JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.
PLoS ONE
PUBLISHED: 08-20-2014
Show Abstract
Hide Abstract
Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng.
Related JoVE Video
Determination of five sulfonylurea herbicides in environmental waters and soil by ultra high performance liquid chromatography with tandem mass spectrometry after extraction using graphene.
J Sep Sci
PUBLISHED: 07-25-2014
Show Abstract
Hide Abstract
A fast and novel analytical method was developed for the determination of trace levels of sulfonylurea herbicides in water and soil samples. Graphene was used as a sorbent for extraction, and ultra high performance liquid chromatography with tandem mass spectrometry was used for quantification. Five sulfonylurea herbicides were preconcentrated from water samples using a graphene-loaded packed cartridge, while extraction from soil samples was performed in a single step using graphene-supported matrix solid-phase dispersion. Under the optimized conditions, the calibration plots were linear in the range between 5 and 1000 ng/L for water samples, and between 1 and 200 ng/g for soil samples. All correlation coefficients (R) were >0.99. The limits of detection for water and soil samples were 0.28-0.53 ng/L and 0.08-0.26 ng/g, respectively. This method was successfully applied to the analysis of spiked samples of environmental water and soil, with recoveries ranging from 84.2-109.3 and 86.12-103.2%, respectively, all with relative standard deviations of <10%.
Related JoVE Video
[Eeffct of multimodality therapies on plasma solube tumor necrosis factor receptor I in OSAHS patients].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 06-26-2014
Show Abstract
Hide Abstract
As a subtype membrane receptor of tumor necrosis factor alpha, not much is known about the link between the soluble TNF receptor-I and obstructive sleep apnea hypopnea syndrome. We hypothesized that the TNF receptor might play an important role in the inflammation in patients with OSAHS, moreover this study was undertakan to investigate the effects of multimodality therapies on its periphery blood level.
Related JoVE Video
Genomic Changes in an Attenuated ZB Strain of Foot-and-Mouth Disease Virus Serotype Asia1 and Comparison with Its Virulent Parental Strain.
Int J Genomics
PUBLISHED: 05-27-2014
Show Abstract
Hide Abstract
The molecular basis of attenuation of foot-and-mouth disease virus (FMDV) serotype Asia1 ZB strain remains unknown. To understand the genetic changes of attenuation, we compared the entire genomes of three different rabbit-passaged attenuated ZB strains (ZB/CHA/58(att), ZBRF168, and ZBRF188) and their virulent parental strains (ZBCF22 and YNBS/58). The results showed that attenuation may be brought about by 28 common amino acid substitutions in the coding region, with one nucleotide point mutation in the 5'-untranslated region (5'-UTR) and another one in the 3'-UTR. In addition, a total of 21 nucleotides silent mutations had been found after attenuation. These substitutions, alone or in combination, may be responsible for the attenuated phenotype of the ZB strain in cattle. This will contribute to elucidation of attenuating molecular basis of the FMDV ZB strain.
Related JoVE Video
Puerarin protects pancreatic ?-cell survival via PI3K/Akt signaling pathway.
J. Mol. Endocrinol.
PUBLISHED: 05-14-2014
Show Abstract
Hide Abstract
Pancreatic ?-cell loss because of apoptosis is the major cause of type 1 diabetes (T1D) and late stage T2D. Puerarin possesses anti-diabetic properties; whether it acts directly on pancreatic ?-cell is not clear. This study was designed to investigate the effects of puerarin on pancreatic ?-cell survival and function. Diabetes was induced in male C57BL/6 mice by a single peritoneal injection of streptozotocin (STZ). Pancreatic ?-cell survival and function were assessed in diabetic mice by measuring ?-cell apoptosis, ?-cell mass, pancreatic insulin content, and glucose tolerance, and in cultured islets and clonial MIN6 ?-cells by measuring ?-cell viability and apoptosis and glucose-stimulated insulin secretion. We found that pre-treatment with puerarin decreased the incidence of STZ-induced diabetes. Puerarin increased pancreatic ?-cell mass via ?-cell apoptosis inhibition in diabetic mice, and increased serum insulin, whereas it decreased blood glucose levels and improved glucose tolerance. In cultured islets and MIN6 cells, puerarin protected ?-cell from cobalt chloride (CoCl2)-induced apoptosis and restored the impaired capacity of glucose-stimulated insulin secretion. Puerarin protection of ?-cell survival involved the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. In conclusion, puerarin protects pancreatic ?-cell function and survival via direct effects on ?-cells, and its protection of ?-cell survival is mediated by the PI3K/Akt pathway. As a safe natural plant extraction, puerarin might serve as a preventive and/or therapeutic approach for diabetes.
Related JoVE Video
Optimization of alkaline extraction and bioactivities of polysaccharides from rhizome of Polygonatum odoratum.
Biomed Res Int
PUBLISHED: 03-24-2014
Show Abstract
Hide Abstract
The present study is to explore the optimal extraction parameters, antioxidant activity, and antimicrobial activity of alkaline soluble polysaccharides from rhizome of Polygonatum odoratum. The optimal extraction parameters were determined as the following: NaOH concentration (A) 0.3 M, temperature (B) 80 °C, ratio of NaOH to solid (C) 10-fold, and extraction time (D) 4 h, in which ratio of NaOH to solid was a key factor. The order of the factors was ratio of NaOH to solid (fold, C) > extraction temperature (°C, B) > NaOH concentration (M, A) > extraction time (h, D). The monosaccharide compositions of polysaccharides from P. odoratum were rhamnose, mannose, xylose, and arabinose with the molecular ratio of 31.78, 31.89, 11.11, and 1.00, respectively. The reducing power, the 1, 1-diphenyl-2-picryl-hydrazil (DPPH) radical scavenging rate, the hydroxyl radicals scavenging rate, and the inhibition rate to polyunsaturated fatty acid (PUFA) peroxidation of the alkaline soluble polysaccharides from P. odoratum at 1 mg/mL were 9.81%, 52.84%, 19.22%, and 19.42% of ascorbic acid at the same concentration, respectively. They also showed antimicrobial activity against pathogenic bacteria Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis, and Escherichia coli.
Related JoVE Video
A study of the interaction between HIV-1 protease and C 2-symmetric inhibitors by computational methods.
J Mol Model
PUBLISHED: 03-16-2014
Show Abstract
Hide Abstract
The human immunodeficiency virus type 1 protease (HIV-1 PR) is a major target for the design of anti-AIDS (acquired immune deficiency syndrome) drugs. Some C2-symmetric inhibitors have been designed for the C2-symmetric binding pocket of HIV-1PR. The crystallographic structures reveal that the binding modes are not C2-symmetric for C2-symmetric inhibitors binding to PR. In this work, four molecular dynamics (MD) simulations were performed to investigate the binding modes between four C2-symmetric inhibitors (6 AD, 6AG, 6FD and 6FG) and PR, as well as the stabilities of these inhibitors in the binding pocket. Analysis of the hydrophobic surface of the binding pocket shows that it is necessary to add a polar group to the P1 (benzyl) and P2 (phenyl) groups of the inhibitor 6AD. Analysis of the hydrogen bonds formed between inhibitors and residues (Asp25/Asp25', Ile50/Ile50') indicates that the steric structures of the inhibitors are not suitable for the binding pocket. The two increased polar groups of trifluoromethyl and formamido meet the needs of the binding pocket for polar molecules. The inhibitor with both these groups (6FG) has stronger stability than the other three inhibitors, which have only one (6AG and 6FD) or none (6AD) of these groups. The ranking of binding free energies calculated by molecular mechanics-generalized born surface area (MM-GBSA) method agrees well with the experimental data. It is expected that this study will provide theoretical guidance for the design of anti-AIDS drugs targeting HIV-1PR.
Related JoVE Video
Erythropoiesis-stimulating agents in the management of cancer patients with anemia: a meta-analysis.
Chin. J. Cancer Res.
