Shwachman-Bodian Diamond Syndrome is a Multi-functional Protein Implicated in Cellular Stress Responses

Human Molecular Genetics. Oct, 2009  |  Pubmed ID: 19602484

Shwachman-Diamond syndrome (SDS; OMIM 260400) results from loss-of-function mutations in the Shwachman-Bodian Diamond syndrome (SBDS) gene. It is a multi-system disorder with clinical features of exocrine pancreatic dysfunction, skeletal abnormalities, bone marrow failure and predisposition to leukemic transformation. Although the cellular functions of SBDS are still unclear, its yeast ortholog has been implicated in ribosome biogenesis. Using affinity capture and mass spectrometry, we have developed an SBDS-interactome and report SBDS binding partners with diverse molecular functions, notably components of the large ribosomal subunit and proteins involved in DNA metabolism. Reciprocal co-immunoprecipitation confirmed the interaction of SBDS with the large ribosomal subunit protein RPL4 and with DNA-PK and RPA70, two proteins with critical roles in DNA repair. Function for SBDS in response to cellular stresses was implicated by demonstrating that SBDS-depleted HEK293 cells are hypersensitive to multiple types of DNA damage as well as chemically induced endoplasmic reticulum stress. Furthermore, using multiple routes to impair translation and mimic the effect of SBDS-depletion, we show that SBDS-dependent hypersensitivity of HEK293 cells to UV irradiation can be distinguished from a role of SBDS in translation. These results indicate functions of SBDS beyond ribosome biogenesis and may provide insight into the poorly understood cancer predisposition of SDS patients.

[Dracorhodin Perchlorate Inhibit High Glucose-induced Connective Tissue Growth Factor Formation in Human Mesangial Cells]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Apr, 2009  |  Pubmed ID: 19623991

To study the effect of dracorhodin perchlorate on high glucose-induced connective tissue growth factor (CTGF) expression in human mesangial cells (HMC), and its mechanism of prevention and treatment on renal fibrosis in diabetic nephropathy (DN).

Levels and Distributions of Polychlorinated Biphenyls in Sewage Sludge of Urban Wastewater Treatment Plants

Journal of Environmental Sciences (China). 2009  |  Pubmed ID: 19634421

Concentrations of polychlorinated biphenyls (PCBs) have been measured in sewage sludge samples from 8 urban wastewater treatment plants in Beijing, China. The PCB congeners were analyzed by isotope dilution high resolution gas chromatography/high resolution mass spectrometry method. The concentration of PCBs ranged from 65.6 to 157 ng/g dry weight (dw), with a mean value of 101 ng/g dw. The dioxin-like PCB WHO-TEQs (World Health Organization-Toxic Equivalents) of the sludge were lower than 1 pg/g dw. Consequently, all the concentrations of PCBs in sludge samples were below the upper limit for land application according to the Chinese legislation law for agriculture use. The PCB homologue profiles in sludge samples were dominated by tri-CBs and tetra-CBs. Similar distributions have been found in one of the Chinese PCB commercial products. The patterns of dioxin-like and indicator congeners observed in this study were quite similar in all samples. The predominant congener for dioxin-like and indicator PCBs were PCB-118 and PCB-28, respectively, while PCB-126 had the highest TEQ value.

[Expression of Human Beta-defensin-3 Induced by Lipopolysaccharide in Human Bronchial Epithelial Cells]

Zhongguo Dang Dai Er Ke Za Zhi = Chinese Journal of Contemporary Pediatrics. Jul, 2009  |  Pubmed ID: 19650994

To study the expression of human beta-defensin-3 (hBD-3) induced by lipopolysaccharide (LPS) in human bronchial epithelial (HBE) cells, and explore the role of hBD-3 in respiratory infection.

[Primary Analysis on Based on Data Mining Medicine Law of Professor Yan Zheng-Hua in Treatment of Stomachache]

Zhongguo Zhong Xi Yi Jie He Za Zhi Zhongguo Zhongxiyi Jiehe Zazhi = Chinese Journal of Integrated Traditional and Western Medicine / Zhongguo Zhong Xi Yi Jie He Xue Hui, Zhongguo Zhong Yi Yan Jiu Yuan Zhu Ban. May, 2009  |  Pubmed ID: 19673340

Binding Sites, Rotational Conformers, and Electronic States of Sc-C6H5X (X = F, CH3, OH, and CN) Probed by Pulsed-field-ionization Electron Spectroscopy

The Journal of Chemical Physics. Aug, 2009  |  Pubmed ID: 19673558

Scandium (Sc) complexes of fluorobenzene (C(6)H(5)F), toluene (C(6)H(5)CH(3)), phenol (C(6)H(5)OH), and benzonitrile (C(6)H(5)CN) are produced in a laser-vaporization molecular beam source. These complexes are studied with pulsed-field-ionization zero-electron-kinetic-energy (ZEKE) spectroscopy and density functional theory calculations. Adiabatic ionization energies and low-frequency metal-ligand and ligand-based vibrational modes are measured from the ZEKE spectra. Metal binding sites and strengths and electronic states are obtained by comparing the ZEKE spectra with the theoretical calculations. The ionization energies of Sc-C(6)H(5)X (X = F, CH(3), OH, and CN) follow the trend of CN > F > OH > CH(3), whereas the bond energies are in the order of CN > CH(3) approximately OH > F. The metal-ligand stretching frequency of Sc(+)-C(6)H(5)CN is nearly twice as those of the other three complexes. All neutral complexes are in low-spin doublet ground states and singly-charged cations are in singlet states. The preferred Sc binding site in these complexes are the phenyl ring with X = F, CH(3), and OH and the nitrile group with CN. For the phenol complex, two rotational conformers are identified in different OH orientations.

Network-assisted Protein Identification and Data Interpretation in Shotgun Proteomics

Molecular Systems Biology. 2009  |  Pubmed ID: 19690572

Protein assembly and biological interpretation of the assembled protein lists are critical steps in shotgun proteomics data analysis. Although most biological functions arise from interactions among proteins, current protein assembly pipelines treat proteins as independent entities. Usually, only individual proteins with strong experimental evidence, that is, confident proteins, are reported, whereas many possible proteins of biological interest are eliminated. We have developed a clique-enrichment approach (CEA) to rescue eliminated proteins by incorporating the relationship among proteins as embedded in a protein interaction network. In several data sets tested, CEA increased protein identification by 8-23% with an estimated accuracy of 85%. Rescued proteins were supported by existing literature or transcriptome profiling studies at similar levels as confident proteins and at a significantly higher level than abandoned ones. Applying CEA on a breast cancer data set, rescued proteins coded by well-known breast cancer genes. In addition, CEA generated a network view of the proteins and helped show the modular organization of proteins that may underpin the molecular mechanisms of the disease.

Impact of Phenolic Substrate and Growth Temperature on the Arthrobacter Chlorophenolicus Proteome

Journal of Proteome Research. Apr, 2009  |  Pubmed ID: 19714879

We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol, or phenol at 5 and 28 degrees C, both for the wild-type and a mutant strain with mass spectrometry based proteomics. A label-free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.

Methodology for Determining Disulfide Linkage Patterns of Closely Spaced Cysteine Residues

Analytical Chemistry. Sep, 2009  |  Pubmed ID: 19715362

We report the development and application of a method for determining bonding patterns in disulfide-linked peptides containing closely spaced cysteine residues. Through the utility of classic N-terminal sequencing chemistry coupled with facile liquid chromatography and mass spectrometric analysis of the cleavage products, we report the ability to demonstrate unambiguous assignment of paired cysteine residues, using human insulin as a model protein. The conditions of the technique were selected and optimized to maintain disulfide integrity. In a forthcoming article, we will present the results of this method as applied to the complete elucidation of linkages in disulfide variants of a therapeutic monoclonal antibody of the IgG2 subclass.

[Repair of Large Skin Defect of Forearm and Hand Using Bilateral Groin Flaps and Abdominal Flaps]

Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi = Zhongguo Xiufu Chongjian Waike Zazhi = Chinese Journal of Reparative and Reconstructive Surgery. Aug, 2009  |  Pubmed ID: 19728608

To investigate an operative method of repairing large skin defect of the forearm and the hand.

Repulsive Axon Guidance Molecule Slit3 is a Novel Angiogenic Factor

Blood. Nov, 2009  |  Pubmed ID: 19741192

Slits are large, secreted repulsive axon guidance molecules. Recent genetic studies revealed that the Slit3 is dispensable for neural development but required for non-neuron-related developmental processes, such as the genesis of the diaphragm and kidney. Here we report that Slit3 potently promotes angiogenesis, a process essential for proper organogenesis during embryonic development. We observed that Slit3 is expressed and secreted by both endothelial cells and vascular smooth muscle cells in vasculature and that the Slit cognate receptors Robo1 and Robo4 are universally expressed by endothelial cells, suggesting that Slit3 may act in paracrine and autocrine manners to regulate endothelial cells. Cellular function studies revealed that Slit3 stimulates endothelial-cell proliferation, promotes endothelial-cell motility and chemotaxis via interaction with Robo4, and accelerates endothelial-cell vascular network formation in vitro with a specific activity comparable with vascular endothelial growth factor. Furthermore, Slit3 stimulates neovessel sprouting ex vivo and new blood vessel growth in vivo. Consistent with these observations, the Slit3 knockout mice display disrupted angiogenesis during embryogenesis. Taken together, our studies reveal that the repulsive axon guidance molecule Slit3 is a novel and potent angiogenic factor and functions to promote angiogenesis in coordinating organogenesis during embryonic development.

Synthesis and Evaluation of Functionalized Isoindigos As Antiproliferative Agents

Bioorganic & Medicinal Chemistry. Nov, 2009  |  Pubmed ID: 19783149

A series of functionalized isoindigos structurally related to meisoindigo (1-methylisoindigo), a therapeutic agent used for the treatment of a form of leukemia, were synthesized and evaluated for antiproliferative activities on a panel of human cancer cells. Two promising compounds (1-phenpropylisoindigo and 1-(p-methoxy-phenethyl)-isoindigo) that were more potent than meisoindigo and comparable to 6-bromoindirubin-3'-oxime on leukemic K562 and liver HuH7 cells were identified. Structure-activity relationships showed the importance of keeping one of the lactam NH in an unsubstituted state. Substitution of the other lactam NH with aryl or arylalkyl side chains retained or improved activity in most instances. An intact exocyclic double bond was also essential, possibly to maintain planarity and rigidity of the isoindigo scaffold. None of the compounds were found to inhibit CDK2 in an in vitro assay, in spite of reports linking the antiproliferative activities of meisoindigo and other isoindigos to CDK2 inhibition. Hence, these functionalized isoindigos disrupted cell growth and proliferation by other mechanistic pathways that did not involve CDK2 inhibition.

The Expression and Significance of Dickkopf-1 in Epithelial Ovarian Carcinoma

The International Journal of Biological Markers. Jul-Sep, 2009  |  Pubmed ID: 19787627

The aim of this study was to investigate the presence and prognostic value of Dickkopf-1 (DKK1) in epithelia ovarian carcinoma. The expression of DKK1 was determined in 56 epithelial ovarian carcinoma tissues, 35 benign ovarian cystadenoma tissues, and 12 normal ovarian tissues by quantitative real-time PCR and immunohistochemistry. The DKK1 mRNA level in the carcinoma tissues was upregulated (5.5+/-2.7-fold increase) compared with that in the normal tissues (p<0.0001). The mRNA level of DKK1 in the cystadenoma tissues (1.1+/-0.4-fold increase) was not statistically different from that in the normal tissues (p=0.486). DKK1 protein expression in the carcinoma tissues was also higher (89.29%) than in cystadenoma (65.71%) and normal tissues (58.33%) (p=0.006 and p=0.009, respectively). In epithelial ovarian carcinoma, DKK1 gene and protein overexpression was associated with advanced FIGO stage (p=0.007, p=0.004) and poor differentiation grade (p=0.027, p=0.010). Elevated DKK1 protein levels in ovarian carcinoma samples were associated with a poor outcome in univariate and multivariate analysis (p<0.0001 and p<0.0001, respectively). The study indicated that DKK1 maymbe a useful prognostic and diagnostic indicator for epithelial ovarian carcinoma.

Evaluation of the Effects of PM101, a Cyclodextrin-based Formulation of Intravenous Amiodarone, on Blood Pressure in Healthy Humans

The American Journal of Cardiology. Oct, 2009  |  Pubmed ID: 19801040

Intravenous amiodarone (AIV) is used to treat cardiac arrhythmias. Hypotension is the dose-limiting adverse event of AIV and is considered to be due to the cosolvents (polysorbate 80 and benzyl alcohol) in the formulation. To minimize hypotension, the initial loading dose of AIV (150 mg) is diluted to 1.5 mg/ml and slowly infused over 10 minutes. PM101 is a cosolvent-free intravenous formulation of amiodarone. The present study was designed to assess any potential hypotensive effect of PM101 (50 mg/ml) on the administration of the loading dose (150 mg) as an undiluted bolus push. This was a randomized, double-blind, placebo- and active-controlled study in healthy human subjects receiving placebo (5% dextrose in water, n = 112) or PM101 (bolus push, n = 112). The primary end point was the noninferiority assessment of placebo versus PM101 for change in systolic blood pressure. For comparison, the standard loading dose of AIV (150 mg) was infused at 1.5 mg/ml over 10 minutes, and a rapid loading dose of AIV (150 mg) was infused undiluted (50 mg/ml) over 15 seconds. PM101 was noninferior to placebo, with changes from baseline systolic blood pressure for placebo and PM101 of -4.25 +/- 4.2 and -4.83 +/- 5.0 mm Hg, respectively. Neither regimen of AIV altered systolic blood pressure compared to placebo. Transient and significant increases in heart rate were observed in both AIV groups and with PM101 but not placebo. In conclusion, the results of this study demonstrate that PM101 is devoid of hypotension in healthy human subjects. The absence of a hypotensive effect of AIV in this population suggests that further evaluation is needed in a patient population with cardiac disease.

[Establishment of a Diabetic-hypertensive Rat Model]

Yao Xue Xue Bao = Acta Pharmaceutica Sinica. Jun, 2009  |  Pubmed ID: 19806885

This study is to establish a diabetic-hypertensive model in rats. After the induction of diabetes by streptozocin (STZ), rats were maintained with free access to rat chow and 1% NaCl drinking water. Blood pressure was monitored at conscious state by tail-cuff weekly till it was 50 mmHg higher than normal animal steadily. Finally, blood pressure was measured by catheterization of the right carotid artery and plasma ET-1 and Ang II, kidney Ang II and angiotensinogen or preproendothelin gene expression in liver or aorta were assayed separately. STZ-diabetic rats that maintained with 1% NaCl drinking water exhibited obviously increasing blood pressure since the third week. Then the pressure reached 150 mmHg at the 6th week and was maintained until the 11th week. Till the 12th week, the blood pressure reached to higher than 160 mmHg. In addition, these high blood pressure rats were accompanied with increased blood plasma ET-1 and Ang II and augmented gene expression levels of angiotensinogen in kidneys and preproendothelin in aorta tissues. Loading sodium chloride chronically to STZ-diabetic rats could prepare a diabetic-hypertensive rat model.

Abdominal Fat Accumulation with Hyperuricemia and Hypercholesterolemia Quail Model Induced by High Fat Diet

Chinese Medical Sciences Journal = Chung-kuo I Hsüeh K'o Hsüeh Tsa Chih / Chinese Academy of Medical Sciences. Sep, 2009  |  Pubmed ID: 19848323

To establish abdominal fat accumulation with hyperuricemia and hypercholesterolemia quail model fed with high fat diet. And then to investigate the pathological characteristics of this quail model.

Astrophysics: Most Distant Cosmic Blast Seen

Nature. Oct, 2009  |  Pubmed ID: 19865159

Surgical Excision of Cervicofacial Giant Macrocystic Lymphatic Malformations in Infants and Children

International Journal of Pediatric Otorhinolaryngology. Jun, 2009  |  Pubmed ID: 19324424

Various modalities have been used to treat lymphatic malformations, such as steroids, the injection of sclerosing agents, aspiration, and surgery. Giant macrocystic lymphangiomas involving the cervicofacial region in infants and children constitute a major therapeutic challenge.

Estimation and Characterization of PCDD/Fs and Dioxin-like PCBs from Secondary Copper and Aluminum Metallurgies in China

Chemosphere. May, 2009  |  Pubmed ID: 19329140

The secondary metallurgy industry is considered as one source of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/Fs). This study investigated the emission factors and total emissions amounts of PCDD/Fs and dioxin-like polychlorinated biphenyls (dioxin-like PCBs) released from secondary aluminum and copper metallurgy industries in China. The congener patterns are shown and the formation mechanism is also discussed in this paper. The toxic equivalency (TEQ) emission factor of PCDD/Fs is higher for secondary copper production, at 14,802 ng TEQ t(-1) than for secondary aluminum production, at 2650 ng TEQ t(-1). However, the TEQ emission factor of dioxin-like PCBs of secondary aluminum production, with 193 ng TEQ t(-1), is higher than that of secondary copper production with 98.1 ng TEQ t(-1). The total estimated emission amount of PCDD/Fs released to air from the production of 2.75 million tons secondary aluminum and 2 million tons secondary copper in 2007 are 7.3 and 37.5 g TEQ yr(-1), respectively, the corresponding dioxin-like PCBs total emission amounts being 0.53 and 0.2 g TEQ yr(-1) respectively. In general, the emission factors and the total emission amounts of the secondary aluminum and copper metallurgies in China stay in the middle level compared to values reported for other countries. The most abundant congener of PCDD/Fs is 2,3,4,7,8-PeCDF and the most abundant congener of dioxin-like PCBs is CB-126 in samples collected from both secondary aluminum and copper metallurgies. According to the distribution of organochlorocompounds (PCDF>PCDD>PCB, PCDF/PCDD>1) and the dominant contribution of higher chlorinated congeners, the de novo synthesis is assumed to be the main formation pathway of PCDD/Fs and PCBs in the secondary copper and aluminum metallurgies.

Ultrafast Dynamics of O-bromofluorobenzene Studied by Time-resolved Photoelectron Imaging

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. Jun, 2009  |  Pubmed ID: 19343750

Photodissociation dynamics and rotational wave packet coherences of o-bromofluorobenzene are studied by femtosecond time-resolved photoelectron imaging [figure: see text]. The decay of different photoelectron rings shows the population decay of states from which the lifetimes of different states are determined. The variation of photoelectron angular distributions reflects the evolution of rotational coherences.Photodissociation dynamics and rotational wave packet coherences of o-bromofluorobenzene are studied by femtosecond time-resolved photoelectron imaging (TR-PEI) spectroscopy combined with the (1+2') resonance-enhanced multiphoton ionization (REMPI). Photoelectron kinetic energy and angular distributions indicate ionization dynamics from some Rydberg states at the (1+1') photon energy. The lifetimes of the S(1) (A') and T(2) (A') states are determined from the decay of the photoelectron signals to be 38 ps and 27 ps. The electron population decay of the two states is attributed to predissociation and tunneling dissociation. The variation of time-dependent anisotropy parameters in the first 5 ps shows the rotational wave coherences of molecule.

Wolbachia Infection in Australasian and North American Populations of Haematobia Irritans (Diptera: Muscidae)

Veterinary Parasitology. Jun, 2009  |  Pubmed ID: 19345018

Buffalo fly (Haematobia irritans exigua) is a major pest of beef and dairy cattle in northern Australia. Global warming is expected to increase the southern range of buffalo fly. Chemical control is compromised by resistance and may not be feasible in extensive production systems and there is rapidly growing market preference for beef and dairy products produced in low-chemical systems. Wolbachia are vertically transmitted intracellular bacteria that can profoundly influence host reproduction and fitness and are of increasing interest for use in biocontrol programs. To determine whether Australian flies are infected with Wolbachia, buffalo flies were collected from 12 cattle herds around Australia and assayed by standard PCR for the Wolbachia wsp gene. H. i. exigua from Indonesia and horn fly (H. i. irritans) from Canada were also tested. All H. i. exigua samples tested were negative for Wolbachia infection whereas a very strong signal for Wolbachia was obtained from H. i. irritans.

Gene Transferability from Transgenic Brassica Napus L. to Various Subspecies and Varieties of Brassica Rapa

Transgenic Research. Oct, 2009  |  Pubmed ID: 19357986

Gene transferability from transgenic rapeseed to various subspecies and varieties of Brassica rapa was assessed in this study. Artificial crossability was studied in 118 cultivars of 7 B. rapa subspecies and varieties with the transgenic rapeseed GT73 (Brassica napus) as the pollen donor. On average 5.7 seeds were obtained per pollination, with a range from 0.05 to 19.4. The heading type of B. rapa L. showed significantly higher crossability than non-heading types of B. rapa. The spontaneous outcrossing rate between B. rapa (female) and the transgenic rapeseed Ms8 x Rf3 (B. napus) (male) ranged from 0.039 to 0.406%, with an average of 0.19%. The fertilization process and the development of the hybrid seeds as shown by fluorescent staining techniques indicated that the number of adhered pollens on the stigma was reduced by 80%, the number of pollen tubes in the style was reduced by 2/3 and the fertilization time was delayed by over 20 h when pollinated with the transgenic rapeseed Ms8 x Rf3 in comparison with the bud self-pollination of B. rapa as control. About 10-70% of the interspecific hybrid embryos were aborted in the course of development. Some seeds looked cracked in mature pods, which showed germination abilities lower than 10%. The spontaneous outcrossing rates were much lower than the artificial crossability, and their survival fitness of the interspecific hybrid was very low, indicating that it should be possible to keep the adventitious presence of the off-plants under the allowed threshold, if proper measures are taken.

The Intersystem Crossing Process of P-bromofluorobenzene Studied with Time-resolved Photoelectron Imaging

The Journal of Chemical Physics. Apr, 2009  |  Pubmed ID: 19368447

Ultrafast processes of p-bromofluorobenzene are studied with femtosecond time-resolved photoelectron imaging spectroscopy. The photoelectron image revealed four photoelectron rings centered at 0.39, 0.86, 1.13, and 1.61 eV, respectively. The inner rings are more anisotropic than the outer rings. The decay traces of the different rings were recorded separately. Sharp photoelectron energy distributions and different anisotropy parameters extracted from the images indicated resonances with Rydberg states at the (1+1(')) photon energy. The quantum defect values of the four Rydberg states were determined to be 0.75, 0.52, 0.36, and approximately 0, respectively, with principal quantum number of 3. The electron dephasing mechanism of the S(1)(B(2)) state corresponds to the intersystem crossing from the S(1)(B(2)) to T(1)(B(2)) state and the predissociation of the S(1)(B(2)) state via the T(1)(B(1)) state. The lifetimes of S(1)(B(2)) and T(1)(B(2)) are determined from the decay of the photoelectron signals to be 40 and 33 ps, respectively. The variety of time-dependent anisotropy parameters in the first 5 ps shows the rotational wave coherences of p-bromofluorobenzene at the S(1)(B(2)) state.

