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Find video protocols related to scientific articles indexed in Pubmed.
Adjuvant effects of recombinant giant panda (Ailuropoda melanoleuca) IL-18 on the canine distemper disease vaccine in mice.
J. Vet. Med. Sci.
PUBLISHED: 11-18-2014
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Canine distemper virus (CDV) is a morbillivirus known to cause morbidity and mortality in a broad range of animals. Giant pandas (Ailuropoda melanoleuca), especially captive ones, are susceptible to natural infection with CDV. Interleukin-18 (IL-18) is a powerful adjuvant molecule that can enhance the development of antigen-specific immunity and vaccine efficacy. In this study, a giant panda IL-18 gene eukaryotic expression plasmid (pcAmIL-18) was constructed. Female BALB/c mice were muscularly inoculated with the plasmids pcAmIL-18, pcDNA3.1 and PBS, respectively. They were subsequently injected with an attenuated CDV vaccine for dogs, and the induced humoral and cellular responses were evaluated. The results showed that pcAmIL-18 remarkably improved the level of specific antibody, IFN-? and IL-2 in mice sera, the T lymphocyte proliferation index and the percentage of CD4(+) and CD8(+) cells. These data indicated that pcAmIL-18 is a potential adjuvant that promotes specific immunity.
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A rapid new approach for the quality evaluation of the folk medicine dianbaizhu based on chemometrics.
Chem. Pharm. Bull.
PUBLISHED: 11-05-2014
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Dianbaizhu, a folk medicine from Gaultheria leucocarpa BLUME var. yunnanensis (FRANCH.) T. Z. HSU & R. C. FANG (Ericaceae) used as an antirheumatic, has multiple plant origins and officinal parts. A rapid high-performance liquid chromatography with diode array detector (HPLC-DAD) method was established for the simultaneous determination of the characteristic ingredient methyl benzoate-2-O-?-D-glucopyranosyl(1?2) [O-?-D-xylopyranosyl(1?6)]-O-?-D-glucopyranoside and seven bioactive constituents in eight Gaultheria species. This chromatographic method is precise, accurate, and stable. Kruskal-Wallis analysis, hierarchical cluster analysis, and factor analysis were used to analyze the content of reference compounds in different Gaultheria species and officinal parts. The analyses showed significant differences (p<0.05) in Gaultheria species but few differences (p>0.05) in their medicinal parts. G. leucocarpa var. yunnanensis appeared to the best among the Gaultheria species tested for the treatment of rheumatic diseases. Taken together, the results show that this simultaneous quanti?cation of multiple active constituents using HPLC-DAD combined with chemometrics can be reliably applied to evaluate the quality of Dianbaizhu.
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[Analysis of differentially expressed genes in placental tissues of early-onset severe preeclampsia patients].
Zhonghua Fu Chan Ke Za Zhi
PUBLISHED: 10-21-2014
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To explore the differentially expressed genes(DEG)involved in the pathogenesis of preeclampsia (PE).
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[Evaluation of Orbscan II plus non-history double-K method in intraocular lens power calculation for patients after refractive surgery].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 10-15-2014
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To explore the accuracy of intraocular lens (IOL) power calculation with non-history method using the keratometric value derived from one zone of Orbscan II topography after laser in situ keratomileusis (LASIK).
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The complete mitochondrial genome of Stump-tailed Macaques (Macaca arctoides).
Mitochondrial DNA
PUBLISHED: 09-23-2014
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Abstract Stump-tailed macaque (Macaca arctoides) has been enlisted as the Near Threatened species in the IUCN Red List. In this study, the complete mitochondial genome of M. arctoides was determined. The mitogenome was 16,559?bp in length with an A?+?T content of 56.8%, containing 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes (PCGs) and a control region (D-loop). Ten protein-coding genes (ND1, COX1, COX2, ND4, COX3, ND4L, ATP8, ATP6, CYTB, ND6) started with ATG codons, while ND2, ND3 and ND5 initiated with ATT, ATC and ATA, respectively. Eight PCGs ended with complete termination codons except for COX3, ND3, ND4, and CYTB terminated with incompleted codon T.
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The degradation of antibiotic amoxicillin in the Fenton-activated sludge combined system.
Environ Technol
PUBLISHED: 09-11-2014
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The present study investigated the removal efficiency of amoxicillin by the Fenton process, individual activated sludge process and Fenton-activated sludge combined system. For the antibiotic at 1?g L(-1), the optimal conditions of the Fenton process included: 4?mL FeSO4·7H2O solution (20.43?g ?L(-1)), 6?mL H2O2 solution (3%) and 40°C. Under the optimal conditions, the removal rate of amoxicillin achieved up to 80% in 70?min. In addition, the impact of amoxicillin on microorganism limited the removal capacity of the activated sludge process. When the concentration of amoxicillin was less than 350?mg?L(-1), 69.04-88.79% of the antibiotic was removed. However, the antibiotic could not be treated by the activated sludge when the concentration increased up to 650?mg?L(-1). On the other hand, ifamoxicillin was pretreated partly by the Fenton process it was then degraded completely by the same activated sludge. Thus, the combined system included two steps: 80% amoxicillin was degraded in step I and was removed completely in the cheaper biological treatment (step II). Our result showed that compared with the individual activated sludge process, the Fenton process improved the removal capacity of the subsequent activated sludge process in the combined system.
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Scutellarin inhibits high glucose-induced and hypoxia-mimetic agent-induced angiogenic effects in human retinal endothelial cells through reactive oxygen species/hypoxia-inducible factor-1?/vascular endothelial growth factor pathway.
J. Cardiovasc. Pharmacol.
PUBLISHED: 09-06-2014
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Scutellarin inhibits hypoxia-induced and moderately high glucose-induced proliferation and vascular endothelial growth factor (VEGF) expression in human retinal endothelial cells (HRECs); thus, it could be a potential therapy for diabetic retinopathy. However, how scutellarin inhibits VEGF is unknown. In our study, HRECs were treated with high glucose and/or hypoxia-mimetic agent cobalt chloride to stimulate cell proliferation, migration, and angiogenesis, and the effects of scutellarin on these processes were analyzed through cell viability assay, Transwell migration assay and endothelial tube formation assay, respectively. The inhibition of angiogenic factor VEGF by scutellarin was confirmed by reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. The mechanisms for VEGF inhibition were examined by luciferase reporter assay, Western blot, immunoprecipitation, and biochemical assays. We found that scutellarin not only concentration-dependently inhibited cell proliferation, migration, and tube formation in HRECs but also decreased their production of VEGF. The reduction of VEGF was due to increased ubiquitination and degradation of hypoxia-inducible factor (HIF)-1? by scutellarin. Furthermore, scutellarin impaired the interaction of HIF-1? with p300, which further decreased the transcriptional activity of HIF-1?. As an inducer of HIF-1?, oxidative stress was attenuated by scutellarin. Our data demonstrate that scutellarin exhibits an antiangiogenic effect via inhibition of oxidative stress, enhancement of HIF-1? degradation, and reduction of VEGF secretion.
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Effect of yiqibushenhuoxue decoction on chronic obstructive pulmonary disease measured by St. George's respiratory disease questionnaire scores and forced expiratory volume.
