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162. Patients with amyotrophic lateral sclerosis have specific denervation patterns
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Introduction: First dorsal interoseous (FDI) atrophy is an early abnormal sign in amyotrophic lateral sclerosis (ALS). Animal models suggest early compromise of fast fatigueable distal muscles. The authors query whether specific needle electromyography (EMG) denervation patterns (e.g., fibrillations [Fbs], positive sharp waves, fasciculations [Fs], polyphasia, decreased recruitment) are characteristic of ALS.
Source: Clinical Neurophysiology - May 25, 2012 Category: Neuroscience Authors: D.B. Rosenfield, M. Al Beear, S.H. Appel, E. Caballero Tags: Abstracts Source Type: research
Use of an Electronic Survey Instrument to Determine Barriers to Certification in Infection ControlEmail this article to a colleague.
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One of our chapter goals for 2011 was to increase certification among our membership. To determine how to best assist members to achieve and/or maintain certification, the APIC-NNJ Board decided to query the membership. A survey was designed to identify barriers to certification for our members, their preferences for overcoming these barriers, and ascertain the value of certification to our members and their employers.
Source: American Journal of Infection Control - May 24, 2012 Category: Infectious Diseases Authors: Anne Maher, Nancy Kerr, Laura Anderson, Norma Atienza, Jane Badaracco, Vicki DeChirico, Mary Ann Kellar, Judith Leschek, Romeo P. Mamon Tags: Staff Training/Competency/Compliance Source Type: research
Nigeria: Sacked Doctors Have Started AppealingEmail this article to a colleague.
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[This Day]
Lagos State Government yesterday claimed that some of the dismissed doctors had started appealing and responding to the query issued them, questioning their strike embarked by them.
Source: AllAfrica News: Health and Medicine - May 24, 2012 Category: African Health Source Type: news
LIPOPREDICT: Bacterial lipoprotein prediction server.Email this article to a colleague.
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Abstract
Bacterial lipoproteins have many important functions owing to their essential nature and roles in pathogenesis and represent a class of possible vaccine candidates. The prediction of bacterial lipoproteins from sequence is thus an important task for computational vaccinology. A Support Vector Machines (SVM) based module for predicting bacterial lipoproteins, LIPOPREDICT, has been developed. The best performing sequence model were generated using selected dipeptide composition, which gave 97% accuracy of prediction. The results obtained were compared very well with those of previously developed methods. AVA...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Kumari SR, Kadam K, Badwaik R, Jayaraman VK Tags: Bioinformation Source Type: research
MEDDB: A medicinal plant database developed with the information gathered from tribal people in and around Madurai, Tamil Nadu.Email this article to a colleague.
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Abstract
Tribal peoples are endowed with enriched traditional wisdom to use available nature resources around them. They are well versed in the usage of plant for treating various diseases. They have used powder or extract or paste form of the plant parts such as root, shoot, whole plant, fruits and leaves etc. The recipe known by the tribal people was passed on only to their family members and community through mouth to mouth practice. Hence, the knowledge is confined to particular people alone. It is always expedient to store information in the database, so that it will be accessible by everyone from everywhere. ...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Mary JA, Priyadharshini KC, Amal GP, Ramya G, Nithya R, Ambika MB, Shenbagarathai R Tags: Bioinformation Source Type: research
HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.Email this article to a colleague.
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Abstract
Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Yin L, Yao J, Gardner BP, Chang K, Yu F, Goodenow MM Tags: Bioinformation Source Type: research
3D-QSAR studies on fluroquinolones derivatives as inhibitors for tuberculosis.Email this article to a colleague.
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Abstract
A quantitative structure activity relationship (QSAR) study was performed on the fluroquinolones known to have anti-tuberculosis activity. The 3D-QSAR models were generated using stepwise variable selection of the four methods - multiple regression (MR), partial least square regression (PLSR), principal component regression (PCR) and artificial neural networks (kNN-MFA). The statistical result showed a significant correlation coefficient q(2) (90%) for MR model and an external test set of (pred_r(2)) -1.7535, though the external predictivity showed to improve using kNN-MFA method with pred_r(2) of -0.4644....