PUBLISHED: 03-10-2014
Show Abstract
Hide Abstract
Erythropoiesis-stimulating agents (ESAs) are widely used in the management of anemia in cancer patients. Despite their apparent effectiveness, recent studies have suggested that ESAs could result in serious adverse events and even higher mortality. The aim of the current study was to evaluate the benefits and risks of ESAs in the management of cancer patients with anemia using a meta-analysis.
Related JoVE Video
Comparative performance of aldolase and lactate dehydrogenase rapid diagnostic tests in Plasmodium vivax detection.
Malar. J.
PUBLISHED: 03-10-2014
Show Abstract
Hide Abstract
Misdiagnosis of malaria by commercial rapid diagnostic tests (RDTs) is a major cause of concern in the diagnosis of malaria. This retrospective study was aimed at assessing the relative performance of four RDTs with emphasis on the detection of two Plasmodium vivax antigens: aldolase and lactate dehydrogenase (LDH).
Related JoVE Video
Combination of dispersive solid-phase extraction and salting-out homogeneous liquid-liquid extraction for the determination of organophosphorus pesticides in cereal grains.
J Sep Sci
PUBLISHED: 03-05-2014
Show Abstract
Hide Abstract
A new analytical method for the determination of organophosphorus pesticides in cereal samples was developed by combining dispersive SPE (d-SPE) and salting-out homogeneous liquid-liquid extraction (SHLLE). The pesticides were first extracted from cereal grains with acetonitrile, followed by d-SPE cleanup. A 2 mL aliquot of the extract was then added to a centrifuge tube containing 9.2 mL water and 3.3 g NaCl for SHLLE. Analysis of the extract was carried out by gas chromatography coupled with flame photometric detection. The d-SPE procedure effectively provides the necessary cleanup of the extract while SHLLE is used as an efficient concentration technique. Experimental parameters influencing the extraction efficiency including amounts of added water and salt were investigated. Recovery studies were carried out at three fortification levels, yielding recoveries in the range of 57.7-98.1% with the RSD from 3.7 to 10.9%. The reported limits of determination obtained from this study were 1 ?g/kg, which is better than the conventional methods. In the analysis of 40 wheat and corn samples taken from Beijing suburbs, only two wheat samples have chlorpyrifos residue over the limits of determination.
Related JoVE Video
SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.
Methods Mol. Biol.
PUBLISHED: 02-28-2014
Show Abstract
Hide Abstract
RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.
Related JoVE Video
Insight into conformational change for 14-3-3? protein by molecular dynamics simulation.
Int J Mol Sci
PUBLISHED: 01-18-2014
Show Abstract
Hide Abstract
14-3-3? is a member of a highly conserved family of 14-3-3 proteins that has a double-edged sword role in human cancers. Former reports have indicated that the 14-3-3 protein may be in an open or closed state. In this work, we found that the apo-14-3-3? is in an open state compared with the phosphopeptide bound 14-3-3? complex which is in a more closed state based on our 80 ns molecular dynamics (MD) simulations. The interaction between the two monomers of 14-3-3? in the open state is the same as that in the closed state. In both open and closed states, helices A to D, which are involved in dimerization, are stable. However, large differences are found in helices E and F. The hydrophobic contacts and hydrogen bonds between helices E and G in apo-14-3-3? are different from those in the bound 14-3-3? complex. The restrained and the mutated (Arg56 or Arg129 to alanine) MD simulations indicate that the conformation of four residues (Lys49, Arg56, Arg129 and Tyr130) may play an important role to keep the 14-3-3? protein in an open or closed state. These results would be useful to evaluate the 14-3-3? protein structure-function relationship.
Related JoVE Video
Analysing and Correcting the Differences between Multi-Source and Multi-Scale Spatial Remote Sensing Observations.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Differences exist among analysis results of agriculture monitoring and crop production based on remote sensing observations, which are obtained at different spatial scales from multiple remote sensors in same time period, and processed by same algorithms, models or methods. These differences can be mainly quantitatively described from three aspects, i.e. multiple remote sensing observations, crop parameters estimation models, and spatial scale effects of surface parameters. Our research proposed a new method to analyse and correct the differences between multi-source and multi-scale spatial remote sensing surface reflectance datasets, aiming to provide references for further studies in agricultural application with multiple remotely sensed observations from different sources. The new method was constructed on the basis of physical and mathematical properties of multi-source and multi-scale reflectance datasets. Theories of statistics were involved to extract statistical characteristics of multiple surface reflectance datasets, and further quantitatively analyse spatial variations of these characteristics at multiple spatial scales. Then, taking the surface reflectance at small spatial scale as the baseline data, theories of Gaussian distribution were selected for multiple surface reflectance datasets correction based on the above obtained physical characteristics and mathematical distribution properties, and their spatial variations. This proposed method was verified by two sets of multiple satellite images, which were obtained in two experimental fields located in Inner Mongolia and Beijing, China with different degrees of homogeneity of underlying surfaces. Experimental results indicate that differences of surface reflectance datasets at multiple spatial scales could be effectively corrected over non-homogeneous underlying surfaces, which provide database for further multi-source and multi-scale crop growth monitoring and yield prediction, and their corresponding consistency analysis evaluation.
Related JoVE Video
Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions). A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC) of 0.77 with high precision (94%) and high sensitivity (65%). We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA)] is available as an on-line server at http://sparks-lab.org.
Related JoVE Video
Monitoring powdery mildew of winter wheat by using moderate resolution multi-temporal satellite imagery.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Powdery mildew is one of the most serious diseases that have a significant impact on the production of winter wheat. As an effective alternative to traditional sampling methods, remote sensing can be a useful tool in disease detection. This study attempted to use multi-temporal moderate resolution satellite-based data of surface reflectances in blue (B), green (G), red (R) and near infrared (NIR) bands from HJ-CCD (CCD sensor on Huanjing satellite) to monitor disease at a regional scale. In a suburban area in Beijing, China, an extensive field campaign for disease intensity survey was conducted at key growth stages of winter wheat in 2010. Meanwhile, corresponding time series of HJ-CCD images were acquired over the study area. In this study, a number of single-stage and multi-stage spectral features, which were sensitive to powdery mildew, were selected by using an independent t-test. With the selected spectral features, four advanced methods: mahalanobis distance, maximum likelihood classifier, partial least square regression and mixture tuned matched filtering were tested and evaluated for their performances in disease mapping. The experimental results showed that all four algorithms could generate disease maps with a generally correct distribution pattern of powdery mildew at the grain filling stage (Zadoks 72). However, by comparing these disease maps with ground survey data (validation samples), all of the four algorithms also produced a variable degree of error in estimating the disease occurrence and severity. Further, we found that the integration of MTMF and PLSR algorithms could result in a significant accuracy improvement of identifying and determining the disease intensity (overall accuracy of 72% increased to 78% and kappa coefficient of 0.49 increased to 0.59). The experimental results also demonstrated that the multi-temporal satellite images have a great potential in crop diseases mapping at a regional scale.
Related JoVE Video
Development of rapid immunochromatographic test for hemagglutinin antigen of H7 subtype in patients infected with novel avian influenza A (H7N9) virus.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Since human infection with the novel H7N9 avian influenza virus was identified in China in March 2013, the relatively high mortality rate and possibility of human-to-human transmission have highlighted the urgent need for sensitive and specific assays for diagnosis of H7N9 infection.
Related JoVE Video
The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins.
Biophys. J.
PUBLISHED: 09-02-2013
Show Abstract
Hide Abstract
Probabilities of disorder for FlgM proteins of 39 species whose optimal growth temperature ranges from 273 K (0°C) to 368 K (95°C) were predicted by a newly developed method called Sequence-based Prediction with Integrated NEural networks for Disorder (SPINE-D). We showed that the temperature-dependent behavior of FlgM proteins could be separated into two subgroups according to their sequence lengths. Only shorter sequences evolved to adapt to high temperatures (>318 K or 45°C). Their ability to adapt to high temperatures was achieved through a transition from a fully disordered state with little secondary structure to a semidisordered state with high predicted helical probability at the N-terminal region. The predicted results are consistent with available experimental data. An analysis of all orthologous protein families in 39 species suggests that such a transition from a fully disordered state to semidisordered and/or ordered states is one of the strategies employed by nature for adaptation to high temperatures.