J Tradit Chin Med
PUBLISHED: 09-05-2014
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To investigate the effects of Yiqibushenhuoxue decoction on stable chronic obstructive pulmonary disease (COPD) by observing its influences on patients' quality of life and airway inflammation.
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Cryptosporidiosis in broiler chickens in Zhejiang Province, China: molecular characterization of oocysts detected in fecal samples.
Parasite
PUBLISHED: 07-31-2014
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Cryptosporidium is one of the most important parasites in poultry, and this pathogen can infect more than 30 avian species. The present study investigated the infection rate of Cryptosporidium among broiler chicken flocks. A total of 385 fecal samples from broiler chickens in 7 regions of Zhejiang Province collected from November 2010 to January 2012 were examined by microscopy. Thirty-eight (10%) samples were positive for Cryptosporidium infection, and 3 genotypes (Cryptosporidium baileyi, Cryptosporidium meleagridis, and avian genotype II) were identified by PCR and sequencing. A phylogenetic tree of the isolates was analyzed. These results suggest that cryptosporidiosis is widespread in poultry in Zhejiang Province, and is a potential threat to public health as well as the economy. This is the first report about the infection rate and molecular characterization of Cryptosporidium in broiler chickens in Zhejiang.
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Triptycene based organometallic complexes: a new class of acceptor synthons for supramolecular ensembles.
Dalton Trans
PUBLISHED: 07-24-2014
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Preparation and characterization of two new triptycene based polytopic Pt(II) organometallic complexes are being reported. These complexes have three trans-bromobis(trialkylphosphine)platinum(II) units directly attached to the central triptycene unit. These organoplatinum complexes were converted to the corresponding nitrate salts for subsequent use in self-assembly reactions. Characterization of these organometallic triptycene complexes by multinuclear NMR, FTIR, mass spectrometry and elemental analyses is described. The molecular structure of one of the organoplatinum triptycene tripods was determined by single-crystal X-ray crystallography. The potential utility of these organometallic tritopic acceptors as building blocks in the construction of metallasupramolecular cages containing the triptycene motif is explored. Additionally, for the first time, 3,3'-bipyridine has been used as a flexible donor tecton for self-assembly of discrete and finite metallacages using triptycene based tritopic organometallic acceptor units. Triptycene motif containing supramolecules were characterized by multinuclear NMR (including (1)H DOSY), mass spectrometry and elemental analyses. Geometry of each supramolecular framework was optimized by employing the PM6 semiempirical molecular orbital method to predict its shape and size.
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[The development of new cerebral circulation analyzer].
Zhongguo Yi Liao Qi Xie Za Zhi
PUBLISHED: 05-21-2014
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In this paper a new type of cerebral circulation is introduced, including the basic principal, parameter algorithms and equipment design. The analyzer is developed on the basis of previous cerebral circulation analyzer and combined with the latest development of hemodynamics. It has the advantages of previous analyzer and overcomes its shortcomings frequently encountered in clinical that unable to finish the analysis without detection of all the intracranial vessels. It provides new functional module and adds indices such as hydraulic power, carotidshear stress, comprehensive index etc. This analyzer can be used for cerebral circulation dynamic analysis and auxiliary diagnosis of cerebrovascular diseases.
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[A case and pedigree report of hereditary hemorrhagic telangiectasia].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 05-16-2014
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A case of hereditary hemorrhagic telangiectasia was reported. Repeated hemorrhage in nasal and digestive system are main clinical manifestation. Capillary expanded on tongue and finger is the main physical sign. Main clinical manifestation and typical physical signs, combined with family history, can help to establish a diagnosis.
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Preparation of carbon quantum dots based on starch and their spectral properties.
Luminescence
PUBLISHED: 05-15-2014
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A simple method for the synthesis of water-soluble carbon quantum dots (CQDs) has been developed based on chemical oxidation of starch. The structures and optical properties of the CQDs were characterized by ultraviolet-visible (UV-Vis) spectroscopy, photoluminescence spectroscopy (PL) and transmission electron microscopy. The CQDs were found to emit bright blue fluorescence and disperse uniformly. The effects of ambient temperature, light and pH on the properties of CQDs were studied. The CQDs exhibited good chemical stability, good photostability and pH sensitivity. Furthermore, the interaction between CQDs and bovine serum albumin (BSA) was investigated. Copyright © 2014 John Wiley & Sons, Ltd.
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PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM.
Bioinformatics
PUBLISHED: 05-09-2014
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In liquid chromatography-mass spectrometry/tandem mass spectrometry (LC-MS/MS), it is necessary to link tandem MS-identified peptide peaks so that protein expression changes between the two runs can be tracked. However, only a small number of peptides can be identified and linked by tandem MS in two runs, and it becomes necessary to link peptide peaks with tandem identification in one run to their corresponding ones in another run without identification. In the past, peptide peaks are linked based on similarities in retention time (rt), mass or peak shape after rt alignment, which corrects mean rt shifts between runs. However, the accuracy in linking is still limited especially for complex samples collected from different conditions. Consequently, large-scale proteomics studies that require comparison of protein expression profiles of hundreds of patients can not be carried out effectively.
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Comparison of fiber lasers based on distributed side-coupled cladding-pumped fibers and double-cladding fibers.
Appl Opt
PUBLISHED: 05-03-2014
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We compare both analytically and numerically the distributed side-coupled cladding-pumped (DSCCP) fiber lasers and double cladding fiber (DCF) lasers. We show that, through optimization of the coupling and absorbing coefficients, the optical-to-optical efficiency of DSCCP fiber lasers can be made as high as that of DCF lasers. At the same time, DSCCP fiber lasers are better than the DCF lasers in terms of thermal management.
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High signal-to-noise ratio, single-frequency 2 ?m Brillouin fiber laser.
Opt Lett
PUBLISHED: 05-03-2014
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A high optical signal-to-noise ratio (OSNR) single-frequency 2 ?m Brillouin fiber laser (BFL) with watt-level output and high transfer efficiency is demonstrated for the first time to the best of our knowledge. The Brillouin pump is constructed with a two-stage thulium-doped fiber amplifier (TDFA) seeded by a 2 ?m laser diode, providing 4.02 W average power with 1 MHz linewidth. Using an optimized length of 14 m for the Brillouin ring cavity, the BFL works stably in single-mode region with 8 kHz linewidth because of the linewidth narrowing effect. The transfer efficiency is 51% with 1.08 W output power and 62 dB OSNR for 3.22 W pump power.
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[Clinical features of rituximab plus chemotherapy as first-line treatment in patients with diffuse large B-cell lymphoma].
Zhonghua Xue Ye Xue Za Zhi
PUBLISHED: 04-25-2014
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A prospective, multicenter and non-interventional prospective study was conducted to evaluate the clinical features of rituximab combined with chemotherapy (R-Chemo) as first-line treatment on newly diagnosed Chinese patients with diffuse large B-cell lymphoma (DLBCL).
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Stem cell-like circulating tumor cells indicate poor prognosis in gastric cancer.
