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Find video protocols related to scientific articles indexed in Pubmed.
[Clinical characteristics of pediatric hemorrhagic fever with renal syndrome.]
Zhongguo Dang Dai Er Ke Za Zhi
PUBLISHED: 11-20-2014
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To study the clinical characteristics of pediatric hemorrhagic fever with renal syndrome (HFRS), and to improve its understanding so as to reduce the misdiagnosis.
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[Advances in actinobacterial proteomics].
Sheng Wu Gong Cheng Xue Bao
PUBLISHED: 10-28-2014
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Protein is the executor of physiological function, and direct embodiment of the life phenomena. Proteomics aims to systematically clarify all or parts of proteins' role and function in life movement. In post genome era, proteomics began to play more important role in life science field. Actinobacteria are closely linked to human production and life, which have produced many clinically important secondary metabolites, including antibiotics, antitumorals and enzymes. Actinobacterial systematics and its model organism Streptomyces coelicolor in 2001 genome sequence laid the foundation for further functional genomic studies. Actinobacterial proteomics was more directly and exactly to interpret the activity of life than genomics and transcriptomics, which grew much faster and received so much attention from scientists in the near years. Complex morphological differention, stronge environment adaptiveness, nitrogen-fixing capacity, metabolic mechanism, pathogenicity and natural produces' discovery were systematically reviewed in this study, which was expected to be the basis for promoting Actinobacterial proteomics study in the near future.
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[Plasmodium vivax specific peptides prediction and screening based on repetitive protein sequences and linear B cell epitope].
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi
PUBLISHED: 10-28-2014
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To establish a method based on repetitive protein sequences and linear B cell epitope to predict and screen specific peptides of Plasmodium vivax.
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[Construction and identification of recombinant Mycobacterium smegmatis vaccine expressing Cysticercus cellulosae cC1 antigen].
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi
PUBLISHED: 10-28-2014
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To construct recombinant Mycobacterium smegmatis vaccine expressing Cysticercus cellulosae cC1 antigen.
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[Dynamic distribution of the avian infectious bronchitis virus isolate strain Jin-13 in SPF chickens].
Bing Du Xue Bao
PUBLISHED: 10-03-2014
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This study aimed to understand the dynamic distribution of infectious bronchitis virus (IBV) Jin-13 strain in SPF chickens. Ninety-day-old SPF chickens were inoculated with Jin-13, a virulent strain, and dissected at day 1, 4, 7, 10, 14, 21, 28 or 35 post-inoculation (dpi). Samples of heart, liver, spleen, lung, trachea, kidney and duodenum were collected and the N gene was detected by Sybr Green I real-time quantitative RT-PCR assays. The established method had a good linear correlation from 7.77 x 10(8) to 10(0) copies/microL. SPF chickens developed typical clinical signs of IBV at the 4th dpi, and the IBV viral concentration of tissues and organs gradually increased with a peak of up to 7.13 x 10(4) copies/microL. The viral concentration of most organs decreased by the 10th dpi, but those of the kidney, trachea and lung remained positive for IBV at 28 dpi and the heart was still positive for IBV at > 35 dpi. The results of this study, showed that the Jin-13 strain can cause prolonged virus excertion in chickens with severe renal damage.
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Clinicopathological correlation of parapapillary atrophy in monkeys with experimental glaucoma and temporary central retinal artery occlusion.
Indian J Ophthalmol
PUBLISHED: 09-30-2014
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To investigate the clinicopathological correlation of parapapillary atrophy.
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[Residues and health risk assessment of sulfonamides in sediment and fish from typical marine aquaculture regions of Guangdong Province, China].
Huan Jing Ke Xue
PUBLISHED: 09-24-2014
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Concentrations of sulfonamides including sulfadiazine (SDZ), sulfadimidin (SM2) and sulfamethoxazole (SMX) in sediments, muscle and liver tissues of 7 kinds of fish species collected from two marine aquaculture regions along the coast of Guangdong Provice were determined by high performance liquid chromatography (HPLC) equipped with a ultraviolet detector. Assessment of the health risks were conducted based on the values of maximum residue limits (MRL) and acceptable daily intake (ADI). The results showed that sulfonamides were found in all the sediment samples. The concentrations (dry wet) ranged from 2.1 - 35.2 ng x g(-1), the detected frequency of the 3 sulfonamide antibiotics ranked as SDZ (85.7%) > SM2 (71.4%) > SMX (28.6%). The detection rate of sulfonamides in samples from Daya Bay was higher than that from Hailing Island. Higher concentrations were detected in liver tissues rather than in muscle tissues (P < 0.05). The residues of SDZ, SM2 and SMX in fish muscle tissues (wet weight) ranged from 11.6-37.9, 16.3-27.8 and 4.9-20.0 ng x g(-1), respectively. The calculated daily intakes of sulfonamides in the present study ranged from 3.37-36.72 ng x kg(-1), which accounted for 0.007% -0.073% of the ADI (50 microg x kg(-1)). Health risks to human body were negligible as the estimated intake was less than 1% ADI, therefore the security of dietary was high.
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[Effect of sand dust weather on major water-soluble ions in PM10 in Lanzhou, China].
Huan Jing Ke Xue
PUBLISHED: 09-24-2014
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The major water-soluble ions (Ca(2+), NH(4+), Mg(2+), K(+), Na(+), SO4(2-), NO3(-) and Cl-(-) in PM10 at 1-h interval were measured by an online analyzer for monitoring of Aerosols and Gases (MARGA) at the campus of Lanzhou University, from April 1 to June 30, 2011. There were 15 days of dust weather during the monitoring period. The main water-soluble ions in PM10 were Ca(2+), SO4(2-) and NO3(-). The concentration of NO3(-) and NH4(+) decreased during blowing sand weather comparing with non-dust, this phenomenon showed that the dust weather had the function of eliminating the local anthropogenic emissions. As the soil pollution marker, the concentration of Mg(2+), Na(+) and Ca(2+) increased during dust weather comparing with non-dust. The correlation coefficients between Na(+) and Mg(2+), Na(+) and Ca(2+), Mg(2+) and Ca(2+) during dust weather were 0.520, 0.659 and 0.671, respectively. The similar correlation coefficients indicated that some fraction of these species was derived from the same sources, such as soil dust. The correlation coefficients between Na(+) and Mg(2+), Na(+) and Ca(2+), Mg(2+) and Ca(2+) during non-dust weather were not strong, only 0.065, 0.131 and 0.163, respectively. The low correlation coefficients indicated that these species were derived from different sources. The mass concentration of Cl(-) in the dust weather was significantly higher than that of floating dust and non dust, indicating that soil dust was the main source of Cl(-).
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Essential Role of the N- and C-terminals of Laccase from Pleurotus florida on the Laccase Activity and Stability.
Appl. Biochem. Biotechnol.