Related JoVE Video
The conformational changes analysis of maltodextrin binding protein based on elastic network model.
Int J Data Min Bioinform
PUBLISHED: 06-27-2013
Show Abstract
Hide Abstract
Maltodextrin Binding Protein (MBP) has provided a model system for investigating open-closed conformation transition based on two coarse-grained elastic network models. GNM results show that the open and closed forms have the same motion hinge axes and the open-closed conformational transition mainly exhibits as a large movement of the N-domain. ANM calculation shows a transition from open/closed to closed/open, which is helpful for ligand binding or release. During the open-closed transition, the residues within the domains move in a highly coupled way, and this indicates that the hinge connecting the domains is flexible, while the domains themselves are rigid.
Related JoVE Video
[Application of computed tomographic angiography in repairing skin defect after scalp avulsion with free latissimus dorsi flap transplantation].
Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi
PUBLISHED: 05-16-2013
Show Abstract
Hide Abstract
To investigate the clinical value of computed tomographic angiography (CTA) and three-dimensional reconstruction technique in repairing scalp avulsion wound with large skull exposure by the free latissimus dorsi flap transplantation.
Related JoVE Video
Ligand selectivity of estrogen receptors by a molecular dynamics study.
Eur J Med Chem
PUBLISHED: 03-09-2013
Show Abstract
Hide Abstract
Estrogen receptors ? (ER?) and ? (ER?) have different physiological functions and expression levels in different tissues. ER? and ER? are highly homologous and have only two residue substitutions in the binding pocket. This high similarity at the active site stimulates the interests for discovering subtype selective ligands. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method have been carried out to analyze the basis of selectivity of three ligands (659, 818 and 041). The calculated binding free energies show that all the ligands bind more tightly to ER? than to ER?. The dominant free energy components of selectivity for 659 are similar to that for 041, but different from that for 818. The decompositions of free energy contributions and structural analysis imply that there are eight residues primarily contributing to the selectivity for 659, five residues for 041, as well as two residues for 818. The structural analysis implies that two residue substitutions in binding packet cause the position of 659 in ER?-659 complex to shift relative to that in ER?-659 complex and also cause the conformational changes of other residues in the binding pocket. The higher selectivity for 041 is mainly caused by three residues, Ile373 (Met421), His475 (His524) and Leu476 (Leu525).
Related JoVE Video
Evaluation of Wondfo influenza A&B fast test based on immunochromatography assay for rapid diagnosis of influenza A H1N1.
Braz J Infect Dis
PUBLISHED: 03-01-2013
Show Abstract
Hide Abstract
Influenza viruses cause significant morbidity and mortality in both children and adults during local outbreaks or epidemics. Therefore, a rapid test for influenza A&B would be useful. This study was conducted to evaluate the clinical performance of the Wondfo influenza A&B test for rapid diagnosis of influenza A H1N1 Infection. The rapid testing assay could distinguish infection of influenza A and B virus. The reference viral strains were cultured in MDCK cells while TCID50 if the viruses were determined. The analytical sensitivity of the Wondfo kit was 100TCID50/ml. The Wondfo kit did not show cross reactivity with other common viruses. 1928 suspected cases of influenza A (H1N1) virus infection were analyzed in the Wondfo influenza A&B test and other commercially available products. Inconsistent results were further confirmed by virus isolation in cell culture. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were 100%, 98.23%, 92.45%, and 100% for flu A, and 96.39%, 99.95%, 98.77%, and 99.84% for flu B respectively. 766 suspected cases of influenza A (H1N1) virus infection were analyzed in the Wondfo influenza A&B test and RT-PCR. The sensitivity, specificity, PPV and NPV were 56.5%, 99.75%, 99.52% and 71.04% for flu A, 25.45%, 99.86%, 93.33% and 94.54% for flu B respectively. These results indicate that the Wondfo influenza A&B test has high positive and negative detection rates. One hundred fifty-six specimens of influenza A (H1N1) confirmed by RT-PCR were analyzed by the Wondfo influenza A&B test and 66.67% were positive while only 18.59% were positive by the reference kit. These results indicate that our rapid diagnostic assay may be useful for analyzing influenza A H1N1 infections in patient specimen.
Related JoVE Video
Global gene expression changes in Candidatus?Liberibacter asiaticus during the transmission in distinct hosts between plant and insect.
Mol. Plant Pathol.
PUBLISHED: 01-22-2013
Show Abstract
Hide Abstract
Huanglongbing (HLB) or citrus greening disease is a destructive disease of citrus worldwide, which is associated with Candidatus?Liberibacter asiaticus. This phloem-limited fastidious pathogen is transmitted by the Asian citrus psyllid, Diaphorina citri, and appears to be an intracellular pathogen that maintains an intimate association with the psyllid or the plant throughout its life cycle. The molecular basis of the interaction of this pathogen with its hosts is not well understood. We hypothesized that, during infection, Ca. L.?asiaticus differentially expresses the genes critical for its survival and/or pathogenicity in either host. To test this hypothesis, quantitative reverse transcription-polymerase chain reaction was performed to compare the gene expression of Ca. L.?asiaticus in?planta and in psyllid. Overall, 381 genes were analysed for their gene expression in?planta and in psyllid. Among them, 182 genes were up-regulated in?planta compared with in psyllid (P?
Related JoVE Video
Plasmodium vivax aldolase-specific monoclonal antibodies and its application in clinical diagnosis of malaria infections in China.
Malar. J.
PUBLISHED: 01-17-2013
Show Abstract
Hide Abstract
Most rapid diagnostic tests (RDTs) currently used for malaria diagnosis cannot distinguish the various Plasmodium infections. The development of a Plasmodium vivax specific RDTs with high sensitivity to sufficiently differentiate the two most common Plasmodium infections would be very crucial for disease treatment and control.
Related JoVE Video
Chemical composition and antimicrobial activity of the volatile oil from Fusarium tricinctum, the endophytic fungus in Paris polyphylla var. yunnanensis.
Nat Prod Commun
PUBLISHED: 12-23-2011
Show Abstract
Hide Abstract
The volatile oil, obtained by hydro-distillation from Fusarium tricinctum, the endophytic fungus isolated from Paris polyphylla var. yunnanensis, was analyzed by gas chromatography-mass spectrometry (GC-MS). trans-1,2,3,3a,4,7a-Hexahydro-7a-methyl-5H-inden-5-one (73.1%), 2-methylene-4,8,8-trimethyl-4-vinyl bicyclo [5.2.0] nonane (12.0%), and 2,6-dimethyl-6-(4-methyl-3-pentenyl) bicyclo [3.1.1] hept-2-ene (4.5%) were the major compounds of the 15 identified components accounting for 95.4% of the volatile oil. The antimicrobial activity of the volatile oil was assayed against eight bacteria and two fungi. The minimum inhibitory concentration (MIC) values of the volatile oil against the test bacteria ranged from 25 to 45 microg/mL. The MIC values against the fungi Candida albicans and Magnaporthe oryzae were 100 and 225 microg/mL, respectively. The mean inhibitory concentration (IC50) values of the volatile oil against the test bacteria ranged from 17.8 to 31.6 microg/mL, and those of the volatile oil against C. albicans and M. oryzae were 84.3 and 204.3 microg/mL, respectively.
Related JoVE Video
Antimicrobial and antioxidant activities of the flower essential oil of Halimodendron halodendron.