Biomed Res Int
PUBLISHED: 04-22-2014
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Circulating tumor cells (CTCs), which have stem cell-like characteristics, might play a crucial role in cancer metastasis. CD44 has been identified as gastric cancer (GC) stem cell (CSC) marker. Here, the prognostic significance of CD44-positive CTCs in GC patients was investigated. CTCs were detected in 27 of 45 GC patients. The presence of CTCs was significantly associated with lymph node metastasis, distant metastasis, and recurrence (P = 0.007, P = 0.035, and P = 0.035, resp.). Nineteen of the 27 CTC-positive patients had CD44-positive CTCs. These patients were more likely to develop metastasis and recurrence than patients with CD44-negative CTCs. CD44-positive CTC counts were higher in recurrent patients than in the nonrecurrent ones (means 4.8 and 1.9, resp.; P = 0.010). Furthermore, 13 of 19 patients with CD44-positive CTCs developed recurrent disease, and the mean time to recurrence was shorter than that in patients with CD44-negative CTCs (10.54 ± 5.55 and 19.13 ± 9.72 months, resp.; P = 0.04). COX proportional hazards model indicated that the presence of CD44-positive CTCs and TNM stage were independent predictors of recurrence for GC (P = 0.030 and 0.008). So identifying the stem cell-like CTC subset may provide more clinically useful prognostic information than only detecting CTCs.
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The process-dependent impacts of dimethoate on the feeding behavior of rotifer.
Chemosphere
PUBLISHED: 04-16-2014
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Traditional toxicological studies usually depict the dose-effect relationship at the given exposure time while ignore how toxic effects vary during and after the exposure. In the present study, feeding depression of the rotifer Brachionus calyciflorus under the impact of dimethoate was evaluated not only in the exposure time but also in the post-exposure time. Both the filtration rates (F) and the ingestion rates (I) of the rotifers varied during the exposure period under any concentration of dimethoate. A three-stepwise stress was observed when the rotifers were exposed to 0.2 and 1.0mgL(-1) of the pesticide respectively, whereas 1.8mgL(-1) dimethoate caused only one-step stress on the rotifers during the whole period. In addition, although the feeding behaviors of the rotifers recovered after the exposure, two feeding rates both got even more depressed at 8h in the post-exposure time. The latent inhibition after exposure was related to the exposure concentrations and the exposure time. Our works indicated that the impact of dimethoate on the feeding behavior of the rotifers was highly process-dependent that caused the stepwise stress during the exposure period and the latent stress after the exposure.
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[Value of second trimester maternal serum sFlt-1, PlGF and their ratio in the prediction of preeclampsia].
Zhonghua Fu Chan Ke Za Zhi
PUBLISHED: 04-04-2014
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To study the value of second trimester maternal serum soluble Fms-like tyrosine kinase 1 (sFlt-1), placenta grouth factor (PlGF) and their ratio in the prediction of preeclampsia.
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Rearrangement structure-independent strategy of CNV breakpoint analysis.
Mol. Genet. Genomics
PUBLISHED: 03-28-2014
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Rare copy number variations (CNVs) generated by human genomic rearrangements have been shown to play an important role in pathogenesis of human diseases and cancers. CNV breakpoint analysis can help define genomic location, genetic content and sequence structure of pathogenic CNVs. This process is vital to elucidate CNV mutational mechanism and etiology of CNV-associated disorders. However, it is technically challenging to map CNV breakpoints at base-pair level, especially in the genomic regions with sequence complexity. In this study, we developed a new method of capture and breakpoint approaching sequencing (CBAS) to efficiently obtain CNV breakpoint sequences. This strategy is independent of CNV structures and applicable to various CNV types. As was demonstrated in CNV-associated patients with neurological disorders, CBAS achieved fine mapping of breakpoint sequences for compound deletion, complex duplication, and translocation. Intriguingly, CBAS also revealed unexpected CNV complexity involving long-range DNA rearrangement. Our observations showed that CBAS is an efficient method for obtaining CNV breakpoint sequence and mapping insertional events as well. This method can facilitate the researches on CNV-associated human diseases and cancers. CBAS is also applicable to mapping the integration sites of retrovirus (such as HIV) and transgenes in model organisms.
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The analysis of the disease spectrum in China.
Biomed Res Int
PUBLISHED: 03-25-2014
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Analysis of the related risks of disease provides a scientific basis for disease prevention and treatment, hospital management, and policy formulation by the changes in disease spectrum of patients in hospital. Retrospective analysis was made to the first diagnosis, age, gender, daily average cost of hospitalized patients, and other factors in the First Affiliated Hospital of Nanjing Medical University during 2006-2013. The top 4 cases were as follows: cardiovascular disease, malignant tumors, lung infections, and noninsulin dependent diabetes mellitus. By the age of disease analysis, we found a younger age trend of cardiovascular disease, and the age of onset of cancer or diabetes was somewhat postponed. The average daily cost of hospitalization and the average daily cost of the main noncommunicable diseases were both on the rise. Noncommunicable diseases occupy an increasingly important position in the constitution of the disease, and they caused an increasing medical burden. People should pay attention to health from the aspects of lifestyle changing. Hospitals should focus on building the appropriate discipline. On the other hand, an integrated government response is required to tackle key risks. Multiple interventions are needed to lower the burden of these diseases and to improve national health.
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Differential expression of STAT1 and p21 proteins predicts pancreatic cancer progression and prognosis.
Pancreas
PUBLISHED: 03-25-2014
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The transcription factor Stat1 is a member of the family of signal transducers and transcription activators and responds to interferon-? stimulation. p21 is a p53-responsive gene for cell cycle regulation and mediates Stat1 antitumor activity. The aim of this study was to analyze their expression for prediction of pancreatic cancer progression and prognosis.
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Segmental relaxation behavior of polystyrene chains in the cores of collapsed dry micelles tethered on the micelle film surface by a poly(acrylic acid) corona.
Soft Matter
PUBLISHED: 03-22-2014
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We present an experimental investigation of the segmental relaxation behavior of polystyrene (PS) chains that are confined in a micellar core tethered by a poly(acrylic acid) (PAA) block corona on the dry film surface, along with various core density and molecular weight of PS block from below to well above the entanglement molecular weight. The results show that the onset temperature of PS chain rearrangement (T(onset)), which was much lower than the T(bulk)(g) of the corresponding PS block and higher than T(film)(g) of ultrathin PS films with corresponding thickness and molecular weights, generally increases with increasing density of the micelle core. It was found that the difference in ?T(onset) with increasing relative density ?/?min obtained from PS154-b-PAA49 and PS278-b-PAA47 micelles was large, while these from PS278-b-PAA47 and PS404-b-PAA63 was negligible, suggesting that entanglement has considerable influence on the density dependence of the T(onset) of PS chains under confinement in the micelle core on the film surface.
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Cassava genome from a wild ancestor to cultivated varieties.
Nat Commun
PUBLISHED: 03-20-2014
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Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
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Study on the fluorescence resonance energy transfer between CdS quantum dots and Eosin Y.