Recombinant T Cell Receptor Ligand Treats Experimental Stroke

Stroke; a Journal of Cerebral Circulation. Jul, 2009  |  Pubmed ID: 19443805

Experimental stroke induces a biphasic effect on the immune response that involves early activation of peripheral leukocytes followed by severe immunodepression and atrophy of the spleen and thymus. In tandem, the developing infarct is exacerbated by influx of numerous inflammatory cell types, including T and B lymphocytes. These features of stroke prompted our use of recombinant T cell receptor ligands (RTL), partial major histocompatibility complex Class II molecules covalently bound to myelin peptides. We tested the hypothesis that RTL would improve ischemic outcome in the brain without exacerbating defects in the peripheral immune system function.

[Discussion on Implications and Research Ideas of Toxic Theory in Natural Characteristics of Chinese Herbal Medicine]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Feb, 2009  |  Pubmed ID: 19459317

The meaning of "poisonous" in Traditional Chinese Medicine (TCM) is different from that of modern medicine. Narrow meaning of "poisonous" in TCM refers to harmful reaction to human body. Otherwise, generalized meaning of "poisonous" has two main implications: general title of drug and eccentric nature for drug. To fully reveal the scientific content of Chinese herbal toxic theory, we should carry out our research on the relationship between Chinese herbal toxicity and body state under the guidance of TCM theory. Moreover, comprehensive study on toxic information is also necessary for clarifying the natural characteristics of Chinese herbal medicine.

Explaining the Inhibition of Cyclin-dependent Kinase 5 by Peptides Derived from P25 with Molecular Dynamics Simulations and MM-PBSA

Journal of Molecular Modeling. May, 2009  |  Pubmed ID: 19466465

A cyclin-dependent kinase (CDK) 5 inhibitory peptide (CIP) from p25 was recently reported to inhibit CDK5/p25 activity in vitro but had no effect on endogenous cdc2 kinase activity. This may lead to a specific CDK5 inhibition strategy in the treatment of neurodegeneration. However, the mechanism of the inhibition remains unclear. In this work, molecular dynamics simulations and energy decomposition calculation models were set up to investigate the deregulation mechanisms of CIP on CDK5 activity. The results show that truncation of the N, and C terminals of p25 introduces important conformational changes into a hydrophobic pocket that is crucial for accommodating Ile153 on the activation loop of CDK5. In addition, such truncations lead to distortion and displacement of the activation loop and consequently affect binding of the substrate peptide. New inhibition sites for selectively inhibiting the activity of CDK5 are also suggested.

Predissociation Dynamics of the B State of CH3I by Femtosecond Pump-probe Technique

Optics Express. Jun, 2009  |  Pubmed ID: 19550446

The laser induced predissociation dynamics of the B Rydberg state of CH(3)I following two-photon absorption of a pump pulse was studied with femtosecond pump-probe photoelectron imaging coupled with time-resolved mass spectroscopy. The predissociation lifetime was measured to be 1.55 ps induced by the crossing between the B state and the repulsive A-band. Two possible predissociation channels were observed originating from (a) direct coupling between the B state and the repulsive (3)Q(0) state and (b) a second crossing between the (3)Q(0) and (1)Q(1) states after the coupling between the B and (3)Q(0) states, respectively.

Estimation and Characterization of PCDD/Fs and Dioxin-like PCB Emission from Secondary Zinc and Lead Metallurgies in China

Journal of Environmental Monitoring : JEM. Apr, 2009  |  Pubmed ID: 19557242

Secondary zinc and lead production is addressed as one of the potential sources of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dioxin-like PCBs) due to the impurity of the raw material. However, the release inventory of PCDD/Fs and dioxin-like PCBs is very scarce for these secondary nonferrous metallurgies. This study selected typical secondary zinc and lead plants to investigate the emissions of PCDD/Fs and dioxin-like PCBs released from such plants in China. The toxic equivalent quantity (TEQ) emission factor of PCDD/Fs and dioxin-like PCBs released into the environment is higher for secondary zinc production, at 52 298.02 ng TEQ ton(-1) than for secondary lead production, at 646.05 ng TEQ ton(-1). The most abundant congeners of PCDD/Fs are 2,3,4,7,8-PeCDF and 1,2,3,4,6,7,8-HpCDF for the secondary zinc and lead metallurgies, respectively. The most abundant congener of dioxin-like PCBs in the samples collected from both metallurgies is CB-126 . According to the distribution of PCDD/Fs (PCDF/PCDD > 1) and the dominant contribution of higher chlorinated congeners, the de novo synthesis is assumed to be the main formation pathway of PCDD/Fs in the secondary zinc metallurgies. For the secondary lead metallurgies, the role of precursor formation is also very important. Based on the emission factor and production level, the total estimated emission amounts of PCDD/Fs and dioxin-like PCBs in both stack gas and fly ash released into the environment from secondary zinc and lead production is estimated to be at least 2.76 and 0.42 g TEQ yr(-1), respectively. The dioxin-like PCBs contribute 2.8% and 0.6% of the total emission from secondary zinc and lead plants, respectively.

[Significance of a Reversal Expression of the Angiopoietin-1 and 2 in Oral Squamous Cell Carcinoma]

Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi = Chinese Journal of Otorhinolaryngology Head and Neck Surgery. May, 2009  |  Pubmed ID: 19567053

To investigate the significance of Angiopoietin-1 (Ang-1), Angiopoietin-2 (Ang-2) expression in angiogenesis, vessel maturation, progress and prognosis of oral squamous cell carcinoma (OSCC).

A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments

Statistical Applications in Genetics and Molecular Biology. 2009  |  Pubmed ID: 19954419

Methods for gene set analysis test for coordinated changes of a group of genes involved in the same biological process or molecular pathway. Higher statistical power is gained for gene set analysis by combining weak signals from a number of individual genes in each group. Although many gene set analysis methods have been proposed for microarray experiments with two groups, few can be applied to time course experiments. We propose a unified statistical model for analyzing time course experiments at the gene set level using random coefficient models, which fall into the more general class of mixed effects models. These models include a systematic component that models the mean trajectory for the group of genes, and a random component (the random coefficients) that models how each gene's trajectory varies about the mean trajectory. We show that the proposed model (1) outperforms currently available methods at discriminating gene sets differentially changed over time from null gene sets; (2) provides more stable results that are less affected by sampling variations; (3) models dependency among genes adequately and preserves type I error rate; and (4) allows for gene ranking based on predicted values of the random effects. We describe simulation studies using gene expression data with "real life" correlations and we demonstrate the proposed random coefficient model using a mouse colon development time course dataset. The agreement between results of the proposed random coefficient model and the previous reports for this proof-of-concept trial further validates this methodology, which provides a unified statistical model for systems analysis of microarray experiments with complex experimental designs when re-sampling based methods are difficult to apply.

Atmospheric Emission of PCDD/Fs, PCBs, Hexachlorobenzene, and Pentachlorobenzene from the Coking Industry

Environmental Science & Technology. Dec, 2009  |  Pubmed ID: 20000510

The coking process is considered to be a potential source of unintentionally produced persistent organic pollutants (UP-POPs). However, intensive studies on the emission of UP-POPs from the coking industry are still very scarce. Emission of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs), dioxin-like polychlorinated biphenyls (dl-PCBs), hexachlorobenzene (HxCBz), and pentachlorobenzene (PeCBz) covered under the Stockholm Convention were investigated for the coking process in this study. Stack gases from some typical coke plants in China were collected and analyzed to estimate the emission of UP-POPs from the coking industry. Emission factors of 28.9 ng WHO-TEQ tonne(-1) for PCDD/Fs, 1.7 ng WHO-TEQ tonne(-1) for dl-PCBs, 596 ng tonne(-1) for HxCBz, and 680 ng tonne(-1) for PeCBz were derived based on the investigated data. The annual emissions from the global coking industry were estimated to be 15.8 g WHO-TEQ for PCDD/Fs, 0.93 g WHO-TEQ for dl-PCBs, 333 g for HxCBz, and 379 g for PeCBz, respectively (reference year 2007). According to the distribution of PCDD/Fs, we argued for the de novo synthesis to be the major pathway of PCDD/F formation. With regard to the characteristics of dl-PCBs, the most abundant congener was CB-118, and the most dominant contributor to the total WHO-TEQ of dl-PCBs was CB-126.

[Prevalence Rates of Overweight and Obesity in Chinese Minority Students in 2005]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Sep, 2009  |  Pubmed ID: 20193227

To analyze the prevalence rates of overweight and obesity in Chinese minority students in 2005.

[Study on the Trend of Minority Students' Health Status from 1995 to 2005 in China]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Sep, 2009  |  Pubmed ID: 20193228

To reveal the trend of minority students' health from 1995 to 2005 in China.

[Study on the Changing Status of Morphological Development Among Minority Students in China, from 1985 to 2005]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Oct, 2009  |  Pubmed ID: 20193384

To identify the changes of morphological development status on minority students in China from 1985 to 2005.

[Changes of Physical Functions Among Chinese Minority Students from 1985 to 2005]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Oct, 2009  |  Pubmed ID: 20193385

To study the changes of physical functions among minority students in China from 1985 to 2005, to provide evidence for health promotion to the minority students in the country.

[Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) Loci in the Genomes of Halophilic Archaea]

Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica. Nov, 2009  |  Pubmed ID: 20112671

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time.

Prevalence and Clinical and Molecular Characterization of Human Metapneumovirus in Children with Acute Respiratory Infection in China

The Pediatric Infectious Disease Journal. Feb, 2010  |  Pubmed ID: 20135829

Human metapneumovirus (HMPV), a newly discovered paramyxovirus, has been associated with acute respiratory tract infections (ARTIs). However, the prevalence and molecular characteristics of HMPV in China are still unclear.

Preparation of Highly Ordered Cubic NaA Zeolite from Halloysite Mineral for Adsorption of Ammonium Ions

Journal of Hazardous Materials. Jun, 2010  |  Pubmed ID: 20172651

Well-ordered cubic NaA zeolite was first synthesized using natural halloysite mineral with nanotubular structure as source material by hydro-thermal method. SEM and HRTEM images indicate that the synthesized NaA zeolite is cubic-shaped crystal with planar surface, well-defined edges and symmetrical and uniform pore channels. The adsorption behavior of ammonium ions (NH(4)(+)) from aqueous solution onto NaA zeolite was investigated as a function of parameters such as equilibrium time, pH, initial NH(4)(+) concentration, temperature and competitive cations. The Langmuir and Freundlich adsorption models were applied to describe the equilibrium isotherms. A maximum adsorption capacity of 44.3 mg g(-1) of NH(4)(+) was achieved. The regeneration and reusable ability of this adsorbent was evaluated, and the results indicated that the recovered adsorbent could be used again for NH(4)(+) removal with nearly constant adsorption capacity. Thermodynamic parameters such as change in free energy (DeltaG(0)), enthalpy (DeltaH(0)) and entropy (DeltaS(0)) were also determined, which indicated that the adsorption was a spontaneous and exothermic process at ambient conditions. Compared with other adsorbents, the as-synthesized NaA zeolite displays a faster adsorption rate and higher adsorption capacity, which implies potential application for removing NH(4)(+) pollutants from wastewaters.

SiO2 Nanoparticles Induce Cytotoxicity and Protein Expression Alteration in HaCaT Cells

Particle and Fibre Toxicology. 2010  |  Pubmed ID: 20180970

Nanometer silicon dioxide (nano-SiO2) has a wide variety of applications in material sciences, engineering and medicine; however, the potential cell biological and proteomic effects of nano-SiO2 exposure and the toxic mechanisms remain far from clear.

High-throughput Multiplexed Transcript Analysis Yields Enhanced Resolution of 5-hydroxytryptamine 2C Receptor MRNA Editing Profiles

Molecular Pharmacology. Jun, 2010  |  Pubmed ID: 20181818

RNA editing is a post-transcriptional modification in which adenosine residues are converted to inosine (adenosine-to-inosine editing). Commonly used methodologies to quantify RNA editing levels involve either direct sequencing or pyrosequencing of individual cDNA clones. The limitations of these methods lead to a small number of clones characterized in comparison to the number of mRNA molecules in the original sample, thereby producing significant sampling errors and potentially erroneous conclusions. We have developed an improved method for quantifying RNA editing patterns that increases sequence analysis to an average of more than 800,000 individual cDNAs per sample, substantially increasing accuracy and sensitivity. Our method is based on the serotonin 2C receptor (5-hydroxytryptamine(2C); 5HT(2C)) transcript, an RNA editing substrate in which up to five adenosines are modified. Using a high-throughput multiplexed transcript analysis, we were able to quantify accurately the expression of twenty 5HT(2C) isoforms, each representing at least 0.25% of the total 5HT(2C) transcripts. Furthermore, this approach allowed the detection of previously unobserved changes in 5HT(2C) editing in RNA samples isolated from different inbred mouse strains and dissected brain regions, as well as editing differences in alternatively spliced 5HT(2C) variants. This approach provides a novel and efficient strategy for large-scale analyses of RNA editing and may prove to be a valuable tool for uncovering new information regarding editing patterns in specific disease states and in response to pharmacological and physiological perturbation, further elucidating the impact of 5HT(2C) RNA editing on central nervous system function.

[Changes in Clinical Manifestations of Mycoplasma Pneumoniae Pneumonia in Children Older Than 3 Years During 2000 - 2006 in Hangzhou]

Zhonghua Er Ke Za Zhi. Chinese Journal of Pediatrics. Jul, 2010  |  Pubmed ID: 21055091

To reveal changes in clinical manifestations of Mycoplasma pneumoniae (Mp) pneumonia in children older than 3 years of age during 2000 - 2006.

[An Antimicrobial Resistance Surveillance of Gram-positive Cocci Isolated from 12 Teaching Hospitals in China in 2009]

Zhonghua Nei Ke Za Zhi [Chinese Journal of Internal Medicine]. Sep, 2010  |  Pubmed ID: 21092441

To investigate antimicrobial resistance among gram-positive cocci in China in 2009.

Estimation and Characterization of Polychlorinated Naphthalene Emission from Coking Industries

Environmental Science & Technology. Nov, 2010  |  Pubmed ID: 20886822

Occurrence of polycyclic aromatic hydrocarbons (PAHs) during the coking process has been widely recognized. The formation of polychlorinated naphthalenes (PCNs) from PAHs during some thermal related processes has been confirmed in many studies. Thus, the coking process is assumed to be a potential source of PCNs. However, intensive investigations on PCN emissions during the coking process are lacking. In order to evaluate PCN emissions from the coking process, an intensive study comprising 11 typical coke plants was undertaken. PCNs were qualified and quantified by isotope dilution HRGC/HRMS techniques. The concentrations of PCNs in stack gas samples collected from the investigated coke plants were in the range of 1.6-91.8 ng Nm(-3) (0.08-4.23 pg TEQ Nm(-3)). The emission factors of PCNs were found to be in the range of 0.77-1.24 ng TEQ per ton of coke production. The estimated annual toxic emissions of PCNs from the global coking industry vary from 430 to 692 mg TEQs. Characteristics of the PCN profiles were dominated by the lower chlorinated homologues, with mono-CN being the most abundant homologue. According to the PCN distribution and correlations of PCN homologues, it was speculated that chlorination is possibly the dominant pathway of PCN formation during the coking process.

[Difference of Hypaconitine Concentration in Serum Between Cold-deficiency and Normal Mice]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Aug, 2010  |  Pubmed ID: 20931857

To investigate the difference of hypaconitine concentration in serum between normal and cold-deficiency mice after administration of aconite decoction. To analyze how the toxic dose of aconite decoction correlate to the metabolic environment.

[Study on the Relation Between Fraction Cover and Mixed Spectra in Karst Environment]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Sep, 2010  |  Pubmed ID: 21105420

Karst rocky desertification is one of the most serious eco-environmental problems of land degradation in karst regions, southwest China. The fractional cover of vegetation and exposed bedrock are the main land surface symptoms and essential assessing indicators of karst rocky desertification. To assess the extent of rocky desertification in complex karst environments, the information of multiple land cover types fraction is needed. Based on in situ spectral reflectance data, this study proposed several spectral indices and explored the relationship between spectral features of main land cover types and their responding fractional cover. The results showed that spectral indices have much higher correlation coefficients with fractional cover than does spectral reflectance. Vegetation indices have good linear relation with fractional cover of photosynthetic vegetation (PV). The proposed spectral indices have high correlation coefficients with fractional cover of non-photosynthetic vegetation (NPV) and bare soil, with R2 0.70 and 0.73, respectively. Lower correlation coefficients (R2 = 0.55) with the factional cover of exposed bedrock, were observed. The absorption depth of four forms of the proposed indices has the highest correlation coefficient with the fractional cover of NPV, bare soil, and exposed rock. This study indicates that hyperspectral remote sensing has the potential for the extraction of karst rocky desertification information.

Intestinal Metabolite Compound K of Ginseng Saponin Potently Attenuates Metastatic Growth of Hepatocellular Carcinoma by Augmenting Apoptosis Via a Bid-mediated Mitochondrial Pathway

Journal of Agricultural and Food Chemistry. Dec, 2010  |  Pubmed ID: 21121651

It was recently shown that compound K (CK), an intestinal bacterial metabolite of ginseng saponin, exhibits antihepatocellular carcinoma (HCC) activity, and Bid is a potential drug target for HCC therapy. This paper reports a novel mechanism of CK-induced apoptosis of HCC cells via Bid-mediated mitochondrial pathway. CK dramatically inhibited HCC cells growth in concentration- and time-dependent manners, and a high dose of CK could induce HCC cell apoptotic cell death. Furthermore, the effective dose of CK potently attenuated the subcutaneous tumor growth and spontaneous HCC metastasis in vivo. At the molecular level, immunohistochemical staining revealed that Bid expression in subcutaneous tumor and liver metastasis tissues decreased dramatically in CK-treated groups compared to untreated controls, which also implies that Bid may play a critical role in the growth and progression of HCC. Further study shows that translocation of full-length Bid to the mitochondria from nuclei during cytotoxic apoptosis was associated with the release of cytochrome c from mitochondria, indicating that full-length Bid is sufficient for the activation of mitochondrial cell death pathways in response to CK treatment in HCC cells. Taken together, the results not only reveal a Bid-mediated mitochondrial pathway in HCC cells induced by CK but also suggest that CK may become a potential cytotoxic drug targeting Bid in the prevention and treatment of HCC.

Lentiviral-mediated RNA Interference Against TGF-beta Receptor Type II in Renal Epithelial and Fibroblast Cell Populations in Vitro Demonstrates Regulated Renal Fibrogenesis That is More Efficient Than a Nonlentiviral Vector

Journal of Biomedicine & Biotechnology. 2010  |  Pubmed ID: 21151672

Lentiviral constructs reportedly can integrate into the genome of non-dividing, terminally differentiated cells and dividing cells, for long-term gene expression. This investigation tested whether a third generation lentiviral-mediated small interfering RNA (siRNA) delivered into renal epithelial and fibroblast cells against type II transforming growth factor-beta receptor (siRNA-TBRII) could better attenuate renal fibrogenesis in comparison with a non-lentiviral construct.

[Surveys on the Nutrition Literacy of 802 Adults in Jiangxi Province]

Wei Sheng Yan Jiu = Journal of Hygiene Research. Nov, 2010  |  Pubmed ID: 21351643

To investigate the nutrition literacy status of adults in Jiangxi province and afford support for nutrition education.

Development and Characterization of Microsatellite Loci in Taihangia Rupestris (Rosaceae), a Rare Cliff Herb

American Journal of Botany. Dec, 2010  |  Pubmed ID: 21616832

• Premise of the study: Microsatellite primers were developed for the rare Taihangia rupestris (Rosaceae) to evaluate genetic diversity, population genetic structure, mating system, and demographic events of this species. • Methods and Results: Ten primer sets were developed using an enriched genomic library and were successfully amplified in T. rupestris var. ciliata and T. rupestris var. rupestris. The number of alleles per locus ranged from 2 to 21; the observed and expected heterozygosities ranged from 0.300 to 0.950 and from 0.328 to 0.956, respectively, in the two varieties. • Conclusions: The markers described here will be useful for studies of genetic variation, genetic structure, and mating systems of T. rupestris, which are important for the future conservation of this rare species.

Estimation and Congener-specific Characterization of Polychlorinated Naphthalene Emissions from Secondary Nonferrous Metallurgical Facilities in China

Environmental Science & Technology. Apr, 2010  |  Pubmed ID: 20201508

Secondary nonferrous production is addressed as one of the potential sources of the unintentionally produced persistent organic pollutants (UP-POPs) due to the impurity of raw material. Although there are inventories of dioxin emissions from secondary nonferrous metallurgical facilities, release inventories of polychlorinated naphthalenes (PCNs) are scarce. This study selected typical secondary copper, aluminum, zinc, and lead plants to investigate the emissions of PCNs in secondary nonferrous production in China. The toxic equivalency (TEQ) emission factor for PCNs released to the environment is highest for secondary copper production, at 428.4 ng TEQ t(-1), followed by secondary aluminum, zinc, and lead production, at 142.8, 125.7, and 20.1 ng TEQ t(-1), respectively. PCNs released in secondary copper, aluminum, lead, and zinc production in China are estimated to be 0.86, 0.39, 0.009, and 0.01 g TEQ a(-1), respectively. Analysis of stack gas emission from secondary nonferrous production revealed that less-chlorinated PCNs are the dominant homologues, with mono- to tri-CNs making the most important contributions to the concentration. However, for fly ash, the more highly chlorinated PCNs such as octa-CN are the dominant homologues.