Nat Prod Commun
PUBLISHED: 12-23-2011
Show Abstract
Hide Abstract
The essential oil obtained by hydro-distillation from the flowers of Halimondendron halodendron (Leguminosae) was analyzed for its chemical composition by gas chromatography-mass spectrometry (GC-MS). Undecane (16.4%), dodecane (15.3%), tridecane (12.5%), decane (8.2%), 6,10,14-trimethyl-pentadecan-2-one (6.3%), methyl palmitate (6.0%), methyl linolenate (4.1%) and ethylcyclohexane (4.1%) were the major compounds of the thirty-five identified components of the oil. The essential oil was shown to have a broad spectrum of antimicrobial activity with MIC values ranging from 100 to 250 microg/mL, and IC50 values from 40.4 to 193.8 microg/mL. The oil also showed strong antioxidant activity, with an especially high metal chelating capacity of ferrous ions with an IC50 value of 7.4 microg/mL on ferrozine-Fe2+ complex formation.
Related JoVE Video
Why the OPLS-AA force field cannot produce the ?-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field?
J. Biomol. Struct. Dyn.
PUBLISHED: 11-10-2011
Show Abstract
Hide Abstract
The optimal combination of force field and water model is an essential problem that is able to increase molecular dynamics simulation quality for different types of proteins and peptides. In this work, an attempt has been made to explore the problem by studying H1 peptide using four different models based on different force fields, water models and electrostatic schemes. The driving force for H1 peptide conformation transition and the reason why the OPLS-AA force field cannot produce the ?-hairpin structure of H1 peptide in solution while the GROMOS 43A1 force field can do were investigated by temperature replica exchange molecular dynamics simulation (T-REMD). The simulation using the GROMOS 43A1 force field preferred to adopt a ?-hairpin structure, which was in good agreement with the several other simulations and the experimental evidences. However, the simulation using the OPLS-AA force field has a significant difference from the simulations with the GROMOS 43A1 force field simulation. The results show that the driving force in H1 peptide conformation transition is solvent exposure of its hydrophobic residues. However, the subtle balances between residue-residue interactions and residue-solvent interaction are disrupted by using the OPLS-AA force field, which induced the reduction in the number of residue-residue contact. Similar solvent exposure of the hydrophobic residues is observed for all the conformations sampled using the OPLS-AA force field. For H1 peptide which exhibits large solvent exposure of the hydrophobic residues, the GROMOS 43A1 force field with the SPC water model can provide more accurate results.
Related JoVE Video
[Research on the relationship of IgE between adenoid and middle ear effusion in children otitis media with effusion cases].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 09-29-2011
Show Abstract
Hide Abstract
To study the expression of IgE in recur repeatedly children otitis media with effusion (OME), and the relativity of IgE between adenoid and middle ear effusion.
Related JoVE Video
Effects of different force fields and temperatures on the structural character of abeta (12-28) Peptide in aqueous solution.
Int J Mol Sci
PUBLISHED: 07-22-2011
Show Abstract
Hide Abstract
The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of A? (12-28) peptide in aqueous solution. Moreover, the structural character of A? (12-28) peptide is compared with other amyloid peptides (such as H1 and ?-syn12 peptide). The two independent temperature replica exchange molecular dynamics (T-REMD) simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC). We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of ?-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of ?-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form ?-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form ?-hairpin with turn located at residues L17-F20.
Related JoVE Video
Even sampling designs generation by charges repulsion simulation.
Environ Monit Assess
PUBLISHED: 06-30-2011
Show Abstract
Hide Abstract
Evenly distributed sampling design is generally considered as an efficient sampling design. It is widely used in sampling for the environmental survey. In this paper, we present a novel method for generating N evenly distributed samples within a given irregular polygon via simulating the movements of some ideal homogeneous point charges. Initially, charges are randomly put into the sampling region; then, they are freed and held orderly; and after enough runs, the charges will finally reach a stable state with all of them having a zero resultant force and velocity; and so they distribute evenly within the region. Their layout can thus be considered as an evenly distributed sampling design. The main advantages of this method are: (1) it is easy to understand and implement; (2) it is efficient in both running and generating better designs. Analysis and experimental results indicate that this method is an efficient and robust method for generating even sampling designs for 2D polygonal sampling region.
Related JoVE Video
[Research on the serum levels of matrix metalloproteinase-9 and free fatty acids in OSAHS cases].
Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 05-11-2011
Show Abstract
Hide Abstract
To study the expression of matrix metalloproteinase-9 (MMP-9) and free fatty acids (FFA) in obstructive sleep apnea-hypopnea syndrome(OSAHS) patients. And the relativity among the serum level of MMP-9, FFA, four factors of blood lipids,hypopnea index (AHI), minimum oxygen saturation, body mass index (BMI) in OSAHS patients.
Related JoVE Video
Study and evaluation of Wondfo rapid diagnostic kit based on nano-gold immunochromatography assay for diagnosis of Plasmodium falciparum.
Parasitol. Res.
PUBLISHED: 04-25-2011
Show Abstract
Hide Abstract
Malaria has been recognized as a human disease for thousands of years and remains one of the most common diseases affecting humans worldwide. Therefore, a method for rapidly detecting Plasmodium falciparum is necessary and useful. We have developed Wondfo rapid diagnostic kit based on nano-gold immunochromatography assay for the detection of P. falciparum in patient specimen. In the present study, we demonstrated the sensitivity and specificity of the rapid diagnostic kit in which nano-gold labeling techniques and the monoclonal antibodies against histidine-rich protein-2 of P. falciparum were used to establish two-antibody sandwich immunochromatographic assay for detecting P. falciparum. By using microscopic examination of blood smears as control, the sensitivity, specificity, and feasibility of Wondfo rapid diagnostic kit was determined in the prompt and accurate diagnosis of malaria. In this study, 1,558 blood samples were collected from outpatient clinics in China and detected by both Wondfo kit and microscopic examination. The Wondfo kit did not show cross-reaction with microfilaria, Toxoplasma gondii, and other parasites in the blood. The patient samples positive for rheumatoid factor, HIV, tuberculosis, and syphilis did not show false positivity when testing with Wondfo kit. The detection sensitivity and specificity of Wondfo rapid diagnostic kit were 95.49% and 99.53%, respectively. These results indicate that our rapid diagnostic assay may be useful for detecting P. falciparum in patient specimen.
Related JoVE Video
Intravenous thrombolysis in Sneddons syndrome.
J Clin Neurosci
PUBLISHED: 04-21-2011
Show Abstract
Hide Abstract
Sneddons syndrome (SS) is an uncommon disorder, characterized by the association of ischemic stroke and widespread livedo reticularis. The treatment options for SS to prevent stroke recurrence and future disability include antiplatelet therapy, anticoagulation, or immunosuppression. We describe a patient with SS who presented with an acute ischemic stroke, and was treated with intravenous recombinant tissue-plasminogen activator with significant neurologic improvement. To our knowledge this is the first report of the use of thrombolysis in SS patients with acute ischemic stroke. It suggests that thrombolytic therapy might be safe and effective in these patients.
Related JoVE Video
Novel Strategies for Drug Discovery Based on Intrinsically Disordered Proteins (IDPs).
Int J Mol Sci
PUBLISHED: 04-01-2011
Show Abstract
Hide Abstract
Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. Numerous IDPs have close relationships with human diseases such as tumor, Parkinson disease, Alzheimer disease, diabetes, and so on. These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. Most of them in the disease datasets have more interactants and hence the size of the disease-associated IDPs interaction network is simultaneously increased. For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 interaction network; ?-synuclein, an intrinsically disordered protein involved in Parkinson diseases, is also a hub of the protein network. The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore, novel strategies for drug discovery based on IDPs are in the ascendant. It is dependent on the features of IDPs to develop the novel strategies. It is found out that IDPs have unique structural features such as high flexibility and random coil-like conformations which enable them to participate in both the "one to many" and "many to one" interaction. Accordingly, in order to promote novel strategies for drug discovery, it is essential that more and more features of IDPs are revealed by experimental and computing methods.
Related JoVE Video
Production and use of DDT containing antifouling paint resulted in high DDTs residue in three paint factory sites and two shipyard sites, China.
