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Find video protocols related to scientific articles indexed in Pubmed.
Molecular Insight into the Role of the N-terminal Extension in the Maturation, Substrate Recognition, and Catalysis of a Bacterial Alginate Lyase from Polysaccharide Lyase Family 18.
J. Biol. Chem.
PUBLISHED: 09-10-2014
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Bacterial alginate lyases, which are members of several polysaccharide lyase (PL) families, have important biological roles and biotechnological applications. The mechanisms for maturation, substrate recognition, and catalysis of PL18 alginate lyases are still largely unknown. A PL18 alginate lyase, aly-SJ02, from Pseudoalteromonas sp. 0524 displays a ?-jelly roll scaffold. Structural and biochemical analyses indicated that the N-terminal extension in the aly-SJ02 precursor may act as an intramolecular chaperone to mediate the correct folding of the catalytic domain. Molecular dynamics simulations and mutational assays suggested that the lid loops over the aly-SJ02 active center serve as a gate for substrate entry. Molecular docking and site-directed mutations revealed that certain conserved residues at the active center, especially those at subsites +1 and +2, are crucial for substrate recognition. Tyr(353) may function as both a catalytic base and acid. Based on our results, a model for the catalysis of aly-SJ02 in alginate depolymerization is proposed. Moreover, although bacterial alginate lyases from families PL5, 7, 15, and 18 adopt distinct scaffolds, they share the same conformation of catalytic residues, reflecting their convergent evolution. Our results provide the foremost insight into the mechanisms of maturation, substrate recognition, and catalysis of a PL18 alginate lyase.
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Comparative genomics provide insights into evolution of trichoderma nutrition style.
Genome Biol Evol
PUBLISHED: 02-01-2014
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Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase-polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, ?-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (?) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.
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An evidence-based proposal for predicting organ failure in severe acute pancreatitis.
Pancreas
PUBLISHED: 10-25-2013
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Early, efficient, and accurate evaluation for organ failure is an important step for improving outcome in severe acute pancreatitis (SAP). We aim to develop a method that can early, efficiently, and accurately evaluate the in-hospital organ failure in patients with SAP.
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[Research on removal of tetrabromobisphenol A from synthetic wastewater by nanoscale zero valent iron supported on organobentonite].
Huan Jing Ke Xue
PUBLISHED: 08-17-2013
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The removal of tetrabromobisphenol A (TBBPA) in methanol aqueous solutions by nanoscale zero valent iron supported on organobentonite (NZVI-CMT) was studied. The effects of temperature, initial concentration of TBBPA and the dose of NZVI-CMT on the degradation and debromination of TBBPA were investigated. The removal rate by NZVI-CMT reached 97.5% within 12 hours at 25 degrees C, when the initial concentration of TBBPA was 10 mg x L(-1). And the removal rate of NZVI-CMT was higher than those of two simple materials, namely organobentonite (CMT) and nanoscale zero valent iron (NZVI), as well as the sum of those two simple materials. In addition, NZVI-CMT exhibited a better reusable attribute, and the rate of the materials remained above 90% after being used for 3 times. Based on the identification of degradation products and analysis of the TBBPA removal by NZVI-CMT, the main reaction mechanism was suggested as adsorption and debromination, and higher reaction temperature was preferable for debromination.
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Identification of biomarkers for hepatocellular carcinoma using network-based bioinformatics methods.
Eur. J. Med. Res.
PUBLISHED: 05-10-2013
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Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide. Despite several efforts to elucidate molecular mechanisms involved in this cancer, they are still not fully understood.
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Prospectively estimating the recoverability of renal function after relief of unilateral urinary obstruction by measurement of renal parenchymal volume.
Acad Radiol
PUBLISHED: 03-19-2013
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Renal parenchymal volume (RPV) has been suggested as an indicator of the potential functional residual capacity for a given kidney. The goal of this study was to determine whether the recoverability of renal function could be predicted by RPV as estimated by computed tomography (CT) before an operation.
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Magnetic properties and spin dynamics in Ba(Fe(1-x)Mn(x))2As2 compounds studied by 57Fe Mössbauer spectroscopy.
