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Find video protocols related to scientific articles indexed in Pubmed.
[Mics of the Clostridium thermocellum in lignocellulose degradation--a review].
Wei Sheng Wu Xue Bao
PUBLISHED: 05-14-2014
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Clostridium thermocellum ( C. thermocellum ) is the dominant microorganism that can efficiently degrade lignocellulose. Extensive studies were done for secreting the cell surface-bound protein complex known as the cellulosome. C. thermocellum is regulated by carbon sources, reflected in overall multiple cellulase production and in the cellulosomal subunit profile. To produce a cellulosomal protein complex is a dynamic assembly process. In recent years, it becomes a hotspot to study how C. thermocellum senses the insoluble substrate, regulates the secretion of relevant enzymes, and assembles the supramolecular-degradation enzyme complex. This review summarized the research advance in genomics, transcriptomics, proteomics and extracellular carbohydrate-sensing mechanism in C. thermocellum, and analyzed the mechanism and dynamic process of C. thermocellum in lignocellulose degradation.
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Mst3b Promotes Spinal Cord Neuronal Regeneration by Promoting Growth Cone Branching Out in Spinal Cord Injury Rats.
Mol. Neurobiol.
PUBLISHED: 04-11-2014
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Spinal cord injury is a severe clinical problem, and research searching activity molecular that can promote spinal cord injury repairing is very prevalent. Mst3b can promote repair of damaged peripheral nerves and the optic nerve, but has been rarely reported in spinal cord injury research. Through detecting its expression in different periods of injured spinal cord, we found that the expression of Mst3b was significantly upregulated in injured spinal cord neurons. Increasing Mst3b expression using adenovirus in vivo and in vitro promoted axonal regeneration of spinal cord neurons, which led to behavioral and electrophysiological improvement. Downregulation of Mst3b level had the adverse effects. Increasing Mst3b expression in PC12 cells resulted in an elevation of P42/44(MAPK) and LIMK/Cofilin activation. These results identified Mst3b as a powerful regulator for promoting spinal cord injury recovery through the P42/44(MAPK) and LIMK/Cofilin signaling pathways.
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Cooperativity of oncogenic K-ras and downregulated p16/INK4A in human pancreatic tumorigenesis.
PLoS ONE
PUBLISHED: 01-01-2014
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Activation of K-ras and inactivation of p16 are the most frequently identified genetic alterations in human pancreatic epithelial adenocarcinoma (PDAC). Mouse models engineered with mutant K-ras and deleted p16 recapitulate key pathological features of PDAC. However, a human cell culture transformation model that recapitulates the human pancreatic molecular carcinogenesis is lacking. In this study, we investigated the role of p16 in hTERT-immortalized human pancreatic epithelial nestin-expressing (HPNE) cells expressing mutant K-ras (K-rasG12V). We found that expression of p16 was induced by oncogenic K-ras in these HPNE cells and that silencing of this induced p16 expression resulted in tumorigenic transformation and development of metastatic PDAC in an orthotopic xenograft mouse model. Our results revealed that PI3K/Akt, ERK1/2 pathways and TGF? signaling were activated by K-ras and involved in the malignant transformation of human pancreatic cells. Also, p38/MAPK pathway was involved in p16 up-regulation. Thus, our findings establish an experimental cell-based model for dissecting signaling pathways in the development of human PDAC. This model provides an important tool for studying the molecular basis of PDAC development and gaining insight into signaling mechanisms and potential new therapeutic targets for altered oncogenic signaling pathways in PDAC.
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Nonlocal denoising using anisotropic structure tensor for 3D MRI.
Med Phys
PUBLISHED: 10-05-2013
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Noise in magnetic resonance imaging (MRI) data is widely recognized to be harmful to image processing and subsequent quantitative analysis. To ameliorate the effects of image noise, the authors present a structure-tensor based nonlocal mean (NLM) denoising technique that can effectively reduce noise in MRI data and improve tissue characterization.
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Proteomics analysis of autophagy-deficient Atg7-/- MEFs reveals a close relationship between F-actin and autophagy.
Biochem. Biophys. Res. Commun.