Chemosphere
PUBLISHED: 03-08-2011
Show Abstract
Hide Abstract
This study provides the first intensive investigation of Dichlorodiphenyltrichloroethanes (DDT) distribution in typical paint factories and shipyards in China where DDT containing antifouling paint were mass produced and used respectively. DDTs were analyzed in soil, sludge and sediment samples collected from three major paint factories and two shipyards. The results showed that the total DDTs concentrations detected in paint factory and shipyard sites ranged from 0.06 to 8387.24 mg kg(-1). In comparison with paint factory sites, the shipyard sites were much more seriously contaminated. However, for both kinds of sites, the DDTs level was found to be largely affected by history and capacity of production and use of DDT containing antifouling paint. (DDE+DDD)/DDT ratios indicated that DDT containing antifouling paint could serve as important fresh input sources for DDTs. It can be seen that most samples in shipyards were in ranges where heavy contamination and potential ecological risk were identified.
Related JoVE Video
Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution.
Acta Biochim. Biophys. Sin. (Shanghai)
PUBLISHED: 02-02-2011
Show Abstract
Hide Abstract
The structural and thermodynamics characters of ?-syn12 (residues 1-12 of the human ?-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational ?-helix and an irregular structure, respectively. Each replica was run for 300 ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded ?-hairpin structure, and favorite conformations. The results showed that the isolated ?-syn12 peptide in water adopted four different conformational states: the first state was a ?-hairpin ensemble with Turn(9-6) and four hydrogen bonds, the second state was a ?-hairpin ensemble with two turns (Turn(9-6) and Turn(5-2)) and three hydrogen bonds, the third state was a disordered structure with both Turn(8-5) and Turn(5-2), and the last state was a ?-helix ensemble. Meanwhile, we studied the free energy change of ?-syn12 peptide from the unfolded state to the ?-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition. The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated ?-syn12 peptide in water by T-REMD.
Related JoVE Video
Antifungal activity of the essential oil of Illicium verum fruit and its main component trans-anethole.
Molecules
PUBLISHED: 10-14-2010
Show Abstract
Hide Abstract
In order to identify natural products for plant disease control, the essential oil of star anise (Illicium verum Hook. f.) fruit was investigated for its antifungal activity on plant pathogenic fungi. The fruit essential oil obtained by hydro-distillation was analyzed for its chemical composition by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). trans-Anethole (89.5%), 2-(1-cyclopentenyl)-furan (0.9%) and cis-anethole (0.7%) were found to be the main components among 22 identified compounds, which accounted for 94.6% of the total oil. The antifungal activity of the oil and its main component trans-anethole against plant pathogenic fungi were determined. Both the essential oil and trans-anethole exhibited strong inhibitory effect against all test fungi indicating that most of the observed antifungal properties was due to the presence of trans-anethole in the oil, which could be developed as natural fungicides for plant disease control in fruit and vegetable preservation.
Related JoVE Video
Flavonoids from Halostachys caspica and their antimicrobial and antioxidant activities.
Molecules
PUBLISHED: 10-11-2010
Show Abstract
Hide Abstract
Seven flavonoids have been isolated from the aerial parts of Halostachys caspica C. A. Mey. (Chenopodiaceae) for the first time. By means of physicochemical and spectrometric analysis, they were identified as luteolin (1), chrysin (2), chrysin 7-O-?-D-glucopyranoside (3), quercetin (4), quercetin 3-O-?-D-glucopyranoside (5), isorhamentin-3-O-?-D-glucopyranoside (6), and isorhamentin-3-O-?-D-rutinoside (7). All flavonoids were evaluated to show a broad antimicrobial spectrum of activity on microorganisms including seven bacterial and one fungal species as well as pronounced antioxidant activity. Among them, the aglycones with relatively low polarity had stronger bioactivity than their glycosides. The results suggested that the isolated flavonoids could be used for future development of antimicrobial and antioxidant agents, and also provided additional data for supporting the use of H. caspica as forage.
Related JoVE Video
Effects of pH and temperature on the structural and thermodynamic character of alpha-syn12 peptide in aqueous solution.
J. Biomol. Struct. Dyn.
PUBLISHED: 10-06-2010
Show Abstract
Hide Abstract
The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and 10.0, respectively. Each replica was run for 300 ns. The structural and thermodynamic characters of alpha syn12 peptide were studied based on the distributions of backbone dihedral angles, the free energy surface, and the stability of different type structure and the favorite conformations of the peptide. The results showed that the simulation at pH = 10.0 produced more sampling in alpha region than the simulation at pH = 7.0. The temperature changes from 283 K to 308 K result in negligible effects on the distributions of backbone dihedral angle. The beta hairpin conformation with Turn(9-6) and four hydrogen bonds (HB(4-11), HB(6-9), HB(9-6) and HB(11-4)) is the lowest free energy state in the simulation at pH = 7.0. However, for the simulation at pH = 10.0, the lowest free energy state corresponds to a structure with Turn(9-6) and two hydrogen bonds (HB(6-10) and HB(10-6)) induced by an overly strong residue-residue interaction effect between lysine residues. For the simulation at pH = 7.0, the free energy change of the alpha-syn12 peptide from the unfolded state to the beta hairpin state was in good agreement with the experiments and molecular dynamics simulation results for the other beta-peptides, the beta hairpin state of the alpha-syn12 peptide included the conformations that not only the Turn(9-6) is formed, but also the terminus are closed together in space. However, the subtle balances between lysine-lysine interactions and lysine-solvent interaction are disrupted in the simulation at pH = 10.0, which induced the assembly of lysine residues, the beta hairpin conformation is destabilized by the deprotonation of the Lys side chain. This study can help us to understand the conformation changes and the thermodynamic character of alpha;-syn12 peptide at atomic level induced by changing pH and temperature, which is propitious to reveal the nosogenesis of Parkinson disease. In our knowledge, this is the first report to study the influence of pH and temperature on isolated alpha-syn12 peptide in water by T-REMD.
Related JoVE Video
Antimicrobial and antioxidant activities of the root bark essential oil of Periploca sepium and its main component 2-hydroxy-4-methoxybenzaldehyde.
Molecules
PUBLISHED: 08-05-2010
Show Abstract
Hide Abstract
The root bark essential oil of Periploca sepium Bunge (Asclepiadaceae/ Apocynaceae) obtained by hydrodistillation was investigated by GC and GC-MS. 2-Hydroxy-4-methoxybenzaldehyde was found to be the main component (78.8% of the total) among 17 identified compounds. 2-Hydroxy-4-methoxybenzaldehyde was separated and purified by preparative thin layer chromatography, and was further identified by means of physicochemical and spectrometric analysis. Both the essential oil and 2-hydroxy-4-methoxybenzaldehyde exhibited antimicrobial activities on all test bacteria and fungi, with MBC/MFC values ranging from 125 microg/mL to 300 microg/mL, MIC values from 80 microg/mL to 300 microg/mL, and IC(50) values from 63.29 microg/mL to 167.30 microg/mL. They also showed moderate antioxidant activity in the DPPH free radical scavenging, beta-carotene bleaching and ferrozine-ferrous ions assays. The results indicated that the major portion of these antimicrobial and antioxidant activities was due to the presence of 2-hydroxy-4-methoxy-benzaldehyde in the oil, which could potentially be developed as an antimicrobial and antioxidant agent in the future.
Related JoVE Video
Chemical analysis and biological activity of the essential oils of two valerianaceous species from China: Nardostachys chinensis and Valeriana officinalis.