Combined Use of PCR-based TCRG and TCRB Clonality Tests on Paraffin-embedded Skin Tissue in the Differential Diagnosis of Mycosis Fungoides and Inflammatory Dermatoses

The Journal of Molecular Diagnostics : JMD. May, 2010  |  Pubmed ID: 20203005

The distinction between mycosis fungoides (MF) and inflammatory dermatoses (ID) by clinicopathologic criteria can be challenging. There is limited information regarding the performance characteristics and utility of TCRG and TCRB clonality assays in diagnosis of MF and ID from paraffin-embedded tissue sections. In this study, PCR tests were performed with both TCRG and TCRB BIOMED-2 clonality methods followed by capillary electrophoresis and Genescan analysis using DNA samples from 35 MF and 96 ID patients with 69 and 133 paraffin-embedded specimens, respectively. Performance characteristics were determined for each test individually and in combination. TCRG and TCRB tests demonstrated identical sensitivity (64%) and specificity (84%) when analyzed as individual assays. The positive predictive value, negative predictive value, and change of posttest MF probability over a range of MF pretest probabilities were obtained. These data were used to construct an algorithm for sequential use of TCRG and TCRB. As single tests, commercially available BIOMED-2 PCR-based TCRG and TCRB clonality tests on paraffin-embedded tissue have no significant difference in terms of sensitivity and specificity. Combined use of the two tests in patients with intermediate pretest probabilities as proposed in the algorithm could improve test utility.

Novel MicroRNAs in Silkworm (Bombyx Mori)

Functional & Integrative Genomics. Aug, 2010  |  Pubmed ID: 20229201

We acquired more than 4 million useful sequences using a high-throughput method from a library for miRNA identification, which is constructed from a mixture of 14 RNA samples from different developmental stages. We mapped 247,410 reads to known silkworm miRNAs in miRBase (13.0), 701,913 reads to other RNA molecules based on sequence homology, and 3,219,395 reads to the silkworm genome. Our analysis identified 54 silkworm known miRNAs. A striking strand bias between miRNAs and their corresponding miRNA*s was found, and was speculated to reflect that transcripts from the passenger strand of pre-miRNAs may have important biological roles. Using an elaborate screening protocol, we predicted 287 candidate novel miRNAs (represent 116,494 short reads), and 59 of them have both miRNA and miRNA* sequences. Most of the previously identified silkworm miRNAs are cross-species conserved with a high abundance, while those predicted candidates tend to be species-specific miRNAs. Our discovery of SNPs among miRNAs implied within-species functional diversity. Target prediction uncovers that considerable silkworm miRNAs may aim at modulating more than one hormone signaling pathway components and/or hormone biosynthesis-related proteins implying their important roles in silkworm development.

Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in Blood and Breast Milk Samples from Residents of a Schistosomiasis Area with Na-PCP Application in China

Chemosphere. Apr, 2010  |  Pubmed ID: 20299071

Schistosomiasis has prevailed in some areas of China for a long time. Chinese technical sodium pentachlorophenate (Na-PCP) has been used to control the spread of snail-borne schistosomiasis since the 1960s. Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), impurities contained in the Na-PCP, enter the soil and may accumulate in the food chain. In order to evaluate their potentially harmful effects on local residents, 50 breast milk samples and 20 blood samples were collected in 2004 from residents in the Dongting Lake area, one of China's known schistosomiasis areas. Levels of 17 PCDD/F congeners were measured in all samples, and DNA damage was simultaneously assessed in blood samples. The PCDD/F congener distribution patterns in human tissue samples from the Dongting Lake area were similar to those in Na-PCP, and the octachlorodibenzodioxin (OCDD) congener was predominant in all samples. We also had a primary investigation that the breast milk WHO-TEQ associated with some factors such as: age, dietary habit, body mass index (BMI) and the total menses times. In blood samples, the samples with higher OCDD level had higher DDS (DNA damage score) values than those samples with low OCDD level, which indicated that the higher DNA damage value in general population might be caused directly or indirectly by PCDD/Fs. The results also indicated that the WHO-TEQ values in blood were associated with age (r=0.6, p=0.007).

Estradiol and G1 Reduce Infarct Size and Improve Immunosuppression After Experimental Stroke

Journal of Immunology (Baltimore, Md. : 1950). Apr, 2010  |  Pubmed ID: 20304826

Reduced risk and severity of stroke in adult females is thought to depend on normal endogenous levels of estrogen, a well-known neuroprotectant and immunomodulator. In male mice, experimental stroke induces immunosuppression of the peripheral immune system, characterized by a reduction in spleen size and cell numbers and decreased cytokine and chemokine expression. However, stroke-induced immunosuppression has not been evaluated in female mice. To test the hypothesis that estradiol (E2) deficiency exacerbates immunosuppression after focal stroke in females, we evaluated the effect of middle cerebral artery occlusion on infarct size and peripheral and CNS immune responses in ovariectomized mice with or without sustained, controlled levels of 17-beta-E2 administered by s.c. implant or the putative membrane estrogen receptor agonist, G1. Both E2- and G1-replacement decreased infarct volume and partially restored splenocyte numbers. Moreover, E2-replacement increased splenocyte proliferation in response to stimulation with anti-CD3/CD28 Abs and normalized aberrant mRNA expression for cytokines, chemokines, and chemokine receptors and percentage of CD4(+)CD25(+)FoxP3(+) T regulatory cells observed in E2-deficient animals. These beneficial changes in peripheral immunity after E2 replacement were accompanied by a profound reduction in expression of the chemokine, MIP-2, and a 40-fold increased expression of CCR7 in the lesioned brain hemisphere. These results demonstrate for the first time that E2 replacement in ovariectomized female mice improves stroke-induced peripheral immunosuppression.

Double-balloon Enteroscopy for Obscure Gastrointestinal Bleeding: a Single Center Experience in China

World Journal of Gastroenterology : WJG. Apr, 2010  |  Pubmed ID: 20355245

To evaluate the diagnostic value of double-balloon enteroscopy (DBE) for obscure gastrointestinal bleeding (OGIB).

BMI Percentile Curves for Chinese Children Aged 7-18 Years, in Comparison with the WHO and the US Centers for Disease Control and Prevention References

Public Health Nutrition. Dec, 2010  |  Pubmed ID: 20359376

To establish BMI percentile curves that describe the contemporary BMI distribution among Chinese children, and to compare their BMI percentile curves with those in two recently developed international references: the WHO and the US Centers for Disease Control and Prevention (US CDC) growth references.

Probing Ultrafast Internal Conversion of O-xylene Via Femtosecond Time-resolved Photoelectron Imaging

Optics Express. Mar, 2010  |  Pubmed ID: 20389596

The dynamics of excited states in o-xylene molecules has been studied by femtosecond time-resolved photoelectron imaging coupled with time-resolved mass spectroscopy. The ultrafast internal conversion from the S(2) state to the vibrationally hot S(1) state on timescale of 60 fs is observed on real time. The secondarily populated high vibronic S(1) state deactivates further to the S(0) state on timescale of 9.85 ps. Interestingly, the lifetime of the low vibronic S(1) state is much longer, extrapolated to ~12.7 ns. The great differences of lifetime of different vibronic S(1) state are due to their different radiationless dynamics.

Identification of Immune-relevant Genes by Expressed Sequence Tag Analysis of Head Kidney from Grass Carp (Ctenopharyngodon Idella)

Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. Jun, 2010  |  Pubmed ID: 20403773

Grass carp is the third largest aquaculture species in global production. However, genomic research of this species has been limited. To identify immune-related genes in grass carp, a normalized full-length cDNA library was constructed from head kidney tissues, and 6432 randomly selected clones were sequenced. 5289 high quality expressed sequence tags (EST) were generated and assembled into 2687 unigenes. Among them, 1585 unigenes showed significant similarity with known sequences in public databases, whereas the remaining 1102 unigenes appeared to be novel sequences with unknown functions. In particular, 136 immune-related genes were identified to encode immunoglobulins, FcRgamma, IFN-related proteins, various CD markers, MHCs, complements and other important immune-related factors; a majority of these genes are reported in grass carp for the first time. Sequence analysis indicated that grass carp has at least three subtypes of immunoglobulin light chains, namely L1, L2 and L3. Furthermore, FCRgamma was found to broadly express in different tissues. Our study constitutes the first EST analysis of lymphatic tissue in grass carp, and could pave the way for further research of immune-related genes and functional genomics in grass carp.

12-O-tetradecanoylphorbol-1, 3-acetate Induces the Negative Regulation of Protein Kinase B by Protein Kinase Calpha During Gastric Cancer Cell Apoptosis

Cellular & Molecular Biology Letters. Sep, 2010  |  Pubmed ID: 20428959

The PKB signaling pathway is essential for cell survival and the inhibition of apoptosis, but its functional mechanisms have not been fully explored. Previously, we reported that TPA effectively inhibited PKB activity and caused PKB degradation, which was correlated with the repression of PKB phosphorylation at Ser473. In this study, we focus on how PKB is regulated by TPA in gastric cancer cells. One of the TPA targets, PKCalpha, was found to mediate the inhibition of PKB phosphorylation and degredation caused by TPA. Furthermore, TPA induced the import of PKCalpha into the nucleus, where PKCalpha exerted an inhibitory effect on PKB expression and phosphorylation. As a result, cancer cell proliferation was arrested. Our study characterizes a novel function of PKCalpha in mediating the negative regulation of PKB by TPA, and suggests a potential application in the clinical treatment of gastric cancer.

[Determination of Monomethylamine and Dimethylamine in Air of Work Places with Headspace Gas Chromatography]

Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi = Zhonghua Laodong Weisheng Zhiyebing Zazhi = Chinese Journal of Industrial Hygiene and Occupational Diseases. Feb, 2010  |  Pubmed ID: 20450810

Photodissociation Dynamics of 2-bromopropane Using Velocity Map Imaging Technique

The Journal of Physical Chemistry. A. Jun, 2010  |  Pubmed ID: 20459145

Photodissociation dynamics of 2-bromopropane in the A band was investigated at several wavelengths between 232 and 267 nm using resonance-enhanced multiphoton ionization technique combined with velocity map ion-imaging detection. The ion images of Br ((2)P(3/2)) and Br* ((2)P(1/2)) were analyzed to yield corresponding total translational energy and angular distributions. The total translational energy distributions showed that the channel leading to Br carried more internal energy in the 2-C(3)H(7) moiety than the channel leading to Br*. The anisotropy parameters of beta (Br) were obtained to be between 0.68 and 1.49, and beta (Br*) between 0.73 and 1.96, indicating that the Br* product originates from direct excitation of the (3)Q(0) state and the (1)Q(1) --> (3)Q(0) nonadiabatic transition, and the Br product from direct excitation of the (1)Q(1) or (3)Q(1) state and the (3)Q(0) --> (1)Q(1) nonadiabatic transition. The curve crossing probabilities were determined to be increase with the wavelength. As compared with the case of CH(3)Br, the two heavier branched CH(3) groups significantly enhance the Br ((2)P(3/2)) production from nonadiabatic contribution. The curve crossing from the (3)Q(0) to the (1)Q(1) surface is much higher than that of the reverse from the (1)Q(1) to the (3)Q(0) surface, which may have resulted from the difference in shape between the potential energy surfaces of the (3)Q(0) and (1)Q(1) states. Finally, based on the experimental data, the partial absorption cross sections of the A band for the (3)Q(0), (3)Q(1), and (1)Q(1) states were extracted.

Proteomics Reveals a Core Molecular Response of Pseudomonas Putida F1 to Acute Chromate Challenge

BMC Genomics. 2010  |  Pubmed ID: 20482812

Pseudomonas putida is a model organism for bioremediation because of its remarkable metabolic versatility, extensive biodegradative functions, and ubiquity in contaminated soil environments. To further the understanding of molecular pathways responding to the heavy metal chromium(VI) [Cr(VI)], the proteome of aerobically grown, Cr(VI)-stressed P. putida strain F1 was characterized within the context of two disparate nutritional environments: rich (LB) media and minimal (M9L) media containing lactate as the sole carbon source.

Co-expression Module Analysis Reveals Biological Processes, Genomic Gain, and Regulatory Mechanisms Associated with Breast Cancer Progression

BMC Systems Biology. 2010  |  Pubmed ID: 20507583

Gene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest. However, individual gene-based signatures usually suffer from low reproducibility and interpretability.

[Secular Growth Trends in Height and Weight of Chinese Children Aged 7 to 18 Year-old from 1985 to 2005]

Beijing Da Xue Xue Bao. Yi Xue Ban = Journal of Peking University. Health Sciences. Jun, 2010  |  Pubmed ID: 20559409

To analyze the secular changes in height and weight of Chinese school children in recent 20 years, in order to take effective preventive strategies and measures to improve their physical fitness and health.

Policy Design and Performance of Emissions Trading Markets: an Adaptive Agent-based Analysis

Environmental Science & Technology. Aug, 2010  |  Pubmed ID: 20590153

Emissions trading is considered to be a cost-effective environmental economic instrument for pollution control. However, the pilot emissions trading programs in China have failed to bring remarkable success in the campaign for pollution control. The policy design of an emissions trading program is found to have a decisive impact on its performance. In this study, an artificial market for sulfur dioxide (SO2) emissions trading applying the agent-based model was constructed. The performance of the Jiangsu SO2 emissions trading market under different policy design scenario was also examined. Results show that the market efficiency of emissions trading is significantly affected by policy design and existing policies. China's coal-electricity price system is the principal factor influencing the performance of the SO2 emissions trading market. Transaction costs would also reduce market efficiency. In addition, current-level emissions discharge fee/tax and banking mechanisms do not distinctly affect policy performance. Thus, applying emissions trading in emission control in China should consider policy design and interaction with other existing policies.

[Mathematical Analysis of the Relationship Between Yang Deficiency Syndrome in Traditional Chinese Medicine and Its Objective Indicators in Clinical Literature]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Jul, 2010  |  Pubmed ID: 20619146

The primary aim of this research is to systematically sort out and analyze available documents for yang deficiency syndrome in traditional Chinese medicine, providing innovative ideas and methods for statistical study of yang deficiency syndrome.

Postconditioning the Human Heart in Percutaneous Coronary Intervention

Clinical Cardiology. Jul, 2010  |  Pubmed ID: 20641122

It has been proved in animal models that postconditioning (PC) could attenuate reperfusion injury. But there are not many clinical studies on the application of PC.

CRISPLD2 Polymorphisms Are Associated with Non-syndromic Cleft Lip with or Without Cleft Palate in a Northern Chinese Population

European Journal of Oral Sciences. Aug, 2010  |  Pubmed ID: 20662919

Non-syndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect. This complex genetic disorder results from interactions between genes and environmental factors. Numerous genes have been reported in studies demonstrating association between the cleft lip and palate phenotypes and the alleles at single-nucleotide polymorphisms (SNPs) within specific genes. Recently, the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) has been revealed to be a novel candidate gene for NSCLP. The SNPs rs1546124, rs4783099 and rs16974880 in CRISPLD2 were highly significant in Caucasian and Hispanic multiplex families but showed no association in Colombian and Irish populations. In the current study, we examined these three SNPs in a northern Chinese population and found an association between these polymorphisms and NSCLP in both single-marker and haplotype analyses. Our data further strengthen the conclusion that altered CRISPLD2 is associated with NSCLP susceptibility.

A Comparison Between Ribo-minus RNA-sequencing and PolyA-selected RNA-sequencing

Genomics. Nov, 2010  |  Pubmed ID: 20688152

To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq method should detect more polyA- or bimorphic transcripts. Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles.

[Independent Component Analysis for Spectral Unmixing in Hyperspectral Remote Sensing Image]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Jun, 2010  |  Pubmed ID: 20707164

Hyperspectral remote sensing plays an important role in earth observation on land, ocean and atmosphere. A key issue in hyperspectral data exploitation is to extract the spectra of the constituent materials (endmembers) as well as their proportions (fractional abundances) from each measured spectrum of mixed pixel in hyperspectral remote sensing image, called spectral un-mixing. Linear spectral mixture model (LSMM) provides an effective analytical model for spectral unmixing, which assumes that there is a linear relationship among the fractional abundances of the substances within a mixed pixel. To be physically meaningful, LSMM is subject to two constraints: the first constraint requires all abundances to be nonnegative and the second one requires all abundances to be summed to one. Independent component analysis (ICA) has been proposed as an advanced tool to un-mix hyperspectral image. However, ICA is based on the assumption of mutually independent sources, which violates the constraint conditions in LSMM. This embarrassment compromises ICA applicability to hyperspectral data. To overcome this problem, the present paper introduces a solution of minimization of total correlation of the components. Interestingly, with the minimization of total correlation of the components, the angle of the direction between each components is invariable. A Parallel oblique-ICA (Pob-ICA) algorithm is proposed to correct the angle of the searching direction between the components. Two novelties result from our proposed Pob-ICA algorithm. First, the algorithm completely satisfies the physical constraint conditions in LSMM and overcomes the limitation of statistical independency assumed by ICA. Second, the last component, which is missed in other existing ICA algorithms, can be estimated by our proposed algorithm. In experiments, Pob-ICA algorithm demonstrates excellent performance in the simulative and real hyperspectral images.

Abundance and Diversity of Tetracycline Resistance Genes in Soils Adjacent to Representative Swine Feedlots in China

Environmental Science & Technology. Sep, 2010  |  Pubmed ID: 20707363

Tetracyclines are commonly used antibiotics in the swine industry for disease treatment and growth promotion. Tetracycline resistance was determined in soils sampled from farmlands in the vicinity of nine swine farms located in three cities in China. Totally, 15 tetracycline resistance (tet) genes were commonly detected in soil samples, including seven efflux pump genes (tetA, tetC, tetE, tetG, tetK, tetL, tetA/P), seven ribosomal protection proteins (RPPs) genes (tetM, tetO, tetQ, tetS, tetT, tetW, tetB/P), and one enzymatic modification gene (tetX). The quantitative real-time PCR was further used to quantify five RPPs genes (tetM, tetO, tetQ, tetW, tetT) and 16S rRNA gene abundances. The concentrations of total tetracyclines (5 typical tetracyclines and 10 of their degradation products) in these soils were measured using liquid chromatography-electrospray tandem mass spectrometry (LC-MS/MS) and were found to range from 5.4 to 377.8 μg·kg(-1) dry soil. Bivariate correlation analysis confirmed that absolute tet gene copies (sum of tetM, tetO, tetQ, tetW genes) were strongly correlated with the concentrations of tetracycline residues (r(2) = 0.45, P < 0.05), ambient bacterial 16S-rRNA gene copies in each soil sample (r(2) = 0.65, P < 0.01), and organic matter in soil (r(2) = 0.46, P < 0.05), respectively. Finally, the phylogenetic analysis on tetM combined with culture-independent molecular techniques revealed at least five genotypes of tetM in nine soil samples.

Ammonium Removal from Aqueous Solution by Zeolite X Synthesized from Halloysite Mineral

Water Science and Technology : a Journal of the International Association on Water Pollution Research. 2010  |  Pubmed ID: 20729599

Zeolite X was successfully synthesized from natural halloysite mineral by hydrothermal method. The synthesized zeolite X was characterized by XRD, SEM, TEM and HRTEM. The characterization indicated that zeolite X had high crystallinity together with symmetrical and uniform pore channels. Ammonium (NH₄+) adsorption properties of zeolite X were studied using batch experiments. The results revealed that high initial concentration and low temperature favored NH₄+ adsorption on zeolite X. Both Langmuir and Freundlich isotherms fit well with the equilibrium data. Kinetic studies showed that the adsorption followed pseudo-second-order model. Intra-particle diffusion analysis demonstrated that NH₄+ diffused quickly among the particles at the initial 20 min of the adsorption process, and then the diffusion slowed down and stabilized. Thermodynamic parameters such as change in free energy (ΔG⁰), enthalpy (ΔH⁰) and entropy (ΔS⁰) indicated that the adsorption was spontaneous and exothermic at ambient conditions. The reusable ability of zeolite X was also evaluated. Due to its low cost, high adsorption capacity and fast adsorption rate, zeolite X synthesized from halloysite could be used as an effective and environmental-friendly adsorbent for NH₄+ removal.

Equipment Setup for Drosophila Electrophysiology

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810624

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. This article describes the components of an electrophysiology setup, commonly referred to as an electrophysiology rig. The rig described here is based on equipment and software used in the Cold Spring Harbor Laboratory (CSHL) course "Neurobiology of Drosophila."

Electrophysiological Recording from a 'model' Cell

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810633

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. This protocol describes the basics of setting up and conducting electrophysiological experiments using a model cell. For the novice, a model cell provides a way to learn the operation of electrophysiology equipment and software without the anxiety of damaging living cells. This protocol also illustrates passive membrane properties such as the input resistance, capacitance, and time constant.

Electrophysiological Recording from Drosophila Larval Body-wall Muscles

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810634

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. This protocol describes the steps for performing intracellular recording from fly larval body-wall muscles and explains how to record and analyze spontaneous and evoked synaptic potentials. Methods used include larval dissection ("filleting"), identification of muscle fibers and their innervating nerves, the use of a micromanipulator and microelectrode in penetrating the muscle membrane, and nerve stimulation to evoke synaptic potentials.

Voltage-clamp Analysis of Synaptic Transmission at the Drosophila Larval Neuromuscular Junction

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810635

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. Although intracellular recording is particularly valuable in revealing membrane potential changes, it has several limitations. Primarily, it does not offer information on the kinetics of membrane currents associated with ion channels or synaptic receptors responsible for the potential change. Furthermore, the resting potential of the Drosophila body-wall muscle varies naturally such that the driving force also varies considerably, making it difficult to accurately compare the amplitude of minis (spontaneous miniature synaptic potentials) or evoked excitatory junction potentials (EJPs). Finally, accurate determination of quantal content based on minis and EJPs is possible only at low release conditions when nonlinear summation is not a major issue. The voltage-clamp technique can overcome these limitations by using negative feedback mechanisms to keep the cell membrane potential steady at any reasonable set points. In the large larval muscle cells of Drosophila, the two-electrode voltage-clamp (TEVC) method is used, in which one electrode monitors the cell membrane potential while the other electrode passes electric currents. This protocol introduces the application of TEVC in analysis of synaptic currents using the larval NMJ preparation.

Focal Recording of Synaptic Currents from Single Boutons at the Drosophila Neuromuscular Junction

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810636

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. Focal recording is an extracellular method designed for the study of synaptic activity of one or a few synaptic boutons rather than the ensemble activity of all of the boutons, as occurs with intracellular recording or the two-electrode voltage-clamp (TEVC) method. This is a useful technique for investigating the properties of different motor neurons that innervate the same muscle, applying statistical analysis to discrete synaptic events, and investigating the heterogeneity of synaptic release properties among boutons.