PUBLISHED: 08-27-2014
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POXA1b is the most thermostable laccase isoenzyme from Pleurotus ostreatus. POXA1b is remarkably stable at alkaline pH (the t1/2 at pH 10 was 30 days), and its C-terminal affects its catalytic and stability properties. We cloned POXA1c from P. florida, which showed 99 % identity with POXA1b. POXA1c was functionally expressed in Pichia pastoris. The functions of the N and C termini of POXA1c were investigated using site-directed mutagenesis. Compared with POXA1c, the N-terminal R5V site effectively increased the specific activities for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and guaiacol by 2- and 3.5-fold, respectively. A C-terminal truncated mutant, POXA1c?13, also increased the specific activities for ABTS and guaiacol by 2.3- and 3.4-fold, respectively. A double mutant, POXA1c?13-R5V, combined the R5V and ?13 effects. The specific activity of this double mutant for ABTS was 1,321 U/mg, which indicated a 4-fold increase compared with the wild type. The role of residue V5 on laccase catalytic properties was also observed for laccases from Trametes versicolor and Rigidoporus lignosus. The specific activities of the V5R of the laccases from T. versicolor and R. lignosus were half of that of the wild type. The pH and thermal stability analysis of POXA1c and its mutants showed that the enzymes were remarkably stable because they showed 63 % residual activity after incubation for 108 h at 30 °C over a pH range of 4.5 to 9.0. Similar results were observed for POXA1c?13-R5V. POXA1c?13-R5V can be widely used in industrial biotechnology because of its excellent catalytic properties.
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INTRAVITREAL VASCULAR ENDOTHELIAL GROWTH FACTOR CONCENTRATION AND AXIAL LENGTH.
Retina (Philadelphia, Pa.)
PUBLISHED: 08-25-2014
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To examine the intravitreal concentration of vascular endothelial growth factor (VEGF) in dependence of the axial length in eyes without intraocular neovascularization.
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Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients.
Sci Rep
PUBLISHED: 08-12-2014
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Lung cancer is the most common cause of cancer mortality worldwide, with an estimated 1.4 million deaths each year. Here we report whole-exome sequencing of nine tumor/normal tissue pairs from Chinese patients with non-small cell lung carcinoma (NSCLC). This allows us to identify a number of significantly mutated genes in NSCLC, which were highly enriched in DNA damage repair, NF-?B pathway, JAK/STAT signaling and chromatin modification. Notably, we identify a histone-lysine methyltransferase gene, namely, MLL2, as one of the most significantly mutated genes in our screen. In a following validation study, we identify deleterious mutations of MLL2 in 12 out of 105 (11.4%) NSCLC patients. Additionally, reduced or lost expression of MLL2 was commonly observed in tumor tissues as compared with paired adjacent non-tumor tissues regardless of mutation status. Together, our study defines the landscape of somatic mutations in Chinese NSCLC and supports the role of MLL2 mutation in the pathogenesis of the disease.
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Expression of cytokines on the iris of patients with neovascular glaucoma.
Acta Ophthalmol
PUBLISHED: 06-15-2014
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To determine the expression levels of cytokines, including growth factors, inflammatory cytokines, and cell migration associated factors on the iris from subjects with neovascular glaucoma (NVG).
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Analytical Morse/long-range model potential and predicted infrared and microwave spectra for a symmetric top-atom dimer: a case study of CH?F-He.
J Chem Phys
PUBLISHED: 06-09-2014
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Four-dimensional ab initio intermolecular potential energy surfaces (PESs) for CH3F-He that explicitly incorporates dependence on the Q3 stretching normal mode of the CH3F molecule and are parametrically dependent on the other averaged intramolecular coordinates have been calculated. Analytical three-dimensional PESs for v3(CH3F) = 0 and 1 are obtained by least-squares fitting the vibrationally averaged potentials to the Morse/Long-Range potential function form. With the 3D PESs, we employ Lanczos algorithm to calculate rovibrational levels of the dimer system. Following some re-assignments, the predicted transition frequencies are in good agreement with experimental microwave data for ortho-CH3F, with the root-mean-square deviation of 0.042 cm(-1). We then provide the first prediction of the infrared and microwave spectra for the para-CH3F-He dimer. The calculated infrared band origin shifts associated with the ?3 fundamental of CH3F are 0.039 and 0.069 cm(-1) for para-CH3F-He and ortho-CH3F-He, respectively.
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Continued decline of aqueous interleukin-8 after multiple intravitreal injections of ganciclovir for cytomegalovirus retinitis.
J Ocul Pharmacol Ther
PUBLISHED: 05-29-2014
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To evaluate the relationship between aqueous inflammation cytokines and cytomegalovirus (CMV) particles in patients with cytomegalovirus retinitis (CMVR), and evaluate the changes in aqueous inflammation cytokines during multiple intravitreal injections of antiviral drugs for CMVR.
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An improved SOM algorithm and its application to color feature extraction.
Neural Comput Appl
PUBLISHED: 05-20-2014
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Reducing the redundancy of dominant color features in an image and meanwhile preserving the diversity and quality of extracted colors is of importance in many applications such as image analysis and compression. This paper presents an improved self-organization map (SOM) algorithm namely MFD-SOM and its application to color feature extraction from images. Different from the winner-take-all competitive principle held by conventional SOM algorithms, MFD-SOM prevents, to a certain degree, features of non-principal components in the training data from being weakened or lost in the learning process, which is conductive to preserving the diversity of extracted features. Besides, MFD-SOM adopts a new way to update weight vectors of neurons, which helps to reduce the redundancy in features extracted from the principal components. In addition, we apply a linear neighborhood function in the proposed algorithm aiming to improve its performance on color feature extraction. Experimental results of feature extraction on artificial datasets and benchmark image datasets demonstrate the characteristics of the MFD-SOM algorithm.
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Optimal cutoff of the waist-to-hip ratio for detecting cardiovascular risk factors among Han adults in Xinjiang.
BMC Cardiovasc Disord
PUBLISHED: 05-15-2014
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The optimal cutoff of the waist-to-hip ratio (WHR) among Han adults in Xinjiang, which is located in the center of Asia, is unknown. We aimed to examine the relationship between different WHRs and cardiovascular risk factors among Han adults in Xinjiang, and determine the optimal cutoff of the WHR.
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Orthogonality breaking induces extraordinary single-mode transparency in an elaborate waveguide with wall corrugations.