PUBLISHED: 06-26-2013
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Autophagy plays a crucial role in a wide array of physiological processes. To uncover the complex regulatory networks and mechanisms underlying basal autophagy, we performed a quantitative proteomics analysis of autophagy-deficient mouse embryonic fibroblast cells (MEFs) using iTRAQ labeling coupled with on-line 2D LC/MS/MS. We quantified a total of 1234 proteins and identified 114 proteins that were significantly altered (90% confidence interval), including 48 up-regulated proteins and 66 down-regulated proteins. We determined that F-actin was disassembled in autophagy-deficient Atg7(-/-) MEFs. Treatment of the WT MEFs with cytochalasin D (CD), which induces F-actin depolymerization, significantly induced autophagosome formation. However, treatment with cytochalasin D also increased the protein level of p62 under starvation conditions, suggesting that depolymerization of F-actin impaired autophagosome maturation and that the intact F-actin network is required for basal and starvation-induced autophagy. Our results demonstrate a close relationship between F-actin and autophagy and provide the basis for further investigation of their interactions.
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Activation of inactive hepatocytes through histone acetylation: a mechanism for functional compensation after massive loss of hepatocytes.
Am. J. Pathol.
PUBLISHED: 05-11-2011
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The mechanisms by which hepatic function is maintained after extensive parenchymal loss are unclear. In this study, we propose a novel concept of "functional heterogeneity" of hepatocytes based on their different expression of acetylated histones, the markers of active gene transcription, to explain the powerful compensatory capability of the liver. In the healthy human liver, only a fraction of the hepatocytes were marked by acetylated histones (ac-H2AK5, ac-H2BK5, ac-H3K9, ac-H3K14, ac-H3K27, and ac-H3K9/14). With the progression of cirrhosis, the ratio of the positive cells was gradually elevated, accompanied by the gradual exhaustion of the negative cells. By examining the global transcriptome of the mouse hepatocytes, we observed that the primed genes in the positive cells were much more numerous than those in negative cells. In a 70% hepatectomized mouse, the remnant hepatocytes were extensively activated, and the liver function was well maintained even when regeneration was severely inhibited. The functional compensation was absolutely dependent on the elevated expression of acetyl-histones. Additionally, when liver regeneration was blocked, the metabolism-related genes seemed to be preferentially transcribed. In conclusion, we demonstrate that normally, part of the active hepatocytes are competent for routine physiological requirements. The inactive hepatocytes, delicately regulated by acetyl-histones, act as a functional reservoir for future activation to restore the liver function after massive parenchymal loss.
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A novel approach for estimating the relationship between the kinetics and thermodynamics of glycoside hydrolases.
Acta Biochim. Biophys. Sin. (Shanghai)
PUBLISHED: 04-02-2011
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A series of experiments were performed, in which p-nitrophenyl-?-D-cellobioside (PNPC) was hydrolyzed by 1, 4-?-D-glucan-cellobiohydrolase (CBHI: EC 3.2.1.91), and O-nitrophenyl-?-D-galactoside (ONPG) was hydrolyzed by ?-galactosidase (EC 3.2.1.23) under different combinations of temperature and time period. The combined effects of temperature and time on p-nitrophenyl and O-nitrophenyl formation were characterized as the change of the instantaneous reaction velocity occurrence per temperature range termed as v(inst)· T(-1). This parameter was used as a stable index to evaluate the apparent activation energy (E(a)) based on the Arrhenius approach, instead of the reaction velocity constant, k. It was found that E(a) for PNPC hydrolysis by CBHI first decreased with temperature increase and then slightly increased at higher temperature, and its minimum value was obtained just at the maximum point of v(inst). In addition, E(a) for PNPC hydrolysis by dilute sulfuric acid was not a constant, but was continuously increased with temperature. The present studies demonstrated that E(a) obtained by Arrhenius approach for the hydrolysis reaction of ?-hydrolases appears to be only an empirical kinetic parameter for the dependence of the reaction velocity on temperature and time, and has no meaning in the sense of thermodynamic energy.
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Construction of a portal implantable functional tissue-engineered liver using perfusion-decellularized matrix and hepatocytes in rats.