J Phys Condens Matter
PUBLISHED: 03-11-2013
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Ba(Fe(1-x)Mn(x))2As2 compounds with x = 0.016 and 0.064 have been studied by (57)Fe Mössbauer spectroscopy in the temperature range from 30 to 300 K. The unusual magnetic splitting spectra at lower temperatures have been analyzed using the distribution of hyperfine field. It is found that the influence of Mn dopant spreads beyond the nearest Fe magnetic moments, and the Fe 3d electrons behave more localized compared with those in the electron-doped compounds. This reduces the hyperfine interactions between iron nucleus and the sounding electrons. The shape of the spin density wave is near-rectangular at 6.4%-Mn doping, indicating quite different interband interactions compared with electron-doped compounds. A distinct broadening of the spectral linewidth around the spin density wave transition temperature has been observed and the spin correlation time is deduced according to the linewidth. The correlation time is further related to the spin-lattice relaxation rate by a simple model and the magnetic fluctuations can be explored effectively. It is found that the magnetic fluctuations of iron spins in Mn-doped compounds can be described well using a phenomenological two-component model and the resulting Curie-Weiss temperature is far from the quantum critical point at the present doping levels.
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The secondary structure of heated whey protein and its hydrolysates antigenicity.
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 06-28-2011
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Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) were used to investigate the conformational changes of heated whey protein (WP) and the corresponding changes in the hydrolysates immunoreactivity were determined by competitive enzyme-linked immunosorbent assay (ELISA). Results showed that the contents of alpha- helix and beta-sheet of WP did not decrease much under mild heating conditions and the antigenicity was relatively high; when the heating intensity increased (70 degrees for 25 min or 75 degrees C for 20 min), the content of alpha- helix and beta-sheet decreased to the minimum, so was the antigenicity; However, when the WP was heated at even higher temperature and for a longer time, the beta-sheet associated with protein aggregation begun to increase and the antigenicity increased correspondingly. It was concluded that the conformations of heated WP and the antigenicity of its hydrolysates are related and the optimum structure for decreasing the hydrolysates antigeniity is the least content of alpha-helix and beta-sheet. Establishing the relationship between the WP secondary structure and WP hydrolysates antigenicity is significant to supply the reference for antigenicity reduction by enzymolysis.
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Synthesis and antitumor activity of 1,2,4-triazoles having 1,4-benzodioxan fragment as a novel class of potent methionine aminopeptidase type II inhibitors.
Bioorg. Med. Chem.
PUBLISHED: 06-24-2011
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A series of 1,2,4-triazole derivatives containing 1,4-benzodioxan (5a-5q) have been designed, synthesized, structurally determined, and their biological activities were evaluated as potential MetAP2 inhibitors. All the synthesized compounds were first reported. Among the compounds, compound 5k showed the most potent biological activity against HEPG2 cancer cell line (IC(50)=0.81 ?M for HEPG2 and IC(50)=0.93 ?M for MetAP2), which was comparable to the positive control. Docking simulation by positioning compound 5k into the MetAP2 structure active site was performed to explore the possible binding model. The results of apoptosis and Western-blot assay demonstrated that compound 5k possessed good antitumor activity against HEPG2 cancer cell line. Therefore, compound 5k with potent inhibitory activity in tumor growth inhibition may be a potential antitumor agent against HEPG2 cancer cell.
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[Effect of lipoxin A(4) on lipopolysaccharide-induced endothelial hyperpermeability in human umbilical vein endothelial cell].
Zhonghua Fu Chan Ke Za Zhi
PUBLISHED: 05-18-2011
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To explore whether lipoxin A(4) (LXA(4))could prevent lipopolysaccharide (LPS)-induced human umbilical vein endothelial cells (HUVEC) monolayer hyperpermeability and its possible mechanism.
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Normal values for renal parenchymal volume and kidney length as measured by non-enhanced multidetector spiral computed tomography.
Acta Radiol
PUBLISHED: 04-20-2011
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Renal parenchymal volume (RPV) is considered an important index for clinical decisions. However, normal values have not been established, which hinders the clinical application of RPV.
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Cardiac shock wave therapy reduces angina and improves myocardial function in patients with refractory coronary artery disease.
Clin Cardiol
PUBLISHED: 11-20-2010
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Safe and effective therapeutic management of refractory coronary artery disease (CAD) in heart patients is critical to enhance cardiovascular function and improve quality of life. Current therapies for refractory CAD are inadequate in ameliorating angina and promoting revascularization of ischemic myocardium.