Sci Rep
PUBLISHED: 05-14-2014
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Orthogonality plays a fundamental role in various mathematical theorems and in physics. The orthogonal eigenfunctions that represent the intrinsic motions of various physical systems can also be regarded as transverse wave modes in a straight waveguide. Because of their orthogonality, these modes propagate independently, without mutual interference. When the wall separation fluctuates, the former mode orthogonality is destroyed because of the change in the Euclidean space of the system. Here, we experimentally demonstrate the extraordinary single-mode transparency that arises as a result of the intense mode interference induced by orthogonality breaking in a waveguide with a varying cross section. A mode diagram is also introduced to illuminate these mode interactions. In particular, measurements of the transverse field distributions indicate that a three-mode interaction leads to a single high-order mode that penetrates through the lower-mode bandgaps when the wall period is carefully selected. The observation of Bessel-like transverse distributions is promising for applications in wave-control engineering.
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Combined application of NMR- and GC-MS-based metabonomics yields a superior urinary biomarker panel for bipolar disorder.
Sci Rep
PUBLISHED: 05-08-2014
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Bipolar disorder (BD) is a debilitating mental disorder that cannot be diagnosed by objective laboratory-based modalities. Our previous studies have independently used nuclear magnetic resonance (NMR)-based and gas chromatography-mass spectrometry (GC-MS)-based metabonomic methods to characterize the urinary metabolic profiles of BD subjects and healthy controls (HC). However, the combined application of NMR spectroscopy and GC-MS may identify a more comprehensive metabolite panel than any single metabonomic platform alone. Therefore, here we applied a dual platform (NMR spectroscopy and GC-MS) that generated a panel of five metabolite biomarkers for BD-four GC-MS-derived metabolites and one NMR-derived metabolite. This composite biomarker panel could effectively discriminate BD subjects from HC, achieving an area under receiver operating characteristic curve (AUC) values of 0.974 in a training set and 0.964 in a test set. Moreover, the diagnostic performance of this panel was significantly superior to the previous single platform-derived metabolite panels. Thus, the urinary biomarker panel identified here shows promise as an effective diagnostic tool for BD. These findings also demonstrate the complementary nature of NMR spectroscopy and GC-MS for metabonomic analysis, suggesting that the combination of NMR spectroscopy and GC-MS can identify a more comprehensive metabolite panel than applying each platform in isolation.
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[Effect of PvMSP1 on differentiation, maturation and function of dendritic cells].
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi
PUBLISHED: 05-08-2014
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To investigate the effects of Plasmodium vivax merozoite surface protein 1 (PvMSP1) on differentiation, maturation and function of dendritic cells (DC) and the mechanisms of PvMSP1 on the activation of DC via toll like receptors (TLR).
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Inhibiton of cytochrome P450 isoenzymes and P-gp activity by multiple extracts of Huang-Lian-Jie-Du decoction.
J Ethnopharmacol
PUBLISHED: 04-03-2014
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Huang-Lian-Jie-Du-Decotion (HLJDD), an important traditional Chinese medicine formula, has been used for various diseases in clinical practice, and thus has high potential to induce cytochrome P450 (CYP) isoenzymes / P-glycoprotein (P-gp) mediated herb-drug interactions (HDIs) with other co-administered drugs.
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Compound facial expressions of emotion.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 03-31-2014
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Understanding the different categories of facial expressions of emotion regularly used by us is essential to gain insights into human cognition and affect as well as for the design of computational models and perceptual interfaces. Past research on facial expressions of emotion has focused on the study of six basic categories--happiness, surprise, anger, sadness, fear, and disgust. However, many more facial expressions of emotion exist and are used regularly by humans. This paper describes an important group of expressions, which we call compound emotion categories. Compound emotions are those that can be constructed by combining basic component categories to create new ones. For instance, happily surprised and angrily surprised are two distinct compound emotion categories. The present work defines 21 distinct emotion categories. Sample images of their facial expressions were collected from 230 human subjects. A Facial Action Coding System analysis shows the production of these 21 categories is different but consistent with the subordinate categories they represent (e.g., a happily surprised expression combines muscle movements observed in happiness and surprised). We show that these differences are sufficient to distinguish between the 21 defined categories. We then use a computational model of face perception to demonstrate that most of these categories are also visually discriminable from one another.
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Lentivirus mediated siRNA against GluN2B subunit of NMDA receptor reduces nociception in a rat model of neuropathic pain.
Biomed Res Int
PUBLISHED: 03-28-2014
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Although neuropathic pain (NP) is still not fully understood by scientists and clinicians alike, studies suggest that N-methyl-D-aspartate (NMDA) receptors play an important role in the induction and maintenance of NP. A promising treatment for NP is through the downregulation of NMDA subunit GluN2B by RNA interference; however, naked siRNA (small interference RNA) is not effective in long-term treatments. In order to concoct a viable prolonged treatment for NP, Lv-siGluN2B (lentivirus carrying siRNA targeting GluN2B subunit) was prepared and the antinociception effects were observed in chronic constriction injury (CCI) rats in the present study. Results showed that Lv-siGluN2B was transduced into spinal cord cells after intrathecal injections and effectively reduced the nociception induced by sciatic nerve ligation while inhibiting the mRNA and protein expression of GluN2B. This antinociception effect lasted approximately 7 weeks. These findings suggest that GluN2B subunit could be a target for NP treatment and Lv-siGluN2B represents a new potential option for long-term treatment of NP.
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Clinical characteristics and current management of hepatitis B and C in China.
World J. Gastroenterol.
PUBLISHED: 03-24-2014
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To describe a population of outpatients in China infected by hepatitis B virus (HBV) and/or hepatitis C virus (HCV), and assess their current management status.
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Fever as a first manifestation of advanced gastric adenosquamous carcinoma: a case report.
World J. Gastroenterol.
PUBLISHED: 03-24-2014
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Gastric adenosquamous carcinoma (ASC) is a rare type of gastric cancer. It is a mixed neoplasm, consisting of glandular cells and squamous cells. It is often diagnosed at an advanced stage, thus carrying a poor prognosis. We describe a case of a 73-year-old male, who presented with refractory fever and an intra-abdominal mass on imaging. He underwent a laparoscopic exploration followed by a successful totally laparoscopic total gastrectomy with D2 lymphadenectomy for gastric cancer. Postoperative pathology revealed primary gastric ASC (T4aN0M0). The patient received adjuvant radiotherapy and chemotherapy with S1 and is alive 20 mo after surgery without recurrence. This is the first case of advanced gastric ASC with fever as the initial presentation treated with totally laparoscopic total gastrectomy reported in the English literature.
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The role of the hybridization between Mn 3d and O 2p orbitals in the existence of the Griffiths phase in La0.85Ca0.15MnO3.
J Phys Condens Matter
PUBLISHED: 03-18-2014
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Favourable conditions for the existence of the Griffiths phase in the La0.85Ca0.15MnO3 compound are experimentally investigated in terms of electronic and lattice structure by temperature-dependent x-ray absorption spectroscopy, valence band photoemission spectroscopy, and x-ray diffraction experiments. The chemical shifts of Mn L-edge and O K-edge x-ray absorption lines in the Griffiths phase are understood to be related to the hybridization between Mn 3d and O 2p states instead of the variation of Mn valence states. Valence band spectra also indicate that the hybridization of O 2p with Mn 3d is enhanced in the Griffiths phase. From a 2D diluted Ising ferromagnet model, this hybridization between Mn 3d and O 2p orbitals surely enhances the Griffiths phase feature.