Luminescence
PUBLISHED: 02-26-2014
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Water-soluble CdS quantum dots (QDs) were prepared using mercaptoacetic acid (TGA) as the stabilizer in an aqueous system. A fluorescence resonance energy transfer (FRET) system was constructed between water-soluble CdS QDs (donor) and Eosin Y (acceptor). Several factors that impacted the fluorescence spectra of the FRET system, such as pH (3.05-10.10), concentration of Eosin Y (2-80 mg/L) and concentration of CdS QDs (2-80 mg/L), were investigated and refined. Donor-to-acceptor ratios, the energy transfer efficiency (E) and the distance (r) between CdS QDs and Eosin Y were obtained. The results showed that a FRET system could be established between water-soluble CdS QDs and Eosin Y at pH 5.0; donor-to-acceptor ratios demonstrated a 1: 8 proportion of complexes; the energy transfer efficiency (E) and the distance (r) between the QDs and Eosin Y were 20.07% and 4.36 nm,respectively. Copyright © 2014 John Wiley & Sons, Ltd.
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Different types of nitrogen deposition show variable effects on the soil carbon cycle process of temperate forests.
Glob Chang Biol
PUBLISHED: 02-14-2014
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Nitrogen (N) deposition significantly affects the soil carbon (C) cycle process of forests. However, the influence of different types of N on it still remained unclear. In this work, ammonium nitrate was selected as an inorganic N (IN) source, while urea and glycine were chosen as organic N (ON) sources. Different ratios of IN to ON (1 : 4, 2 : 3, 3 : 2, 4 : 1, and 5 : 0) were mixed with equal total amounts and then used to fertilize temperate forest soils for 2 years. Results showed that IN deposition inhibited soil C cycle processes, such as soil respiration, soil organic C decomposition, and enzymatic activities, and induced the accumulation of recalcitrant organic C. By contrast, ON deposition promoted these processes. Addition of ON also resulted in accelerated transformation of recalcitrant compounds into labile compounds and increased CO2 efflux. Meanwhile, greater ON deposition may convert C sequestration in forest soils into C source. These results indicated the importance of the IN to ON ratio in controlling the soil C cycle, which can consequently change the ecological effect of N deposition.
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The complete mitochondrial genome of Assamese Macaques (Macaca assamensis).
Mitochondrial DNA
PUBLISHED: 02-06-2014
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Abstract The complete mitochondrial genome of Assamese macaques (Macaca assamensis) was sequenced in this study. The genome is 16,542?bp long, consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding areas. Eight PCGs (COI, COII, ATP6, COIII, ND4L, ND4, ND6, CYTB) initiate with the start codon ATG and another two genes (ND1, ATP8) use GTG, while ND2, ND3 and ND5 start with ATT, ATC and ATA, respectively. Five genes (COII, ATP8, ATP6, ND4L and ND5) use the complete stop codon TAA, whereas four genes have incomplete stop codons, TA- (COIII) and T-?- (ND3, ND4, CYTB), while others use standard canonical TAA as their termination codons. The largest non-coding control region with the length of 1091?bp is located between the tRNA-Pro and tRNA-Phe genes.
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Expression and characterization of a soluble VEGF receptor 2 protein.
Cell Biosci
PUBLISHED: 01-31-2014
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To clone and express a truncated, soluble vascular endothelial growth factor receptor 2 (sVEGFR2) possessing the combined-functional domains 1-3 and 5 in eukaryotic cells and to test the inhibitory effects of full length VEGFR2 in vivo.
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Chronic gastritis in China: a national multi-center survey.
BMC Gastroenterol
PUBLISHED: 01-27-2014
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Chronic gastritis is one of the most common findings at upper endoscopy in the general population, and chronic atrophic gastritis is epidemiologically associated with the occurrence of gastric cancer. However, the current status of diagnosis and treatment of chronic gastritis in China is unclear.
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[Early compliance and efficacy of sublingual immunotherapy in patients with allergic rhinitis].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 12-24-2013
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The study aimed to investigate the efficacy and adverse effects of sublingual immunotherapy (SLIT) of dust mite drops to allergic rhinitis with mite allergy. The compliance and satisfaction of SLIT were also assessed.
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Efficient dual-wavelength Nd:LuLiF4 laser.
Opt Lett
PUBLISHED: 11-02-2013
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We report an efficient continuous-wave (CW) and passively Q-switched dual-wavelength Nd:LuLiF4 laser at 1314 and 1321 nm for the first time. Maximum CW output power of 6.08 W is obtained, giving an optical-to-optical conversion efficiency of 30.2% and a slope efficiency of 32.1%. Even using high doping V3+:YAG as the saturable absorber to passively Q-switch the laser, stable dual-wavelength operation remains. Maximum pulse energy extracted from the resonator is 108.7 ?J at 17.2 kHz pulse-repetition rate, and maximum peak power is 885 W.
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FancJ regulates interstrand crosslinker induced centrosome amplification through the activation of polo-like kinase 1.
Biol Open
PUBLISHED: 10-15-2013
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DNA damage response (DDR) and the centrosome cycle are two of the most critical processes for maintaining a stable genome in animals. Sporadic evidence suggests a connection between these two processes. Here, we report our findings that six Fanconi Anemia (FA) proteins, including FancI and FancJ, localize to the centrosome. Intriguingly, we found that the localization of FancJ to the mother centrosome is stimulated by a DNA interstrand crosslinker, Mitomycin C (MMC). We further show that, in addition to its role in interstrand crosslinking (ICL) repair, FancJ also regulates the normal centrosome cycle as well as ICL induced centrosome amplification by activating the polo-like kinase 1 (PLK1). We have uncovered a novel function of FancJ in centrosome biogenesis and established centrosome amplification as an integral part of the ICL response.
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Efficient 1856 nm emission from Tm,Mg:LiNbO3 laser.
Opt Express
PUBLISHED: 10-10-2013
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Efficient continuous-wave laser emission at 1856 nm from a Tm,Mg:LiNbO(3) crystal slab with high Tm(3+) doping concentration is reported. A maximum output power of 2.62 W is realized with a slope efficiency of 19.6% and the beam quality factor M(2) of 1.7 at room temperature. We believe that this is the first demonstration of watt-level laser operation in Tm,Mg:LiNbO(3) crystal and the output power is four orders of magnitude higher than that reported previously in Tm-doped LiNbO(3) crystal. Performance degradation due to the photorefractive effect under high intensity 1856 nm laser is not observed thanks to the co-doping of magnesium ions. Quantitative analysis about the long-term photorefractive effect is also provided. Multi-wavelength laser operation is realized by using different narrow-band output couplers. This demonstration opens up a viable pathway towards 2-?m integrated optic devices for achieving laser oscillation, electro-optic and nonlinear optical effects within just one sample simultaneously.
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Experimental study on the all-fiberized continuous-wave ytterbium-doped laser operating near 980 nm.
Appl Opt
PUBLISHED: 10-03-2013
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All-fiberized continuous-wave Yb-doped fiber lasers operating near 980 nm are fabricated, and 1.73 W, 980 nm lasing is obtained. Moreover, the output properties of the 980 nm fiber laser are studied by experiment. It is demonstrated, for the first time to the best of our knowledge, that the output power curve versus the active fiber length experiences double-peak values, which are caused by the red shift of the lasing wavelength induced by the longitudinal-mode competition. It is also demonstrated that the pump threshold increases exponentially with the active fiber length. The relationship between the pump threshold and the optimum active fiber length is examined.
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BRCA1 downregulates the kinase activity of Polo-like kinase 1 in response to replication stress.