Molecules
PUBLISHED: 07-30-2010
Show Abstract
Hide Abstract
In order to investigate essential oils with biological activity from local wild plants, two valerianaceous species, Nardostachys chinensis and Valeriana officinalis, were screened for their antimicrobial and antioxidant activity. The essential oils were obtained from the roots and rhizomes of the two plants by hydro-distillation, and were analyzed for their chemical composition by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Calarene (25.31%), aristolone (13.35%), ?-selinene (7.32%) and ?-maaliene (6.70%) were the major compounds of the 23 identified components which accounted for 92.76% of the total oil of N. chinensis. Patchoulol (16.75%), ?-pinene (14.81%), and ?-humulene (8.19%) were the major compounds among the 20 identified components, which accounted for 88.11% of the total oil of V. officinalis. Both oils were rich in sesquiterpene hydrocarbons as well as their oxygenated derivatives. Essential oils were shown to have broad spectrum antibacterial activity with MIC values that ranged from 62.5 ?g/mL to 400 ?g/mL, and IC(50) values from 36.93 ?g/mL to 374.72 ?g/mL. The oils were also shown to have moderate antifungal activity to Candida albicans growth as well as inhibition of spore germination of Magnaporthe oryzae. Two essential oils were assessed by 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, ?-carotene bleaching and ferrozine-ferrous ions assays, respectively, to show moderate antioxidant activity. Results suggest that the isolated essential oils could be used for future development of antimicrobial and antioxidant agents.
Related JoVE Video
Preparative separation of phenolic compounds from Halimodendron halodendron by high-speed counter-current chromatography.
Molecules
PUBLISHED: 07-30-2010
Show Abstract
Hide Abstract
Three phenolic compounds, p-hydroxybenzoic acid (1), isorhamnetin-3-O-?-D-rutinoside (2), and 3,3-di-O-methylquercetin (5), along with a phenolic mixture were successfully separated from the ethyl acetate crude extract of Halimodendron halodendron by high-speed counter-current chromatography (HSCCC) with chloroform-methanol-water-acetic acid (4:3:2:0.05, v/v) as the two-phase solvent system. The phenolic mixture from HSCCC was further separated by preparative HPLC and purified by Sephadex LH-20 to afford quercetin (3) and 3-O-methylquercetin (4). Seven hundred mg of ethyl acetate crude extract was separated by HSCCC to obtain six fractions which were then analyzed by high performance liquid chromatography (HPLC). The HSCCC separation obtained total of 80 mg of the mixture of quercetin (3) and 3-O-methylquercetin (4) (26.43% and 71.89%, respectively) in fraction 2, 14 mg of 3,3-di-O-methylquercetin (5) at 95.14% of purity in fraction 3, 15 mg of p-hydroxybenzoic acid (1) at 92.83% of purity in fraction 5, 12 mg of isorhamnetin-3-O-?-D-rutinoside (2) at 97.99% of purity in fraction 6. This is the first time these phenolic compounds have been obtained from H. halodendron, and their chemical structures identified by means of physicochemical and spectrometric analysis.
Related JoVE Video
Beauvericin from the endophytic fungus, Fusarium redolens, isolated from Dioscorea zingiberensis and its antibacterial activity.
Nat Prod Commun
PUBLISHED: 06-05-2010
Show Abstract
Hide Abstract
From the fungal endophyte, Fusarium redolens Dzf2, isolated from rhizomes of the Chinese medicinal plant Dioscorea zingiberensis, beauvericin was obtained by TLC in combination with bioautographic antibacterial assay. The compound was identified by spectroscopic and physicochemical means. The median effective inhibitory concentration (IC50) values of beauvericin against six test bacteria (Bacillus subtilis, Staphylococcus haemolyticus, Pseudomonas lachrymans, Agrobacterium tumefaciens, Escherichia coli and Xanthomonas vesicatoria) were between 18.4 and 70.7 microg/mL. The beauvericin content of F. redolens Dzf2 mycelia was 9.60 mg/g dw, and beauvericin yield 62.4 mg/L. The obtained results show the potential use of the endophytic fungus for its biological role in providing its host plant with protection, as well as the possible development of beauvericin as an antibacterial.
Related JoVE Video
Extraction of pesticides in water samples using vortex-assisted liquid-liquid microextraction.
J Chromatogr A
PUBLISHED: 06-02-2010
Show Abstract
Hide Abstract
A simple solvent microextraction method termed vortex-assisted liquid-liquid microextraction (VALLME) coupled with gas chromatography micro electron-capture detector (GC-microECD) has been developed and used for the pesticide residue analysis in water samples. In the VALLME method, aliquots of 30 microL toluene used as extraction solvent were directly injected into a 25 mL volumetric flask containing the water sample. The extraction solvent was dispersed into the water phase under vigorously shaking with the vortex. The parameters affecting the extraction efficiency of the proposed VALLME such as extraction solvent, vortex time, volumes of extraction solvent and salt addition were investigated. Under the optimum condition, enrichment factors (EFs) in a range of 835-1115 and limits of detection below 0.010 microg L(-1) were obtained for the determination of target pesticides in water. The calculated calibration curves provide high levels of linearity yielding correlation coefficients (r(2)) greater than 0.9958 with the concentration level ranged from 0.05 to 2.5 microg L(-1). Finally, the proposed method has been successfully applied to the determination of pesticides from real water samples and acceptable recoveries over the range of 72-106.3% were obtained.
Related JoVE Video
Isolation and identification of a putative scent-related gene RhMYB1 from rose.
Mol. Biol. Rep.
PUBLISHED: 02-09-2010
Show Abstract
Hide Abstract
Rose fragrances play an important role in attracting pollinators and commercial value. However, some genes involved in rose floral scent metabolism are less well understood. Here, wild-type scented rose (WR) and its spontaneous non-scented mutant rose (MR) were analyzed. SPME-GC/MS analysis showed that relative content of 1-ethenyl-4-methoxy-benzene represented was significantly different between WR and MR. We have isolated an EST encoding a MYB family of transcription factor from SSH libraries of the two roses in the previous studies, and designated RhMYB1. In the study, the full-length cDNA of RhMYB1 was identified and characterized by rapid amplification of cDNA ends (RACE). The RhMYB1 full-length cDNA was 1,125 bp containing an 882 bp open reading frame, which encodes a precursor protein of 294 amino acids. Sequence alignments revealed that RhMYB1 shared high similarity with other plants R-type MYB, and RhMYB1 contained a DNA binding domain. Northern blot analysis revealed that RhMYB1 was expressed specifically in flower petal, moreover, the expression level of RhMYB1 in WR increased along with scent emission, and decreased when the scent emission decreased. It is suggested that RhMYB1 might be a putative identification of gene involved in the biosynthesis of rose scent.
Related JoVE Video
A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations.
J. Biomol. Struct. Dyn.
PUBLISHED: 01-21-2010
Show Abstract
Hide Abstract
The dynamics and thermodynamics character of H1 peptide in aqueous solution has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations using two different force fields (OPLS-AA and GROMOS 43A1). The two independent T-REMD simulations were completed starting from initial conformations alpha-helix and beta-sheet, respectively. Each replica was run for 300 ns. The performance of each force field was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, root mean square deviations (RMSD) of C(alpha) atoms and all heavy atoms, formation of beta-turn, the stability of folded beta-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from alpha-helix structure sampled the conformation cluster which C(alpha) RMSD was 0.05 nm from beta-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in P(II)region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the alpha region, but the probabilities of the conformations including any helical content were only 1-2%. Under the both force fields, the beta-turn structures exhibited higher stability than alpha-helix structures and the folded beta-hairpin structures. In the GROMOS 43A1 force field, the free energy change from the unfolded state to the hairpin state was in good agreement with the results of several experiments about some beta-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded beta-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.
Related JoVE Video
Application of bioaugmentation in the rapid start-up and stable operation of biological processes for municipal wastewater treatment at low temperatures.
Bioresour. Technol.
PUBLISHED: 01-14-2010
Show Abstract
Hide Abstract
To accelerate the start-up of biological municipal wastewater treatment processes at low temperatures and ensure their daily stable performances, bioaugmentation was adopted with the addition of specialized mixed bacteria. As a result, three types of biological processes were successfully started within 15days and showed stable and efficient daily performances. Results of PCR-DGGE analysis demonstrated the long-term predominance of the bioaugmented specialized bacteria in the bioaugmented systems. And results of BIOLOG analysis showed that the bacterial community structure and catabolic capability of the biological systems varied with wastewater temperature variations. However, the stability of the bacterial community under normal operating conditions and adaptability to perturbations enabled the long-term stable and efficient performances of the biological systems. In conclusion, bioaugmentation was successful for rapid start-up and stable performances of three typical biological municipal wastewater treatment processes at low temperatures.