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Glial-derived neurotrophic factor regulates intestinal epithelial barrier function and inflammation and is therapeutic for murine colitis.
J. Pathol.
PUBLISHED: 07-16-2010
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Although enteric glial cells (EGCs) have been demonstrated to play a key role in maintaining intestinal epithelial barrier integrity, it is not known how EGCs regulate this integrity. We therefore hypothesized that glial-derived neurotrophic factor (GDNF) produced by EGCs might be involved in this regulation. Here we investigated the role of GDNF in regulating epithelial barrier function in vivo. Recombinant adenoviral vectors encoding GDNF (Ad-GDNF) were administered intracolonically in experimental colitis induced by dextran sulphate sodium (DSS). The disease activity index (DAI) and histological score were measured. Epithelial permeability was assayed using Evans blue dye. The anti-apoptotic potency of GDNF in vivo was evaluated. The expression of tumour necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta), and myeloperoxidase (MPO) activity were measured by ELISA assay and/or RT-PCR. The expression of ZO-1, Akt, caspase-3, and NF-kappaB p65 was analysed by western blot assay. Our results showed that GDNF resulted in a significant reduction in enhanced permeability, inhibited MPO activity, IL-1beta and TNF-alpha expression, and increased ZO-1 and Akt expression. Moreover, GDNF strongly prevented apoptosis in vivo and significantly ameliorated experimental colitis. Our findings indicate that GDNF participates directly in restoring epithelial barrier function in vivo via reduction of increased epithelial permeability and inhibition of mucosal inflammatory response, and is efficacious in DSS-induced colitis. These findings support the notion that EGCs are able to regulate intestinal epithelial barrier integrity indirectly via their release of GDNF in vivo. GDNF is namely an important mediator of the cross-talk between EGCs and mucosal epithelial cells. GDNF may be a useful therapeutic approach to the treatment of inflammatory bowel disease.
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Amelioration of dextran sulfate sodium-induced colitis by neuropeptide Y antisense oligodeoxynucleotide.
Int J Colorectal Dis
PUBLISHED: 05-21-2010
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Neuropeptide Y (NPY) from enteric neurons has been shown to play an important role in immune and inflammatory responses. The purpose of the present study was to investigate the effects of NPY antisense oligodeoxynucleotides (ODNs) on an experimental model of ulcerative colitis (UC).
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[Effect of lipoxin A(4) on lipopolysaccharide-induced oxidant stress in human umbilical vein endothelial cells].
Zhonghua Fu Chan Ke Za Zhi
PUBLISHED: 05-09-2010
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To explore the effects of lipoxin A(4) (LXA(4)) on lipopolysaccharide (LPS)-induced oxidative stress in human umbilical veins endothelial cells (HUVEC) and the possible mechanism.
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[Characterization of Cr (VI) removal and total Cr equilibrium adsorption by sulfate reducing granular sludge in stimulant wastewater].
Huan Jing Ke Xue
PUBLISHED: 03-10-2010
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Sulfate reducing granular sludge (SRGS) cultivated in small scale EGSB reactor was used for Cr (VI) removing. Characterization of Cr (VI) removal and total Cr equilibrium adsorption was studied, and the adsorption isotherm was fitted. Results showed that removal of Cr (VI) was in connection with the structure and chemical composition of SRGS and several environmental factors. The Cr (VI) removal rate increased with the dosage of granular sludge; the increasing of oscillation speed and temperature could enhance Cr (VI) removal and total Cr adsorption, but while the oscillation speed reached 150 r x min(-1) or the temperature came to 40 degrees C, the physical structure of granular sludge would be affected and the granular sludge discrete, and total Cr equilibrium adsorption decreased; lower pH value caused higher Cr (VI) removal rate, however the sulfate on the surface of granular sludge was affected by lower pH value easily and would translate into H2S, then total Cr adsorption rate decreased. Cr (VI) removal would be influenced by physical, chemical and biological factors, and the process included reduction and adsorption mainly. The maximum adsorption of total Cr by granular sludge was 6.84 mg x g(-1), and the total Cr adsorbing process fitted in with Langmuir adsorption isotherm.
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[Preparation and characterization of human phage display antibody against peroxiredoxin I of lung adenocarcinoma].