Cell Cycle
PUBLISHED: 09-27-2013
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In response to DNA damage or replication stress, proliferating cells are arrested at different cell cycle stages for DNA repair by downregulating the activity of both the cyclin-dependent kinases (CDKs) and other important cell cycle kinases, including Polo-like kinase 1 (PLK1) . The signaling pathway to inhibit CDKs is relatively well understood, and breast cancer gene 1 (BRCA1) and other DNA damage response (DDR) factors play a key role in this process. However, the DNA damage-induced inhibition of PLK1 is still largely a mystery. Here we show that DNA damage and replication stress stimulate the association between BRCA1 and PLK1. Most importantly, we demonstrate that BRCA1 downregulates the kinase activity of PLK1 by modulating the dynamic interactions of Aurora A, hBora, and PLK1. Together with previous findings, we propose that in response to replication stress and DNA damage, BRCA1 plays a critical role in downregulating the kinase activity of both CDKs and PLK1.
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Layered Li2MnO3·3LiNi(0.5-x)Mn(0.5-x)Co(2x)O2 microspheres with Mn-rich cores as high performance cathode materials for lithium ion batteries.
Phys Chem Chem Phys
PUBLISHED: 08-20-2013
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Layered Li2MnO3·3LiNi0.5-xMn0.5-xCo2xO2 (x = 0, 0.05, 0.1, 0.165) microspheres with Mn-rich core were successfully synthesized by a simple two-step precipitation calcination method and intensively evaluated as cathode materials for lithium ion batteries. The X-ray powder diffractometry (XRD) results indicate that the growth of Li2MnO3-like regions is impeded due to the presence of cobalt (Co) in the material. The field-emission scanning electron microscopy (FESEM) data reveal the core-shell-like structure with a Mn-rich core in the as-prepared particles. The charge-discharge testing reveals that the capacity is markedly improved by adding Co. The activation of the cathode after Co doping becomes easier and can be accomplished completely when charged to 4.6 V at the C/40 rate in the initial cycle. Superior electrochemical performances are obtained for samples with x = 0.05 and 0.1. The corresponding initial discharge capacities are separately 281 and 285 mA h g(-1) at C/40 between 2 and 4.6 V at room temperature. After 250 cycles at C/2, the respective capacity retentions are 71.2% and 70.4%, which are better compared to the normal Li-excess Li2MnO3·3LiNi0.4Mn0.4Co0.2O2 sample with a uniform distribution of Mn element in the particles. The initial discharge capacities of both samples are approximately 250 mA h g(-1) at a rate of C/2 between 2 and 4.6 V at 55 °C after activation. Furthermore, the samples are investigated by electrochemical impedance spectroscopy (EIS) at room and elevated temperature, revealing that the key factor affecting electrochemical performance is the charge transfer resistance in the particles.
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Degradation and bound-residue formation of nonylphenol in red soil and the effects of ammonium.
Environ. Pollut.
PUBLISHED: 08-08-2013
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Fate of nonylphenol (NP) in soils and the effects of nitrogen fertilizers are unclear. Using (14)C-tracer, we studied the aerobic and anaerobic degradation of 4-NP111 in a paddy red soil amended without and with ammonium chloride. Under oxic conditions, 4-NP111 had a half-life of 16.1 ± 1.6 days and minor mineralization (3.84 ± 0.02%), forming no extractable metabolite but abundant bound residues (60.9 ± 1.7%, mostly bound to humin) after 49 days of incubation. The ammonium amendment (8 mmol/kg soil) significantly inhibited the degradation (half-life of 68.0 ± 7.7 days), mineralization (2.0 ± 1.1%), and bound-residue formation (23.7 ± 0.2%). Under anoxic conditions, 4-NP111 did not degrade during 49 days of incubation and the ammonium amendment (40 mmol/kg soil) did not affect its persistence. Our results demonstrate that bound-residue formation was a major mechanism for NP dissipation in the red soil under oxic conditions and that chemical nitrogen fertilizer at average field application rate may already considerably increase NP recalcitrance in agricultural soils.
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BRCA1 promotes the ubiquitination of PCNA and recruitment of translesion polymerases in response to replication blockade.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-30-2013
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Breast cancer gene 1 (BRCA1) deficient cells not only are hypersensitive to double-strand breaks but also are hypersensitive to UV irradiation and other agents that cause replication blockade; however, the molecular mechanisms behind these latter sensitivities are largely unknown. Here, we report that BRCA1 promotes cell survival by directly regulating the DNA damage tolerance pathway in response to agents that create cross-links in DNA. We show that BRCA1 not only promotes efficient mono- and polyubiquitination of proliferating cell nuclear antigen (PCNA) by regulating the recruitment of replication protein A, Rad18, and helicase-like transcription factor to chromatin but also directly recruits translesion polymerases, such as Polymerase eta and Rev1, to the lesions through protein-protein interactions. Our data suggest that BRCA1 plays a critical role in promoting translesion DNA synthesis as well as DNA template switching.
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Degradation, metabolism, and bound-residue formation and release of Tetrabromobisphenol A in soil during sequential anoxic-oxic incubation.
Environ. Sci. Technol.
PUBLISHED: 07-24-2013
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Tetrabromobisphenol A (TBBPA) is one of the most commonly used flame retardants and has become an environmental contaminant worldwide. We studied the fate of (14)C-labeled TBBPA in soil under static anoxic (195 days) and sequential anoxic (125 days)-oxic (70 days) conditions. During anoxic incubation, TBBPA dissipated with a half-life of 36 days, yielding four debromination metabolites: bisphenol A (BPA) and mono-, di-, and tribrominated BPA. At the end of anoxic incubation, all four brominated BPAs completely disappeared, leaving BPA (54% of initial TBBPA) as the sole detectable organic metabolite. TBBPA dissipation was accompanied by trace mineralization (<1.3%) and substantial bound-residue formation (35%), probably owing to chemical binding to soil organic matter. Subsequent oxic incubation was effective in degrading accumulated BPA (half-life 11 days) through mineralization (6%) and bound-residue formation (62%). However, 42% of the anoxically formed bound residues was released as TBBPA and lower brominated BPAs, which were then persistent during oxic incubation. Our results provide the first evidence for release of bound residues during alteration of the redox environment and indicate that sequential anoxic-oxic incubation approaches-considered effective in remediation of environments containing halogenated xenobiotics-do not completely remove xenobiotics from environmental matrices.
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Amphiphilic peptide-loaded nanofibrous calcium phosphate microspheres promote hemostasis in vivo.
Acta Biomater
PUBLISHED: 06-08-2013
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Most fatalities from trauma occur due to severe blood loss. There is a need for improved hemostatic biomaterials that can address this problem. The aim of this study was to determine the in vivo efficacy of nanofibrous microspheres (NFM) loaded with hemostatic peptides, specifically ideal amphipathic peptides (IAP) that have been demonstrated to possess both procoagulant and antifibrinolyic activities. We demonstrate that IAP can be coupled to NFM (IAP-NFM) to form matrices that exhibit substantial hemostatic activity. IAP-NFM matrices were compared to a commercial zeolitic hemostatic biomaterial (QuikClot) and have superior efficacy in reducing bleeding in vivo. In both a murine tail transection and a murine hepatic injury model, bleeding times were significantly reduced (P<0.05) with the use of IAP-NFM as compared with equal masses of either QuikClot or NFM alone, or no treatment. Importantly, histological examination revealed no tissue injury when IAP-NFM or NFM were applied to hepatic lacerations. In contrast, QuikClot caused widespread hepatocyte degeneration and necrosis, with higher average injury zone thickness as determined by semiquantitative analysis. In summary, NFM was able to maintain the pro-coagulant properties of IAP in our preclinical model, caused no observable tissue damage at the site of application and had better performance than QuikClot controls.