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Bhattacharjee A, Mylliemngap BJ, Velmurugan D Tags: Bioinformation Source Type: research
Molecular modeling and evaluation of binding mode and affinity of artemisinin-quinine hybrid and its congeners with Fe-protoporphyrin-IX as a putative receptor.Email this article to a colleague.
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Abstract
A recent rational approach to anti-malarial drug design is characterized as "covalent biotherapy" involves linking of two molecules with individual intrinsic activity into a single agent, thus packaging dual activity into a single hybrid molecule. In view of this background and reported anti malaria synergism between artemisinin and quinine; we describe the computer-assisted docking to predict molecular interaction and binding affinity of Artemisinin-Quinine hybrid and its derivatives with the intraparasitic haeme group of human haemoglobin. Starting from a crystallographic structure of Fe-protoporphyrin-I...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Mahapatra RK, Behera N, Naik PK Tags: Bioinformation Source Type: research
Automation of a primer design and evaluation pipeline for subsequent sequencing of the coding regions of all human Refseq genes.Email this article to a colleague.
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Abstract
Screening for mutations in human disease-causing genes in a molecular diagnostic environment demands simplicity with a view to allowing high throughput approaches. In order to advance these requirements, we have developed and applied a primer design program, termed BatchPD, to achieve the PCR amplification of coding exons of all known human Refseq genes. Primer design, in silico PCR checks and formatted primer information for subsequent web-based interrogation are queried from existing online tools. BatchPD acts as an intermediate to automate queries and results processing and provides exon-specific inform...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Lai D, Love DR Tags: Bioinformation Source Type: research
Relevance of systems biological approach in the differential diagnosis of invasive lobular carcinoma & invasive ductal carcinoma.Email this article to a colleague.
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Relevance of systems biological approach in the differential diagnosis of invasive lobular carcinoma & invasive ductal carcinoma.
Bioinformation. 2012;8(8):359-64
Authors: Ragunath P, Reddy BV, Abhinand P, Ahmed SS
Abstract
Breast cancer is a malignant neoplasm originating from breast tissue, most commonly from the inner lining of milk ducts or the lobules that supply the ducts with milk. ILCs and IDCs vary from each other with respect to various histological, biological and clinical features. Remarkably, ductal tumors tending to form glandular structures, whereas lobular tumors are less cohesive and te...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Ragunath P, Reddy BV, Abhinand P, Ahmed SS Tags: Bioinformation Source Type: research
Comparative QSAR analysis of cyclo-oxygenase2 inhibiting drugs.Email this article to a colleague.
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This study shall help in rational drug design and synthesis of new selective cyclo-oxygenase 2 inhibitors with predetermined affinity and activity.
PMID: 22570515 [PubMed - in process]
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Mohanapriya A, Achuthan D Tags: Bioinformation Source Type: research
Designing cyclopentapeptide inhibitor as potential antiviral drug for dengue virus ns5 methyltransferase.Email this article to a colleague.
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This study was conducted to design cyclic peptide ligands as enzyme inhibitors of dengue virus NS5 Mtase through computational approach. Cyclopentapeptides were designed as ligand of SAM binding site as much as 1635 and 736 cyclopentpeptides were designed as ligand of RNA-cap binding site. Interaction between ligand and NS5 Mtase has been conducted on the Docking simulation. The result shows that cyclopentapeptide CTWYC was the best peptide candidate on SAM binding site, with estimated free binding energy -30.72 kca/mol. Cyclopentapeptide CYEFC was the best peptide on RNA-cap binding site with estimated free binding energy...
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Idrus S, Tambunan US, Zubaidi AA Tags: Bioinformation Source Type: research
Analysis of aminoacids pattern in receptor tyrosine kinase using Boolean Association Rule.Email this article to a colleague.