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Isolation and characterization of recombinant variable domain of heavy chain anti-idiotypic antibodies specific to aflatoxin B1.
Biomed. Environ. Sci.
PUBLISHED: 03-15-2014
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Some unique subclasses of Camelidae antibodies are devoid of the light chain, and the antigen binding site is comprised exclusively of the variable domain of the heavy chain (VHH). The recombinant VHHs have a high potential as alternative reagents for the next generation of immunoassay. In particular, they might be very useful for molecular mimicry. The present study demonstrated an alpaca immunized with the F(ab')2 fragment of anti-aflatoxin B1 mAb and developed an important anti-idiotypic (anti-Id) responses. Antigen-specific elution method was used for panning private anti-Id VHHs from the constructed alpaca VHH library. The selected VHHs were expressed, renatured, purified, and then identified by a competitive enzyme-linked immunosorbent assay (ELISA). Our findings indicated that the VHH would be an alternative tool for haptens mimicry studies.
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Complete mitochondrial genome of the orange clownfish Amphiprion percula (Pisces: Perciformes, Pomacentridae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract In this study we determined the complete mitochondrial (mt) genome of the orange clownfish Amphiprion percula. The circular mtDNA molecule was 16,645?bp in size and the overall nucleotide composition of the H-strand was 29.20% A, 25.80% T, 16.03% G and 28.98% C, with an A?+?T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region (D-loop), with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. The similarity of the complete mitogenomes between A. percula and A. ocellaris (AP006017) was 95.60%, clearly different at molecular level.
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Complete mitochondrial genome of the yellowtail clownfish Amphiprion clarkii (Pisces: Perciformes, Pomacentridae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract In this study we determined the complete mitochondrial (mt) genome of the yellowtail clownfish Amphiprion clarkii using eight consensus primer pairs with a long PCR technique. The circular mtDNA molecule was 16,976?bp in size and the overall nucleotide composition of the H-strand was 29.15% A, 26.15% T, 15.67% G and 29.03% C, with an A?+?T bias. The complete mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region (D-loop), and the gene order was typical of vertebrate mitogenomes. We determined five complete continuity tandem repeat units and one imperfect tandem repeat, all located downstream in the control region.
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Proteinase-activated receptor 1 contributed to up-regulation of enkephalin in keratinocytes of patients with obstructive jaundice.
Anesthesiology
PUBLISHED: 03-12-2014
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Skin synthesis of endogenous opioids such as enkephalin is considered to be increased in cholestatic rodents, which may induce antinociception in cholestatic liver disease. No studies have reported yet the expression of skin enkephalin in patients with cholestasis.
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Clinical features and outcome of acute hepatitis B in pregnancy.
BMC Infect. Dis.
PUBLISHED: 03-03-2014
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The impact of pregnancy on the clinical course of acute hepatitis B (AHB) is still largely unclear, mainly because most studies have not included matched controls. This study was conducted to investigate the clinical features and outcome of AHB in pregnancy using matched controls.
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Congenital malaria in China.
PLoS Negl Trop Dis
PUBLISHED: 03-01-2014
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Congenital malaria, in which infants are directly infected with malaria parasites from their mother prior to or during birth, is a potentially life-threatening condition that occurs at relatively low rates in malaria-endemic regions. It is recognized as a serious problem in Plasmodium falciparum-endemic sub-Saharan Africa, where recent data suggests that it is more common than previously believed. In such regions where malaria transmission is high, neonates may be protected from disease caused by congenital malaria through the transfer of maternal antibodies against the parasite. However, in low P. vivax-endemic regions, immunity to vivax malaria is low; thus, there is the likelihood that congenital vivax malaria poses a more significant threat to newborn health. Malaria had previously been a major parasitic disease in China, and congenital malaria case reports in Chinese offer valuable information for understanding the risks posed by congenital malaria to neonatal health. As most of the literature documenting congenital malaria cases in China are written in Chinese and therefore are not easily accessible to the global malaria research community, we have undertaken an extensive review of the Chinese literature on this subject.
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The role of IL-17 promotes spinal cord neuroinflammation via activation of the transcription factor STAT3 after spinal cord injury in the rat.
Mediators Inflamm.
PUBLISHED: 02-19-2014
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In this study, we investigated the role of IL-17 via activation of STAT3 in the pathophysiology of SCI.
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Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor.
Appl. Environ. Microbiol.
PUBLISHED: 01-31-2014
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Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.
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Global identification of O-GlcNAc transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome.
Proteomics
PUBLISHED: 01-23-2014
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O-Linked ?-N-acetylglucosamine (O-GlcNAcylation) is an important protein PTM, which is very abundant in mammalian cells. O-GlcNAcylation is catalyzed by O-GlcNAc transferase (OGT), whose substrate specificity is believed to be regulated through interactions with other proteins. There are a handful of known human OGT interactors, which is far from enough for fully elucidating the substrate specificity of OGT. To address this challenge, we used a human proteome microarray containing ~17,000 affinity-purified human proteins to globally identify OGT interactors and identified 25 OGT-binding proteins. Bioinformatics analysis showed that these interacting proteins play a variety of roles in a wide range of cellular functions and are highly enriched in intra-Golgi vesicle-mediated transport and vitamin biosynthetic processes. Combining newly identified OGT interactors with the interactors identified prior to this study, we have constructed the first OGT interactome. Bioinformatics analysis suggests that the OGT interactome plays important roles in protein transportation/localization and transcriptional regulation. The novel OGT interactors that we identified in this study could serve as a starting point for further functional analysis. Because of its high-throughput and parallel analysis capability, we strongly believe that protein microarrays could be easily applied for the global identification of regulators for other key enzymes.
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Effect of oxidative stress on heme oxygenase-1 expression in patients with gestational diabetes mellitus.