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MicroRNA-143 downregulates interleukin-13 receptor alpha1 in human mast cells.
Int J Mol Sci
PUBLISHED: 06-03-2013
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MicroRNA-143 (miR-143) was found to be downregulated in allergic rhinitis, and bioinformatics analysis predicted that IL-13R?1 was a target gene of miR-143. To understand the molecular mechanisms of miR-143 involved in the pathogenesis of allergic inflammation, recombinant miR-143 plasmid vectors were constructed, and human mast cell-1(HMC-1) cells which play a central role in the allergic response were used for study. The plasmids were transfected into HMC-1 cells using a lentiviral vector. Expression of IL-13R?1 mRNA was then detected by reverse transcriptase polymerase chain reaction (RT-PCR) and Western Blotting. The miR-143 lentiviral vector was successfully stably transfected in HMC-1 cells for target gene expression. Compared to the control, the target gene IL-13R?1 was less expressed in HMC-1 transfected with miR-143 as determined by RT-PCR and Western Blotting (p < 0.05); this difference in expression was statistically significant and the inhibition efficiency was 71%. It indicates that miR-143 directly targets IL-13R?1 and suppresses IL-13R?1 expression in HMC-1 cells. Therefore, miR-143 may be associated with allergic reaction in human mast cells.
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The swimming speed alteration of two freshwater rotifers Brachionus calyciflorus and Asplanchna brightwelli under dimethoate stress.
Chemosphere
PUBLISHED: 05-21-2013
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Two common freshwater rotifer species Brachionus calyciflorus and Asplanchna brightwelli were employed as test organisms to investigate the toxic effects of the widely used organophosphate pesticide, dimethoate. The swimming angular speed and linear speed alteration of two rotifers were evaluated under the toxic stress in four concentrations (0.4, 0.8, 1.2, and 1.6 mg L(-1)). For B. calyciflorus, the rotifer swimming angular speed and linear speed were both adversely affected as a function of the toxicant concentrations. After a 2h exposure, the angular speeds at four concentrations were 39.37, 30.74, 26.68 and 23.96° s(-1), 65.30%, 50.98%, 44.25% and 39.74% of that of the control, respectively, while the mean linear speed decreased from 194.80 to 91.85×10(-3) mm s(-1), which was 70.12%, 48.14%, 34.02% and 33.06% of that of the control (277.82×10(-3) mm s(-1)), respectively. The pesticide also significantly inhibited the swimming angular speed of A. brightwelli. After a 2h exposure, the angular speeds of this rotifer at four concentrations were 39.37, 30.74, 26.68 and 23.96° s(-1), only 22.99%, 17.16%, 16.21% and 13.63% of that of the control (170.80° s(-1)), respectively. Compared with the results of B. calyciflorus, A. brightwelli was more sensitive on the swimming angular speed when exposed to the toxicant. It implied that A. brightwelli should be an alternative candidate model species about the toxicities of aquatic pollutants. In addition, when the rotifer A. brightwelli was exposed to four pesticide concentrations, the swimming linear speed displayed symptoms of hormesis, characterized by the conversion of low-concentration stimulate to high-concentration inhibition. Our results show that dimethoate had a significant effect on swimming of freshwater rotifers.
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Simultaneous Screening and Identifying Four Categories of Particular Flavonoids in the Leaves of Murraya exotica L. by HPLC-DAD-ESI-MS-MS.
J Chromatogr Sci
PUBLISHED: 01-11-2013
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Polymethoxylated flavonoids (PMFs), the particular flavonoid subclass in which all or almost all hydroxyls are capped by methylation, have high oral bioavailability and various activities. A sensitive high-performance liquid chromatography-diode array detection-electrospray ionization tandem mass spectrometry (HPLC-DAD-ESI-MS-MS) method was established to screen and identify the PMFs in the leaves of Murraya exotica. Eight PMF standards, including two polymethoxylated flavones, two polymethoxylated flavanones, two polymethoxylated chalcones and two PMF glycosides, were first to be analyzed in positive mode by collision-induced dissociation MS-MS. On the basis of the ESI-MS, characterizations were deduced, and in the results of the extracted ion chromatogram MS-MS experiment, 26 PMFs, including 18 flavones, five flavanones or chalcones and three PMF glycosides, were screened out from the complex extract of the leaves of M. exotica. Among them, 24 PMFs were hydroxylated polymethoxyflavonoids, whereas the rest were all permethoxylated PMFs. This was the first systematic report on the presence of PMFs in the leaves of M. exotica. The results indicated that the established analytical method could be adopted as a rapid, effective technique for the structural characterization of PMFs from the complex extracts of traditional Chinese medicines.
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Degradation of methyl blue using Fe-tourmaline as a novel photocatalyst.
Molecules
PUBLISHED: 01-08-2013
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This study investigated the photocatalytic activity of tourmaline by itself. Under irradiation of a 13 W, 254 nm UV lamp, 50% of methyl blue disappeared in the presence of 130 mg·L?¹ tourmaline. The reaction was inhibited by the addition of ethanol, Cl?, SO?²? and Cu²?, and promoted a little by addition of 50 mg/L Mg²?, which supports the inference of involvement of •OH radicals. This is the first proposal of tourmaline as a single photocatalyst without the need to add any artificial chemical products. Results from this study might contribute to the broadened usage of this mineral to approach the goals of saving energy and eliminate direct or indirect environmental pollution.
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RNA interference targeting CD147 inhibits the invasion of human cervical squamous carcinoma cells by downregulating MMP-9.
Cell Biol. Int.
PUBLISHED: 01-03-2013
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Cervical squamous carcinoma is a highly invasive tumour that has a great capacity to metastasise. Extracellular matrix metalloproteinase inducer (EMMPRIN or CD147), a member of the immunoglobulin superfamily, is a widely distributed cell surface glycoprotein. It is highly expressed on malignant tumour cell surfaces, including human cervical squamous carcinoma. It also plays a critical role in the invasive and metastatic activity of malignant cells by stimulating the expression of matrix metalloproteinases (MMPs). The anti-invasive effect of small interfering RNA (siRNA) against CD147 on human cervical squamous carcinoma cells and its possible pathways has been investigated. The downregulation of CD147 by transfection with siRNA resulted in MMP-9 expression and decreased activity in the cervical squamous carcinoma cell line SiHa. In vitro analysis showed that the invasive capacity of SiHa cells decreased. Thus CD147 inhibition and subsequent MMP-9 deletion may have anti-tumour effects by inhibiting the invasiveness of human cervical squamous carcinoma cells.
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A molecular evolution approach to study the roles of tropomyosin in fission yeast.