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In conclusion, results from this study supports our hypothesis that cancer cells may resemble lower organisms since functionally cancer cells are unresponsive to external signals and various regulatory mechanisms typically found in higher eukaryotes are largely absent.
PMID: 22570513 [PubMed - in process]
Source: Bioinformation - May 19, 2012 Category: Bioinformatics Authors: Kalita P, Kumar BS, Krishnaswamy S, Nachimuthu SK Tags: Bioinformation Source Type: research
RCDB: Renal Cancer Gene DatabaseEmail this article to a colleague.
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Conclusions:
It is hoped that this database would serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in RCC genetics.
Source: BMC Research Notes - May 18, 2012 Category: Research Authors: Jayashree Ramana Source Type: research
Google goes cancer: Search engine algorithm finds cancer biomarkersEmail this article to a colleague.
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The strategy used by Google to decide which pages are relevant for a search query can also be used to determine which proteins in a patient's cancer are relevant for the disease progression.
Source: ScienceDaily Headlines - May 17, 2012 Category: Science Source Type: news
Google goes cancer: Researchers use search engine algorithm to find cancer biomarkersEmail this article to a colleague.
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(Public Library of Science) The strategy used by Google to decide which pages are relevant for a search query can also be used to determine which proteins in a patient's cancer are relevant for the disease progression.
Source: EurekAlert! - Cancer - May 17, 2012 Category: Cancer & Oncology Source Type: news
Children Injured by Violence in the United States: Emergency Department Utilization, 2000–2008Email this article to a colleague.
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Conclusions: ED visits among children for violent injury still represent an important clinical, public health, and economic challenge. The ED could be considered as a potential venue for prevention and intervention efforts.
Source: Academic Emergency Medicine - May 17, 2012 Category: Emergency Medicine Authors: Michael C. Monuteaux, Lois Lee, Eric Fleegler Source Type: research
Patterns of compliance with prenatal iron supplementation among Peruvian womenEmail this article to a colleague.
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In conclusion, women comply highly with prenatal supplementation within a prenatal care model in which supplies are maintained and reinforcing messages are provided.
Source: Maternal and Child Nutrition - May 16, 2012 Category: Nutrition Authors: Nelly Zavaleta, Laura E. Caulfield, Alberto Figueroa, Ping Chen Source Type: research
A Protein Block based Fold Recognition method for the Annotation of Twilight Zone Sequences.Email this article to a colleague.
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Abstract
The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications. Here, we present a...
Source: Protein and Peptide Letters - May 16, 2012 Category: Biochemistry Authors: Suresh V, Ganesan K, Parthasarathy S Tags: Protein Pept Lett Source Type: research
Detecting internet activity for erectile dysfunction using search engine query data in the Republic of IrelandEmail this article to a colleague.
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CONCLUSIONS• The advent of recent Internet media campaigns and increasing number of Irish web pages is associated with a significant increase in online activity for ED in the Republic of Ireland.• Novel online technologies appear to provide a useful tool for educating the general public on the symptoms and treatment options available for ED.
Source: BJU International - May 15, 2012 Category: Urology & Nephrology Authors: Niall F. Davis, Lisa G. Smyth, Hugh D. Flood Source Type: research
CytoITMprobe: a network information flow plugin for CytoscapeEmail this article to a colleague.
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Conclusions:
The main strength of CytoITMprobe is its flexibility. It allows the user to specify as input any Cytoscape network, rather than being restricted to the pre-compiled protein-protein interaction networks available through the ITM Probe web service. Users may supply their own edge weights and directionalities. Consequently, as opposed to ITM Probe web service, CytoITMprobe can be applied to many other domains of network-based research beyond protein-networks. It also enables seamless integration of ITM Probe results with other Cytoscape plugins having complementary functionality for data analysis.