Fabrication of Microelectrodes, Suction Electrodes, and Focal Electrodes

Cold Spring Harbor Protocols. Sep, 2010  |  Pubmed ID: 20810637

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. This protocol details some basic methods for manufacturing microelectrodes used for intracellular recording and two-electrode voltage-clamp (TEVC), and loose patch electrodes used for focal recording. In addition, a method is provided for manufacturing homemade suction electrodes used for nerve stimulation.

A Genetic Mosaic Approach for Neural Circuit Mapping in Drosophila

Proceedings of the National Academy of Sciences of the United States of America. Sep, 2010  |  Pubmed ID: 20810922

Transgenic manipulation of subsets of brain cells is increasingly used for studying behaviors and their underlying neural circuits. In Drosophila, the GAL4-upstream activating sequence (UAS) binary system is powerful for gene manipulation, but GAL4 expression is often too broad for fine mapping of neural circuits. Here, we describe the development of unique molecular genetic tools to restrict GAL4 expression patterns. Building on the GAL4-UAS system, our method adds two components: a collection of enhancer-trap recombinase, Flippase (ET-FLP), transgenic lines that provide inheritable, reproducible, and tissue-specific FLP and an FRT-dependent GAL80 "flip-in" construct that converts FLP expression into tissue-specific repression of GAL4 by GAL80. By including a UAS-encoded fluorescent protein, circuit morphology can be simultaneously marked while the circuit function is assessed using another UAS transgene. In a proof-of-principle analysis, we applied this ET-FLP-induced intersectional GAL80/GAL4 repression (FINGR) method to map the neural circuitry underlying fly wing inflation. The FINGR system is versatile and powerful in combination with the vast collection of GAL4 lines for neural circuit mapping as well as for clonal analysis based on the infusion of the yeast-derived FRT/FLP system of mitotic recombination into Drosophila. The strategies and tactics underlying our FINGR system are also applicable to other genetically amenable organisms in which transgenes including the GAL4, UAS, GAL80, and FLP factors can be applied.

[Determination of Indicator Toxaphene in Soil by Isotope Dilution-gas Chromatography-tandem Mass Spectrometry]

Se Pu = Chinese Journal of Chromatography / Zhongguo Hua Xue Hui. May, 2010  |  Pubmed ID: 20812620

Although toxaphene is now banned in use, the analysis of toxaphene has attracted increasing interest due to its persistence and widespread atmospheric transport in the environment. A new method based on isotope dilution-gas chromatography-tandem mass spectrometry (ID-GC-MS/MS) has been developed for the determination of three toxaphene specific congeners comprised of Parlar No. 26 (P26), Parlar No. 50 (P50) and Parlar No. 62 (P62) in soil. (13)C10-labeled indicator toxaphene solution was added to the sample prior to pretreatment. Then the sample was extracted using pressurized liquid extraction (PLE) followed by purification on multilayer acidic silica column and neutral silica column. The eluent was concentrated under gentle nitrogen gas flow and spiked with the injection of internal standard of (13)C10-chlordane. Identification and quantification of the analytes were carried out in the multiple reaction monitoring (MRM) mode after the GC separation. The linear range was 20-800 microg/L for three congeners, limits of detection (LOD) ranged from 3.0 to 6.0 pg. The five point calibration curves showed a good linearity for all the congeners (R2 > 0.99). The relative standard deviations (RSDs) were below 11% for and the spiked recoveries were in the range of 55%-110%. The developed analytical method is suitable for the determination of toxaphene specific congeners in soil.

[Determination of Trace Organochlorine Pesticides in Soil Using Isotope Dilution-high Resolution Gas Chromatography]

Se Pu = Chinese Journal of Chromatography / Zhongguo Hua Xue Hui. May, 2010  |  Pubmed ID: 20812621

A method for the determination of trace organochlorine pesticides (OCPs) in soil using isotope dilution and high resolution gas chromatography-high resolution mass spectrometry (ID-HRGC-HRMS) was developed. The sample was extracted by accelerated solvent extractor (ASE) and cleaned-up by a Florisil solid phase extraction (SPE) cartridge. The analytes were separated by HRGC on a DB-5MS column (30 mx 0.25 mm x 0.25 microm) and determined by HRMS. The identifications of OCPs were based on the retention time of 13C-labelled standard and the abundance ratio of the two exact mass-to-charge ratios. The quantitative analysis was performed using the ratios of the integrated areas of the 13C-labelled standards. This method has the recoveries ranging from 77.3% to 114.5% and the relative standard deviations (RSD) less than 10.81% (n=5). The limits of detection (LODs) of this method for all OCPs were lower than 0.04 pg/g. The results indicated that the method is rapid, selective and sensitive for precise determination requirements of organochlorine pesticides at trace level in soil.

[Effects of Gutuo Qingfu Decoction Via Gastro-enteric Perfusion on 16SrRNA in Blood of Severe Multitraumatic Patients]

Zhongguo Zhong Xi Yi Jie He Za Zhi Zhongguo Zhongxiyi Jiehe Zazhi = Chinese Journal of Integrated Traditional and Western Medicine / Zhongguo Zhong Xi Yi Jie He Xue Hui, Zhongguo Zhong Yi Yan Jiu Yuan Zhu Ban. Jun, 2010  |  Pubmed ID: 20815272

To observe the effects of Gutuo Qingfu Decoction (GQD) via gastro-enteric perfusion on blood level of bacterial 16S rRNA gene in severe multi-traumatic (SMT) patients at early stage.

The Cysteine Protease Domain of Porcine Reproductive and Respiratory Syndrome Virus Non-structural Protein 2 Antagonizes Interferon Regulatory Factor 3 Activation

The Journal of General Virology. Dec, 2010  |  Pubmed ID: 20826620

There is growing evidence that porcine reproductive and respiratory syndrome virus (PRRSV) has developed mechanisms to subvert the host innate immune response. PRRSV non-structural protein 2 (Nsp2) was suggested previously as a potential interferon (IFN) antagonist. This study focused on Nsp2 to investigate its inhibitory mechanism of IFN induction. It was demonstrated that Nsp2 strongly inhibited IFN-β production by antagonizing activation of the IFN regulatory factor 3 (IRF-3) pathway induced by the Sendai virus (SeV). Further studies revealed that the cysteine protease domain (PL2) of Nsp2 was necessary for IFN antagonism. Additionally, both full-length Nsp2 and the PL2 protease domain of Nsp2 were found to inhibit SeV-induced phosphorylation and nuclear translocation of IRF-3. These findings suggest that Nsp2 is likely to play an important role in subversion of IRF-3-dependent innate antiviral defences, providing a basis for elucidating the mechanisms underlying PRRSV pathogenesis.

[Research on Crop-weed Discrimination Using a Field Imaging Spectrometer]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Jul, 2010  |  Pubmed ID: 20827980

Discrimination of weeds from crop is the first and important step for variable herbicides application and precise physical weed control. Using a new field imaging spectrometer developed by our group, hyperspectral images in the wavelength range 380-870 nm were taken in the wild for the investigation of crop-weed discrimination. After normalizing the data to reduce or eliminate the influence of varying illuminance, stepwise forward variable selection was employed to select the proper band sets and fisher linear discriminant analysis (LDA) was performed to discriminate crop and weeds. For the case of considering each species as a different class, classification accuracy reached 85% with eight selected bands while for the case of considering overall weed species as a class, classification accuracy was higher than 91% with seven selected bands. In order to develop a low-cost device and system in future, all combinations of two and three bands were evaluated to find the best combinations. The result showed that the best three bands can achieve a performance of 89% comparable to the performance achieved by five bands selected using stepwise selection. The authors also found that "red edge" could afford abundant information in the discrimination of weed and crop.

Study on the Adsorption of Neutral Red from Aqueous Solution Onto Halloysite Nanotubes

Water Research. Mar, 2010  |  Pubmed ID: 20003999

Halloysite nanotubes (HNTs), a low-cost available clay mineral, were tested for the ability to remove cationic dye, Neutral Red (NR), from aqueous solution. Natural HNTs used as adsorbent in this work were initially characterized by XRD, FT-IR, TEM and BET. The effect of adsorbent dose, initial pH, temperature, initial concentration and contact time were investigated. Adsorption increased with increase in adsorbent dose, initial pH, temperature and initial concentration. The equilibrium data were well described by both the Langmuir and Freundlich isotherm models. The maximum adsorption capacity was 54.85, 59.24 and 65.45mg/g at 298, 308 and 318K, respectively. Batch kinetic experiments showed that the adsorption followed pseudo-second-order kinetic model with correlation coefficients greater than 0.999. Thermodynamic parameters of DeltaG(0), DeltaH(0) and DeltaS(0) indicated the adsorption process was spontaneous and endothermic. The results above confirmed that HNTs had the potential to be utilized as low-cost and relatively effective adsorbent for cationic dyes removal.

Mechanism of CDK5 Activation Revealed by Steered Molecular Dynamics Simulations and Energy Calculations

Journal of Molecular Modeling. Jun, 2010  |  Pubmed ID: 20013135

In the current work, CDK5/p25 complexes were pulled apart by applying external forces with steered molecular dynamics (SMD) simulations. The crucial interactions between the kinase and the activation protein were investigated and the SMD simulations showed that several activation-relevant motifs of CDK5 leave p25 in sequence during the pulling and lead to an apo-CDK2 like CDK5 structure after separation. Based on systematic examination of hydrogen bond breaking and classical MD/molecular mechanics-generalized Born/surface area) (MM-GBSA) calculations, a CDK5 activation mechanism by p25 is suggested. This is the first step towards the systemic development of CDK inhibitors and the mechanism proposed could lead to a better understanding of the protein-protein recognition characteristics between the kinase and its activator.

Photodissociation of Cis-, Trans-, and 1,1-dichloroethylene in the Ultraviolet Range: Characterization of Cl((2)P(J)) Elimination

The Journal of Physical Chemistry. A. Jan, 2010  |  Pubmed ID: 20020718

By using photofragment velocity imaging detection coupled with a (2 + 1) resonance-enhanced multiphoton ionization technique, the elimination channel of spin-orbit chlorine atoms in photodissociation of cis-, trans-, and 1,1-dichloroethylene at two photolysis wavelengths of 214.5 and 235 nm is investigated. Translational energy and angular distributions of Cl((2)P(J)) fragmentation are acquired. The Cl((2)P(J)) fragments are produced by two competing channels. The fast dissociation component with higher translational energy is characterized by a Gaussian distribution, resulting from a curve crossing of the initially excited (pi, pi*) state to nearby repulsive (pi, sigma*) and/or (n, sigma*). In contrast, the slow component with a lower translational energy is characterized by a Boltzmann distribution, which dissociates on the vibrationally hot ground state relaxed from the (pi, pi*) state via internal conversion. cis-C(2)H(2)Cl(2) is found to have a larger branching of Boltzmann component than the other two isomers. The fraction of available energy partitioning into translation increases along the trend of cis- < trans- < 1,1-C(2)H(2)Cl(2). This trend may be fitted by a rigid radical model and interpreted by means of a torque generated during the C-Cl bond cleavage. The anisotropy parameters are determined, and the transition dipole moments are expected to be essentially along the C horizontal lineC bond axis. The results are also predicted theoretically. The relative quantum yields of Cl((2)P(J)) have a similar value for the three isomers at the two photolysis wavelengths.

Determination of Fab-hinge Disulfide Connectivity in Structural Isoforms of a Recombinant Human Immunoglobulin G2 Antibody

Analytical Chemistry. Feb, 2010  |  Pubmed ID: 20039682

The detection and characterization of unexpected disulfide-mediated structural variants of human immunoglobulin G2 (IgG2) antibodies was recently the subject of two copublications. In this paper, we present data to confirm the previously reported structures and elucidate the complete disulfide connectivity of each variant through the application of a novel analytical methodology. In this manner, the data illustrate the presence of at least five structural variants, including the classical structure with independent Fab domains and a hinge region. Multiple subvariants of the IgG2-A/B and IgG2-B structures are identified; these subvariants of each structure differ through the order of attachment of Fab peptides to the sequential hinge cysteines. Furthermore, the connectivity of a novel subvariant of IgG2-B containing an intrachain disulfide linkage in the lower hinge region is elucidated. The results presented in this paper reveal that the population of IgG2 disulfide structural variants is yet more complex than recently reported.

CanProVar: a Human Cancer Proteome Variation Database

Human Mutation. Mar, 2010  |  Pubmed ID: 20052754

Identification and annotation of mutated genes or proteins involved in oncogenesis and tumor progression are crucial for both cancer biology and clinical applications. We have developed a human Cancer Proteome Variation Database (CanProVar) by integrating information on protein sequence variations from various public resources, with a focus on cancer-related variations (crVAR). We have also built a user-friendly interface for querying the database. The current version of CanProVar comprises 8,570 crVARs in 2,921 proteins derived from existing genome variation databases and recently published large-scale cancer genome resequencing studies. It also includes 41,541 non-cancer specific variations (ncsVARs) in 30,322 proteins derived from the dbSNP database. CanProVar provides quick access to known crVARs in protein sequences along with related cancer samples, relevant publications, data sources, and functional information such as Gene Ontology (GO) annotations for the proteins, protein domains in which the variation occurs, and protein interaction partners with crVARs. CanProVar also helps reveal functional characteristics of crVARs and proteins bearing these variations. Our analysis showed that crVARs were enriched in certain protein domains. We also showed that proteins bearing crVARs were more likely to interact with each other in the protein interaction network. CanProVar can be accessed from http://bioinfo.vanderbilt.edu/canprovar.

Distinct Transcriptomes Define Rostral and Caudal Serotonin Neurons

The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Jan, 2010  |  Pubmed ID: 20071532

The molecular architecture of developing serotonin (5HT) neurons is poorly understood, yet its determination is likely to be essential for elucidating functional heterogeneity of these cells and the contribution of serotonergic dysfunction to disease pathogenesis. Here, we describe the purification of postmitotic embryonic 5HT neurons by flow cytometry for whole-genome microarray expression profiling of this unitary monoaminergic neuron type. Our studies identified significantly enriched expression of hundreds of unique genes in 5HT neurons, thus providing an abundance of new serotonergic markers. Furthermore, we identified several hundred transcripts encoding homeodomain, axon guidance, cell adhesion, intracellular signaling, ion transport, and imprinted genes associated with various neurodevelopmental disorders that were differentially enriched in developing rostral and caudal 5HT neurons. These findings suggested a homeodomain code that distinguishes rostral and caudal 5HT neurons. Indeed, verification studies demonstrated that Hmx homeodomain and Hox gene expression defined an Hmx(+) rostral subtype and Hox(+) caudal subtype. Expression of engrailed genes in a subset of 5HT neurons in the rostral domain further distinguished two subtypes defined as Hmx(+)En(+) and Hmx(+)En(-). The differential enrichment of gene sets for different canonical pathways and gene ontology categories provided additional evidence for heterogeneity between rostral and caudal 5HT neurons. These findings demonstrate a deep transcriptome and biological pathway duality for neurons that give rise to the ascending and descending serotonergic subsystems. Our databases provide a rich, clinically relevant resource for definition of 5HT neuron subtypes and elucidation of the genetic networks required for serotonergic function.

Identification of Immune Genes of the Agamaki Clam (Sinonovacula Constricta) by Sequencing and Bioinformatic Analysis of ESTs

Marine Biotechnology (New York, N.Y.). Jun, 2010  |  Pubmed ID: 19590922

The Agamaki clam (Sinonovacula constricta) is an economically important shellfish in Asia. However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. The objective of this study was to generate expressed sequence tags (ESTs) from a normalized liver complementary DNA library and to identify genes that function in immune defense. A total of 5,296 ESTs were sequenced, from which 540 contigs and 3,473 singletons were identified. BLAST homology analysis indicated that only 20.7% of these ESTs were homologues of known genes while the remaining 79.3% appeared to be novel sequences. Based on sequence similarities, 43 putative immune genes were identified that encode proteases and protease inhibitors, adhesive proteins, stress proteins, lysosomal enzymes, and signal transduction regulators. Our study thus provides both a large collection of novel transcripts and a detailed annotation of immune genes for an important bivalve species.

Cohort Profile: The China Health and Nutrition Survey--monitoring and Understanding Socio-economic and Health Change in China, 1989-2011

International Journal of Epidemiology. Dec, 2010  |  Pubmed ID: 19887509

Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Patients with Colon Cancer

Gastroenterology. Mar, 2010  |  Pubmed ID: 19914252

Staging inadequately predicts metastatic risk in patients with colon cancer. We used a gene expression profile derived from invasive, murine colon cancer cells that were highly metastatic in an immunocompetent mouse model to identify patients with colon cancer at risk of recurrence.

[Trend of Milk Consumption Among Chinese Children and Adolescents Aged 7 to 17 Years Old in 9 Provinces from 1991 to 2006.]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Dec, 2010  |  Pubmed ID: 21223662

OBJECTIVE: To investigate the trend of milk consumption among Chinese children and adolescents in 9 provinces from 1991 to 2006. METHODS: The paper was based on data collected in the China Health and Nutrition Survey in 1991, 1993, 1997, 2000, 2004, 2006 and the subjects aged 7 to 17 years old with complete 24-hour-dietary data for 3 days. Milk consumption in this paper was defined as intake offresh milk, powdered milk or yogurt, excluding other milk products and milk drinks. RESULTS: There were increasing trends of milk drinking rate and average amount of milk consumption per day in the period of 1991 - 2006, in which milk drinking rate among Chinese children and adolescents increased from 2.88% in 1991 to 13.88% in 2006. The average milk consumption per day increased from 3.90 g/day in 1991 to 26.11 g/day in 2006. There were significant differences regarding milk consumption, both on regional and economic levels. Although milk intake had been increasing in the past 15 years, there was still huge gap between the amount of consumption and the criterion of 300 g/day, proposed by the Chinese Dietary Guidelines (2007). The prevalence of dietary calcium intake under Adequate Intake value was still over 97%, indicating the need of more efforts to be made. CONCLUSION: The condition of milk intake was improved significantly from 1991 to 2006. However, there was widespread deficiency in milk consumption among Chinese children and adolescents, calling for strengthening the macro-control, optimizing the production and conducting education on nutrition, and improving milk consumption among the Chinese children and adolescents.

{μ(2)-6,6'-Dimeth-oxy-2,2'-[butane-1,4-diylbis(nitrilo-methyl-idyne)]diphenolato}trinitratocopper(II)neodymium(III)

Acta Crystallographica. Section E, Structure Reports Online. 2010  |  Pubmed ID: 21588850

In the title complex, [CuNd(C(20)H(22)N(2)O(4))(NO(3))(3)], the Cu(II) ion is coordinated in a distorted square-planar environment by two O atoms and two N atoms of a tetra-dentate Schiff base ligand. The Nd(III) ion is ten-coordinated by three bis-chelating nitrate groups and four O atoms of the Schiff base ligand. The atoms of one of the nitrato ligands are disordered over two sets of sites, with refined occupancies of 0.567 (13) and 0.433 (17).

Relating Protein Adduction to Gene Expression Changes: a Systems Approach

Molecular BioSystems. Jul, 2011  |  Pubmed ID: 21594272

Modification of proteins by reactive electrophiles such as the 4-hydroxy-2-nonenal (HNE) plays a critical role in oxidant-associated human diseases. However, little is known about protein adduction and the mechanism by which protein damage elicits adaptive effects and toxicity. We developed a systems approach for relating protein adduction to gene expression changes through the integration of protein adduction, gene expression, protein-DNA interaction, and protein-protein interaction data. Using a random walk strategy, we expanded a list of responsive transcription factors inferred from gene expression studies to upstream signaling networks, which in turn allowed overlaying protein adduction data on the network for the prediction of stress sensors and their associated regulatory mechanisms. We demonstrated the general applicability of transcription factor-based signaling network inference using 103 known pathways. Applying our workflow on gene expression and protein adduction data from HNE-treatment not only rediscovered known mechanisms of electrophile stress but also generated novel hypotheses regarding protein damage sensors. Although developed for analyzing protein adduction data, the framework can be easily adapted for phosphoproteomics and other types of protein modification data.

Elimination Mechanisms of Br(2)+ and Br+ in Photodissociation of 1,1- and 1,2-dibromoethylenes Using Velocity Imaging Technique

The Journal of Chemical Physics. May, 2011  |  Pubmed ID: 21599064

Elimination pathways of the Br(2)(+) and Br(+) ionic fragments in photodissociation of 1,2- and 1,1-dibromoethylenes (C(2)H(2)Br(2)) at 233 nm are investigated using time-of-flight mass spectrometer equipped with velocity ion imaging. The Br(2)(+) fragments are verified not to stem from ionization of neutral Br(2), that is a dissociation channel of dibromoethylenes reported previously. Instead, they are produced from dissociative ionization of dibromoethylene isomers. That is, C(2)H(2)Br(2) is first ionized by absorbing two photons, followed by the dissociation scheme, C(2)H(2)Br(2)(+) + hv→Br(2)(+) + C(2)H(2). 1,2-C(2)H(2)Br(2) gives rise to a bright Br(2)(+) image with anisotropy parameter of -0.5 ± 0.1; the fragment may recoil at an angle of ∼66° with respect to the C=C bond axis. However, this channel is relatively slow in 1,1-C(2)H(2)Br(2) such that a weak Br(2)(+) image is acquired with anisotropy parameter equal to zero, indicative of an isotropic recoil fragment distribution. It is more complicated to understand the formation mechanisms of Br(+). Three routes are proposed for dissociation of 1,2-C(2)H(2)Br(2), including (a) ionization of Br that is eliminated from C(2)H(2)Br(2) by absorbing one photon, (b) dissociation from C(2)H(2)Br(2)(+) by absorbing two more photons, and (c) dissociation of Br(2)(+). Each pathway requires four photons to release one Br(+), in contrast to the Br(2)(+) formation that involves a three-photon process. As for 1,1-C(2)H(2)Br(2), the first two pathways are the same, but the third one is too weak to be detected.

Phenanthrenes from Juncus Effusus with Anxiolytic and Sedative Activities

Natural Product Research. Oct, 2011  |  Pubmed ID: 22017742

Eight phenanthrenes, 7-carboxy-2-hydroxy-1-methyl-5-vinyl-phenanthrene (1); 2,7-dihydroxy-1-methyl-5-aldehyde-9,10-dihydrophenanthrene (2); dehydroeffusol (3); dehydrojuncusol (4); 7-carboxy-2-hydroxy-1-methyl-5-vinyl-9,10-dihydrophenanthrene (5); 8-carboxy-2-hydroxy-1-methyl-5-vinyl-9,10-dihydrophenanthrene (6); effusol (7) and juncusol (8), were isolated from the aerial part of Juncus effusus. Compounds 1 and 2 were identified as new constituents. Compounds 7 and 8 showed anxiolytic and sedative activities.