Related JoVE Video
Isoquinoline alkaloids from Macleaya cordata active against plant microbial pathogens.
Nat Prod Commun
PUBLISHED: 12-09-2009
Show Abstract
Hide Abstract
Bioassay-guided fractionation of the crude extract of the whole plant of Macleaya cordata R. Br. led to the isolation of four alkaloids, which were identified as sanguinarine (1), chelerythrine (2), protopine (3) and alpha-allocryptopine (4) on the basis of their physicochemical and spectrometric data. Compounds 1 and 2 demonstrated a significant antifungal activity against the six test fungi with median inhibitory concentrations (IC50) ranging from 0.47 to 6.13 microg/mL. Compound 1 was the most effective with an IC50 of 0.47 microg/mL on Rhizoctonia solani. Furthermore, compounds 1 and 2 also demonstrated strong antibacterial activity, with IC50 values ranging from 5.01 to 11.3 microg/mL, and minimum inhibitory concentrations (MIC) ranging from 8.0 to 32.0 microg/mL. This is the first report on the activity of the alkaloids from M. cordata against economically important phytopathogenic fungi and bacteria.
Related JoVE Video
Analysis of the changes of vegetation coverage of western Beijing mountainous areas using remote sensing and GIS.
Environ Monit Assess
PUBLISHED: 07-09-2009
Show Abstract
Hide Abstract
Mentougou District acts as a crucial component in the ecological buffer in western Beijing mountainous areas, Beijing, China. Using two Landsat MSS/TM images acquired on July 14, 1979 and July 23, 2005, the vegetation coverage of Mentougou District was calculated based on normalized difference vegetation index and spectral mixture analysis (NDVI-SMA) model. Its temporal and spatial changes were analyzed according to digital elevation model (DEM) image, social and economic data. The results showed that the vegetation coverage decreased from 76.4% in 1979 to 72.7% in 2005. Vegetation degradation was probably the result of human disturbance, such as outspreading of resident areas, and coal and stone mining activities, while vegetation restoration might be contributed by the combined effects of both natural processes and ecological construction effort. Vegetation changes were closely related to topographical characteristics. Plants at high altitude were more stable and less degraded than the plants at low altitude, while the plants on steep slope or northwest aspect were more vulnerable to degradation. During the period of 26 years, landscape appeared to become more fragmental, and ecological quality of the land seemed deteriorated sharply in that highly-covered vegetation area has been decreased by 24%.
Related JoVE Video
Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples.
Mol. Biol. Rep.
PUBLISHED: 06-23-2009
Show Abstract
Hide Abstract
We developed and evaluated the specificity and sensitivity of a loop-mediated isothermal amplification (LAMP) method for rapid detection of the food-borne Escherichia coli O157 strains. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on three targets, which were rfbE, stx1 and stx2. The detection limits were found to be 100, 100 and 10 fg DNA/tube for rfbE, stx1 and stx2, respectively. Application of LAMP assays were performed on 417 food-borne E. coli strains, the sensitivity of LAMP assays for the rfbE, stx1 and stx2 was 100, 95.3 and 96.3%, and the negative predictive value was 100, 96.7 and 97.1%, respectively; with a 100% specificity and positive predictive value for all three targets.
Related JoVE Video
Antimicrobial phenolic compounds from Anabasis aphylla L.
Nat Prod Commun
PUBLISHED: 05-06-2009
Show Abstract
Hide Abstract
Bioassay-guided fractionation of an ethyl acetate extract from the aerial parts of Anabasis aphylla, a Chenopodiaceous species widely distributed in the northwest of China, led to the isolation of six phenolic compounds, which were identified by means of spectrometric analysis as 1-(2-hydroxy-4,6-dimethoxyphenyl)-ethanone (1), 3,4-dihydroxy cinnamic acid tetracosyl ester (2), 4-hydroxy-3-methoxy benzoic acid (3), 2-hydroxy benzoic acid (4), 3,4-dihydroxy cinnamic acid methyl ester (5) and 4-hydroxy benzoic acid pentadecane ester (6). These compounds were further screened for their minimum inhibitory concentration (MIC) and median inhibitory concentration (IC50) by use of the micro-dilution-MTT assay for antimicrobial activity against one Gram-positive bacterium (Bacillus subtilis), three Gram-negative bacteria (Agrobacterium tumefaciens, Pseudomonas lachrymans, and Xanthomonas vesicatoria), and one yeast (Candida albicans). Apart from compound 6, which had no activity against any of the tested microorganisms, the other compounds showed selective inhibitory activity. This is the first report on the antimicrobial activity of the phenolic compounds isolated from A. aphylla. The obtained results provide promising baseline information for the potential use of the extract and some isolated compounds from this plant as antimicrobial agents to control plant and animal diseases.
Related JoVE Video
PRO-GRADE: GIS toolkits for ground water recharge and discharge estimation.
Ground Water
PUBLISHED: 03-10-2009
Show Abstract
Hide Abstract
PRO-GRADE is an ESRI ArcGIS 9.2 plug-in package that consists of two separate toolkits: (1) the pattern recognition organizer for geographic information system (PRO-GIS) and (2) the ground water recharge and discharge estimator for GIS (GRADE-GIS). PRO-GIS is a collection of several existing image-processing algorithms into one user interface to offer the flexibility to extract spatial patterns according to the users needs. GRADE-GIS is a ground water recharge and discharge estimation interface using a mass balance method that requires only hydraulic conductivity, water table, and bedrock elevation data for simulating two-dimensional steady-state unconfined aquifers. PRO-GRADE was developed to assist ongoing assessments of the water resources in Illinois and Wisconsin, and is being used to assist several ground water resource studies in several locations in the United States. The advantage of using PRO-GRADE is to enable fast production of initial recharge and discharge maps that can be further enhanced by using a follow-up ground water flow model with parameter estimation codes. PRO-GRADE leverages ArcGIS to provide a computer-assisted framework to support expert judgment in order to efficiently select alternative recharge and discharge maps that can be used as (1) guidelines for field study planning and decision making; (2) initial conditions for numerical simulation; and (3) screening for alternative model selection and prediction/parameter uncertainty evaluation. In addition, PRO-GRADE allows for more easy and rapid correlation of those maps with other hydrologically relevant geospatial data.
Related JoVE Video
Studying the unfolding process of protein G and protein L under physical property space.
BMC Bioinformatics
PUBLISHED: 01-30-2009
Show Abstract
Hide Abstract
The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topologies have been studied under Cartesian space and the results indicate that some proteins share the similar folding/unfolding characters.
Related JoVE Video
Development and evaluation of reverse-transcription loop-mediated isothermal amplification for rapid detection of human immunodeficiency virus type 1.
Indian J Med Microbiol
Show Abstract
Hide Abstract
The objective of this study was to establish a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of human immunodeficiency virus type 1 (HIV-1).
Related JoVE Video
Comparison of the structural characteristics of Cu(2+)-bound and unbound ?-syn12 peptide obtained in simulations using different force fields.