Source: BMC Research Notes - May 15, 2012 Category: Research Authors: Aleksandar StojmirovicAlexander BliskovskyYi-Kuo Yu Source Type: research
Solid Organ Transplant Recipients Presenting for Mohs Micrographic Surgery: A Retrospective Case–Control StudyEmail this article to a colleague.
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ConclusionsSOTR referred for MMS have disproportionately more and different types of skin cancers than controls.
Source: Dermatologic Surgery - May 15, 2012 Category: Dermatology Authors: Edward Upjohn, Rafia Bhore, R. Stan Taylor Tags: Original Article Source Type: research
Ligand‐Based Virtual Screening and Molecular Docking Studies to Identify the Critical Chemical Features of Potent Cathepsin D InhibitorsEmail this article to a colleague.
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Cathepsin D is a major component of lysosomes and plays a major role in catabolism and degenerative diseases. The quantitative structure–activity relationship study was used to explore the critical chemical features of cathepsin D inhibitors. Top 10 hypotheses were built based on 36 known cathepsin D inhibitors using HypoGen/Discovery Studio v2.5. The best hypothesis Hypo1 consists of three hydrophobic, one hydrogen bond acceptor lipid, and one hydrogen bond acceptor features. The selected Hypo1 model was cross‐validated using Fischer’s randomization method to identify the strong correlation between experimental and ...
Source: Chemical Biology and Drug Design - May 14, 2012 Category: Biology Authors: Sugunadevi Sakkiah, Sundarapandian Thangapandian, Keun Woo Lee Tags: Research Article Source Type: research
SIS: a program to generate draft genome sequence
scaffolds for prokaryotesEmail this article to a colleague.
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Conclusions:
SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-aloneand as a web server. The good performance of SIS in our tests adds evidence thatlarge-scale inversions are widespread in prokaryotic genomes.
Source: BMC Bioinformatics - Latest articles - May 14, 2012 Category: Bioinformatics Authors: Zanoni DiasUlisses DiasJoao Setubal Source Type: research
3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparisonEmail this article to a colleague.
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Conclusions:
The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible molecularshape comparison and enhance navigation for user's interaction. 3DMolNavi can be accessed viahttps://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
Source: BMC Bioinformatics - Latest articles - May 14, 2012 Category: Bioinformatics Authors: Yu-Shen LiuMeng WangJean-Claude PaulKarthik Ramani Source Type: research
Informatics in Radiology: Use of CouchDB for Document-based Storage of DICOM Objects [Informatics]Email this article to a colleague.
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Picture archiving and communication systems traditionally have depended on schema-based Structured Query Language (SQL) databases for imaging data management. To optimize database size and performance, many such systems store a reduced set of Digital Imaging and Communications in Medicine (DICOM) metadata, discarding informational content that might be needed in the future. As an alternative to traditional database systems, document-based key-value stores recently have gained popularity. These systems store documents containing key-value pairs that facilitate data searches without predefined schemas. Document-based key-val...
Source: Radiographics recent issues - May 11, 2012 Category: Radiology Authors: Rascovsky, S. J., Delgado, J. A., Sanz, A., Calvo, V. D., Castrillon, G. Tags: Informatics Source Type: research
MFG-E8 Released by Apoptotic Endothelial Cells Triggers Anti-Inflammatory Macrophage Reprogramming.Email this article to a colleague.
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In this study, we report that apoptosis of human and mouse endothelial cells triggers the release of milk fat globule-epidermal growth factor 8 (MFG-E8) and reprograms macrophages into an anti-inflammatory cells. We demonstrated that MFG-E8 is released by apoptotic endothelial cells in a caspase-3-dependent manner. When macrophages were exposed to conditioned media from serum-starved apoptotic endothelial cells, they adopt a high anti-inflammatory, low pro-inflammatory cytokine/chemokine secreting phenotype that is lost if MFG-E8 is absent from the media. Macrophage treatment with recombinant MFG-E8 recapitulates the effec...