Estimation and Characterization of PCDD/Fs, Dl-PCBs, PCNs, HxCBz and PeCBz Emissions from Magnesium Metallurgy Facilities in China

Chemosphere. Dec, 2011  |  Pubmed ID: 22024095

Magnesium production is considered to be one potential source of unintentional persistent organic pollutants (unintentional POPs). However, studies on the emissions of unintentional POPs from magnesium metallurgy are still lacking. Emissions of unintentional POPs, such as polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs), dioxin-like polychlorinated biphenyls (dl-PCBs), polychlorinated naphthalenes (PCNs), hexachlorobenzene (HxCBz) and pentachlorobenzene (PeCBz) are covered under the Stockholm Convention. In this study, these emissions were investigated through a magnesium smelting process. Stack gas and fly ash samples from a typical magnesium plant in China were collected and analyzed to estimate the emissions of unintentional POPs from magnesium metallurgy. Emissions factors of 412 ng TEQ t(-1) for PCDD/Fs, 18.6 ng TEQ t(-1) for dl-PCBs, 3329 μg t(-1) for PCNs, 820 μg t(-1) for HxCBz, and 1326 μg t(-1) for PeCBz were obtained in 2009. Annual emissions from magnesium metallurgy in China were estimated to be 0.46 g WHO-TEQ for PCDD/Fs and dl-PCBs, 1651 g for PCNs, 403 g for HxCBz and 653 g for PeCBz, respectively.

[The Status and Trend of Cereal Consumption Among Chinese Adults in Nine Provinces (municipality) from 1989 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Sep, 2011  |  Pubmed ID: 22177301

To explore the status and trend of cereal consumption among Chinese adults aged 18 to 59 years in nine provinces (municipality) from 1989 to 2006.

Controlling Air Pollution from Coal Power Plants in China: Incremental Change or a Great Leap Forward

Environmental Science & Technology. Dec, 2011  |  Pubmed ID: 22111961

Wireless Intra-brain Communication for Image Transmission Through Mouse Brain

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. Aug, 2011  |  Pubmed ID: 22254951

We demonstrate wireless image data transmission through a mouse brain. The transmission characteristics of mouse brain is measured. By inserting electrodes into the brain, the transmission efficiency is drastically increased. An AM signal modulated with the image data from an implantable image sensor was launched into the brain and the received signal was demodulated. The data was successfully transmitted through the brain and the image was reproduced.

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

Genomics, Proteomics & Bioinformatics / Beijing Genomics Institute. Dec, 2011  |  Pubmed ID: 22289480

The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn't taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net.

The Role of Vanin-1 and Oxidative Stress-related Pathways in Distinguishing Acute and Chronic Pediatric ITP

Blood. Apr, 2011  |  Pubmed ID: 21325602

Pediatric immune thrombocytopenia (ITP) is usually self-limited. However, approximately 20% of children develop chronic ITP, which can be associated with significant morbidity because of long-term immunosuppression and splenectomy in refractory cases. To explore the molecular mechanism of chronic ITP compared with acute ITP, we studied 63 pediatric patients with ITP. Gene expression analysis of whole blood revealed distinct signatures for acute and chronic ITP. Oxidative stress-related pathways were among the most significant chronic ITP-associated pathways. Overexpression of VNN1, an oxidative stress sensor in epithelial cells, was most strongly associated with progression to chronic ITP. Studies of normal persons demonstrated VNN1 expression in a variety of blood cells. Exposure of blood mononuclear cells to oxidative stress inducers elicited dramatic up-regulation of VNN1 and down-regulation of PPARγ, indicating a role for VNN1 as a peripheral blood oxidative stress sensor. Assessment of redox state by tandem mass spectrometry demonstrated statistically significant lower glutathione ratios in patients with ITP versus healthy controls; lower glutathione ratios were also seen in untreated patients with ITP compared with recently treated patients. Our work demonstrates distinct patterns of gene expression in acute and chronic ITP and implicates oxidative stress pathways in the pathogenesis of chronic pediatric ITP.

[Analysis on the Status of Vitamin A Deficiency Among Children Under 5 Years Old in Poor Rural Areas of 6 Western Chinese Provinces in 2009]

Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. Dec, 2011  |  Pubmed ID: 22336605

To analyze the status of vitamin A deficiency among children under 5 years old in poor rural areas of 6 Western Chinese provinces in 2009.

[Mathematical Analysis of Characteristics of Glucocorticoid-induced Yang Deficiency or Yin Deficiency Syndrome in Animal Models Based on Information Entropy Theory]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Jan, 2011  |  Pubmed ID: 21227028

Based on information entropy theory, this study analyzes the experimental indicators of glucocorticoid-induced traditional Chinese medicine yang deficiency or yin deficiency syndrome in animal models, thus laying the foundation of defining and interpreting the model state.

Therapeutic Efficacy of Stemazole in a Beta-amyloid Injection Rat Model of Alzheimer's Disease

European Journal of Pharmacology. Apr, 2011  |  Pubmed ID: 21316359

Alzheimer's disease is one of the most devastating neurodegenerative disorders and is characterized by severe memory and cognitive decline. The deposition of beta-amyloid (Aβ) protein is the primary pathology associated with Alzheimer's disease. Current treatments for Alzheimer's disease only offer limited symptomatic alleviation, and more effective therapies are needed for Alzheimer's disease. Our primary data showed that stemazole, a novel small molecule, protected SH-SY5Y cells from toxicity induced by hydrogen peroxide and Aβ aggregates in vitro. In this study, we evaluated the therapeutic effects of a 14-day stemazole treatment in Aβ1-40 aggregate injection rat model of Alzheimer's disease. Administration of stemazole reversed learning and memory deficits induced by the Aβ1-40 aggregates in a dose-dependent manner, as assessed by a Morris water maze task. In addition, the number of Aβ1-40 aggregates was reduced in the hippocampus, as demonstrated by micro-positron emission tomography/computerized tomographic scanning. Finally, stemazole treatment reduced degeneration and the loss of neurons in the hippocampus, as shown by histology and immunohistochemical analysis. The neuroprotective effects of stemazole may be important for its therapeutic efficacy. These results demonstrate that stemazole is effective in the treatment of Aβ1-40 aggregates injection rat model, suggesting that this compound may be used as a therapeutic agent against Alzheimer's disease.

Salvianic Borneol Ester Reduces β-amyloid Oligomers and Prevents Cytotoxicity

Pharmaceutical Biology. Oct, 2011  |  Pubmed ID: 21936627

The destabilization of β-amyloid (Aβ) peptide aggregates and the protection of functional cells are the attractive therapeutic strategies for Alzheimer's disease (AD). Some active ingredients of Salvia miltiorrhiza f. alba C.Y.Wu & H.W.Li (Lamiaceae) (SM) have attracted increasing attention for the treatment of neurodegenerative diseases.

Evaluation of Apparent Diffusion Coefficient Mappings in Amnestic Mild Cognitive Impairment Using an Image Analysis Software Brain Search

Acta Radiologica (Stockholm, Sweden : 1987). Dec, 2011  |  Pubmed ID: 21969707

The apparent diffusion coefficient (ADC) from diffusion-weighted imaging (DWI) can quantify alterations in water diffusivity resulting from microscopic structural changes from amnestic mild cognitive impairment (aMCI) and Alzheimer's disease (AD).

DNA Methylation in the Rat Livers Induced by Low Dosage Isoniazid Treatment

Environmental Toxicology and Pharmacology. Nov, 2011  |  Pubmed ID: 22004970

As a first-line anti-tuberculosis drug, isoniazid has a serious adverse side effect: hepatotoxicity. Therefore, the assessment and monitoring of hepatotoxicity from isoniazid to prevent liver injury are great concerns. In this experiment, we compared the levels of ALT in plasma and DNA methylation. 30 male SD rats were allocated randomly into two groups, a control group and an isoniazid group, and treated, respectively, with pure water and isoniazid at low dosage (10 mg/(kg day)) for 42 days by oral gavage. Five rats per group were sacrificed after 14, 28, and 42 days of isoniazid treatment. The levels of methylation in the genome and LINE-1 were measured, in which hypomethylation in the whole genome and LINE-1 repetitive sequences was observed in the INH group during the later period of the experiment (the 42nd day) accompanied with pathological changes in the liver. Thus, our results suggest that low dose of isoniazid can induce liver injury and that level of DNA methylation may be a more sensitive marker for monitoring drug-induced hepatotoxicity than aminotransferase.

Quantifying the Relationships of Blood Pressure with Weight, Height and Body Mass Index in Chinese Children and Adolescents

Journal of Paediatrics and Child Health. Nov, 2011  |  Pubmed ID: 22050622

Aim:  The aim of this study was to quantify the relationships of height, weight and body mass index (BMI) with blood pressure (BP) levels in Chinese children and adolescents. Methods:  Height, weight, BMI and BP measurements were obtained from a nationally representative sample of 231 227 children aged 7-18 years. Body size measurements were converted to age- and sex-specific standard deviation (SD) scores. The relationships between body size and BP measurements were assessed using linear regression analysis. Results:  All body size measurements were significantly associated with BP levels. Systolic BP increased 4.14, 3.70 and 2.88 mmHg in boys and 2.98, 2.63 and 1.87 mmHg in girls, corresponding to 1 SD increase in weight, BMI and height, respectively. A similar pattern was also observed for diastolic BP. After adjustment for height, systolic BP increased substantially with increasing weight (3.96 mmHg/SD increase for boys and 2.92 mmHg for girls). With adjustment for weight, systolic BP increased slightly with 1 SD increase in height (0.27 mmHg for boys and 0.10 mmHg for girls). The strength of the association between a body size measurement and BP varied among different ages, peaked at 10-11 years in girls and around 12-14 years in boys. Conclusions:  Weight is the most powerful driving force of BP in children and adolescents, followed by BMI and height. Height has little impact on BP in children with a given weight, while weight has considerable impact on BP in children with a given height.

{μ-6,6'-Dimeth-oxy-2,2'-[butane-1,4-diylbis(nitrilo-methanylyl-idene)]diphenolato}trinitratocopper(II)samarium(III)

Acta Crystallographica. Section E, Structure Reports Online. Sep, 2011  |  Pubmed ID: 22058850

In the monomeric dinuclear title complex, [CuSm(C(20)H(22)N(2)O(4))(NO(3))(3)], the four-coordinate Cu(II) ion has a square-planar geometry involving two O atoms and two N atoms of the deprotonated Schiff base ligand. The Sm(III) ion is ten-coordinate, chelated by four O donor atoms of the Schiff base and two O atoms each from three bidentate nitrate groups, one of which is disordered over two sites in a 0.55 (7):0.45 (7) ratio.

Multifunctional Gold-silica Nanostructures for Ultrasensitive Electrochemical Immunoassay of Streptomycin Residues

ACS Applied Materials & Interfaces. Dec, 2011  |  Pubmed ID: 22059488

A facile and simple electrochemical immunoassay for ultrasensitive determination of streptomycin residues (STR) in food was designed by using nanogold-assembled mesoporous silica (GMSNs) as bionanolabels on a three-dimensional redox-active organosilica-functionalized sensing interface. To construct such a sensing interface, we initially synthesized organosilica colloids by using wet chemical method, and then utilized the prepared colloidal organosilica nanocomposites for the immobilization of monoclonal anti-STR antibodies on a glassy carbon electrode based on a sol-gel method. The bionanolabels were prepared based on coimmobilization of horseradish peroxidase (HRP) and STR-bovine serum albumin conjugates (STR-BSA) on the GMSNs. With a competitive-type immunoassay format, the assay toward STR analyte was carried out in pH 5.5 acetate acid buffer (ABS) by using redox-active organosilica nanocomposites as electron mediators, biofunctionalized GMSNs as traces, and hydrogen peroxide (H(2)O(2)) as enzyme substrate. Under optimal conditions, the reduction current of the electrochemical immunosensor decreased with the increase in STR level in the sample, and displayed a wide dynamic range of 0.05-50 ng mL(-1) with a low detection limit (LOD) of 5 pg mL(-1) at 3s(B). Intra- and interassay coefficients of variation were less than 8.7 and 9.3% for STR detection, respectively. In addition, the methodology was validated with STR spiked samples including honey, milk, kidney, and muscle, receiving a good correspondence with the results obtained from high-performance liquid chromatography (HPLC).

Elevated Levels of the Vesicular Monoamine Transporter and a Novel Repetitive Behavior in the Drosophila Model of Fragile X Syndrome

PloS One. 2011  |  Pubmed ID: 22087250

Fragile X Syndrome (FXS) is characterized by mental impairment and autism in humans, and it often features hyperactivity and repetitive behaviors. The mechanisms for the disease, however, remain poorly understood. Here we report that the dfmr1 mutant in the Drosophila model of FXS grooms excessively, which may be regulated differentially by two signaling pathways. Blocking metabotropic glutamate receptor signaling enhances grooming in dfmr1 mutant flies, whereas blocking the vesicular monoamine transporter (VMAT) suppresses excessive grooming. dfmr1 mutant flies also exhibit elevated levels of VMAT mRNA and protein. These results suggest that enhanced monoamine signaling correlates with repetitive behaviors and hyperactivity associated with FXS.

[Meta-analysis of Surgical Techniques for Preventing Frey Syndrome and a Concave Facial Deformity After Parotidectomy]

Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi = Chinese Journal of Otorhinolaryngology Head and Neck Surgery. Jul, 2011  |  Pubmed ID: 22088289

To explore the curative effects on surgical methods for the prevention of Frey syndrome and a concave facial deformity after parotidectomy.

[Effects of PTHrP and Notch Signaling on the Proliferation of Epiphysis Stem Cells]

Zhonghua Yi Xue Za Zhi. Aug, 2011  |  Pubmed ID: 22093939

To study the regulation of the proliferation of epiphysis stem cells by the PTHrP (parathyroidhormone related peptide) and Notch signaling systems.

[A Method of Endmember Extraction in Hyperspectral Remote Sensing Images Based on Discrete Particle Swarm Optimization (D-PSO)]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Sep, 2011  |  Pubmed ID: 22097848

For the inaccuracy of endmember extraction caused by abnormal noises of data during the mixed pixel decomposition process, particle swarm optimization (PSO), a swarm intelligence algorithm was introduced and improved in the present paper. By re-defining the position and velocity representation and data updating strategies, the algorithm of discrete particle swarm optimization (D-PSO) was proposed, which made it possible to search resolutions in discrete space and ultimately resolve combinatorial optimization problems. In addition, by defining objective functions and feasible solution spaces, endmember extraction was converted to combinatorial optimization problem, which can be resolved by D-PSO. After giving the detailed flow of applying D-PSO to endmember extraction and experiments based on simulative data and real data, it has been verified the algorithm's flexibility to handle data with abnormal noise and the reliability of endmember extraction were verified. Furthermore, the influence of different parameters on the algorithm's performances was analyzed thoroughly.

Maternal Cigarette Smoking and the Associated Risk of Having a Child with Orofacial Clefts in China: a Case-control Study

Journal of Cranio-maxillo-facial Surgery : Official Publication of the European Association for Cranio-Maxillo-Facial Surgery. Jul, 2011  |  Pubmed ID: 20832329

We investigated whether maternal and paternal cigarette smoking during early pregnancy could increase the risk of delivering an infant with an orofacial cleft.

Expression of the C-terminal ORF2 Protein of Duck Astrovirus for Application in a Serological Test

Journal of Virological Methods. Jan, 2011  |  Pubmed ID: 20863856

Duck astrovirus (DAstV) is an important pathogen causing duck viral hepatitis (DVH), a highly contagious and fatal disease in young ducklings. To provide an antigen for a diagnostic serum test, the C-terminus of DAstV ORF2 protein was expressed in Escherichia coli. Four positive and 30 negative sera were used to validate the purified ORF2 protein by developing an indirect enzyme-linked immunosorbent assay (ELISA). No cross-reactions were found against other duck pathogens, including duck hepatitis A virus, duck plague herpesvirus, duck reovirus, Newcastle disease virus, and Riemerella anatipestifer 12/19 (63.2%) and 26/51 (51%) sera samples from two flocks of ducks that survived DAstV infections in commercial duck farms were positive for DAstV by this method, respectively. Interestingly, DAstV-specific antibodies were also detected in 12 (28.6%) of 42 sera samples from a different flock without DVH, indicating a wide distribution of subclinical infections caused by DAstV.

[Progress of Cohort Study and Its Inspiration to China Health and Nutrition Survey]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624321

[Milk Consumption and Its Changing Trend of Chinese Adult Aged 18 - 44 in Nine Provinces (autonomous Region) from 1991 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624323

To investigate the age, gender and region specified milk consumption and its changing trends of Chinese 18 - 44 years old adults in 9 provinces (autonomous region) from 1991 to 2006.

[The Status of Dietary Sodium Intake of Chinese Population in Nine Provinces (autonomous Region) from 1991 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624324

To analyze the status of dietary sodium intake of 18 - 65 years old Chinese people in nine provinces (autonomous region) in 1991 and 2006.

[Milk Consumption and Effects on Dietary Nutrients and Growth Status Among Chinese Children in Nine Provinces (autonomous Region) from 1991 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624325

To investigate milk consumption and effects on dietary nutrients and growth status among 7 - 17 years-old Chinese children in 9 provinces (autonomous region) from 1991 to 2006.

[Trends of the Dietary Fiber Intake Among Chinese Aged 18 - 45 in Nine Provinces (autonomous Region) from 1989 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624326

To analyze the status and trend of dietary fiber intake and its food sources among Chinese residents aged 18 - 45 years old in 9 provinces (autonomous region), from 1989 to 2006.

[Status and Trend of Alcohol Consumption Among Adults in Nine Provinces (antonomous Region) of China from 1993 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624327

To understand the status and trend of alcohol consumption among adult people living in 9 provinces (autonomous region) of China from 1993 to 2006.

[Food Consumption Trend of Chinese Adults in Nine Provinces (autonomous Region) from 1989 to 2006]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Apr, 2011  |  Pubmed ID: 21624328

To analyze the trends of food consumption among Chinese residents aged from 18 to 59 years old in 9 provinces (autonomous region) from 1989 to 2006.

Analytical Characterization of a Novel Degradation Product in a PEGylated Recombinant Protein

Journal of Pharmaceutical Sciences. Nov, 2011  |  Pubmed ID: 21647888

We report the identification and characterization of a novel degradation product associated with PEGylation of a recombinant protein. After several months of storage at 2°C-8°C, an unexpected increase was observed in the proportion of an impurity that eluted with the native unPEGylated protein by size exclusion chromatography--from less than 0.01% at the start of storage to more than 0.25% at 12 months. An investigation into the nature of the impurity determined the presence of an N-terminal adduction with a mass increase of +58 Da over the native unPEGylated protein species, demonstrating that this impurity was the result of degradation. The impurity was subjected to thorough analytical characterization using orthogonal methods to establish its identity, and a mechanistic model proposed for its formation. The data implicate the presence of a monomethoxy polyethylene glycol (mPEG)-acetal aldehyde impurity in the mPEG-aldehyde raw material, indicating the need for diligent raw material testing prior to use.

[Classification of 365 Chinese Medicines in Shennong's Materia Medica Classic Based on a Semi-supervised Incremental Clustering Method]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Jun, 2011  |  Pubmed ID: 21669172

Evidence of the pharmacological activity of traditional Chinese medicine (TCM) provides the basis for clinical prescription. Study of the classification of Chinese medicines according to these activities is key to understanding the general active tendencies of medicinal prescriptions, exploring their material basis, investigating their properties and searching for their alternatives. Taking the herbal classic Shennong's Materia Medica Classic (Shennong Bencao Jing) for the data source, this paper studied the classification of Chinese medicines based on semi-supervised incremental clustering algorithm using "micro-cluster" concept in order to investigate the complex similarity among Chinese medicines. The results showed that 253 Chinese medicines were reasonably classified into 14 types, such as invigoration, clearing heat, diuresis, dredging blockages in the channels, treating gynecological conditions and treating strange diseases caused by ghosts. The results also showed that the other 112 Chinese medicines were classified into 112 individual types and the same high similarity to different known types was the main reason for this. The semi-supervised incremental clustering algorithm employed in the study had a high quality and a good development for clustering which is suitable for classification of Chinese medicines. This study illustrated the diversity of Chinese medicines and their complex similarities, thus aiming to provide innovative ideas and methods for related research.

[Geographic Distribution and Secular Trend of Menarche in 9-18 Year-old Chinese Han Girls]

Beijing Da Xue Xue Bao. Yi Xue Ban = Journal of Peking University. Health Sciences. Jun, 2011  |  Pubmed ID: 21681264

To analyze the characteristics and secular trend of age at menarche (age at menarche, AAM) in Chinese girls aged 9-18.

First BRET-based Screening Assay Performed in Budding Yeast Leads to the Discovery of CDK5/p25 Interaction Inhibitors

Biotechnology Journal. Jul, 2011  |  Pubmed ID: 21681968

The protein kinase CDK5 (cyclin-dependent kinase 5) is activated through its association with a cyclin-like protein p35 or p39. In pathological conditions (such as Alzheimer's disease and various other neuropathies), truncation of p35 leads to the appearance of the p25 protein. The interaction of p25 with CDK5 up-regulates the kinase activity and modifies the substrate specificity. ATP-mimetic inhibitors of CDK5 have already been developed. However, the lack of selectivity of such inhibitors is often a matter of concern. An alternative approach can be used to identify highly specific inhibitors that disrupt protein interactions involving protein kinases. We have developed a bioluminescence resonance energy transfer (BRET)-based screening assay in yeast to discover protein-protein interaction inhibitors (P2I2). Here, we present the first use of BRET in yeast for the screening of small molecule libraries. This screening campaign led to the discovery of one molecule that prevents the interaction between CDK5 and p25, thus inhibiting the protein kinase activity. This molecule may give rise to high-specificity drug candidates.