Exp Ther Med
PUBLISHED: 01-08-2014
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The anti-oxidative stress effect of heme oxygenase-1 (HO-1) expression is being increasingly studied. However, few studies regarding HO-1 have been conducted in patients with gestational diabetes mellitus (GDM). In the present study, HO-1 expression was compared in peripheral blood mononuclear cells at 24-28 weeks of pregnancy in patients with GDM and healthy females, to investigate the correlation between HO-1 and oxidative stress by calculation of MDA content in the peripheral blood serum (thiobarbituric acid method), tested ROS (flow cytometry method), HO-1mRNA (RT-PCR method), and HO-1 protein (western blotting method) of Mononuclear cells. The results show that the levels of serum malonaldehyde (MDA), reactive oxygen species (ROS), HO-1 mRNA and HO-1 protein expression in peripheral blood mononuclear cells were higher in the GDM group than in the control group. Correlation analysis showed that the expression levels of HO-1 protein were positively correlated with the HO-1 mRNA expression levels (r=0.680; P=0.000), and the levels of ROS (r=0.572; P=0.000) and MDA (r=0.614; P=0.000). HO-1 mRNA expression levels were found to positively correlate with the levels of MDA (r=0.451; P=0.010) and fasting plasma glucose (FPG; r=0.337; P=0.039). Partial correlation analysis demonstrated that, after removing the effects of body mass index, FPG and 2-h plasma glucose, HO-1 protein expression levels were positively correlated with the levels of HO-1 mRNA expression (r=0.611; P=0.005), ROS (r=0.526; P=0.021) and MDA (r=0.519; P=0.015). These findings indicate that pregnant females with GDM may be protected against oxidative injury due to the induction of adaptive and compensatory expression of HO-1 to guard against oxidative stress induced by high glucose levels.
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Intraocular pressure and associations in children. The gobi desert children eye study.
PLoS ONE
PUBLISHED: 01-01-2014
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To assess the intraocular pressure (IOP) and its association in children in a population living in an oasis in the Gobi Desert.
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Mechanisms of GOLPH3 Associated with the Progression of Gastric Cancer: A Preliminary Study.
PLoS ONE
PUBLISHED: 01-01-2014
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To investigate the specific mechanisms by which Golgi phosphoprotein 3 (GOLPH3) affects the progression of gastric cancer and to explore its clinical significance.
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Excavation of Pid3 orthologs with differential resistance spectra to Magnaporthe oryzae in rice resource.
PLoS ONE
PUBLISHED: 01-01-2014
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Twenty-six orthologs of the rice blast resistance gene Pid3 from cultivated varieties and wild rice accessions distributed in different areas were cloned by allele mining. Sequence analysis showed that while each of the orthologous genes from indica varieties and most wild accessions encodes a complete NBS-LRR protein, each of the proteins encoded by those from japonica varieties and few wild rice accessions presents a premature termination. Eleven of the 26 orthologs were selected for blast resistance testing by transforming into the blast susceptible rice variety TP309, respectively. Inoculation of 23 M. oryzae strains collected from diverse regions of China to the respective transgenic plants revealed that 6 Pid3 orthologs showed susceptible to all the tested strains, while the other 5 orthologs showed differential resistance spectra in a gradually spectrum-widen order as Pid3-W3, Pid3-W4, Pid3-I3, Pid3-W5 and Pid3-I1. Amino acid sequences alignment of these orthologs indicated that the sequence diversities between the blast resistance orthologs were mostly located in the LRR domain such as the substitutions of Q694H,D856H,Q896R,D899E etc. However, the differences between the resistance orthologs and the susceptible ones were mostly located in the NBS domain. The present experiments provide an example of that the ortholog evaluation of plant R genes could be an efficient way to expand the rice blast resistance and some other plant disease resistance as well for breeding.
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Straw mulching reduces the harmful effects of extreme hydrological and temperature conditions in citrus orchards.
PLoS ONE
PUBLISHED: 01-01-2014
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Extreme weather conditions with negative impacts can strongly affect agricultural production. In the Danjiangkou reservoir area, citrus yields were greatly influenced by cold weather conditions and drought stress in 2011. Soil straw mulching (SM) practices have a major effect on soil water and thermal regimes. A two-year field experiment was conducted to evaluate whether the SM practices can help achieve favorable citrus fruit yields. Results showed that the annual total runoff was significantly (P<0.05) reduced with SM as compared to the control (CK). Correspondingly, mean soil water storage in the top 100 cm of the soil profile was increased in the SM as compared to the CK treatment. However, this result was significant only in the dry season (Jan to Mar), and not in the wet season (Jul to Sep) for both years. Interestingly, the SM treatment did not significantly increase citrus fruit yield in 2010 but did so in 2011, when the citrus crop was completely destroyed (zero fruit yield) in the CK treatment plot due to extremely low temperatures during the citrus overwintering stage. The mulch probably acted as an insulator, resulting in smaller fluctuations in soil temperature in the SM than in the CK treatment. The results suggested that the small effects on soil water and temperature changes created by surface mulch had limited impact on citrus fruit yield in a normal year (e.g., in 2010). However, SM practices can positively impact citrus fruit yield in extreme weather conditions.
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Impact of fertilizing pattern on the biodiversity of a weed community and wheat growth.
PLoS ONE
PUBLISHED: 01-01-2014
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Weeding and fertilization are important farming practices. Integrated weed management should protect or improve the biodiversity of farmland weed communities for a better ecological environment with not only increased crop yield, but also reduced use of herbicides. This study hypothesized that appropriate fertilization would benefit both crop growth and the biodiversity of farmland weed communities. To study the effects of different fertilizing patterns on the biodiversity of a farmland weed community and their adaptive mechanisms, indices of species diversity and responses of weed species and wheat were investigated in a 17-year field trial with a winter wheat-soybean rotation. This long term field trial includes six fertilizing treatments with different N, P and K application rates. The results indicated that wheat and the four prevalent weed species (Galium aparine, Vicia sativa, Veronica persica and Geranium carolinianum) showed different responses to fertilizer treatment in terms of density, plant height, shoot biomass, and nutrient accumulations. Each individual weed population exhibited its own adaptive mechanisms, such as increased internode length for growth advantages and increased light interception. The PK treatment had higher density, shoot biomass, Shannon-Wiener and Pielou Indices of weed community than N plus P fertilizer treatments. The N1/2PK treatment showed the same weed species number as the PK treatment. It also showed higher Shannon-Wiener and Pielou Indices of the weed community, although it had a lower wheat yield than the NPK treatment. The negative effects of the N1/2PK treatment on wheat yield could be balanced by the simultaneous positive effects on weed communities, which are intermediate in terms of the effects on wheat and weeds.
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[Protein budget: cost estimating criteria for synthetic biology].
Sheng Wu Gong Cheng Xue Bao
PUBLISHED: 12-25-2013
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The aim of synthetic biology is to design artificial life systems. Such system is hoped to create a better production process with desired ability for bioproduction, biotransformation, adaption and environmental monitoring. However, to design a life system involves understanding the cellular regulation networks at multiple levels, in which the controls of protein level, subcelluar location, and activity are especially critical. Thus tuning protein expression has become essential tools in synthetic biology studies, such as part design, module assembly and compatibility optimization. Protein budget, just like budget for a factory, can be thought as the cost estimating criteria for an artificial cell factory. Protein budget control has provided a powerful optimization strategy for synthetic biology.
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Involvement of SpoVG in hemolysis caused by Bacillus subtilis.