Source: Atherosclerosis - May 10, 2012 Category: Cardiology Authors: Brissette MJ, Lepage S, Lamonde AS, Sirois I, Groleau J, Laurin LP, Cailhier JF Tags: PLoS One Source Type: research
Hematopoietic miR155 Deficiency Enhances Atherosclerosis and Decreases Plaque Stability in Hyperlipidemic Mice.Email this article to a colleague.
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In conclusion, in this hyperlipidemic mouse model miR155 acts as an anti-inflammatory, atheroprotective microRNA. Additionally, besides a known role in lymphoid cell development, we show a crucial role of miR155 in myeloid lineage differentiation.
PMID: 22558252 [PubMed - in process]
Source: Atherosclerosis - May 10, 2012 Category: Cardiology Authors: Donners MM, Wolfs IM, Stöger LJ, van der Vorst EP, Pöttgens CC, Heymans S, Schroen B, Gijbels MJ, de Winther MP Tags: PLoS One Source Type: research
Hyperlipidemia and atherosclerotic lesion development in ldlr-deficient mice on a long-term high-fat diet.Email this article to a colleague.
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CONCLUSIONS/SIGNIFICANCE: Ldlr-deficient mice on the HF diet tend to develop site-selective and size-specific atherosclerotic lesions over time. The current study should provide information on diet induction or drug intervention times and facilitate estimation of the appropriate locations of atherosclerotic lesions in Ldlr(-/-) mice.
PMID: 22558236 [PubMed - in process]
Source: Atherosclerosis - May 10, 2012 Category: Cardiology Authors: Ma Y, Wang W, Zhang J, Lu Y, Wu W, Yan H, Wang Y Tags: PLoS One Source Type: research
Connection between Telomerase Activity in PBMC and Markers of Inflammation and Endothelial Dysfunction in Patients with Metabolic Syndrome.Email this article to a colleague.
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In conclusion, in patients with MS characterised by a strong dyslipidemic profile and low diabetes prevalence, significant telomerase activity was detected in circulating PBMC, along with elevated markers of inflammation and endothelial dysfunction. These findings suggest a prolonged activity of inflammatory cells in the studied state of this metabolic disorder that could represent a contributory pathway in the pathogenesis of atherosclerosis.
PMID: 22558213 [PubMed - in process]
Source: Atherosclerosis - May 10, 2012 Category: Cardiology Authors: Rentoukas E, Tsarouhas K, Kaplanis I, Korou E, Nikolaou M, Marathonitis G, Kokkinou S, Haliassos A, Mamalaki A, Kouretas D, Tsitsimpikou C Tags: PLoS One Source Type: research
ProteinTracker: an application for managing protein production and purificationEmail this article to a colleague.
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Conclusions:
ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.
Source: BMC Research Notes - May 10, 2012 Category: Research Authors: Stefan PonkoDavid Bienvenue Source Type: research
A comparative evaluation of sequence classification programsEmail this article to a colleague.
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Conclusions:
We found significant variability in classification accuracy, precision, and resource consumption of sequenceclassification programs when used to analyze various metagenomics data sets. However, we observe somegeneral trends and patterns that will be useful to researchers who use sequence classification programs.
Source: BMC Bioinformatics - Latest articles - May 10, 2012 Category: Bioinformatics Authors: Adam BazinetMichael Cummings Source Type: research
The Prognostic Value of suPAR Compared to Other Inflammatory Markers in Patients with Severe Sepsis.Email this article to a colleague.
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Abstract
It has been suggested that soluble urokinase plasminogen activator (suPAR) can be used as a marker of disease severity and risk of mortality in sepsis. The aim with the present study was to compare plasma levels of suPAR in patients with severe sepsis to control subjects and correlate it with the level of inflammatory activation, severity and mortality. Samples were collected from 27 sepsis patients at the intensive care unit (ICU), Lund, Sweden; 90-day mortalities were registered. The suPAR level was significantly elevated in sepsis patients compared to controls, but not significantly higher in nonsurvivo...