J Mol Model
Show Abstract
Hide Abstract
The effects of Cu(2+) binding and the utilization of different force fields when modeling the structural characteristics of ?-syn12 peptide were investigated. To this end, we performed extensive temperature replica exchange molecular dynamics (T-REMD) simulations on Cu(2+)-bound and unbound ?-syn12 peptide using the GROMOS 43A1, OPLS-AA, and AMBER03 force fields. Each replica was run for 300 ns. The structural characteristics of ?-syn12 peptide were studied based on backbone dihedral angle distributions, free-energy surfaces obtained with different reaction coordinates, favored conformations, the formation of different Turn structures, and the solvent exposure of the hydrophobic residues. The findings show that AMBER03 prefers to sample helical structures for the unbound ?-syn12 peptide and does not sample any ?-hairpin structure for the Cu(2+)-bound ?-syn12 peptide. In contrast, the central structure of the major conformational clusters for the Cu(2+)-bound and unbound ?-syn12 peptide according to simulations performed using the GROMOS 43A1 and OPLS-AA force fields is a ?-hairpin with Turn(9-6). Cu(2+) can also promote the formation of the ?-hairpin and increase the solvent exposure of hydrophobic residues, which promotes the aggregation of ?-syn12 peptide. This study can help us to understand the mechanisms through which Cu(2+) participates in the fibrillation of ?-syn12 peptide at the atomic level, which in turn represents a step towards elucidating the nosogenesis of Parkinsons disease.
Related JoVE Video
Phenolic Compounds from Halimodendron halodendron (Pall.) Voss and Their Antimicrobial and Antioxidant Activities.
Int J Mol Sci
Show Abstract
Hide Abstract
Halimodendron halodendron has been used as forage in northwestern China for a long time. Its young leaves and flowers are edible and favored by indigenous people. In this study, eleven phenolic compounds were bioassay-guided and isolated from the aerial parts of H. halodendron for the first time. They were identified by means of physicochemical and spectrometric analysis as quercetin (1), 3,5,7,8,4-pentahydroxy-3-methoxy flavone (2), 3-O-methylquercetin (3), 3,3-di-O-methylquercetin (4), 3,3-di-O-methylquercetin-7-O-?-d-glucopyranoside (5), isorhamentin-3-O-?-d-rutinoside (6), 8-O-methylretusin (7), 8-O-methylretusin-7-O-?-d-glucopyranoside (8), salicylic acid (9), p-hydroxybenzoic acid (ferulic acid) (10), and 4-hydroxy-3-methoxy cinnamic acid (11). They were sorted as flavonols (1-6), soflavones (7 and 8), and phenolic acids (9-11). Among the compounds, flanools 1-4 revealed a strong antibacterial activity with minimum inhibitory concentration (MIC) values of 50-150 ?g/mL, and median inhibitory concentration (IC(50)) values of 26.8-125.1 ?g/mL. The two isoflavones (7 and 8) showed moderate inhibitory activity on the test bacteria. Three phenolic acids (9, 10 and 11) showed strong antibacterial activity with IC(50) values of 28.1-149.7 ?g/mL. Antifungal activities of the compounds were similar to their antibacterial activities. All these phenolic compounds showed significant antimicrobial activity with a broad spectrum as well as antioxidant activity based on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging and ?-carotene-linoleic acid bleaching assays. In general, the flavonol aglycones with relatively low polarity exhibited stronger activities than the glycosides. The results suggest the potential of this plant as a source of functional food ingredients and provide support data for its utilization as forage as well.
Related JoVE Video
Microbial community analysis of three municipal wastewater treatment plants in winter and spring using culture-dependent and culture-independent methods.
World J. Microbiol. Biotechnol.
Show Abstract
Hide Abstract
Low temperatures can result in start-up and operational problems in wastewater treatment plants. The microbial community structures of three full-scale biological processes for municipal wastewater treatment, namely, anoxic-oxic activated sludge (A/O) process, oxidation ditch, and sequencing batch reactor, in winter and spring were investigated. The performances of the three biological processes were all stable during winter and spring. Comparing all three plants, the NH(4) (+)-N removal efficiency using the A/O process was found to be the highest during both winter and spring. According to the similarity coefficient of the polymerase chain reaction and denaturing gradient gel electrophoresis analysis determined via the culture-independent method, the microbial community structure is the most stable using the A/O process at different temperatures. The dominant members primarily belonged to Proteobacteria, Nitrospira, and Bacteroidetes. In addition, Proteobacteria was the dominant member in the activated sludge utilizing peptone, glucose, and fatty acid. Compared with other biological processes, the A/O process was superior at low temperatures based on its pollution removal performance and stable microbial community sturcture.
Related JoVE Video
Upregulation of Gp96 correlates with the radiosensitivity and five-year survival rate of nasopharyngeal carcinoma.
ORL J. Otorhinolaryngol. Relat. Spec.
Show Abstract
Hide Abstract
Gp96 (GRP94) is a chaperone that is responsible for molecular folding and assembly of proteins. To investigate correlations among Gp96 expression, sensitivity to radiotherapy and clinical features of nasopharyngeal carcinoma (NPC), the expression of Gp96 in 98 NPC samples was analyzed by immunohistochemistry and Western blotting at the protein level, and by real-time PCR at the mRNA level. Clinicopathological features, including stage, sex, grade and survival, were compared between the high and low Gp96 expression groups. As a result, Gp96 was expressed at a higher level in NPC tissues than in noncancerous nasopharyngeal mucosa (p = 0.001). Univariate analysis suggested that a higher Gp96 expression level was associated with significantly decreased disease-free and 5-year survival rates (p = 0.000, p = 0.000, respectively). Multivariate Cox proportional-hazard regression analysis, which adjusts for clinicopathological variables, indicated that it was only associated with the 5-year overall survival rate (p = 0.002). Furthermore, patients with high Gp96 expression levels were significantly more resistant to radiotherapy (p = 0.001). These data are the first indication of a positive correlation between Gp96 expression levels and radiosensitivity and 5-year survival rate. Gp96 might serve as a novel candidate marker for predicting the long-term prognostic outcome of NPC.
Related JoVE Video
Multivariate and geostatistical analyses of the spatial distribution and origin of heavy metals in the agricultural soils in Shunyi, Beijing, China.
Sci. Total Environ.
Show Abstract
Hide Abstract
An extensive survey was conducted in this study to determine the spatial distribution and possible sources of heavy metals in the agricultural soils in Shunyi, a representative agricultural suburb in Beijing, China. A total of 412 surface soil samples were collected at a density of one sample per km(2), and concentrations of As, Cd, Cu, Hg, Pb and Zn were analyzed. The mean values of the heavy metals were 7.85±2.13, 0.136±0.061, 22.4±6.31, 0.073±0.049, 20.4±5.2, and 69.8±16.5 mg kg(-1) for As, Cd, Cu, Hg, Pb, and Zn, respectively, slightly higher than their background values of Beijing topsoil with the exception of Pb, but lower than the guideline values of Chinese Environmental Quality Standard for Soils. Multivariate and geostatistical analyses suggested that soil contamination of Cd, Cu and Zn was mainly derived from agricultural practices. Whereas, As and Pb were due mainly to soil parent materials, and Hg was caused by the atmospheric deposits from Beijing City. The identification of heavy metal sources in agricultural soils is a basis for undertaking appropriate action to protect soil quality.
Related JoVE Video
The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation.
Int J Mol Sci
Show Abstract
Hide Abstract
To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.
Related JoVE Video
Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z.
J Mol Model
Show Abstract
Hide Abstract
Aquaporin Z (AQPZ) is a tetrameric protein that forms water channels in the cell membrane of Escherichia coli. The histidine residue (residue 174) in the selectivity filter (SF) region plays an important role in the transport of water across the membrane. In this work, we perform equilibrium molecular dynamics (MD) simulations to illustrate the gating mechanism of the SF and the influences of residue 174 in two different protonation states: Hsd174 with the proton at N?, and Hse174 with the proton at N?. We calculate the pore radii in the SF region versus the simulation time. We perform steered MD to compute the free-energy profile, i.e., the potential of mean force (PMF) of a water molecule through the SF region. We conduct a quantum mechanics calculation of the binding energy of one water molecule with the residues in the SF region. The hydrogen bonds formed between the side chain of Hsd174 and the side chain of residue 189 (Arg189) play important roles in the selectivity mechanism of AQPZ. The radii of the pores, the hydrogen-bond analysis, and the free energies show that it is easier for water molecules to permeate through the SF region of AQPZ with residue 174 in the Hse state than in the Hsd state.
Related JoVE Video

What is Visualize?

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

How does it work?

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

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

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