Cell Transplant
PUBLISHED: 11-05-2010
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Innovative cell-based therapies, including hepatic tissue engineering following hepatocyte transplantation, are considered as theoretical alternatives to liver transplant or for partial replacement of liver function in patients. However, recent progress in hepatic tissue engineering has been hampered by low initial hepatocyte engraftment and insufficient blood supply in vivo. We developed an intact 3D scaffold of an extracellular matrix (ECM) derived from a decellularized liver lobe, with layer-by-layer (LbL) heparin deposition to avoid thrombosis, which we repopulated with hepatocytes and successfully implanted as a tissue-engineered liver (TEL) into the portal system. The TEL provided sufficient volume for transplantation of cell numbers representing up to 10% of whole-liver equivalents and was perfused by portal vein blood. Treatment of extended hepatectomized rats with a TEL improved liver function and prolonged survival; mean lifespan was extended from 16 to 72 h. At 72 h postoperation, the TEL sustained functional and viable hepatocytes. In conclusion, we propose the TEL as a state-of-the-art substitute for whole-liver transplantation and as a proof of concept for the technology that will eventually allow for the transplantation of a reconstituted liver.
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A novel approach for assessing the susceptibility of Escherichia coli to antibiotics.
Sci China Life Sci
PUBLISHED: 06-29-2010
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The dynamic growth process of Escherichia coli CVCC249 under different concentrations of antibiotics was analyzed. The results suggested that the main reason that definitive results cannot be obtained by antibiotic susceptibility testing (AST) is that the ratio of drug concentration to the population of bacteria and the combined effect of drug concentration and action time cannot be completely determined with the methods used. Based on the analysis of the growth process with a series of concentrations of gentamicin acting for a certain time, and according to the forward difference method, a novel method for AST was proposed. The net increase in turbidity of the bacterial population was used to eliminate the existing effects of resting cells, and then the recurrent coefficient for a growing sequence was used to characterize the effect of antibiotics on bacterial division, and the contour plot was used to display and analyze the combined effect of drug concentration and action time. The inhibition rate of the antibiotics can be characterized as the dynamic change in the composite function of the antibiotic concentration and action time, which indicated that the inhibition rate was dependent on the combined effect of time and concentration of antibiotics. The effectiveness of this new method has been verified with different kinds of antibiotics, such as enrofloxacin, levofloxacin, and ceftriaxone, having different antibacterial mechanisms.
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Polyhydroxy steroids and saponins from China Sea starfish Asterina pectinifera and their biological activities.
Chem. Pharm. Bull.
PUBLISHED: 06-05-2010
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A new polyhydroxy sterol ester, (25S)-5alpha-cholestane-3beta,6alpha,7alpha,8,15alpha,16beta-hexahydroxyl-26-O-14Z-eicosenoate (1), together with seven known steroid derivatives (2-8), were isolated from the EtOH extract of the whole body of China Sea starfish Asterina pectinifera. The structure of 1 was determined by using extensive spectra analysis (IR, 1D and 2D NMR, and MS), chemical degradation, and comparison with the known compound (25S)-5alpha-cholestane-3beta,6alpha,7alpha,8,15alpha,16beta,26-heptol (2). All the isolates were evaluated for their antiviral activity against herpes simplex virus type 1 (HSV-1) and their cytotoxicity against human liver carcinoma HepG2 cell line in vitro. Compounds 3-6, and 8 exhibited antiviral activity against HSV-1 virus with the minimal inhibitory concentration (MIC) values of 0.2, 0.05, 0.2, 0.22, and 0.07 microM, respectively. While compounds 4 and 5 exhibited cytotoxicity against HepG2 cells with IC(50) values of 0.2 and 1.6 microM, respectively.
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Urinary connective tissue growth factor increases far earlier than histopathological damage and functional deterioration in early chronic renal allograft injury.
Scand. J. Urol. Nephrol.
PUBLISHED: 11-20-2009
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To date, serum biochemistry examination and routine biopsy are the most commonly used methods to assess renal function after allogenic kidney transplantation. Connective tissue growth factor (CTGF) has been considered as a biomarker of chronic renal allograft injury characterized by tubular atrophy and interstitial fibrosis (TA/IF). This study explored the potential value of urinary CTGF as an early predictor of TA/IF using a rat model.
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A modified suspension test for estimating the mutagenicity of samples containing free and (or) protein-bound histidine.
Can. J. Microbiol.