Source: Biomarker Insights - May 9, 2012 Category: Journals (General) Authors: Gustafsson A, Ljunggren L, Bodelsson M, Berkestedt I Tags: Biomark Insights Source Type: research
Mining Gene Ontology Data with AGENDA.Email this article to a colleague.
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Abstract
The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-base...
Source: Bioinformatics and Biology Insights - May 9, 2012 Category: Bioinformatics Authors: Ovezmyradov G, Lu Q, Göpfert MC Tags: Bioinform Biol Insights Source Type: research
White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection.Email this article to a colleague.
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Abstract
Acute cardiac allograft rejection is a serious complication of heart transplantation. Investigating molecular processes in whole blood via microarrays is a promising avenue of research in transplantation, particularly due to the non-invasive nature of blood sampling. However, whole blood is a complex tissue and the consequent heterogeneity in composition amongst samples is ignored in traditional microarray analysis. This complicates the biological interpretation of microarray data. Here we have applied a statistical deconvolution approach, cell-specific significance analysis of microarrays (csSAM), to whol...
Source: Bioinformatics and Biology Insights - May 9, 2012 Category: Bioinformatics Authors: Shannon CP, Hollander Z, Wilson-McManus J, Balshaw R, Ng RT, McMaster R, McManus BM, Keown PA, Tebbutt SJ Tags: Bioinform Biol Insights Source Type: research
PhyLAT: a phylogenetic local alignment toolEmail this article to a colleague.
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Motivation: The expansion of DNA sequencing capacity has enabled the sequencing of whole genomes from a number of related species. These genomes can be combined in a multiple alignment that provides useful information about the evolutionary history at each genomic locus. One area in which evolutionary information can productively be exploited is in aligning a new sequence to a database of existing, aligned genomes. However, existing high-throughput alignment tools are not designed to work effectively with multiple genome alignments.
Results: We introduce PhyLAT, the phylogenetic local alignment tool, to compute local align...
Source: Bioinformatics - May 9, 2012 Category: Bioinformatics Authors: Sun, H., Buhler, J. D. Tags: SEQUENCE ANALYSIS Source Type: research
VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program.Email this article to a colleague.
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Abstract
Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs. One of the beneficial properties of the VMD is its ability to be extendable by designing new plug-in. We introduce here a new facility of the VMD for distance analysis and radius of gyration of biopolymers such as protein and DNA. AVAILABILITY: The database is available for free at http://trc.ajums.ac.ir/HomePage.aspx/?TabID/=12618/&Site/=t...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Falsafi-Zadeh S, Karimi Z, Galehdari H Tags: Bioinformation Source Type: research
Comparative modeling of CCRL1, a key protein in masked immune diseases and virtual screening for finding inhibitor of this protein.Email this article to a colleague.
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In this study we predicted 3D structure of CCRL1 using comparative modeling and Hiddebn Markov Model algorithm. Final predicted model optimized by Modeller v9.8 and minimized regarding energy level using UCSF chimera candidate version1.5.3. ClasPro webserver was used to find interacting residues between CCRL1 and CCL21. Interacting residues were used as target for chemical inhibitors by simulated docking study. For finding potential inhibitors, library of KEGG compounds screened and 97 obtained chemicals docked against interacting residues between CCRL1- CCL21 and MolDock was used as docking scoring function. Results indic...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Behjati M, Torktaz I, Mohammadpour M, Ahmadian G, Easton AJ Tags: Bioinformation Source Type: research
Receptor modification as a therapeutic approach against viral diseases.Email this article to a colleague.
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This study will play an important role for bridging computational biology to other fields of applied biology and also will provide an insight to develop resistance against viral diseases. It is also expected that same approach can also be applicable against other viruses like HCV, HIV and other in near future.