PLoS ONE
PUBLISHED: 01-01-2013
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Tropomyosin, a coiled-coil protein that binds along the length of the actin filament, is a universal regulator of the actin cytoskeleton. We have taken a bioinformatics/proteomic approach to studying structure-function relationships in this protein. The presence of a single, essential tropomyosin gene, cdc8, in fission yeast, Schizosaccharomyces pombe, enables a systems-based approach to define the residues that are important for cellular functions. Using molecular evolution methodologies we identified the most conserved residues and related them to the coiled coil structure. Mutants in which one or more of 21 of the most conserved surface residues was mutated to Ala were tested for the ability to rescue growth of a temperature-sensitive cdc8 mutant when overexpressed at the restrictive temperature. Based on altered morphology of the septum and actin cytoskeleton, we selected three sets of mutations for construction of mutant cdc8 strains using marker reconstitution mutagenesis and analysis of recombinant protein in vitro: D16A.K30A, V114S.E117A.H118A and R121A.D131A.E138A. The mutations have sequence-specific effects on cellular morphology including cell length, organization of cytoskeletal structures (actin patches, actin cables and contractile rings), and in vitro actin affinity, lending credence to the proteomic approach introduced here. We propose that bioinformatics is a valid analysis tool for defining structure-function relationships in conserved proteins in this model organism.
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Accurate LC peak boundary detection for ¹?O/¹?O labeled LC-MS data.
PLoS ONE
PUBLISHED: 01-01-2013
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In liquid chromatography-mass spectrometry (LC-MS), parts of LC peaks are often corrupted by their co-eluting peptides, which results in increased quantification variance. In this paper, we propose to apply accurate LC peak boundary detection to remove the corrupted part of LC peaks. Accurate LC peak boundary detection is achieved by checking the consistency of intensity patterns within peptide elution time ranges. In addition, we remove peptides with erroneous mass assignment through model fitness check, which compares observed intensity patterns to theoretically constructed ones. The proposed algorithm can significantly improve the accuracy and precision of peptide ratio measurements.
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[The influence of denervation on myofiber morphology of the adductor and abductor in patients with recurrent laryngeal nerve paralysis].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 12-15-2011
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To investigate the influence of denervation on myofiber morphology of the adductor and the abductor in patients with recurrent laryngeal nerve (RLN) paralysis and to provide experimental evidence for the clinical feasibility of RLN repair.
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BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.
Bioinformatics
PUBLISHED: 12-06-2011
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Peptide detection is a crucial step in mass spectrometry (MS) based proteomics. Most existing algorithms are based upon greedy isotope template matching and thus may be prone to error propagation and ineffective to detect overlapping peptides. In addition, existing algorithms usually work at different charge states separately, isolating useful information that can be drawn from other charge states, which may lead to poor detection of low abundance peptides.
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Processing methods for signal suppression of FTMS data.
Proteome Sci
PUBLISHED: 10-14-2011
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Fourier Transform Mass Spectrometry coupled with Liquid Chromatography(LC-FTMS) has been widely used in proteomics. Past investigation has revealed that there exists an intensity dependent random suppression in peptide elution profiles in LC-FTMS data. The suppression is homogenous for the same peptide but non-homogenous for different peptides. The correction of suppressed profiles and an estimation on the range of suppression are necessary for accurate and reliable quantification using FTMS data.
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Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks.
Proteome Sci
PUBLISHED: 10-14-2011
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Transcriptional regulation by transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of transcriptional regulatory network a difficult task.
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Chemical characterization of a procyanidin-rich extract from sorghum bran and its effect on oxidative stress and tumor inhibition in vivo.
J. Agric. Food Chem.
PUBLISHED: 07-29-2011
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The present study was to characterize a procyanidin-rich extract (PARE) from sorghum ( Sorghum bicolor (L.) Moench) bran and assess its biological activities. The procyanidin oligomers were separated and identified by normal-phase HPLC equipped with fluorescence (FLD) and mass spectrometry (MS) detectors. In addition, the effects of PARE on oxidative stress in mice induced by D-galactose as well as tumor inhibition in C57BL/6J mice bearing Lewis lung cancer were investigated. Administration of D-galactose significantly (p < 0.05) lowered the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). This was accompanied by a significant (p < 0.05) increase in malondialdehyde (MDA) levels in both liver and serum. Administration of PARE (150 mg/kg) significantly (p < 0.05) reversed the d-galactose-induced oxidative stress by enhancing the activities of antioxidant enzymes. Furthermore, PARE administration inhibited tumor growth and metastasis formation by suppressing vascular endothelial growth factor (VEGF) production. The results suggested that PARE had antioxidant and antitumor activities.
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[The expression of myosin heavy chain isoforms of human normal laryngeal muscles and the difference between the adductor and abductor].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 06-28-2011
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To investigate the expression of myosin heavy chain (MHC) in normal laryngeal muscle and the difference between the adductor and abductor.
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Continuous wave, dual-wavelength-pumped supercontinuum generation in an all-fiber device.
Appl Opt
PUBLISHED: 06-16-2011
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We propose a continuous wave dual-wavelength-pumped scheme for visible supercontinuum (SC) generation. The scheme is numerically studied in this paper. In the scheme, the dual-wavelength pump source is produced through a four-wave mixing process in a photonic crystal fiber. SC generation is numerically investigated by solving the generalized nonlinear Schrödinger equation. The results verify that the visible SC can be generated by the scheme, which implies that the scheme is promising for generating visible SC with high spectral power densities.
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SCFIA: a statistical corresponding feature identification algorithm for LC/MS.
BMC Bioinformatics
PUBLISHED: 06-15-2011
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Identifying corresponding features (LC peaks registered by identical peptides) in multiple Liquid Chromatography/Mass Spectrometry (LC-MS) datasets plays a crucial role in the analysis of complex peptide or protein mixtures. Warping functions are commonly used to correct the mean of elution time shifts among LC-MS datasets, which cannot resolve the ambiguity of corresponding feature identification since elution time shifts are random. We propose a Statistical Corresponding Feature Identification Algorithm(SCFIA) based on both elution time shifts and peak shape correlations between corresponding features. SCFIA first trains a set of statistical models, and then, all candidate corresponding features are scored by the statistical models to find the maximum likelihood solution.
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High-power air-cooled SiC-clad Nd:YVO4 slab lasers.
Opt Lett
PUBLISHED: 05-20-2011
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We demonstrate a diode-pumped, air-cooled, 100 W class SiC-clad Nd:YVO(4) active slab laser based on diffusion bonding of two SiC plates to a thin Nd:YVO(4) slab. We obtained 83 W of cw output power with a slope efficiency of 27% without water cooling. This demonstration initiates a novel (to the best of our knowledge) cooling design for efficient removal of waste heat generated from the diode edge-pumped high-power slab laser at room temperature.
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Pregnancy in women with systemic lupus erythematosus: a retrospective study of 111 pregnancies in Chinese women.
J. Matern. Fetal. Neonatal. Med.
PUBLISHED: 04-19-2011
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The impact of pregnancy on lupus activity has been controversial especially in Chinese women. Research looking at predictive factors in this population are sparse. The aim of this study was therefore twofold: to determine the frequencies of abnormal pregnancy outcomes in a Chinese cohort and to identify clinical and laboratory factors predicting adverse fetal and maternal outcomes in Chinese women with systemic lupus erythematosus.