PUBLISHED: 03-20-2009
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The Ames test has not been very effective in estimating the mutagenicity of histidine-containing samples because external free and (or) protein-bound histidine in these samples would allow the histidine auxotrophs in such test samples to grow more compared with the negative controls that were used as the reference. This could give rise to a false positive.n this study, a modified suspension mutagenicity assay (MS assay) was developed. The tester strains were incubated in Luria-Bertani (LB) broth containing different concentrations of traditional Chinese medicines (TCMs) until the declining phase, and the test samples were assayed to be mutagenic or not by observing whether statistically significant differences were demonstrated in the relative reversion frequencies (RRFs) between the negative control groups and the test groups. Collectively, using LB broth as the test medium and comparing the RRFs in the declining phase made this assay less influenced by the presence of histidine in the test samples.The mutagenicity of some TCMs was measured with the MS assay. The results in MS assay were consistent with those in the mammalian bone marrow chromosomal aberration test, which indicated that the MS assay was appropriate to estimate the mutagenicity of samples containing free and (or) protein-bound histidine.
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Discussion on research methods of bacterial resistant mutation mechanisms under selective culture--uncertainty analysis of data from the Luria-Delbrück fluctuation experiment.
Sci China Life Sci
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Whether bacterial drug-resistance is drug-induced or results from rapid propagation of random spontaneous mutations in the flora prior to exposure, remains a long-term key issue concerned and debated in both genetics and medicinal fields. In a pioneering study, Luria and Delbrück exposed E. coli to T1 phage, to investigate whether the number of resistant colonies followed the Poisson distribution. They deduced that the development of resistant colonies is independent of phage presence. Similar results have since been obtained on solid medium containing antibacterial agents. Luria and Delbrücks conclusions were long considered a gold standard for analyzing drug resistance mutations. More recently, the concept of adaptive mutation has triggered controversy over this approach. Microbiological observation shows that, following exposure to drugs of various concentrations, drug-resistant cells emerge and multiply depending on the time course, and show a process function, inconsistent with the definition of Poisson distribution (which assumes not only that resistance is independent of drug quantity but follows no specific time course). At the same time, since cells tend to aggregate after division rather than separating, colonies growing on drug plates arise from the multiplication of resistant bacteria cells of various initial population sizes. Thus, statistical analysis based on equivalence of initial populations will yield erroneous results. In this paper, 310 data from the Luria-Delbrück fluctuation experiment were reanalyzed from this perspective. In most cases, a high-end abnormal value, resulting from the non-synchronous variation of the two above-mentioned time variables, was observed. Therefore, the mean value cannot be regarded as an unbiased expectation estimate. The ratio between mean value and variance was similarly incomparable, because two different sampling methods were used. In fact, the Luria-Delbrück data appear to follow an aggregated, rather than Poisson distribution. In summary, the statistical analysis of Luria and Delbrück is insufficient to describe rules of resistant mutant development and multiplication. Correction of this historical misunderstanding will enable new insight into bacterial resistance mechanisms.
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Cofilin 1-mediated biphasic F-actin dynamics of neuronal cells affect herpes simplex virus 1 infection and replication.
J. Virol.
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Herpes simplex virus 1 (HSV-1) invades the nervous system and causes pathological changes. In this study, we defined the remodeling of F-actin and its possible mechanisms during HSV-1 infection of neuronal cells. HSV-1 infection enhanced the formation of F-actin-based structures in the early stage of infection, which was followed by a continuous decrease in F-actin during the later stages of infection. The disruption of F-actin dynamics by chemical inhibitors significantly reduced the efficiency of viral infection and intracellular HSV-1 replication. The active form of the actin-depolymerizing factor cofilin 1 was found to increase at an early stage of infection and then to continuously decrease in a manner that corresponded to the remodeling pattern of F-actin, suggesting that cofilin 1 may be involved in the biphasic F-actin dynamics induced by HSV-1 infection. Knockdown of cofilin 1 impaired HSV-1-induced F-actin assembly during early infection and inhibited viral entry; however, overexpression of cofilin 1 did not affect F-actin assembly or viral entry during early infection but decreased intracellular viral reproduction efficiently. Our results, for the first time, demonstrated the biphasic F-actin dynamics in HSV-1 neuronal infection and confirmed the association of F-actin with the changes in the expression and activity of cofilin 1. These results may provide insight into the mechanism by which HSV-1 productively infects neuronal cells and causes pathogenesis.
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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.