Nan Fang Yi Ke Da Xue Xue Bao
PUBLISHED: 02-02-2010
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To construct a human phage antibody library and screen the single chain variable fragment (ScFv) antibudies to peroxiredoxin I (Prx I) of lung adenocarcinoma.
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Production and radioimmunoimaging of novel fully human phage display recombinant antibodies and growth inhibition of lung adenocarcinoma cell line overexpressing Prx I.
Cancer Biol. Ther.
PUBLISHED: 07-14-2009
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The Peroxiredoxin I (Prx I) is a member of the Peroxiredoxin family, which is overexpressed in many diverse tumor types and is an anti-apoptosis protein for tumor cell proliferation and survival. Therapeutic strategies targeting the Prx I may therefore be effective broad-spectrum anticancer agents. We constructed a phage display single-chain variable fragment (scFv) antibody library and sieve out the fully human, lung adenocarcinoma-sepcific monoclonal antibodies. The selection on Prx I was performed using above-mentioned lung adenocarcinoma-sepcific monoclonal antibodies with high affinity to Prx I overexpressing lung adenocarcinoma cells. The candidate scFv sequences, based on enzyme-linked immunosorbent assay (ELISA) screening data, were chosen for soluble expression, and a 30 kDa band was observed on polyacrylamide gel electrophoresis as predicted. The purified antibodies were characterized by immunoblotting and showed high specificity to Prx I-overexpressing lung adenocarcinoma cells A549. Radioimmunoimaging was taken to evaluate specificity and distribution of antibodies in vivo. The radiolocalization index (RI) of tumor/serum and tumor/muscle gradually increased, reaching its peak (4.06 +/- 0.13 and 5.17 +/- 0.97, respectively) at 48 h postadministration. Single photon emission computed tomography (SPECT) imaging showed the radioactivity was aggregated in tumor locations and tumor imaging was clearly observed. The internalized scFv resulted in antibody-mediated cell apoptosis and downregulation of Prx I expression. These results demonstrate that the scFv possesses strong antitumor activity on lung adenocarcinoma and may therefore be an effective therapeutic candidate for the treatment of cancers that are dependent on Prx I for growth and survival.
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Streptamer versus tetramer-based selection of functional cytomegalovirus-specific T cells.
J. Formos. Med. Assoc.
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Cytomegalovirus (CMV) disease constitutes a serious complication after stem cell transplantation and has been treated by adoptive transfer of donor-derived CMV-specific CD8(+) T cells. CMV-specific CD8(+) T cells were selected by multimers, and the technologies may alter the function of these T cells. Therefore, here we evaluated the impact of multimer reagents on the function of CD8(+) T lymphocytes.
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Surgical Treatment of Gynecomastia: Mastectomy Compared to Liposuction Technique.
Ann Plast Surg
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BACKGROUND: Gynecomastia was a benign enlargement of the male breast. Yet, the enlarged breasts caused much anxiety, embarrassment, psychosocial discomfort, and fear of breast cancer. The aim of this study was to assess the experience of gynecomastia patients undergoing mastectomy and liposuction surgery. METHODS: Seven hundred thirty-three patients were analyzed for age, chief complaint, position, grade, operation approach, biopsy, and complication between mastectomy group and liposuction group, from 1990 to 2010. RESULTS: Four hundred two patients (436 breasts) were treated with mastectomy and 331 patients (386 breasts) were treated with liposuction techniques. Three hundred thirty (82%) patients complained of breast lump and lump with pain in mastectomy group, and 204 (61%) patients complained of enlargement breast and enlargement with pain in liposuction group (P < 0.05). All excision specimens were performed for routine histological analysis which showed pathologic diagnosis in patients with mastectomy (100%). One hundred fifty-nine (41%) patients with liposuction acquired pathologic diagnosis through fine needle aspiration and/or core biopsy (P < 0.05). The reoperation rates in mastectomy group and liposuction group were 1.4% and 0.5%, respectively. There were no nipple/areola necrosis and scars in liposuction group. CONCLUSIONS: The surgical treatment of gynecomastia required an individual approach, depending on symptoms (lump or enlargement) and requirements of patients. Patients who chose mastectomy were looking for reassurance that their pathologic diagnosis was benign. The increase in the number of liposuction patients was reflected in our study because it was associated with superior esthetic results and few complications.
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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.