Biochem. Biophys. Res. Commun.
PUBLISHED: 11-27-2013
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Bacillus subtilis is a facultative anaerobic Gram-positive non-pathogenic bacterium that includes members displaying hemolytic activity. To identify the genes responsible for hemolysis, a random mariner-based transposon insertion mutant library of B. subtilis 168 was constructed. More than 20,000 colonies were screened for the hypohemolytic phenotype on blood agar plates. One mutant showed significantly less pronounced hemolytic phenotype than the wild type. DNA sequencing and Southern blot analysis showed this mutant has a single transposable element inserted into the open reading frame (ORF) of the spoVG gene; complementation of the spoVG-disrupted mutant with a wild-type copy restored its hemolytic phenotype. It was therefore concluded that the spoVG gene, which plays a role in regulating asymmetric septation during sporulation in B. subtilis, is involved in hemolysis by B. subtilis.
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Analysis of kidney biopsy data from a single center in the midland rural area of china, 1996-2010.
Curr Ther Res Clin Exp
PUBLISHED: 11-11-2013
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To survey the clinical epidemiology and correlations between pathology and clinical features of major groups of kidney diseases in a rural area of China.
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[Construction of Escherichia coli gene knock-out mutants for engineering of fatty acid metabolism].
Wei Sheng Wu Xue Bao
PUBLISHED: 09-14-2013
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Gene knock out technique is very important for gene function study. We developed a simple and efficient method to knock out chromosomal genes in Escherichia coli.
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Pseudomonas chengduensis sp. nov., isolated from landfill leachate.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-10-2013
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Strain MBRT was isolated from landfill leachate in a solid-waste disposal site in Chengdu, Sichuan, China. An analysis of 16S rRNA gene sequences revealed that the isolate was closely related to members of the genus Pseudomonas, sharing the highest sequence similarities to P. toyotomiensis HT-3T(99.8%), P. alcaliphila AL15-21T(99.7%) and P.oleovorans ATCC 8062T(99.4%). Multi-locus sequence analysis (MLSA) based on three housekeeping genes (gyrB, rpoB and rpoD) exhibited higher resolution at species level than that of 16S rRNA gene sequence, which was further confirmed by less than 70% DNA-DNA relatedness between the isolate and P. toyotomiensis H-3T ( 61.3%), P. alcaliphila AL15-21T (51.5%) and P. oleovorans ATCC 8062T(57.8%). The DNA G+C content of strain MBRT was 61.9 mol% and the major ubiquinone was Q-9. The major cellular fatty acids (>10%) were C18:1?7c and/or C18:1?6c, C16:0, and C16:1 ?7c and/or 16:1?6c. Polyphasic analysis indicates that strain MBR T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas chengduensis sp. nov. is proposed. The type strain is MBRT (CGMCC 2318T= DSM 26382T ).
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Meta-analysis of the effect of intravitreal bevacizumab versus intravitreal triamcinolone acetonide in central retinal vein occlusion.
J Ocul Pharmacol Ther
PUBLISHED: 08-24-2013
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To further evaluate the effect of intravitreal bevacizumab (IVB) for the treatment of central retinal vein occlusion (CRVO) by meta-analysis.
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[Induction of UGT1A1 expression by praeruptorin A and praeruptorin C through hCAR pathway].
Yao Xue Xue Bao
PUBLISHED: 07-30-2013
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This study is purposed to investigate the effects of praeruptorin A (PA) and praeruptorin C (PC) on UGT1A1 in HepG2 cells through hCAR pathway. PA and PC were incubated with HepG2 cells for 24 h and 48 h, mRNA and protein expressions of UGT1A1 were determined by real-time PCR and Western blotting assays. Additionally, effects of PA and PC on UGT1A1 mRNA and protein expressions were also measured after transient transfection of a specific CAR siRNA for 72 h in HepG2 cells. UGT1A1 mRNA and protein expression levels were significantly increased by PA and PC after incubation for 48 h. Moreover, the mRNA and protein up-regulations of UGT1A1 were attenuated by transient transfection of a specific CAR siRNA, suggesting the induction was mediated by CAR. The results suggest that PA and PC can significantly up-regulate UGT1A1 expression partially via the CAR-mediated pathway.
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Synthesis and antitumor activity evaluation of maleopimaric acid N-aryl imide atropisomers.
Bioorg. Med. Chem. Lett.
PUBLISHED: 07-25-2013
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Maleopimaric acid N-aryl imides (2) and methyl maleopimaric acid N-aryl imides (3) were designed and synthesized. Their atropisomers (A and B) were separated into their enantiomeric pure forms and the anti-proliferative activity was tested against NCI, A549, Hep G-2, MGC-803 and Hct-116 cell lines, respectively. A significant difference in the level of cytotoxicity was observed between R and S conformers. Atropisomers A with an R configuration exhibited significant toxicity (the IC50 values ranging from 7.51 to 32.1?M). Further experiments proved that antitumor activity of 2A was achieved through the induction of cell apoptosis by G1 cell-cycle arrest.
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Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
BMC Genomics
PUBLISHED: 07-04-2013
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Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.
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Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.
BMC Genomics
PUBLISHED: 06-28-2013
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Usually, next generation sequencing (NGS) technology has the property of ultra-high throughput but the read length is remarkably short compared to conventional Sanger sequencing. Paired-end NGS could computationally extend the read length but with a lot of practical inconvenience because of the inherent gaps. Now that Illumina paired-end sequencing has the ability of read both ends from 600 bp or even 800 bp DNA fragments, how to fill in the gaps between paired ends to produce accurate long reads is intriguing but challenging.
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Presence of Fe(3+) and Zn(2+) promoted biotransformation of Cd-citrate complex and removal of metals from solutions.
J. Hazard. Mater.
PUBLISHED: 05-28-2013
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The promotion to Cd-citrate complex biotransformation via addition of Fe(3+) and Zn(2+) was investigated. Single Fe(III)- or Zn-citrate complex was completely degraded by Pseudomonas sp. MBR, Cd-citrate complex was not. In the Cd-citrate media with molar ratio of 1:2 and 1:3, pH increase obtained from the metabolism of excess citrate slightly promoted the biotransformation of Cd-citrate complex, Cd remained in solutions. The presence of Fe(3+) and Zn(2+) resulted in complete biotransformation of Cd-citrate complex in the 1:1:2 Fe:Cd:citrate and Zn:Cd:citrate and 1:1:1:3 Fe:Zn:Cd:citrate media. Alkaline pH obtained from biotransformation of metal-citrate complexes caused almost complete removal of metals (>98%) through precipitation and co-precipitation. Pseudomonas sp. MBR potentially could be used to treat wastewater containing mixed citrate complexes of Fe(III), Zn and Cd.
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[Malaria epidemiologic characteristics in Wuhe County of Anhui Province from 2009 to 2011].