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Peroxisomal alterations in Alzheimers disease.
Acta Neuropathol.
PUBLISHED: 04-18-2011
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In Alzheimers disease (AD), lipid alterations are present early during disease progression. As some of these alterations point towards a peroxisomal dysfunction, we investigated peroxisomes in human postmortem brains obtained from the cohort-based, longitudinal Vienna-Transdanube Aging (VITA) study. Based on the neuropathological Braak staging for AD on one hemisphere, the patients were grouped into three cohorts of increasing severity (stages I-II, III-IV, and V-VI, respectively). Lipid analyses of cortical regions from the other hemisphere revealed accumulation of C22:0 and very long-chain fatty acids (VLCFA, C24:0 and C26:0), all substrates for peroxisomal ?-oxidation, in cases with stages V-VI pathology compared with those modestly affected (stages I-II). Conversely, the level of plasmalogens, which need intact peroxisomes for their biosynthesis, was decreased in severely affected tissues, in agreement with a peroxisomal dysfunction. In addition, the peroxisomal volume density was increased in the soma of neurons in gyrus frontalis at advanced AD stages. Confocal laser microscopy demonstrated a loss of peroxisomes in neuronal processes with abnormally phosphorylated tau protein, implicating impaired trafficking as the cause of altered peroxisomal distribution. Besides the original Braak staging, the study design allowed a direct correlation between the biochemical findings and the amount of neurofibrillary tangles (NFT) and neuritic plaques, quantified in adjacent tissue sections. Interestingly, the decrease in plasmalogens and the increase in VLCFA and peroxisomal volume density in neuronal somata all showed a stronger association with NFT than with neuritic plaques. These results indicate substantial peroxisome-related alterations in AD, which may contribute to the progression of AD pathology.
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MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments.
BMC Bioinformatics
PUBLISHED: 03-15-2011
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Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.
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Continuous wave and passively Q-switched Nd:Lu xY1-x VO4 laser at 1.34 ?m with V3+:YAG as the saturable absorber.
Opt Express
PUBLISHED: 03-04-2011
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We demonstrated a diode-pumped continuous wave and passively Q-switched Nd:Lu(x)Y(1-x)VO4 laser at 1.34 ?m with V3+:YAG as the saturable absorber. The crystal Nd:Lu(x)Y(1-x)VO4 with equal ionic ratio (x = 0.5) shows better laser performance. The maximum continuous wave output power of 1.45 W was obtained with the optical efficiency of 20.1% and the slope efficiency of 24.5%. For the pulsed operation, the minimum pulse width achieved was 42 ns with the pulse repetition frequency of 142 kHz, and the single pulse energy and the peak power were estimated to be 6.62 ?J and 157.6 W, respectively.
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Efficient Q-switched Tm:YAG ceramic slab laser.
Opt Express
PUBLISHED: 01-26-2011
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Characteristics of Tm:YAG ceramic for high efficient 2-?m lasers are analyzed. Efficient diode end-pumped continuous-wave and Q-switched Tm:YAG ceramic lasers are demonstrated. At the absorbed pump power of 53.2W, the maximum continuous wave (cw) output power of 17.2 W around 2016 nm was obtained with the output transmission of 5%. The optical conversion efficiency is 32.3%, corresponding to a slope efficiency of 36.5%. For Q-switched operation, the shortest width of 69 ns was achieved with the pulse repetition frequency of 500 Hz and single pulse energy of 20.4 mJ, which indicates excellent energy storage capability of the Tm:YAG ceramic.
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Suppression correction and characteristic study in liquid chromatography/Fourier transform mass spectrometry measurements.
Rapid Commun. Mass Spectrom.
PUBLISHED: 01-25-2011
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Analysis of peptide profiles from liquid chromatography/Fourier transform mass spectrometry (LC/FTMS) reveals a nonlinear distortion in intensity. Investigation of the measured C(13)/C(12) ratios comparing with theoretical ones shows that the nonlinearity can be attributed to signal suppression of low abundance peptide peaks. We find that the suppression is homogenous for different isotopes of identical peptides but non-homogenous for different peptides. We develop an iterative correction algorithm that corrects the intensity distortions for peptides with relatively high abundance. This algorithm can be applied in a wide range of applications using LC/FTMS. We also analyze the distortion characteristics of the instrument for lower abundance peptides, which should be considered when interpreting quantification results of LC/FTMS.
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A method to enhance cell survival on Bruchs membrane in eyes affected by age and age-related macular degeneration.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
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To determine whether conditioned medium (CM) derived from bovine corneal endothelial cells (BCECs) can support transplanted cells on aged and age-related macular degeneration (AMD) Bruchs membrane (BM).
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Comparison of FRPE and human embryonic stem cell-derived RPE behavior on aged human Bruchs membrane.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
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To compare RPE derived from human embryonic stem cells (hES-RPE) and fetal RPE (fRPE) behavior on human Bruchs membrane (BM) from aged and AMD donors.
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Cell-deposited matrix improves retinal pigment epithelium survival on aged submacular human Bruchs membrane.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
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To determine whether resurfacing submacular human Bruchs membrane with a cell-deposited extracellular matrix (ECM) improves retinal pigment epithelial (RPE) survival.
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High-power gain-switched Tm(3+)-doped fiber laser.
Opt Express
PUBLISHED: 12-18-2010
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Gain-switched by a 1.914-µm Tm:YLF crystal laser, a two-stage Tm(3+) fiber laser has been achieved 100-W level ~2-µm pulsed laser output with a slope efficiency of ~52%. With the 6-m length of Tm fiber, the laser wavelength was centered at 2020 nm with a bandwidth of ~25 nm. Based on an acousto-optic switch, the pulse repetition rate can be modulated from 500 Hz to 50 kHz, and the laser pulse width can be tuned between 75 ns and ~1 µs. The maximum pulse energy was over 10 mJ, and the maximum pulse peak power was 138 kW. By using the fiber-coiling-induced mode-filtering effect, laser beam quality of M2 = 1.01 was obtained. Further scaling the pulse energy and average power from such kind of gain-switched fiber lasers was also discussed.
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ICPD-a new peak detection algorithm for LC/MS.
BMC Genomics
PUBLISHED: 12-01-2010
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The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise and sample variability, whose statistical characteristics are still elusive, making computational identification of low abundance proteins extremely challenging. As a result, the inability of identifying low abundance proteins in a proteomic study is the main bottleneck in protein biomarker discovery.
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Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry.
IEEE Trans Signal Process
PUBLISHED: 11-08-2010
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In this paper, we address the issue of peptide ion peak detection for high resolution time-of-flight (TOF) mass spectrometry (MS) data. A novel Bayesian peptide ion peak detection method is proposed for TOF data with resolution of 10 000-15 000 full width at half-maximum (FWHW). MS spectra exhibit distinct characteristics at this resolution, which are captured in a novel parametric model. Based on the proposed parametric model, a Bayesian peak detection algorithm based on Markov chain Monte Carlo (MCMC) sampling is developed. The proposed algorithm is tested on both simulated and real datasets. The results show a significant improvement in detection performance over a commonly employed method. The results also agree with experts visual inspection. Moreover, better detection consistency is achieved across MS datasets from patients with identical pathological condition.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.