PMID: 22553391 [PubMed - in process]
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Farid R, Khan MH, Rashid H Tags: Bioinformation Source Type: research
Isolation and characterization of protease producing bacteria from upper respiratory tract of wild chicken.Email this article to a colleague.
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Abstract
Bacterial samples isolated from the upper respiratory tract of a healthy broiler chicken and a wild chicken suffering from influenza which were collected locally revealed proteolytic activity as detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and zymogram analysis. Among five protease producing strains screened, one was selected as promising protease producer. The activity of the protease produced by this organism is stable up to 620C. Optimum yield was achieved after 19 hours of culture, at pH 9.0 and 450C. The desired protein was precipitated from the crude extract by usi...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Raut S, Sen SK, Kabir NA, Satpathy S, Raut S Tags: Bioinformation Source Type: research
Virtual screening and in vitro assay of potential drug like inhibitors from spices against Glutathione-S-Transferase of Meloidogyne incognita.Email this article to a colleague.
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Abstract
Glutathione S-transferases (GSTs) enzymes are critical antioxidant and detoxification system responsible for long-term existence of nematodes in host species. Hence, 16 phytochemicals predicted and reported to have potential nematicidal activity have been docked to GST enzyme of Meloidogyne incognita to assess their binding affinity and inhibitory activity. In vitro effects of these phytochemicals from in silico results have been done for validation of docking studies and efficacy in GST inhibition of following compounds such as alpha- pinene, alpha- terpineol, beta- caryophyllene, capsaicin, cinnamic acid...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Babu RO, Moorkoth D, Azeez S, Eapen SJ Tags: Bioinformation Source Type: research
Sequence and structure based assessment of nonsynonymous SNPs in hypertrichosis universalis.Email this article to a colleague.
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Abstract
Hairs are complex structures, making a protective layer and serves different biological functions. TRPS1, a transcription factor is one of the candidate genes causing congenital hypertrichosis, an excessive hair growth at inappropriate body parts. SNPs of TRPS1 were retrieved from dbSNP which were screened by SIFT and PolyPhen servers based on their functional impacts. Out of the screened SNPs, rs181507248 and rs146506752 were predicted as intolerant and damaging by both the servers. The predicted tertiary structure of the native TRPS1 after refinement and validation was successfully submitted to the Prote...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Waheed R, Khan MH, Bano R, Rashid H Tags: Bioinformation Source Type: research
Categorization of metabolome in bacterial systems.Email this article to a colleague.
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In this study, metabolome of bacterial systems with reliable annotations are analyzed and a simple method is developed to categorize pathways hierarchically, using rational approach. Ninety-four bacterial systems having for each ≥ 250 annotated metabolic pathways were used to identify a set of common pathways. 42 pathways were present in all bacteria which are termed as Core/Stage I pathways. This set of pathways was used along with interacting compounds to categorize pathways in the metabolome hierarchically. In each metabolome non-interacting pathways were identified including at each stage. The case study of Escherich...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Kolhi S, Kolaskar AS Tags: Bioinformation Source Type: research
Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies.Email this article to a colleague.
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In this study, chemical feature based pharmacophore models of MMP-1, MMP-8 and MMP-13 inhibitors have been developed with the aid of HypoGen module within Catalyst program package. In MMP-1 and MMP-13, all the compounds in the training set mapped HBA and RA, while in MMP-8, the training set mapped HBA and HY. These features revealed responsibility for the high molecular bioactivity, and this is further used as a three dimensional query to screen the knowledge based designed molecules. These pharmacophore models for collagenases picked up some potent and novel inhibitors. Subsequently, docking studies were performed for the...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Kalva S, Vadivelan S, Sanam R, Jagarlapudi SA, Saleena LM Tags: Bioinformation Source Type: research
Homology modeling, docking studies and functional analysis of various azoreductase accessory interacting proteins of Nostoc sp.PCC7120.Email this article to a colleague.