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi
PUBLISHED: 05-22-2013
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To understand the malaria epidemiologic characteristics in Wuhe County, Anhui Province from 2009 to 2011, so as to provide the evidence for formulating effective malaria control and prevention interventions.
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[The result of BAHA fitting in single sided deafness].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 05-08-2013
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To learn the benefit of the unilateral profound sensorineural hearing loss patients wear bone conduction hearing aid BAHA.
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High saturated fatty acids proportion in Escherichia coli enhances the activity of ice-nucleation protein from Pantoea ananatis.
FEMS Microbiol. Lett.
PUBLISHED: 05-01-2013
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The ice-nucleation protein (INP) from Pantoea ananatis was expressed in Escherichia coli. INP expression increased the freezing point of the E. coli culture by a few degrees. Deletion of FabH, an important enzyme in fatty acid biosynthesis, significantly inhibited the ice-nucleation activity. Increased unsaturated fatty acids in the fabH mutant cells decreased the ice-nucleation activity. Adding exogenous saturated fatty acids increased both E. coli fatty acid saturation and the ice-nucleation activity. In contrast, adding unsaturated fatty acids exhibited the opposite effects. Furthermore, an E. coli MG1655-fadR strain with high saturated fatty acids content was constructed, in which the INP activity was enhanced by about 17% compared with its activity in the wild-type MG1655 strain.
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Identification of a critical region in the Drosophila ryanodine receptor that confers sensitivity to diamide insecticides.
Insect Biochem. Mol. Biol.
PUBLISHED: 04-29-2013
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Anthranilic diamides, which include the new commercial insecticide, chlorantraniliprole, are an exciting new class of chemistry that target insect ryanodine receptors. These receptors regulate release of stored intracellular calcium and play a critical role in muscle contraction. As with insects, nematodes express ryanodine receptors and are sensitive to the plant alkaloid, ryanodine. However the plant parasitic nematode, Meloidogyne incognita, is insensitive to anthranilic diamides. Expression of a full-length Drosophila melanogaster ryanodine receptor in an insect cell line confers sensitivity to the receptor agents, caffeine and ryanodine along with nanomolar sensitivity to anthranilic diamides. Replacement of a 46 amino acid segment in a highly divergent region of the Drosophila C-terminus with that from Meloidogyne results in a functional RyR which lack sensitivity to diamide insecticides. These findings indicate that this region is critical to diamide sensitivity in insect ryanodine receptors. Furthermore, this region may contribute to our understanding of the differential selectivity diamides exhibit for insect over mammalian ryanodine receptors.
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Zoledronic acid inhibits growth of hepatocellular carcinoma cells in vitro and in vivo.
Chin. Med. J.
PUBLISHED: 04-19-2013
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Growing preclinical evidence shows that zoledronic acid (ZOL) exhibits direct antitumor activity in various cancer cell lines. However, the cytotoxic effects of ZOL on human hepatocellular carcinoma (HCC) cells have not been established. In the present study, we investigated the effect of ZOL on HCC both in vitro and in vivo.
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Meta-analysis of the effect of intravitreal bevacizumab in branch retinal vein occlusion.
J Ocul Pharmacol Ther
PUBLISHED: 03-28-2013
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To further evaluate the effect of intravitreal bevacizumab (IVB) for the treatment of branch retinal vein occlusion in a meta-analysis of previous studies.
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Neuroprotective effect of minocycline in a rat model of branch retinal vein occlusion.
Exp. Eye Res.
PUBLISHED: 03-12-2013
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Branch retinal vein occlusion (BRVO) is the second most frequent retinal vascular disorder. Currently the first-line therapies for BRVO include anti-VEGF and dexamethasone implant treatment, however, with direct or indirect damage on retinal neurons, it has limited effect in improving patients visual acuity. Therefore, novel treatments with neuroprotective effect for BRVO retina were expected. Minocycline is a semisynthetic, broad spectrum tetracycline antibiotic with high penetration through the blood brain barrier. The neuroprotective effects of minocycline have been shown in various central nervous system (CNS) disease. Since both CNS and retina were composed of neurons and glials, it is reasonable to expect a neuroprotective effect by minocycline for BRVO retina. Therefore, the aim of the present study was to study whether minocycline has neuroprotective effect in branch retinal vein occlusion (BRVO) and the possible underlying molecular basis. We created BRVO in rats using laser photocoagulation. The animals were then randomly divided into 4 groups to evaluate the effect of minocycline: group A: minocycline 45 mg/kg intraperitoneal injection (i.p.), group B: minocycline 90 mg/kg i.p., group C: normal saline i.p., group D: sham injection. Fundus photography and fluorescein angiography (FA) were conducted. The changes in thickness of retinal layers were measured with optical coherence tomography (OCT) in vivo. We found that retinal edema occurred predominantly in the inner retinal layers. Intraperitoneal administration of minocycline significantly ameliorated retinal edema in the early stage of BRVO. We performed Full field Electroretinography (ffERG) to evaluate retinal function and found that the reduction of b wave amplitude decreased in the combined maximal response. The expressional levels of apoptosis related genes (Bax, Bcl-2) and inflammation related genes (IL-1 ?, TNF ?, MCP-1 and CCR2) were measured by real-time PCR, the results showed that minocycline treatment upregulated Bcl-2 expression and inhibits TNF ? expression since early stage of BRVO. We also performed Hematoxylin-Eosin (HE) and immunostaining for Iba 1 (a microgilal marker), active caspase-3, Bax, Bcl-2, IL-1 ?, TNF ? and found that minocycline inhibits retinal microglial activation, prevents retinal ganglion cell loss, and inhibits retinal caspase-3 activation. Thus, our study indicates that systemic administration of minocycline ameliorates retinal edema and preserves retinal function in the early stage of BRVO possibly via inhibiting microglia activation and protecting RGC from apoptosis.
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Draft genome sequence of the mulberry tree Morus notabilis.
Nat Commun
PUBLISHED: 03-05-2013
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Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant-herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants.
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Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.
Nature
PUBLISHED: 02-20-2013
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About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of bakers flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae.?tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.
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Draft genome of the wheat A-genome progenitor Triticum urartu.
Nature
PUBLISHED: 02-08-2013
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Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A?genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m)A(m)), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A?genome is the diploid wild einkorn wheat T.?urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T.?urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T.?urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.
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Assessment of organochlorine pesticide contamination in relation to soil properties in the Pearl River Delta, China.
Sci. Total Environ.