An in Silico Approach for the Discovery of CDK5/p25 Interaction Inhibitors

Biotechnology Journal. Jul, 2011  |  Pubmed ID: 21681969

The lack of selectivity of all existing ATP competitive inhibitors for a single cyclin-dependent kinase (CDK) has led us to redirect the structure-based molecule design from targeting the classic ATP-binding pocket in CDK5 toward the CDK5/p25 interface. The aim was to seek novel inhibition mechanisms to interrupt protein-protein interactions. A combined strategy of alanine-scanning calculations for locating binding sites, virtual screening for small molecules, molecular dynamics simulations for examining the binding stability of virtual screening hits and bio-assays for testing the level of inhibition was set up and used to explore novel inhibitors capable of interrupting the interactions between the proteins, and consequently of inhibiting the kinase activity. Two compounds were shown to inhibit the complex formation between CDK5 and p25 through p25 binding. They could open avenues for the discovery of new types of structures that prevent interactions between CDK5 and p25 or other CDK and activator proteins, and, more importantly, provide leads in the development of selective inhibitors among CDKs.

Characterization of EhaJ, a New Autotransporter Protein from Enterohemorrhagic and Enteropathogenic Escherichia Coli

Frontiers in Microbiology. 2011  |  Pubmed ID: 21687429

Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are diarrheagenic pathotypes of E. coli that cause gastrointestinal disease with the potential for life-threatening sequelae. While certain EHEC and EPEC virulence mechanisms have been extensively studied, the factors that mediate host colonization remain to be properly defined. Previously, we identified four genes (ehaA, ehaB, ehaC, and ehaD) from the prototypic EHEC strain EDL933 that encode for proteins that belong to the autotransporter (AT) family. Here we have examined the prevalence of these genes, as well as several other AT-encoding genes, in a collection of EHEC and EPEC strains. We show that the complement of AT-encoding genes in EHEC and EPEC strains is variable, with some AT-encoding genes being highly prevalent. One previously uncharacterized AT-encoding gene, which we have termed ehaJ, was identified in 12/44 (27%) of EHEC and 2/20 (10%) of EPEC strains. The ehaJ gene lies immediately adjacent to a gene encoding a putative glycosyltransferase (referred to as egtA). Western blot analysis using an EhaJ-specific antibody indicated that EhaJ is glycosylated by EgtA. Expression of EhaJ in a recombinant E. coli strain, revealed EhaJ is located at the cell surface and in the presence of the egtA glycosyltransferase gene mediates strong biofilm formation in microtiter plate and flow cell assays. EhaJ also mediated adherence to a range of extracellular matrix proteins, however this occurred independent of glycosylation. We also demonstrate that EhaJ is expressed in a wild-type EPEC strain following in vitro growth. However, deletion of ehaJ did not significantly alter its adherence or biofilm properties. In summary, EhaJ is a new glycosylated AT protein from EPEC and EHEC. Further studies are required to elucidate the function of EhaJ in colonization and virulence.

Evolutionary Conserved MicroRNAs Are Ubiquitously Expressed Compared to Tick-specific MiRNAs in the Cattle Tick Rhipicephalus (Boophilus) Microplus

BMC Genomics. 2011  |  Pubmed ID: 21699734

MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus.

Study of Ultrafast Dynamics of 2-picoline by Time-resolved Photoelectron Imaging

The Journal of Chemical Physics. Jun, 2011  |  Pubmed ID: 21702550

The dynamics of electronically excited states in 2-picoline is studied using femtosecond time-resolved photoelectron imaging spectroscopy. The internal conversion from the S(2) state to the vibrationally excited S(1) state is observed in real time. The secondarily populated high vibronic S(1) state deactivates further to the S(0) state. Photoelectron energy and angular distributions reveal the feature of ionization from the singlet 3p Rydberg states. In addition, variation of time-dependent anisotropy parameters indicates the rotational coherence of the molecule.

Loss of Drosophila Melanogaster P21-activated Kinase 3 Suppresses Defects in Synapse Structure and Function Caused by Spastin Mutations

Genetics. Sep, 2011  |  Pubmed ID: 21705760

Microtubules are dynamic structures that must elongate, disassemble, and be cleaved into smaller pieces for proper neuronal development and function. The AAA ATPase Spastin severs microtubules along their lengths and is thought to regulate the balance between long, stable filaments and shorter fragments that seed extension or are transported. In both Drosophila and humans, loss of Spastin function results in reduction of synaptic connections and disabling motor defects. To gain insight into how spastin is regulated, we screened the Drosophila melanogaster genome for deletions that modify a spastin overexpression phenotype, eye size reduction. One suppressor region deleted p21-activated kinase 3 (pak3), which encodes a member of the Pak family of actin-regulatory enzymes, but whose in vivo function is unknown. We show that pak3 mutants have only mild synaptic defects at the larval neuromuscular junction, but exhibit a potent genetic interaction with spastin mutations. Aberrant bouton morphology, microtubule distribution, and synaptic transmission caused by spastin loss of function are all restored to wild type when pak3 is simultaneously reduced. Neuronal overexpression of pak3 induces actin-rich thin projections, suggesting that it functions in vivo to promote filopodia during presynaptic terminal arborization. pak3 therefore regulates synapse development in vivo, and when mutated, suppresses the synaptic defects that result from spastin loss.

Coherence Generation and Population Transfer by Stimulated Raman Adiabatic Passage and π Pulse in a Four-level Ladder System

Optics Express. Jun, 2011  |  Pubmed ID: 21716434

We propose a new scheme for achieving the complete population transfer and the optimal coherence generation between the ground state and the Rydberg state in a four-level ladder system by combining the STIRAP or fractional STIRAP technique and the π pulse technique. We consider, in particular, two different situations where spontaneous emission from the two highest states are neglected or not. Our numerical calculations show that the time width and the delay time of the π pulse are two critical parameters for attaining the maximal population transfer and coherence generation in this scheme.

Rapid Growth of a Hepatocellular Carcinoma and the Driving Mutations Revealed by Cell-population Genetic Analysis of Whole-genome Data

Proceedings of the National Academy of Sciences of the United States of America. Jul, 2011  |  Pubmed ID: 21730188

We present the analysis of the evolution of tumors in a case of hepatocellular carcinoma. This case is particularly informative about cancer growth dynamics and the underlying driving mutations. We sampled nine different sections from three tumors and seven more sections from the adjacent nontumor tissues. Selected sections were subjected to exon as well as whole-genome sequencing. Putative somatic mutations were then individually validated across all 9 tumor and 7 nontumor sections. Among the mutations validated, 24 were amino acid changes; in addition, 22 large indels/copy number variants (>1 Mb) were detected. These somatic mutations define four evolutionary lineages among tumor cells. Separate evolution and expansion of these lineages were recent and rapid, each apparently having only one lineage-specific protein-coding mutation. Hence, by using a cell-population genetic definition, this approach identified three coding changes (CCNG1, P62, and an indel/fusion gene) as tumor driver mutations. These three mutations, affecting cell cycle control and apoptosis, are functionally distinct from mutations that accumulated earlier, many of which are involved in inflammation/immunity or cell anchoring. These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth.

Less Traditional Diets in Chinese Mothers and Children Are Similarly Linked to Socioeconomic and Cohort Factors but Vary with Increasing Child Age

The Journal of Nutrition. Sep, 2011  |  Pubmed ID: 21734061

Global shifts toward an increasingly Western diet and rises in nutrition-related noncommunicable diseases necessitate systematic examination of dietary change in adults and children. This study longitudinally examined mother and child dietary intakes and their relationship with socioeconomic factors across 4 mutually exclusive cohorts followed over 6- to 7-y time periods (cohort A: 1991-1997, cohort B: 1993-2000, cohort C: 1997-2004, cohort D: 2000-2006). The cohorts included 966 mother-child pairs (children 3-5 y at baseline) from the China Health and Nutrition Survey. Dietary intake was assessed using 24-h recall and household food consumption data; dietary variables were the percentage of total energy from animal-source foods (ASF), fats/oils, and grains. Mother-child comparison of dietary variables used average annual change measures, Spearman partial correlations, random effects models, and seemingly unrelated regression models and estimation. Whereas children were earlier adopters and maintainers of a less traditional Chinese diet, mothers experienced greater shifts away from the traditional Chinese diet with increasing child age. Mother-child correlations for the dietary variables ranged from 0.46 to 0.89 (P < 0.001). Similar increased intake of ASF and decreased intake of grains were reported for mothers and children of urban (vs. rural) residence and with higher levels of maternal education (P < 0.001). A comparable cohort effect was shown, with mothers and children consuming a less traditional Chinese diet in the later (C and D) compared to earlier (A and B) cohorts (P < 0.05). Our findings provide insight into dietary changes in mothers and children within the context of a rapidly changing nutrition and socioeconomic environment.

[Study of Biological Performance of Chinese Materia Medica with Either a Cold or Hot Property Based on the Three-element Mathematical Analysis Model]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Jul, 2011  |  Pubmed ID: 21749821

The properties of Chinese materia medica are believed to be the summarization of the effects of biological performance on the various body states. Systemic discussion of chemical-factor elements, body-condition elements, biological-performance elements and their interrelationships is needed for research into the properties of Chinese materia medica. Following the practical characteristics of Chinese medicine, the three-element mathematical model was formed by introducing some mathematical concepts and methods and was used to study the cold or hot property of Chinese medicine, and to investigate the difference in biological performances of the two properties.

[A Study of Association Rules in Three-dimensional Property-taste-effect Data of Chinese Herbal Medicines Based on Apriori Algorithm]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Jul, 2011  |  Pubmed ID: 21749832

The theory of four properties (Qi) and five tastes (Wei) is the core of the property theory of Chinese materia medica. It is known that Qi and Wei are associated with the pharmacological effects (Xiao) of herbs. This study took records of all 365 Chinese herbs in Shennong's Classic of Materia Medica (Shennong Ben Cao Jing) as the data resource and established a three-dimensional data cube, in the purpose of finding out and analyzing the frequent patterns and valued association rules of Qi, Wei and Xiao based on Apriori algorithm. The results of this study may give rise to innovative ideas and methods in research of traditional Chinese materia medica.

Nuclear Factor-κB and Apoptosis in Patients with Intracerebral Hemorrhage

Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia. Oct, 2011  |  Pubmed ID: 21782444

Studies using rat models have indicated that neuronal apoptosis is involved in the pathogenesis of intracerebral hemorrhage (ICH); however, the mechanism by which apoptosis occurs is unclear. In the present study, we aimed to quantify the number of nuclear factor-κB (NF-κB)-positive cells and apoptotic cells in specimens of middle temporal gyrus taken from 46 human subjects with hypertensive ICH. We also investigated the roles that intercellular adhesion molecule-1 (ICAM-1) and interleukin (IL)-1β play in apoptosis following ICH. At about 24 hours after ICH, some neurons exhibited nuclear swelling and incomplete cellular structures were visible. The mean percentage of apoptotic cells was 39.28 ± 21.83% at 49-72 hours after ICH. NF-κB immunoreactivity varied with time after ICH: the number of immunostained neurons increased during the 2-6 hours after ICH, and reached a maximum at 7-48 hours. The number of IL-1β-immunostained neurons reached a maximum at 2-6 hours after ICH. The number of ICAM-1-immunostained neurons increased during the 48 hours after ICH and reached a maximum at 49-72 hours. These observations indicate that apoptosis has a major role in pathological cell death after ICH and that activation of NF-κB is positively related to the progress of apoptosis. Additionally, activation of ICAM-1 and IL-1β seem to be involved in apoptosis after ICH.

[Detection and Clinical Study on Coronavirus HKU1 with Acute Lower Respiratory Tract Infections of Hospitalized Children in Changsha]

Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi = Zhonghua Shiyan He Linchuang Bingduxue Zazhi = Chinese Journal of Experimental and Clinical Virology. Feb, 2011  |  Pubmed ID: 21789840

In order to understand the epidemiological and virologic characteristics of coronavirus HKU1 infection in hospitalized children with acute respiratory tract infection (ARTI) in Changsha.

[The Research of Saffold Virus in Children with Lower Respiratory Tract Infection in Changsha]

Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi = Zhonghua Shiyan He Linchuang Bingduxue Zazhi = Chinese Journal of Experimental and Clinical Virology. Feb, 2011  |  Pubmed ID: 21789842

To investigate prevalence of Saffold virus (SAFV) in Changsha area of hospitalized children with respiratory tract infection, and to discuss whether this virus is related to respiratory tract infection of children.

GoldMag Nanocomposite-functionalized Graphene Sensing Platform for One-step Electrochemical Immunoassay of Alpha-fetoprotein

Biosensors & Bioelectronics. Oct, 2011  |  Pubmed ID: 21803566

A new flow-through electrochemical immunosensor was designed for sensitive detection of alpha-fetoprotein (AFP) in human serum by using nanogold-functionalized magnetic graphene nanosheets as immunosensing probes. Initially, amino functionalized magnetic beads were covalently immobilized on the surface of graphene oxide nanosheets (MGPs), then nanogold particles were adsorbed on the amino groups of the MGPs to construct GoldMag nanocomposites functionalized graphene nanosheets (GMGPs), and then horseradish peroxidase-anti-AFP conjugates (HRP-anti-AFP) were assembled onto the surface of nanogold particles (bio-GMGP). With the aid of an external magnet, the formed bio-GMGPs were attached onto the base electrode in the flow system. With a non-competitive immunoassay format, the injected sample containing AFP antigens was produced transparent immunoaffinity reaction with the immobilized HRP-anti-AFP on the bio-GMGPs. The formed immunocomplex inhibited partly the active center of HRP, and decreased the labeled HRP toward the reduction of H(2)O(2). The performance and factors influencing the performance of the immunosensor were investigated in detail. Under optimal conditions, the electrochemical immunosensor displayed a wide working range of 0.01-200 ng mL(-1) with a low detection limit (LOD) of 1.0 pg mL(-1) AFP (at 3s(B)). Intra- and inter-assay coefficients of variation (CV) were below 10%. In addition, the methodology was validated with real serum samples, receiving a good correlation with the results obtained from commercially available electrochemiluminescence automated analyzer.

17β-Estradiol Promotes Cell Proliferation in Rat Osteoarthritis Model Chondrocytes Via PI3K/Akt Pathway

Cellular & Molecular Biology Letters. Dec, 2011  |  Pubmed ID: 21847664

Osteoarthritis (OA) is the most common cause of musculoskeletal pain and disability. The importance of chondrocytes in the pathogenesis of OA is unequivocal. 17β-estradiol (E2) has a potential protective effect against OA. However, the mechanism of E2 in OA chondrocytes remains unclear. In this study, we investigated the regulative effect of E2 on cell growth and the relationship between E2 and the PI3K/Akt pathway in rat OA model chondrocytes (pretreated with interleukin-1β). We found that E2 induced chondrocyte proliferation, and increased the expression level of Akt simultaneously, especially the expression level of P-Akt. Furthermore, the inhibition of P-Akt could block chondrocyte proliferation induced by E2. These results suggest that PI3K/Akt activation induced by E2 may be an important factor in the mechanism of E2 in cell proliferation in rat OA model chondrocytes, and help further understanding the role of E2 in OA progression.

[A Mathematical Model for Re-analysis of the Relationship Between Essence of Syndromes in Traditional Chinese Medicine and Clinical Biochemical Indicators Based on the Residual-split Method and Its Application]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Aug, 2011  |  Pubmed ID: 21849144

Studying the essence of syndromes (Zheng) in traditional Chinese medicine (TCM) is a fundamental challenge in basic theoretical research of TCM. The relationship between any given syndrome and biochemical indicators is one of the important aspects of the study. As the indexes selected in each study are specific to a particular Western medical disease diagnosis, and the disease factor is inevitably introduced into the study, the effect of disease factor on the index changes cannot be assessed effectively by traditional data processing methods. This is known as "the same syndrome with different reasons", which has resulted in confusion in TCM research. This study aimed at providing a mathematical tool to address this issue. Based on information theory and the residual-split method, the syndrome information, which was covered in the index variation, was quantitatively calculated in this paper as an independent part of the disease factor. A mathematical model capable of objectively assessing and statistically testing the effect of the syndrome factor on the index changes was established. Applying this model to literature data of studies on the relationship between cyclic nucleotides and yang-deficiency syndrome showed following results. First, the values of yang-deficiency syndrome information were negative for cyclic adenosine monophosphate (cAMP) while positive for cyclic guanosine monophosphate (cGMP) in all included literature. This indicated that the group of yang-deficiency syndrome was correlated with an obvious trend of reduced cAMP levels and increased cGMP levels. Second, the statistical test results of yang-deficiency syndrome information of the two indexes were different among the literature included. The quality of original data was considered as a possible reason. Third, the significant differences between the yang-deficiency group of a specific disease and the normal group may, in some cases, be caused by a disease factor rather than a syndrome factor. The mathematical model provided a reasonable mathematical tool for the analysis of disease factor and syndrome factor in clinical research of TCM, suggesting that the mathematical model may give rise to innovative ideas and methods in the study of syndromes.

93-kDa Twin-domain Serine Protease Inhibitor (Serpin) Has a Regulatory Function on the Beetle Toll Proteolytic Signaling Cascade

The Journal of Biological Chemistry. Oct, 2011  |  Pubmed ID: 21862574

Serpins are protease inhibitors that play essential roles in the down-regulation of extracellular proteolytic cascades. The core serpin domain is highly conserved, and typical serpins are encoded with a molecular size of 35-50 kDa. Here, we describe a novel 93-kDa protein that contains two complete, tandemly arrayed serpin domains. This twin serpin, SPN93, was isolated from the larval hemolymph of the large beetle Tenebrio molitor. The N-terminal serpin domain of SPN93 forms a covalent complex with the Spätzle-processing enzyme, a terminal serine protease of the Toll signaling cascade, whereas the C-terminal serpin domain of SPN93 forms complexes with a modular serine protease and the Spätzle-processing enzyme-activating enzyme, which are two different enzymes of the cascade. Consequently, SPN93 inhibited β-1,3-glucan-mediated Toll proteolytic cascade activation in an in vitro system. Site-specific proteolysis of SPN93 at the N-terminal serpin domain was observed after activation of the Toll proteolytic cascade in vivo, and down-regulation of SPN93 by RNAi sensitized β-1,3-glucan-mediated larval death. Therefore, SPN93 is the first serpin that contains twin tandemly arrayed and functionally active serpin domains that have a regulatory role in the larval Toll proteolytic signaling cascade.

LongSAGE Gene-expression Profiling of Botrytis Cinerea Germination Suppressed by Resveratrol, the Major Grapevine Phytoalexin

Fungal Biology. Sep, 2011  |  Pubmed ID: 21872179

The ascomycetes Botrytis cinerea is one of the most studied necrotrophic phytopathogens and one of the main fungal parasites of grapevine. As a defense mechanism, grapevine produces a phytoalexin compound, resveratrol, which inhibits germination of the fungal conidium before it can penetrate the plant barriers and lead to host cell necrotrophy. To elucidate the effect of resveratrol on transcriptional regulation in B. cinerea germlings, two LongSAGE (long serial analysis of gene expression) libraries were generated in vitro for gene-expression profiling: 41 428 tags and among them, 15 665 unitags were obtained from resveratrol-treated B. cinerea germlings and 41 358 tags, among them, 16 362 unitags were obtained from non-treated B. cinerea germlings. In-silico analysis showed that about half of these unitags match known genes in the complete B. cinerea genome sequence. Comparison of unitag frequencies between libraries highlighted 110 genes that were transcriptionally regulated in the presence of resveratrol: 53 and 57 genes were significantly down- and upregulated, respectively. Manual curation of their putative functional categories showed that primary metabolism of germinating conidia appears to be markedly affected under resveratrol treatment, along with changes in other putative metabolic pathways, such as resveratrol detoxification and virulence-effector secretion, in B. cinerea germlings. We propose a hypothetical model of cross talk between B. cinerea germinating conidia and resveratrol-producing grapevine at the very early steps of infection.

Microsatellite Markers for Dayaoshania Cotinifolia (Gesneriaceae), a Critically Endangered Perennial Herb

American Journal of Botany. Sep, 2011  |  Pubmed ID: 21875974

• Premise of the study: Microsatellite primers were developed for the critically endangered species Dayaoshania cotinifolia (Gesneriaceae) to evaluate population genetic diversity and detect population history. • Methods and Results: In our study, 15 primer sets were developed using an enriched genomic library. These are the first microsatellite loci developed for this genus. Genetic diversity was measured using 40 individuals. The number of alleles per locus ranged from one to six, and the incidence of observed heterozygosities was 0.365 and 0.410 in two populations. • Conclusions: The described markers will be useful in future population genetics studies of this critically endangered species.

Semi-supervised Learning Improves Gene Expression-based Prediction of Cancer Recurrence

Bioinformatics (Oxford, England). Nov, 2011  |  Pubmed ID: 21893520

Gene expression profiling has shown great potential in outcome prediction for different types of cancers. Nevertheless, small sample size remains a bottleneck in obtaining robust and accurate classifiers. Traditional supervised learning techniques can only work with labeled data. Consequently, a large number of microarray data that do not have sufficient follow-up information are disregarded. To fully leverage all of the precious data in public databases, we turned to a semi-supervised learning technique, low density separation (LDS).

A Novel Antimicrobial Protein for Plant Protection Consisting of a Xanthomonas Oryzae Harpin and Active Domains of Cecropin A and Melittin

Microbial Biotechnology. Nov, 2011  |  Pubmed ID: 21895994

Discoveries about antimicrobial peptides and plant defence activators have made possible the de novo and rational design of novel peptides for use in crop protection. Here we report a novel chimeric protein, Hcm1, which was made by linking the active domains of cecropin A and melittin to the hypersensitive response (HR)-elicitor Hpa1 of Xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak. The resulting chimeric protein maintained not only the HR-inducing property of the harpin, but also the antimicrobial activity of the cecropin A-melittin hybrid. Hcm1 was purified from engineered Escherichia coli and evaluated in terms of the minimal inhibitory concentration (MIC) and the 50% effective dose (ED(50)) against important plant pathogenic bacteria and fungi. Importantly, the protein acted as a potential pesticide by inducing disease resistance for viral, bacterial and fungal pathogens. This designed drug can be considered as a lead compound for use in plant protection, either for the development of new broad-spectrum pesticides or for expression in transgenic plants.

[Ridit Analysis of Experimental Data from Animal Models of Yang Deficiency Induced by Different Doses of Hydrocortisone]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Sep, 2011  |  Pubmed ID: 21906518

Hydrocortisone-induced yang-deficiency animal model has now become the generally accepted model of yang deficiency. However, assessing the most appropriate dose of hydrocortisone is a long-term challenge. For analyzing the modeling dose, the authors have built several kinds of yang-deficiency models induced by hydrocortisone at different doses, and analyzed the experimental data with various mathematical statistical methods. In order to discuss the effects of the modeling dose on the basis of previous research, the authors introduced Ridit analysis.