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Abstract
Azo dyes have become a threat to public health because of its toxicity and carcinogenicity. Azoreductase enzyme plays a pivotal role in the degradation of azodyes released by industrial effluents and other resources. The degradation pathway has to be studied in detail for increasing the activity of azoreductase and for better degradation of azo dyes. But the data available on cyanobacterial azoreductase enzyme and its degradation pathway are still very less. Therefore the present work explored the azoreductase pathway of the cyanobacterium Nostoc sp. PCC7120 for better understanding of the degradation path...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Philem PD, Adhikari S Tags: Bioinformation Source Type: research
Disseminating the best available evidence: New challenges in public reporting of health care.Email this article to a colleague.
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Abstract
As a direct benefit of the Health Care Reform Act (2010), concerted effort has been deployed to define and characterize the process by which the best available evidence for diagnosis or treatment intervention prognosis can be obtained. The science of research synthesis in health care has established the systematic research protocol by which randomized clinical trials and other clinical studies must be reviewed and compared for the level and quality of the evidence presented, as well as the consensus of the best available evidence synthesized and shared. This process of systematic review yields a reliable a...
Source: Bioinformation - May 8, 2012 Category: Bioinformatics Authors: Barkhordarian A, Ramchandani MH, Dousti M, Kelly-Gleason L, Chiappelli F Tags: Bioinformation Source Type: research
PHYLOViZ: Phylogenetic Inference and Data Visualization
for Sequence Based Typing MethodsEmail this article to a colleague.
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Conclusions:
PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbialepidemiological and population studies. It is freely available at http://www.phyloviz.net.
Source: BMC Bioinformatics - Latest articles - May 8, 2012 Category: Bioinformatics Authors: Alexandre FranciscoCátia VazPedro MonteiroJosé Melo-CristinoMário RamirezJoão André Carriço Source Type: research
Augmented annotation and orthologue analysis for
Oryctolagus cuniculus: Better BunnyEmail this article to a colleague.
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Conclusions:
We have developed a freely available web-accessible bioinformatics tool that enables investigators to quickly and easily perform extensive functional analysis of rabbit genes. The software application fills a critical void for a wide range of biomedical research that relies on the rabbit model and requires characterization of biological function for large sets of genes.
Source: BMC Bioinformatics - Latest articles - May 8, 2012 Category: Bioinformatics Authors: Douglas CraigSujatha KannanAlan Dombkowski Source Type: research
The Cancer Survival Query System: Making survival estimates from the Surveillance, Epidemiology, and End Results program more timely and relevant for recently diagnosed patientsEmail this article to a colleague.
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CONCLUSIONS:Nomograms of this type can be used as one tool to assist cancer physicians and their patients to better understand their prognosis and to weigh alternative treatment and palliative strategies. Cancer 2012. © 2012 American Cancer Society.
Source: Cancer - May 8, 2012 Category: Cancer & Oncology Authors: Eric J. Feuer, Minjung Lee, Angela B. Mariotto, Kathy A. Cronin, Steve Scoppa, David F. Penson, Mark Hachey, Laurie Cynkin, Ginger A. Carter, David Campbell, Antoinette Percy‐Laurry, Zhaohui Zou, Deborah Schrag, Benjamin F. Hankey Tags: Original Article Source Type: research
Are We Born to Be Religious? (preview)Email this article to a colleague.
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A deep question pervades the debates surrounding religion--whether God exists, sure, but that one is mighty difficult to answer. Instead we can ask a related, more approachable query: Why does God exist for some of us but not for others? Theologians and ministers preach that faith is preeminently a matter of personal choice. Is it, really? [More]
Source: Scientific American - Official RSS Feed - May 5, 2012 Category: Science Tags: More Science,Environment,History of Science,Society & Policy,Thought Cognition,Evolution,Evolutionary Biology,Neuroscience,Biology,Everyday Science Source Type: research