PUBLISHED: 02-01-2013
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High levels of organochlorine pesticides (OCPs) such as hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) have been found in soil of the Pearl River Delta (PRD), attributable to high pesticide application in this area. Consequently, the occurrence and environmental effect of HCHs and DDTs in the PRD have attracted considerable attention. However, study focusing on the influence of potential factors such as soil property on the environmental fate of HCHs and DDTs in the PRD has been rare. The present study aimed to investigate the impact of soil physiochemical properties on the distribution patterns and fate of soil HCHs and DDTs on a large spatial scale. Levels of HCHs (sum of ?-, ?-, ?- and ?-HCH) and DDTs (sum of 1,1,1-trichloro-2,2-bis-(p-chlorophenyl)ethane (p,p-DDT), 1,1-dichloro-2,2-bis-(p-chlorophenyl)ethane (p,p-DDD), and 1,1-dichloro-2,2-bis-(p-chlorophenyl)ethylene (p,p-DDE)) in 151 soil samples covering all areas of the PRD and physiochemical parameters related to soil properties including pH, total organic carbon (TOC), total Fe (TFe), DCB-Fe (DFe), amorphous-Fe (AFe), complexed-Fe (CFe), total Mn (TMn), DCB-Mn (DMn), amorphous-Mn (AMn), complexed-Mn (CMn) and cation exchange capacity (CEC) were determined. The residual levels of HCHs and DDTs in soils of the present study, which are mainly controlled by soil TOC and CFe content and varying spatially with land use types, may potentially pose ecological risk to plants and animals. On the other hand, transformation of soil HCHs may be affected by pH and DDT transformation correlated significantly with AFe and CFe. Currently, soil has become an important secondary source of OCPs and the re-emission potential of OCPs in soil was mainly affected by soil OCP concentrations and land use types.
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Enhanced production of N-acetyl-D-neuraminic acid by multi-approach whole-cell biocatalyst.
Appl. Microbiol. Biotechnol.
PUBLISHED: 01-31-2013
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N-Acetyl-D-neuraminic acid (Neu5Ac) has attracted considerable interest due to its promising potential applications in medicine. Significant efforts have been made in whole-cell biocatalyst for Neu5Ac production, but the processes often result in suboptimal performance due to poor expression of enzymes, imbalances of pathway components, disturbance of competing pathways, and barriers of mass transport. In this study, we engineered Escherichia coli strains capable of producing Neu5Ac by assembling a two-step heterologous pathway consisting of N-acetyl-D-glucosamine 2-epimerase (AGE) and Neu5Ac aldolase (NanA). Multiple approaches were used to improve the efficiency of the engineered pathway and process for enhanced Neu5Ac production. Firstly, we identified that NanA was the rate-controlling enzyme in this pathway. With increased expression of NanA, a ninefold increase in Neu5Ac production (65 mM) was observed. Secondly, knocking out nanTEK genes blocked Neu5Ac uptake and the competing pathway, which kept the reactions to the synthetic direction as the final product went outside of the cells and enhanced the Neu5Ac production by threefold, resulting in 173.8 mM of Neu5Ac. Thirdly, we improved the performance of the system by promoting substrate transport and optimizing concentrations of substrates. An overall whole-cell biocatalytic process was developed and a maximum titer of 240 mM Neu5Ac (74.2 g/L) was achieved, with productivity of 6.2 g Neu5Ac/L/h and conversion yield of 40 % from GlcNAc. The engineered strain could be reused for at least five cycles with a productivity of >6 g/L/h. It is a cost-effective process for Neu5Ac production with potential applications in large-scale industrial production.
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Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.
BMC Genomics
PUBLISHED: 01-18-2013
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Genomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-sized regions are limited when the sequencing coverage is low.
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Apelin-13 regulates proliferation, migration and survival of retinal Müller cells under hypoxia.
Diabetes Res. Clin. Pract.
PUBLISHED: 01-15-2013
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To investigate the effect of apelin-13 and the antagonist of apelin receptor (F13A) on retinal Müller cells in vitro.
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Carbon dioxide flux from rice paddy soils in central China: effects of intermittent flooding and draining cycles.
PLoS ONE
PUBLISHED: 01-11-2013
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A field experiment was conducted to (i) examine the diurnal and seasonal soil carbon dioxide (CO(2)) fluxes pattern in rice paddy fields in central China and (ii) assess the role of floodwater in controlling the emissions of CO(2) from soil and floodwater in intermittently draining rice paddy soil. The soil CO(2) flux rates ranged from -0.45 to 8.62 µmol.m(-2).s(-1) during the rice-growing season. The net effluxes of CO(2) from the paddy soil were lower when the paddy was flooded than when it was drained. The CO(2) emissions for the drained conditions showed distinct diurnal variation with a maximum efflux observed in the afternoon. When the paddy was flooded, daytime soil CO(2) fluxes reversed with a peak negative efflux just after midday. In draining/flooding alternating periods, a sudden pulse-like event of rapidly increasing CO(2) efflux occured in response to re-flooding after draining. Correlation analysis showed a negative relation between soil CO(2) flux and temperature under flooded conditions, but a positive relation was found under drained conditions. The results showed that draining and flooding cycles play a vital role in controlling CO(2) emissions from paddy soils.
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Apelin in epiretinal fibrovascular membranes of patients with retinopathy of prematurity and the changes after intravitreal bevacizumab.
Retina (Philadelphia, Pa.)
PUBLISHED: 01-09-2013
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Apelin, a novel cytokine, was reported to regulate angiogenesis. The aim of this study was to investigate the correlation between apelin and retinopathy of prematurity (ROP), between apelin and the other known angiogenic cytokines including vascular endothelial growth factor (VEGF) and hypoxia-induced factor-1a (HIF-1a).
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Inhibition of GAP-43 by propentofylline in a rat model of neuropathic pain.
Int J Clin Exp Pathol
PUBLISHED: 01-01-2013
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Neural plasticity within the spinal nociceptive network may be fundamental to the chronic nature of neuropathic pain. The relation of growth-associated protein-43 (GAP-43), a protein involved in the nerve fiber growth and sprouting, to pain hypersensitivity has been investigated. Glial activation and inflammatory cytokines released by microglia and astrocytes are considered to be involved in the neural sprouting and plasticity. In the present study, the anti-nociception effect of propentofylline, a glial modulating agent, was investigated in a rat chronic constriction injury (CCI) model aiming to explore the role of GAP-43 expression. Our results demonstrated that propentofylline could attenuate the CCI-induced mechanical allodynia and thermal hyperalgesia and inhibit the astrocyte activation and production of IL-1?. GAP-43 expression was also down-regulated by intrathecal propentofylline. These findings suggest that astrocyte activation is involved in the regulation of GAP-43 expression and propentofylline might be used in the treatment of neuropathic pain.
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[Analysis of the correlation between parapapillary atrophy zones and visual field loss].
Beijing Da Xue Xue Bao
PUBLISHED: 12-20-2011
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To analyze the association between parapapillary atrophy zones and mean sensibility (MS) and mean defect (MD) from visual field examination.
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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.

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

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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.