[Pharmacological Effects of Oleum Cinnamomi and Water Extract of Cortex Cinnamomi in Rats with Yang-deficiency Cold Syndrome and the Mathematical Analysis]

Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. Sep, 2011  |  Pubmed ID: 21906523

To compare the effects of Oleum Cinnamomi and water extract of Cortex Cinnamomi in rats with yang-deficiency cold syndrome based on mathematical analysis.

[Study of Geographic Distribution and 10 Years' Change of Spermarche in Chinese Boys of Han-group Aged 11 to 18]

Zhonghua Yu Fang Yi Xue Za Zhi [Chinese Journal of Preventive Medicine]. Jun, 2011  |  Pubmed ID: 21914335

To analyze the geographic distribution and 10 years' change of spermarche in Chinese boys of Hangroup aged 11 - 18.

Complete Genome Sequence of Alicyclobacillus Acidocaldarius Strain Tc-4-1

Journal of Bacteriology. Oct, 2011  |  Pubmed ID: 21914900

Alicyclobacillus acidocaldarius strain Tc-4-1 was initially isolated from a hot spring in Tengchong, China. This organism is both thermophilic and acidophilic. It can produce heat- and acid-stable enzymes, such as amylase and esterase, which may be important in industry. Here we report the whole genome sequence of the strain.

Synthesis of Oxidized Guar Gum by Dry Method and Its Application in Reactive Dye Printing

International Journal of Biological Macromolecules. Dec, 2011  |  Pubmed ID: 21925204

The aim of this study was to prepare oxidized guar gum with a simple dry method, basing on guar gum, hydrogen peroxide and a small amount of solvent. To obtain a product with suitable viscosity for reactive dye printing, the effects of various factors such as the amount of oxidant and solvent, reaction temperature and time were studied with respect to the viscosity of reaction products. The product was characterized by Fourier transform infrared spectroscopy, size exclusion chromatography, scanning electron microscopy and differential scanning calorimetry. The hydrated rate of guar gum and oxidized guar gum was estimated through measuring the required time when their solutions (1%, w/v) reached the maximum viscosity. The effects of the salt concentration and pH on viscosity of the resultant product were studied. The mixed paste containing oxidized guar gum and carboxymethyl starch was prepared and its viscosity was determined by the viscometer. The rheological property of the mixed paste was appraised by the printing viscosity index. In addition, the applied effect of mixed paste in reactive dye printing was examined by assessing the fabric stiffness, color yield and sharp edge to the printed image in comparison with sodium alginate. And the results indicated that the mixed paste could partially replace sodium alginate as thickener in reactive dye printing. The study also showed that the method was low cost and eco-friendly and the product would have an extensive application in reactive dye printing.

Degradation Mechanism and Control of Silk Fibroin

Biomacromolecules. Apr, 2011  |  Pubmed ID: 21361368

Controlling the degradation process of silk is an important and interesting subject in the field of biomaterials. In the present study, silk fibroin films with different secondary conformations and nanostructures were used to study degradation behavior in buffered protease XIV solution. Different from previous studies, silk fibroin films with highest β-sheet content achieved the highest degradation rate in our research. A new degradation mechanism revealed that degradation behavior of silk fibroin was related to not only crystal content but also hydrophilic interaction and then crystal-noncrystal alternate nanostructures. First, hydrophilic blocks of silk fibroin were degraded. Then, hydrophobic crystal blocks that were formerly surrounded and immobilized by hydrophilic blocks became free particles and moved into solution. Therefore, on the basis of the mechanism, which enables the process to be more controllable and flexible, controlling the degradation behavior of silk fibroin without affecting other performances such as its mechanical or hydrophilic properties becomes feasible, and this would greatly expand the applications of silk as a biomedical material.

Cigarette Smoke Exposure Before Pregnancy and the Associated Risk of Having a Child with Orofacial Clefts in China: a Case-control Study

Plastic and Reconstructive Surgery. Mar, 2011  |  Pubmed ID: 21364386

Real-time Visualization of the Dynamic Evolution of CS2 4d and 6s Rydberg Wave Packet Components

Optics Express. Feb, 2011  |  Pubmed ID: 21369286

The dynamic evolution of CS2 4d and 6s Rydberg wave packet components has been experimentally visualized via femtosecond time-resolved photoelectron imaging coupled with time-resolved mass spectroscopy. The temporal evolution of the four components of the prepared Rydberg wave packet is directly observed as time-dependent changes of the intensities of different parts in the main photoelectron peak. Furthermore, time-resolved photoelectron angular distributions (PADs) clearly reflect the different component characters of 4d and 6s molecular orbitals. The lifetime of Rydberg wave packets is determined to be about 830fs and their decay is attributed to predissociation. Our results suggest the possibility of directly visualizing and determining the amplitudes and relative phases of different electronic and vibrational wave packet components in polyatomic molecules.

Functional and Morphologic Outcome After Stapled Transanal Rectal Resection for Obstructed Defecation Syndrome

Diseases of the Colon and Rectum. Apr, 2011  |  Pubmed ID: 21383561

Stapled transanal rectal resection is a novel surgery for obstructed defecation syndrome. Few data on the functional and morphologic outcome after the surgery have been reported.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics

Molecular & Cellular Proteomics : MCP. May, 2011  |  Pubmed ID: 21389108

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics.

Genetic Dissection of the Gpnmb Network in the Eye

Investigative Ophthalmology & Visual Science. Jun, 2011  |  Pubmed ID: 21398278

To use a systematic genetics approach to investigate the regulation of Gpnmb, a gene that contributes to pigmentary dispersion syndrome (PDS) and pigmentary glaucoma (PG) in the DBA/2J (D2) mouse.

[Value of Fluorescence Quantitative PCR Assay of Bronchoalveolar Lavage Fluid Samples in the Diagnosis of Mycoplasma Pneumoniae Pneumonia in Children]

Zhongguo Dang Dai Er Ke Za Zhi = Chinese Journal of Contemporary Pediatrics. Mar, 2011  |  Pubmed ID: 21426633

To study the value of fluorescence quantitative polymerase chain reaction (FQ-PCR) for detecting Mycoplasma pneumoniae (MP)-DNA in bronchoalveolar lavage fluid (BALF) in the early diagnosis of Mycoplasma pneumoniae pneumonia (MPP).

Splicing of an Intervening Sequence by Protein-free Human SnRNAs

RNA Biology. May-Jun, 2011  |  Pubmed ID: 21445000

Significant structural and mechanistic similarities between the spliceosomal snRNAs and catalytically critical domains of self-splicing group II introns have led to the hypothesis that the spliceosomes and group II introns may be evolutionarily related. We have previously shown that in vitro-transcribed, protein-free U6 and U2 snRNAs can catalyze a two-step splicing reaction in trans on two short RNA oligonucleotides that is identical to the splicing reactions performed by many self-splicing group II introns. Here we show that the same two snRNAs can perform splicing in cis by removal of an intervening sequence from a model substrate. These results prove that the protein-free snRNAs are competent to perform splicing on pre-mRNAs and further strengthen the possibility of an evolutionary relationship to group II introns.

Development of Self-assembled 3D Fe(x)Oy Micro/nano Materials for Application in Hexachlorobenzene Degradation

Journal of Nanoscience and Nanotechnology. Mar, 2011  |  Pubmed ID: 21449355

Self-assembled three dimensional (3D) hierarchical, flower-like iron oxide micro/nano materials, including pure Fe3O4, alpha-Fe2O3/Fe3O4 composite and pure alpha-Fe2O3, were developed to degrade hexachlorobenzene (HCB) at 300 degrees C. It was found that pure Fe3O4 exhibited the highest activity with the reaction rate constant at 0.959 min(-1). Identified degradation products with lower chlorinated benzenes suggest a stepwise hydrodechlorination was occurring for the degradation of HCB on the synthesized Fe3O4. The characterization of the synthesized iron oxides after reaction indicates the Fe3O4 phase was partially transformed into alpha-Fe2O3 phase and in return accelerated progress of hydrodechlorination of HCB. The superior performance of as-prepared Fe3O4 could be attributed to its structural feature such as surface area and pore structure, as well as its phase transformation during HCB degradation.

Characterization of Medium-chain Triacylglycerol (MCT)-enriched Seed Oil from Cinnamomum Camphora (Lauraceae) and Its Oxidative Stability

Journal of Agricultural and Food Chemistry. May, 2011  |  Pubmed ID: 21456611

Medium-chain triacylglycerol (MCT)-enriched oil was extracted by supercritical fluid extraction of carbon dioxide (SFE-CO(2)) from Cinnamomum camphora seeds. The SFE-CO(2) process was optimized using the Box-Behnken design (BBD). The maximum oil yield (42.82%) was obtained under the optimal SFE-CO(2) conditions: extraction pressure, 21.16 MPa; extraction temperature, 45.67 °C; and extraction time, 2.38 h. Subsequently, the physicochemical characteristics, fatty acid composition, triacylglycerol (TAG) composition, tocopherol content, and DSC profile as well as oxidative stabilities of C. camphora seed oil (CCSO) were studied. Results showed that CCSO contained two major medium-chain fatty acids, capric acid (53.27%) and lauric acid (39.93%). The predominant TAG species in CCSO was LaCC/CLaC (ECN 32, 79.29%). Meanwhile, it can be found that CCSO had much higher oxidative stabilities than coconut oil due to the higher content of tocopherols in CCSO (α-tocopherol, 8.67 ± 0.51 mg/100 g; γ-tocopherol, 22.6 ± 1.02 mg/100 g; δ-tocopherol, 8.38 ± 0.47 mg/100 g). Conclusively, CCSO with such a high level of MCTs and high oxidative stabilities could be potentially applied in special food for specific persons such as weak patients and overweight persons because oils enriched in MCTs can be rapidly absorbed into body to provide energy without fat accumulation.

Synthesis of Patterned Nanogold and Mesoporous CoFe2O4 Nanoparticle Assemblies and Their Application in Clinical Immunoassays

Nanoscale. May, 2011  |  Pubmed ID: 21465042

Herein, we describe a facile and feasible synthesis method for patterning nanogold particles onto magnetic mesoporous CoFe(2)O(4) nanostructures (Au-MMNs) by using poly(vinyl pyrrolidone) (PVP) as cross-linker. Initially, mesoporous CoFe(2)O(4) nanoparticles were initially synthesized with a thermal decomposition method by using mesoporous silica nanoparticles as templates, and then nanometre-sized gold particles were produced through the in situ reduction of the Au(III) on the PVP-functionalized CoFe(2)O(4). The as-prepared Au-MMNs were characterized by transmission electron microscopy (TEM), N(2) adsorption-desorption isotherms, UV-visible adsorption spectrometer, vibrating sample magnetometer (VSM) and X-ray photoelectron spectroscopy (XPS). Furthermore, we also demonstrate the conjugation capacity of the synthesized Au-MMNs toward biomolecules by using quartz crystal microbalance (QCM), and the possible application in the electrochemical immunoassays. Experimental results indicated that the resulting Au-MMNs display good conjugation capability toward the biomolecules, and excellent analytical properties for determination of target molecules.

Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms

Molecular Biology and Evolution. Oct, 2011  |  Pubmed ID: 21504891

Population genetics of species living in marginal habitats could be particularly informative about the genetics of adaptation, but such analyses have not been readily feasible until recently. Sonneratia alba, a mangrove species widely distributed in the Indo-West Pacific, provides a very suitable system for the study of local adaptation. In this study, we analyzed DNA variation by pooling 71 genes from 85-100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained ~2,500 × coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 × coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the presence of a small number of highly differentiated loci.

Adult Mouse Epicardium Modulates Myocardial Injury by Secreting Paracrine Factors

The Journal of Clinical Investigation. May, 2011  |  Pubmed ID: 21505261

The epicardium makes essential cellular and paracrine contributions to the growth of the fetal myocardium and the formation of the coronary vasculature. However, whether the epicardium has similar roles postnatally in the normal and injured heart remains enigmatic. Here, we have investigated this question using genetic fate-mapping approaches in mice. In uninjured postnatal heart, epicardial cells were quiescent. Myocardial infarction increased epicardial cell proliferation and stimulated formation of epicardium-derived cells (EPDCs), which remained in a thickened layer on the surface of the heart. EPDCs did not adopt cardiomyocyte or coronary EC fates, but rather differentiated into mesenchymal cells expressing fibroblast and smooth muscle cell markers. In vitro and in vivo assays demonstrated that EPDCs secreted paracrine factors that strongly promoted angiogenesis. In a myocardial infarction model, EPDC-conditioned medium reduced infarct size and improved heart function. Our findings indicate that epicardium modulates the cardiac injury response by conditioning the subepicardial environment, potentially offering a new therapeutic strategy for cardiac protection.

[Protective Effects of Lidocaine on Hyperoxia-exposed Type …�alveolar Epithelial Cells from Premature Rats]

Zhongguo Dang Dai Er Ke Za Zhi = Chinese Journal of Contemporary Pediatrics. Apr, 2011  |  Pubmed ID: 21507302

To investigate the effects of lidocaine on apoptosis and proliferation of hyperoxia-exposed type Ⅱalveolar epithelial cells (AECⅡ) from premature rats.

An Active Sampler for Monitoring Polychlorinated Dibenzo-p-dioxins and Furans in Ambient Air

Bulletin of Environmental Contamination and Toxicology. Jul, 2011  |  Pubmed ID: 21516452

An active sampler for monitoring polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) in air was developed using an automobile air filter set. The performance of the mobile air sampler was evaluated. Recoveries of PCDD/F congeners ranged from 62.3% to 64.5% with sampling volumes of 500-1,800 m³. Air samples were collected between April and June, 2007 in Beijing. The monitoring results of PCDD/F levels by the mobile sampler were comparable to results obtained by a conventional stationary high-volume active sampler. The results suggest this mobile air sampling technology is a promising new strategy for the assessment of air quality in urban areas.

Characteristics of Air Pollution by Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in the Typical Industrial Areas of Tangshan City, China

Journal of Environmental Sciences (China). 2011  |  Pubmed ID: 21516996

The ambient air in vicinity of different industrial sources for PCDD/PCDFs was sampled by TSP/PM10 active samplers and passive PUF disk samplers in Tangshan City, a metropolis containing clusters of various industrial plants. The TEQ concentrations of PCDD/PCDFs ranged from 44.2 to 394.1 fg I-TEQ/m3 with an average of 169.9 fg I-TEQ/m3. 2,3,4,7,8-PeCDF was the dominant contributor to sigma TEQ, contributing 41% (12% to 55%), while 1,2,3,4,6,7,8-HpCDF, OCDD and OCDF were the major congeners for the total concentrations. The ratios of sigma PCDF/ sigma PCDD reached 2.54 on average, suggesting that de novo synthesis in thermal processes played an important role to the airborne pollution of PCDD/PCDFs. The similarities congener profiles indicated that TSP and PM10 active sampling methods are comparable for the determination of the PCDD/PCDFs in ambient air, and the ratios of concentrations determined by the two methods suggested that the PCDD/PCDFs tended to stay in fine particles. It was found that 2,3,7,8-TCDF and OCDD were the dominating congeners in the passive PUF disks samples. Through principal components analysis, the coke industry was suggested to be a relatively high potential emission source for PCDD/PCDFs in the ambient air of Tangshan, which was possibly formed by de novo synthesis mechanism. In this study, the atmospheric impacts to the environment from different industrial sources could be ranked as follows (from high to low): coking, iron sintering, steel making, power generation and chlorinate alkali chemical production industries.

Cooking Process: a New Source of Unintentionally Produced Dioxins?

Journal of Agricultural and Food Chemistry. May, 2011  |  Pubmed ID: 21517073

To improve understanding of human background exposure to dioxins, the influence of cooking on dioxin concentrations in food has received much attention. Studies have focused on changes in the distribution of dioxins that originate from raw foods. However, the possibility of dioxin formation during cooking has been neglected. In this study, cooking experiments were designed to investigate the generation of dioxins during cooking at high temperature and with flavorings containing organic chlorine. Solid, liquid, and gas phase samples were collected during cooking. The results indicate that dioxins can be generated during some cooking processes, such as burning, or when cooking with reactive organic chlorides, and the dioxins are more likely to be present in the smoke (gas phase) than the edible portion (solid and liquid phases). Thus, more attention should be given to cooking of raw foods and organic chlorine-containing flavorings at high temperature. Maintaining good ventilation during cooking is also necessary to reduce human exposure risk to dioxins.

[Characteristic Wavelengths Analysis for Remote Sensing Reflectance on Water Surface in Taihu Lake]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Jul, 2011  |  Pubmed ID: 21942046

The research on characteristic wavelengths analysis of reflectance spectrum is a very important and basic task for remote sensing of inland-water color. The present paper analyzed remote sensing reflectances of 312 samples measured in Taihu Lake between 2006 and 2009, and these reflectances were separated into three classes by chlorophyll-a concentrations. The reflectance spectra smoothed by Savitzky-Golay algorithm were calculated by first- and second-order derivatives. Then, zero values were located in the derivatives and counted at all wavelengths. Thus the frequency distribution of zeros at each wavelength was got. At which wavelength a local maximum of the frequencies appears a characteristic wavelength will most likely be there. These characteristic wavelengths are corresponding to maximum, minimum, from-concave-to-convex inflection point and from-convex-to-concave inflection point of a spectrum curve. At last the paper provided the characteristic wavelengths for Taihu Lake water at the spectral coverage from 350 to 900 nm, which are 359, 440, 464, 472, 552, 566, 583, 628, 636, 645, 660, 676, 689, 706, 728, 791, 806, and 825 nm. In addition, these wavelengths we found were explained by absorption of phytoplankton pigments and components of water in Taihu Lake. Being able to distinguish overlaps between peaks and vales at the same wavelength in different measurements, the method to analyze characteristic wavelengths is universally applicable to various spectrum curves. The characteristic wavelengths chosen by the paper are helpful to improving some algorithms of retrieval of water quality parameters.

A Novel Splice Donor Mutation in the Thrombopoietin Gene Leads to Exon 2 Skipping in a Filipino Family with Hereditary Thrombocythemia

Blood. Dec, 2011  |  Pubmed ID: 22194398

[Status of Malnutrition and Its Influencing Factors in Children Under 5 Years of Age in Poor Areas of China in 2009]

Wei Sheng Yan Jiu = Journal of Hygiene Research. Nov, 2011  |  Pubmed ID: 22279663

To study the status of malnutrition and its influencing factors in children less than 5 years of age in poor areas of China in 2009.

Fast Network Centrality Analysis Using GPUs

BMC Bioinformatics. 2011  |  Pubmed ID: 21569426

With the exploding volume of data generated by continuously evolving high-throughput technologies, biological network analysis problems are growing larger in scale and craving for more computational power. General Purpose computation on Graphics Processing Units (GPGPU) provides a cost-effective technology for the study of large-scale biological networks. Designing algorithms that maximize data parallelism is the key in leveraging the power of GPUs.

Tracking the Implementation of Green Credit Policy in China: Top-down Perspective and Bottom-up Reform

Journal of Environmental Management. Apr, 2011  |  Pubmed ID: 21220183

The Chinese government has introduced the green credit policy to mitigate the environmental impact of industrialization by reining in credit loans to companies and projects with poor environmental performance. This research investigated the implementation of the green credit policy both at the national and provincial levels. Our results show that the green credit policy is not fully implemented. The wide-ranging impact on high-polluting and high energy-consuming industries, vague policy details unclear implementing standards, and lack of environmental information are the main problems in the implementation of the green credit policy in China. On the other hand, the practice at local level (Jiangsu Province) is more practical by integrating green credit policy with the environmental performance rating system. Finally, suggestions are outlined to improve China's green credit policy.

Networked-based Characterization of Extracellular Matrix Proteins from Adult Mouse Pulmonary and Aortic Valves

Journal of Proteome Research. Feb, 2011  |  Pubmed ID: 21133377

A precise mixture of extracellular matrix (ECM) secreted by valvular cells forms a scaffold that lends the heart valve the exact mechanical and tensile strength needed for accurate hemodynamic performance. ECM proteins are a key component of valvular endothelial cell (VEC)-valvular interstitial cell (VIC) communication essential for maintenance of the valve structure. This study reports the healthy adult pulmonary and aortic valve proteomes characterized by LC-MS/MS, resulting in 2710 proteins expressed by 1513 genes, including over 300 abundant ECM proteins. Surprisingly, this study defines a distinct proteome for each semilunar valve. Protein-protein networking (PPN) was used as a tool to direct selection of proteomic candidates for biological investigation. Local PPN for nidogen 1 (Nid1), biglycan (Bgn), elastin microfibril interface-located protein 1 (Emilin-1), and milk fat globule-EGF factor 8 protein (Mfge8) were enriched with proteins essential to valve function and produced biological functions highly relevant to valve biology. Immunofluorescent investigations demonstrated that these proteins are functionally distributed within the pulmonary and aortic valve structure, indicative of important contribution to valve function. This study yields new insight into protein expression contributing to valvular maintenance and health and provides a platform for unbiased assessment of protein alterations during disease processes.

Mechanism of Polychlorinated Diphenyl Ether Formation on a Simulated Fly Ash Surface

Journal of Hazardous Materials. Feb, 2011  |  Pubmed ID: 21146922

Polychlorinated diphenyl ethers (PCDEs) are a focus of current environmental concern. The formation of PCDEs was investigated using laboratory-scale flow reactors under air and under nitrogen at 350°C. The results show the amount of PCDEs formed from the condensation of pentachlorophenol (PCP) and 1,2,4,5-tetrachlorobenzene (1,2,4,5-Cl(4)Bz) was lower with oxygen than without oxygen, and the PCDE homologue distribution was different under both atmospheres. The presence of oxygen influenced the process of PCDE formation from precursors on the fly ash surface. Furthermore, 2,2',3,4,4',5,5',6-octachlorodiphenyl ether (OCDE) is the dominant PCDE homologue product formed on the surface of SiO(2), whereas decachlorodiphenyl ether (DecaCDE) was the predominant product formed on the SiO(2)/FeCl(3) and SiO(2)/CuCl(2) surfaces. The PCDE homologue distribution shifted toward the more chlorinated species in the presence of FeCl(3) and CuCl(2). The simultaneous formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) was also observed during the formation of PCDEs from heterogeneous reactions of precursors. These findings suggest that the emission of PCDEs from municipal waste incineration plants should be considered, and careful and sophisticated control is required to prevent the formation of pollutants.

Protective Immunity Induced by Toxoplasma Gondii Rhoptry Protein 16 Against Toxoplasmosis in Mice

Clinical and Vaccine Immunology : CVI. Jan, 2011  |  Pubmed ID: 21106780

Toxoplasma gondii can infect a large variety of domestic and wild animals and human beings, sometimes causing severe pathology. Rhoptries are involved in T. gondii invasion and host cell interaction and have been implicated as important virulence factors. In this study, we constructed a DNA vaccine expressing rhoptry protein 16 (ROP16) of T. gondii and evaluated the immune responses it induced in Kunming mice. The gene sequence encoding ROP16 was inserted into the eukaryotic expression vector pVAX I. We immunized Kunming mice intramuscularly. After immunization, we evaluated the immune response using a lymphoproliferative assay, cytokine and antibody measurements, and the survival times of mice challenged lethally. The results showed that mice immunized with pVAX-ROP16 developed a high level of specific antibody responses against T. gondii ROP16 expressed in Escherichia coli, a strong lymphoproliferative response, and significant levels of gamma interferon (IFN-γ), interleukin-2 (IL-2), IL-4, and IL-10 production compared with results for other mice immunized with either empty plasmid or phosphate-buffered saline, respectively. The results showed that pVAX-ROP16 induces significant humoral and cellular Th1 immune responses. After lethal challenge, the mice immunized with pVAX-ROP16 showed a significantly (P < 0.05) prolonged survival time (21.6 ± 9.9 days) compared with control mice, which died within 7 days of challenge. Our data demonstrate, for the first time, that ROP16 triggers a strong humoral and cellular response against T. gondii and that ROP16 is a promising vaccine candidate against toxoplasmosis, worth further development.

Structural and Functional Characterization of a Highly Specific Serpin in the Insect Innate Immunity

The Journal of Biological Chemistry. Jan, 2011  |  Pubmed ID: 21047786

The Toll signaling pathway, an essential innate immune response in invertebrates, is mediated via the serine protease cascade. Once activated, the serine proteases are irreversibly inactivated by serine protease inhibitors (serpins). Recently, we identified three serpin-serine protease pairs that are directly involved in the regulation of Toll signaling cascade in a large beetle, Tenebrio molitor. Of these, the serpin SPN48 was cleaved by its target serine protease, Spätzle-processing enzyme, at a noncanonical P1 residue of the serpin's reactive center loop. To address this unique cleavage, we report the crystal structure of SPN48, revealing that SPN48 exhibits a native conformation of human antithrombin, where the reactive center loop is partially inserted into the center of the largest β-sheet of SPN48. The crystal structure also shows that SPN48 has a putative heparin-binding site that is distinct from those of the mammalian serpins. Ensuing biochemical studies demonstrate that heparin accelerates the inhibition of Spätzle-processing enzyme by a proximity effect in targeting the SPN48. Our finding provides the molecular mechanism of how serpins tightly regulate innate immune responses in invertebrates.

Complete Genome Sequence of Bifidobacterium Longum Subsp. Longum BBMN68, a New Strain from a Healthy Chinese Centenarian

Journal of Bacteriology. Feb, 2011  |  Pubmed ID: 21097614

Bifidobacterium longum subsp. longum BBMN68 was isolated from the feces of a healthy centenarian living in an area of BaMa, Guangxi, China, known for longevity. Here we report the main genome features of B. longum strain BBMN68 and the identification of several predicted proteins associated with the ecological niche of longevity.

Anxiolytic and Sedative Effects of Dehydroeffusol from Juncus Effusus in Mice

Planta Medica. Mar, 2011  |  Pubmed ID: 21104609

Dehydroeffusol, a phenanthrene isolated from Juncus effusus L., possesses characteristic anxiolytic and sedative properties, as determined by an array of behavioral tests in mice. In the elevated plus-maze test, dehydroeffusol significantly increased the number of entries into the open arms and the time the mice spent in these arms in a dose-dependent manner, with a minimum effective dose of 2.5 mg/kg. Dehydroeffusol also significantly increased the head-dips of mice in the hole-board test in a dose-dependent manner, with a minimum effective dose of 5 mg/kg. Dehydroeffusol reduced mouse locomotion in the open-field test with a minimum effective dose of 5 mg/kg. In the rota-rod test, 1-5 mg/kg dehydroeffusol did not decrease the fall-down time of mice. The above results confirm that dehydroeffusol possesses anxiolytic and sedative properties and does not affect the general movement coordination of mice. This suggests that dehydroeffusol is a novel anxiolytic chemical derived from herbal medicines.

Pharmacokinetics and Platelet Aggregation Inhibitory Effects of a Novel Intravenous Formulation of Clopidogrel in Humans

Clinical and Experimental Pharmacology & Physiology. Jan, 2012  |  Pubmed ID: 21933229

1. PM103 is an intravenous formulation of clopidogrel being developed as an alternative to oral clopidogrel to provide for dosing flexibility in the emergent clinical setting. The present first-in-human study assessed the pharmacokinetic and pharmacodynamic effects of PM103 and its safety in 144 healthy human subjects. 2. The present was a randomized open-label parallel-group trial. Single intravenous doses of PM103 (0.1, 1.0, 10, 30, 100 or 300 mg) were administered to each group (n = 24 subjects per group). Platelet aggregation was assessed at baseline and then 15 and 30 min and 2, 5 and 24 h after drug administration. Determination of plasma concentrations of clopidogrel, clopidogrel carboxylic acid metabolite and the clopidogrel thiol metabolite were assessed at baseline and at 1, 5, 10, 20 and 30 min and 1, 2, 3, 4, 6, 8, 12 and 24 h after drug administration. 3. PM103 produced a rapid, persistent and dose-related inhibition of platelet aggregation. The onset of the ant platelet effect paralleled the appearance in plasma of the clopidogrel thiol active metabolite. PM103 was well tolerated and no subjects discontinued treatment because of adverse events. 4. These data suggest that PM103 may be a suitable alternative to oral clopidogrel for patients in whom the desired clinical management would include administration of clopidogrel after coronary angiography but prior to percutaneous coronary intervention.

Corn Porous Starch: Preparation, Characterization and Adsorption Property

International Journal of Biological Macromolecules. Jan, 2012  |  Pubmed ID: 22100869

This study was carried out to develop a new type of modified starch based on α-amylase and glucoamylase. The structural and chemical characteristics of the porous starch were determined by Fourier-transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD) and differential scanning calorimetry (DSC). The potential application of the porous starch as an adsorbent was evaluated using methyl violet as an adsorbed model. The adsorption capacity was optimized by investigating the reaction factors, including the mass ratio of α-amylase to glucoamylase (m(α-amylase)/m(glucoamylase)), the mass ratio of total amount of enzymes to starch (m(enzyme)/m(St)), the ratio of liquid volume to starch mass (V(H2O)/M(St)), pH value of the reaction solution, enzymatic reaction temperature, and enzymatic reaction time. The hydrolysis ratio of each sample was also determined to investigate the effect of different reaction conditions on the hydrolysis degree. The results suggest that the porous starch has a more excellent adsorption capacity than the native starch, and may be expected to have wide potential applications in many fields.

Proteomic Consequences of a Single Gene Mutation in a Colorectal Cancer Model

Journal of Proteome Research. Feb, 2012  |  Pubmed ID: 22103262

The proteomic effects of specific cancer-related mutations have not been well characterized. In colorectal cancer (CRC), a relatively small number of mutations in key signaling pathways appear to drive tumorigenesis. Mutations in adenomatous polyposis coli (APC), a negative regulator of Wnt signaling, occur in up to 60% of CRC tumors. Here we examine the proteomic consequences of a single gene mutation by using an isogenic CRC cell culture model in which wildtype APC expression has been ectopically restored. Using LC-MS/MS label free shotgun proteomics, over 5000 proteins were identified in SW480Null (mutant APC) and SW480APC (APC restored). We observed 155 significantly differentially expressed proteins between the two cell lines, with 26 proteins showing opposite expression trends relative to gene expression measurements. Protein changes corresponded to previously characterized features of the APCNull phenotype: loss of cell adhesion proteins, increase in cell cycle regulators, alteration in Wnt signaling related proteins, and redistribution of β-catenin. Increased expression of RNA processing and isoprenoid biosynthetic proteins occurred in SW480Null cells. Therefore, shotgun proteomics reveals proteomic differences associated with a single gene change, including many novel differences that fall outside known target pathways.

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

Journal of Proteome Research. Feb, 2012  |  Pubmed ID: 22103967

The standard shotgun proteomics data analysis strategy relies on searching MS/MS spectra against a context-independent protein sequence database derived from the complete genome sequence of an organism. Because transcriptome sequence analysis (RNA-Seq) promises an unbiased and comprehensive picture of the transcriptome, we reason that a sample-specific protein database derived from RNA-Seq data can better approximate the real protein pool in the sample and thus improve protein identification. In this study, we have developed a two-step strategy for building sample-specific protein databases from RNA-Seq data. First, the database size is reduced by eliminating unexpressed or lowly expressed genes according to transcript quantification. Second, high-quality nonsynonymous coding single nucleotide variations (SNVs) are identified based on RNA-Seq data, and corresponding protein variants are added to the database. Using RNA-Seq and shotgun proteomics data from two colorectal cancer cell lines SW480 and RKO, we demonstrated that customized protein sequence databases could significantly increase the sensitivity of peptide identification, reduce ambiguity in protein assembly, and enable the detection of known and novel peptide variants. Thus, sample-specific databases from RNA-Seq data can enable more sensitive and comprehensive protein discovery in shotgun proteomics studies.

Temporary Reduction and Slow Recovery of Integrin ανβ3 in Endometrium After Uterine Arterial Embolization

European Journal of Obstetrics, Gynecology, and Reproductive Biology. Jan, 2012  |  Pubmed ID: 22015245

We aimed to study the effect of uterine arterial embolization (UAE) on the level of endometrial integrin ανβ3 in guinea pigs.

Intestinal Metabolite Compound K of Panaxoside Inhibits the Growth of Gastric Carcinoma by Augmenting Apoptosis Via Bid-mediated Mitochondrial Pathway

Journal of Cellular and Molecular Medicine. Jan, 2012  |  Pubmed ID: 21323864

Compound K (20-O-β-D-glucopyranosyl-20(S)-protopanaxadiol, CK), an intestinal bacterial metabolite of panaxoside, has been shown to inhibit tumour growth in a variety of tumours. However, the mechanisms involved are largely unknown. We use human gastric carcinoma cell lines BGC823, SGC7901 and human gastric carcinoma xenograft in nude mice as models to study the mechanisms of CK in gastric cancers. We found that CK significantly inhibits the viabilities of BGC823 and SGC7901 cells in dose- and time-dependent manners. CK-induced BGC823 and SGC7901 cells apoptosis and cell cycle arrest in G2 phase by up-regulation of p21 and down-regulation of cdc2 and cyclin B1. Further studies show that CK induces apoptosis in BGC823 and SGC7901 cells mainly through mitochondria-mediated internal pathway, and that CK induces the translocation of nuclear Bid to mitochondria. Finally, we found that CK effectively inhibited the tumour formation of SGC7901 cells in nude mice. Our studies show that CK can inhibit the viabilities and induce apoptosis of human gastric carcinoma cells via Bid-mediated mitochondrial pathway.

[Viral Etiology of 1165 Hospitalized Children with Acute Lower Respiratory Tract Infection]

Zhongguo Dang Dai Er Ke Za Zhi = Chinese Journal of Contemporary Pediatrics. Jan, 2012  |  Pubmed ID: 22289748

To explore the viral etiology of acute low respiratory tract infection (ALRTI) among hospitalized children in Changsha of Hunan Province of China.

Silk Self-assembly Mechanisms and Control from Thermodynamics to Kinetics

Biomacromolecules. Mar, 2012  |  Pubmed ID: 22320432

Silkworms and spiders generate fibers that exhibit high strength and extensibility. The underlying mechanisms involved in processing silk proteins into fiber form remain incompletely understood, resulting in the failure to fully recapitulate the remarkable properties of native fibers in vitro from regenerated silk solutions. In the present study, the extensibility and high strength of regenerated silks were achieved by mimicking the natural spinning process. Conformational transitions inside micelles, followed by aggregation of micelles and their stabilization as they relate to the metastable structure of silk are described. Subsequently, the mechanisms to control the formation of nanofibrous structures were elucidated. The results clarify that the self-assembly of silk in aqueous solution is a thermodynamically driven process where kinetics also play a key role. Four key factors, molecular mobility, charge, hydrophilic interactions, and concentration underlie the process. Adjusting these factors can balance nanostructure and conformational composition, and be used to achieve silk-based materials with properties comparable to native fibers. These mechanisms suggest new directions to design silk-based multifunctional materials.

Synthesis and Characterization of a Novel Potato Starch Derivative with Cationic Acetylcholine Groups

International Journal of Biological Macromolecules. Jan, 2012  |  Pubmed ID: 22266328

A novel substance, cationic acetylcholine potato starch (CAPS), was developed for the first time. The synthesis process had three steps: first, carboxymethyl potato starch (CMPS) was synthesized under sodium hydroxide alkaline condition and in isopropyl alcohol organic media; second, bromocholine chloride (BCC) was synthesized with sulphuric acid as a catalytic agent; finally, CAPS was synthesized by the reaction of CMPS with BCC in N,N'-dimethylformamide (DMF). The degree of substitution (DS) of CAPS was determined by ammonia gas-sensing electrode and elemental analysis. CAPS was characterized by Fourier transformed infrared (FTIR) and near infrared (FTNIR) spectroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD) and differential scanning calorimetry (DSC).

Nanogold-functionalized Magnetic Beads with Redox Activity for Sensitive Electrochemical Immunoassay of Thyroid-stimulating Hormone

Analytica Chimica Acta. Jan, 2012  |  Pubmed ID: 22152790

A new electrochemical immunosensor for sensitive determination of thyroid-stimulating hormone (TSH) was designed by using redox-active nanogold-functionalized magnetic beads (GoldMag) as signal tags on the nanogold-graphene interface. To construct such GoldMag nanostructures, polyethyleneimine-functionalized magnetic beads (PEI-MBs) were initially prepared by using a wet chemical method, and the electroactive thionine molecules and gold nanoparticles were then alternately immobilized on the surface of PEI-MBs by using an opposite-charged adsorption technique and an in situ synthesis method, respectively. The synthesized GoldMag nanostructures were utilized as signal tags for the label of horseradish peroxidase-anti-TSH conjugates (HRP-anti-TSH). With a sandwich-type immunoassay format, the conjugated signal tags on the transducer were increased with the increasing TSH concentration in the sample, thus enhancing the signal of the electrochemical immunosensor due to the labeled HRP toward the catalytic reduction of H(2)O(2). Under optimal conditions, the current was proportional to the logarithm of TSH concentration ranging from 0.01 to 20 μIU mL(-1) in pH 6.0 HAc-NaAc containing 6 mM H(2)O(2). The detection limit (LOD) was 0.005 μIU mL(-1) TSH at 3s(B). The immunosensor displayed an acceptable reproducibility, stability and selectivity. In addition, the methodology was evaluated with human serum specimens, receiving good correlation with results from commercially available electrochemiluminescent analyzer.

Polycomb Repressive Complex 2 Regulates Normal Development of the Mouse Heart

Circulation Research. Feb, 2012  |  Pubmed ID: 22158708

Rationale: Epigenetic marks are crucial for organogenesis, but their role in heart development is poorly understood. Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27, which establishes H3K27me3 repressive epigenetic marks that promote tissue-specific differentiation by silencing ectopic gene programs. Objective: We studied the function of PRC2 in murine heart development using a tissue-restricted conditional inactivation strategy. Methods and Results: Inactivation of the PRC2 subunit Ezh2 by Nkx2-5(Cre) (Ezh2(NK)) caused lethal congenital heart malformations, namely, compact myocardial hypoplasia, hypertrabeculation, and ventricular septal defect. Candidate and genome-wide RNA expression profiling and chromatin immunoprecipitation analyses of Ezh2(NK) heart identified genes directly repressed by EZH2. Among these were the potent cell cycle inhibitors Ink4a/b (inhibitors of cyclin-dependent kinase 4 A and B), the upregulation of which was associated with decreased cardiomyocyte proliferation in Ezh2(NK). EZH2-repressed genes were enriched for transcriptional regulators of noncardiomyocyte expression programs such as Pax6, Isl1, and Six1. EZH2 was also required for proper spatiotemporal regulation of cardiac gene expression, because Hcn4, Mlc2a, and Bmp10 were inappropriately upregulated in ventricular RNA. PRC2 was also required later in heart development, as indicated by cardiomyocyte-restricted TNT-Cre inactivation of the PRC2 subunit Eed. However, Ezh2 inactivation by TNT-Cre did not cause an overt phenotype, likely because of functional redundancy with Ezh1. Thus, early Ezh2 inactivation by Nk2-5(Cre) caused later disruption of cardiomyocyte gene expression and heart development. Conclusions: Our study reveals a previously undescribed role of EZH2 in regulating heart formation and shows that perturbation of the epigenetic landscape early in cardiogenesis has sustained disruptive effects at later developmental stages.

Increased 5S RRNA Oxidation in Alzheimer's Disease

Journal of Alzheimer's Disease : JAD. Jan, 2012  |  Pubmed ID: 22232003

It is widely accepted that oxidative stress is involved in neurodegenerative disorders such as Alzheimer's disease (AD). Ribosomal RNA (rRNA) is one of the most abundant molecules in most cells and is affected by oxidative stress in the human brain. Previous data have indicated that total rRNA levels were decreased in the brains of subjects with AD and mild cognitive impairment concomitant with an increase in rRNA oxidation. In addition, level of 5S rRNA, one of the essential components of the ribosome complex, was significantly lower in the inferior parietal lobule (IP) brain area of subjects with AD compared with control subjects. To further evaluate the alteration of 5S rRNA in neurodegenerative human brains, multiple brain regions from both AD and age-matched control subjects were used in this study, including IP, superior and middle temporal gyro, temporal pole, and cerebellum. Different molecular pools including 5S rRNA integrated into ribosome complexes, free 5S rRNA, cytoplasmic 5S rRNA, and nuclear 5S rRNA were studied. Free 5S rRNA levels were significantly decreased in the temporal pole region of AD subjects and the oxidation of ribosome-integrated and free 5S rRNA was significantly increased in multiple brain regions in AD subjects compared with controls. Moreover, a greater amount of oxidized 5S rRNA was detected in the cytoplasm and nucleus of AD subjects compared with controls. These results suggest that the increased oxidation of 5S rRNA, especially the oxidation of free 5S rRNA, may be involved in the neurodegeneration observed in AD.

Body Fat and Blood Pressure: Comparison of Blood Pressure Measurements in Chinese Children with Different Body Fat Levels

The British Journal of Nutrition. Jan, 2012  |  Pubmed ID: 22243661

Children in China are experiencing a rapid increase in the prevalence of obesity, which is associated with hypertension. To compare the effect of body fat on blood pressure (BP) with that of the normal physical growth, we compared BP levels in Chinese children with different body fat levels. In the present population-based study, 13 972 children in the highest-skinfold-thickness-quartile group were individually matched to 13 972 children in the lowest-skinfold-thickness-quartile group by height and weight. Similarly, 5103 children in the highest-waist-circumference-quartile group were matched to the same number of children in the lowest-waist-circumference-quartile group. The high- and low-fat groups had similar height and weight but the high-fat group had significantly higher skinfold and waist circumference measurements. The differences in systolic BP (SBP) between the high- and low-skinfold-thickness groups were small: 0·01 (95 % CI - 0·41, 0·44) mmHg in boys and 0·20 (95 % CI - 0·15, 0·54) mmHg in girls. The differences in diastolic BP (DBP) were also small (0·39 and 0·38 mmHg for boys and girls, respectively) but were statistically significant. The differences in both SBP and DBP between the high- and low-waist-circumference groups were small but not statistically significant. For a given body size as measured by height and weight, relative body fat had little impact on BP levels in these children. Fat mass and lean mass may have a similar quantitative impact on BP in healthy-weight children.

Long-term Persistence of Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in Air, Soil and Sediment Around an Abandoned Pentachlorophenol Factory in China

Environmental Pollution (Barking, Essex : 1987). Mar, 2012  |  Pubmed ID: 22243858

Air, soils and sediments surrounding an abandoned pentachlorophenol (PCP) factory were sampled to determine the levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), unintentionally formed during PCP production. The mean concentration of PCDD/Fs in ambient air was one order of magnitude higher than that of the reference site. A trend of decreasing concentrations with increasing distance from the factory was observed, suggesting this site has a significant influence on the regional ambient air. As for soil samples collected within 3 km from the factory and sediment samples from the adjacent rivers, high levels of contamination were found with WHO-TEQ concentrations of 193 ± 211 pg/g and 667 ± 978 pg/g, respectively. The PCDD/F homologue profiles of all samples were consistent with those found in the technical product of PCP, with OCDD as the dominant congener. These results indicate PCDD/Fs in the historical contaminated site pose a long-term impact on surrounding environment.

The Small Heat Shock Protein ODF1/HSPB10 is Essential for Tight Linkage of Sperm Head to Tail and Male Fertility in Mice

Molecular and Cellular Biology. Jan, 2012  |  Pubmed ID: 22037768

Sperm motility and hence male fertility strictly depends on proper development of the sperm tail and its tight anchorage to the head. The main protein of sperm tail outer dense fibers, ODF1/HSPB10, belongs to the family of small heat shock proteins that function as molecular chaperones. However, the impact of ODF1 on sperm tail formation and motility and on male fecundity is unknown. We therefore generated mutant mice in which the Odf1 gene was disrupted. Heterozygous mutant male mice are fertile while sperm motility is reduced, but Odf1-deficient male mice are infertile due to the detachment of the sperm head. Although headless tails are somehow motile, transmission electron microscopy revealed disturbed organization of the mitochondrial sheath, as well as of the outer dense fibers. Our results thus suggest that ODF1, besides being involved in the correct arrangement of mitochondrial sheath and outer dense fibers, is essential for rigid junction of sperm head and tail. Loss of function of ODF1, therefore, might account for some of the cases of human infertility with decapitated sperm heads. In addition, since sperm motility is already affected in heterozygous mice, impairment of ODF1 might even account for some cases of reduced fertility in male patients.