MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Bioinformation' source. Thu, 19 Nov 2009 16:19:15 +0100 http://www.medworm.com/index.php?rid=2810290&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759809%26dopt%3DAbstract Authors: Ghozlane A, Joseph AP, Bornot A, de Brevern AG Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy level. Here we report a large scale-analysis of chameleon sequences to estimate their propensities to be associ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810290 Sun, 20 Sep 2009 05:38:05 +0100 2810290 http://www.medworm.com/index.php?rid=2810289&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759810%26dopt%3DAbstract Authors: Dassanayake RS, Rodrigo WW, Karunanayake EH, Weerasena OV, Chandrasekharan NV Expressed sequence tags (ESTs) are an effective approach for discovery of novel genes. In the current study, approximately 250 ESTs of the cattle parasitic nematode Setaria digitata were examined and a cDNA clone identified whose coding sequence could not be functionally annotated by searching over publicly available genome, protein, EST and STS databases. Here, we report the extensive characterization of this ORF (UP) and its homologues using a bioinformatic approach. Uncharacterized protein (SDUP) of S. digitata consists of 204 amino acids with a predicted molecular weight and isoelectric point of 22.8KDa and 9.94, respectively. A search carried out using SDUP over nucleotide, EST and protein datab... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810289 Sun, 20 Sep 2009 05:38:05 +0100 2810289 http://www.medworm.com/index.php?rid=2810288&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759811%26dopt%3DAbstract In this study, computational analysis of sequence homology of 546 bp 5' region of 16SrRNA gene of Bacillus sp. strain SJ-101 resulted in identification of promoter-like sequences within the rrn gene. Using BPROM tool, the regulatory motifs like -35 and -10 boxes were mapped at 392 and 411 positions, respectively. Furthermore, the cis-acting elements as the binding sites for transcription factors (TF) cpxR and argR were identified at positions 413 and 416 at the upstream of an open reading frame (ORF). The probable functions of the putative TFs were predicted through the Uni-Prot/Swiss-Prot protein database. Search for the Shine-Dalgarno sequence (SD) found the presence of highly conserved SD sequence (AATACC), and a short 42 bp coding sequence/ORF bounded with characteristic transcription ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810288 Sun, 20 Sep 2009 05:38:05 +0100 2810288 http://www.medworm.com/index.php?rid=2810287&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759812%26dopt%3DAbstract Authors: Yadav V, Prakash S, Srivastava S, Verma PC, Gupta V, Basu V, Rawat AK A bacterial strain Bz02 was isolated from a water sample collected from river Gomti at the Indian city of Lucknow. We characterized the strain using 16S rRNA sequence. Phylogenetic analysis showed that the strain formed a monophyletic clade with members of the genus Comamonas. The closest phylogenetic relative was Comamonas testosteroni with 95% 16S rRNA gene sequence similarity. It is proposed that the identified strain Bz02 be assigned as the type strain of a species of the genus Comamonas (Comamonas sp Bz02) based on 16S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases together with the phylogenetic tree analysis. The sequence is deposted in GenB... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810287 Sun, 20 Sep 2009 05:38:05 +0100 2810287 http://www.medworm.com/index.php?rid=2810286&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759813%26dopt%3DAbstract In this study, we have formulated few rules to assess the ability to prolong QT interval and thereby discriminate between cardiotoxic and -safe drugs. These rules have clearly determined that cardio-toxic drugs are more likely to obey Lipinski rule of 5 and Oprea lead-like rule. Moreover, the cardio-toxic drugs have been found to have in common values of -0.5 to 6.5 log P, 1-5 nitrogen atoms, up to 4 oxygen atoms, 5-27 hydrophobic atoms, and 15-53 single bonds. Matthews Correlation Coefficient with the value of 0.6 was also attained and nearly 96% of the cardio-toxic drugs were successfully covered. Thus, despite the simplicity of this methodology, we have obtained interesting and informative results. The proposed set of these simple rules could be employed to infer cardio-toxicity or -saf... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810286 Sun, 20 Sep 2009 05:38:05 +0100 2810286 http://www.medworm.com/index.php?rid=2810285&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759814%26dopt%3DAbstract Authors: Mishra S, Dwivedi SP, Dwivedi N, Kumar A, Rawat A, Kamisaka Y Acyl CoA diacylglycerol acyltransferase (DGAT, EC 2.3.120) is recognized as a key player of cellular diacylglycerol metabolism. It catalyzes the terminal, yet the committed step in triacylglycerol synthesis using diacylglycerol and fatty acyl CoA as substrates. The protein sequence of diacylglycerol acyltransferse (DGAT) Type 2B in Moretierella ramanniana var. angulispora (Protein_ID = AAK84180.1) was retrieved from GenBank. However, a structure is not yet available for this sequence. The 3D structure of DGAT Type 2B was modeled using a template structure (PDB ID: 1K30) obtained from Protein databank (PDB) identified by searching with position specific iterative BLAST (PSI-BLAST). The template (PDB ID: 1K30) describ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810285 Sun, 20 Sep 2009 05:38:05 +0100 2810285 http://www.medworm.com/index.php?rid=2810284&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759815%26dopt%3DAbstract Authors: Hatti KS, Diwakar L, Rao GV, Kush A, Reddy GC Abyssinones and related flavonoids were screened against 3 enzymes (3betaHSD, 17betaHSD and Aromatase) of steroidogenesis pathway. The virtual screening experiment shows high affinity for flavonones than their respective chalcones. A 4' -OH blocked prenylated flavonone 2b (2-(2', 2'-dimethyl chroman-6'-yl)-7-hydroxy chroman-4-one) had consistent binding affinity to all the three enzymes used in this study showing higher binding affinity to aromatase. A good correlation was observed between cytotoxic data (MCF-7, breast cancer cell line) and docking results indicating flavonone as a better steroidogenesis modulator in hormone dependent cancer. PMID: 19759815 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810284 Sun, 20 Sep 2009 05:38:05 +0100 2810284 http://www.medworm.com/index.php?rid=2810283&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759816%26dopt%3DAbstract Authors: Soam SS, Khan F, Bhasker B, Mishra BN Binding of peptides to specific Major Histo-compatibility Complex (MHC) molecule is important for understanding immunity and has applications to vaccine discovery and design of immunotherapy. Artificial neural networks (ANN) are widely used by predictions tools to classify the peptides as binders or non-binders (BNB). However, the number of known binders to a specific MHC molecule is limited in many cases, which poses a computational challenge for prediction of BNB and hence, needs improvement in learning of ANN. Here, we describe, the application of probability distribution functions to initialize the weights and biases of the artificial neural network in order to predict HLA-A*0201 binders and non-binders. The 10-fold cross validation ha... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810283 Sun, 20 Sep 2009 05:38:05 +0100 2810283 http://www.medworm.com/index.php?rid=2810282&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759817%26dopt%3DAbstract We describe the role of LHR in complete set of protein sequences in 15 different species. That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate more LHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent at window length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteins compared to other model organisms. PMID: 19759817 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810282 Sun, 20 Sep 2009 05:38:05 +0100 2810282 http://www.medworm.com/index.php?rid=2810281&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759860%26dopt%3DAbstract Authors: Ordog R, Szabadka Z, Grolmusz V The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi-monomer ligands, and the server also offers the preprocessed ligand-protein decomposition of the complete PDB for downloading (up to size: 5GB) AVAILABILITY: http://decomp.pitgroup.org. PMID: 19759860 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810281 Sun, 20 Sep 2009 05:38:05 +0100 2810281 http://www.medworm.com/index.php?rid=2810280&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759861%26dopt%3DAbstract Authors: Sen N, Mishra M, Khan F, Meena A, Sharma A Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight m... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810280 Sun, 20 Sep 2009 05:38:05 +0100 2810280 http://www.medworm.com/index.php?rid=2810279&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759862%26dopt%3DAbstract Authors: Kushwaha SK, Shakya M Cellular processes are regulated by interaction of various proteins i.e. multiprotein complexes and absences of these interactions are often the cause of disorder or disease. Such type of protein interactions are of great interest for drug designing. In host-parasite diseases like Tuberculosis, non-homologous proteins as drug target are first preference. Most potent drug target can be identifying among large number of non-homologous protein through protein interaction network analysis. Drug target should be those non-homologous protein which is associated with maximum number of functional proteins i.e. has highest number of interactants, so that maximum harm can be caused to pathogen only. In present work, Protein Interaction Network Analysis Tool (PINAT)... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810279 Sun, 20 Sep 2009 05:38:05 +0100 2810279 http://www.medworm.com/index.php?rid=2810278&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759863%26dopt%3DAbstract Authors: Kumar GR, Subazini TK, Subha K, Rajadurai CP, Prabakar L The advent of genomic and proteomic technologies in this post-genomic era has urged the researchers to develop novel research strategies against cancer by targeting the human genes that would greatly facilitate to identify more promising treatment and to develop accurate early diagnosis for cancer. To harness the power of cancer genetic information towards better treatment we have developed a cancer gene database called CanGeneBase (CGB). It is a comprehensive data collection of cancer-related genes with the intention of helping the researchers to stay on a single platform to gain exclusive information on the genes of their interest. According to the Cancer Gene Data Curation Project, about 4,700 genes have been identifi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810278 Sun, 20 Sep 2009 05:38:05 +0100 2810278 http://www.medworm.com/index.php?rid=2810277&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759864%26dopt%3DAbstract Authors: Shrivastava S, Poddar R, Shukla P, Mukhopadhyay K Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bioinformatics tools. Multivariate analysis has been used as a tool to study codon bias perspectives of xylanases. It was further observed that the codon usage of xylanases genes from different fungal sources is not similar and to reveal this phenomenon the relative synonymous codon usage (RSCU) and base composition variation in fungal xylan... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810277 Sun, 20 Sep 2009 05:38:05 +0100 2810277 http://www.medworm.com/index.php?rid=2810276&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759865%26dopt%3DAbstract Authors: Sharma RD, Lynn AM, Sharma PK, Rajnee , Jawaid S The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classical molecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an amidase-03 domain which is known to exhibit the catalytic activity of N-acetylmuramoyl-L-alanine amidase (digesting MurNAc-Lalanine linkage of bacterial cell wall). The amidase-03 enzyme has stability at high temperature due to the core formed by the combination of several secondary structure elements made of beta-sheets. We used root-mean-square-displacement (RMSD) of the simulated structure from its initial state to demonstrate the unfolding of the enzyme using its secondary structural elements. Results show t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810276 Sun, 20 Sep 2009 05:38:05 +0100 2810276 http://www.medworm.com/index.php?rid=2810275&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759866%26dopt%3DAbstract Authors: Somvanshi P, Seth PK Dengue fever, dengue hemorrhagic fever and dengue shock syndrome are the prevalent mosquito borne viral infections worldwide. The dengue virus belongs to the genus flavivirus with conserved RNA domains peptidase_S7 and dexHc among its members. The secondary structures for RNA domains peptidase_S7 and DexHc are hence predicted and discussed with other known viral RNA structures to glean structural insights through comparison. PMID: 19759866 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810275 Sun, 20 Sep 2009 05:38:05 +0100 2810275 http://www.medworm.com/index.php?rid=2810274&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759867%26dopt%3DAbstract Authors: Singh P, Suman S, Chandna S, Das TK Alzheimer's disease (AD) is a common neurodegenerative disease characterized by both extra- as well as intracellular deposition of amyloid beta peptides (Abeta). The accumulation of Abeta in mitochondria is associated with mitochondrial dysfunction and oxidative stress in AD. Recent evidences suggest the involvement of Abeta interaction with mitochondrial proteins such as cyclophilin-D (CypD) in oxidative stress, mitochondrial permeability transition (MPT) and Alzheimer's associated neurodegeneration. The present study is an effort to elucidate the molecular interaction of Abeta with other proteins involved in MPT like adenine nucleotide translocase (ANT). Based on our prediction for sub-cellular localization using WolfPSORT and other experi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810274 Sun, 20 Sep 2009 05:38:05 +0100 2810274 http://www.medworm.com/index.php?rid=2810273&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759868%26dopt%3DAbstract In this study, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of xylanases. Physico-chemical properties were predicted and prediction of motifs, disulfide bridges and secondary structure was performed for functional characterization. Apart from these analyses, three dimensional structures were constructed and stereo-chemical quality was evaluated by different structure validation tools. Comparative catalytic site analysis and assessment was performed to extract information about the important residues. Asn72 was found to be the common residue in the active sites of the proteins P35809 and Q12603. PMID: 19759868 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810273 Sun, 20 Sep 2009 05:38:05 +0100 2810273 http://www.medworm.com/index.php?rid=2810272&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19759869%26dopt%3DAbstract Authors: Wu Q, Wang J, Yan H Nucleosome positioning can affect the accessibility of the underlying DNA to the nuclear environment and as such plays an essential role in the regulation of cellular processes. Specific patterns have been found in the underlying DNA sequences of the nucleosome, and one of the most important patterns includes dinucleotides distributed every 10 to 11 base pairs. Based on this property, we propose to match each dinucleotide in the sequence against its mirror occurrences for 10 to 11 base pairs on both left-hand and right-hand sides. A large number of matches in a local region will then signify the existence of a nucleosome. In this paper, we propose the matched mirror position filters for efficient matching of periodic dinucleotide patterns and computationall... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2810272 Sun, 20 Sep 2009 05:38:05 +0100 2810272 http://www.medworm.com/index.php?rid=2742153&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707293%26dopt%3DAbstract Authors: Singh A, Sivaprasad C Insect pests are the major cause of damage to commercially important agricultural crops. The continuous application of synthetic pesticides resulted in severe insect resistance by plants. This causes irreversible damage to the environment. Bacillus thuringiensis (Bt) emerged as a valuable biological alternative in pest control. However, insect resistance against Bt has been reported in many cases. Insects develop resistance to insecticides through mechanisms that reduce the binding of toxins to gut receptors. Nonetheless, the molecular mechanism of insect resistance is not fully understood. Therefore, it is important to study the mechanism of toxin resistance by analyzing amino-peptidase-N (APN) receptor of the insect M. sexta. A homology model of APN was... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742153 Sat, 29 Aug 2009 04:38:03 +0100 2742153 http://www.medworm.com/index.php?rid=2742152&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707294%26dopt%3DAbstract Authors: Upadhyay J, Misra K Vitamin E is a mixture of eight compounds alpha, beta, gamma, delta- tocopherols and alpha, beta, gamma, delta- tocotrienols. Their individual role in cellular transport as antioxidants and in metabolic pathways has been highlighted in the present work. All the eight compounds have been docked with the respective metabolizing enzymes (alpha-tocopherol transfer protein (ATTP), alpha-tocopherol associated protein (TAP), P-glycoprotein (P-gly) and human serum albumin (HSA)) to understand molecular interactions for pharmacokinetics. These have been structurally aligned against the four human phospholipids in order to reveal their individual role in chylomicron formation and hence the mechanism of cellular transport. The study of their binding with their metabol... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742152 Sat, 29 Aug 2009 04:38:03 +0100 2742152 http://www.medworm.com/index.php?rid=2742151&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707295%26dopt%3DAbstract Authors: Oluwadara O, Chiappelli F Nasopharyngeal carcinoma (NpC) is a malignant disease associated with Epstein-Barr virus infection, and often diagnosed at an advanced stage. This significantly curtails patient survival. We hypothesize that a panel of biomarkers can be assembled to assess NpC incidence, early detection, and tumor progression during therapeutic intervention. Our thesis rests on a model of successfully predicting high-risk gliomas by means of a carefully crafted panel of molecular mitotic biomarkers (i.e., securin, survivin and MCM2). The strategy we propose holds strong promise for prevention and cure of NpC. The approach we propose seeks to identify certain biomarkers from viral materials, patient tissues and assessment of related diseases, whose signatures, taken to... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742151 Sat, 29 Aug 2009 04:38:03 +0100 2742151 http://www.medworm.com/index.php?rid=2742150&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707296%26dopt%3DAbstract Authors: Daura-Oller E, Cabre M, Montero MA, Paternain JL, Romeu A Giving coding region structural features a role in the hypomethylation of specific genes, the occurrence of G+C content, CpG islands, repeat and retrotransposable elements in demethylated genes related to cancer has been evaluated. A comparative analysis among different cancer types has also been performed. In this work, the inter-cancer coding region features comparative analysis carried out, show insights into what structural trends/patterns are present in the studied cancers. PMID: 19707296 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742150 Sat, 29 Aug 2009 04:38:03 +0100 2742150 http://www.medworm.com/index.php?rid=2742149&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707297%26dopt%3DAbstract Authors: Kim C, Kwon S, Lee G, Lee H, Choi J, Kim Y, Hahn J The AllergenPro database has developed a web-based system that will provide information about allergen in microbes, animals and plants. The database has three major parts and functions:(i) database list; (ii) allergen search; and (iii) allergenicity prediction. The database contains 2,434 allergens related information readily available in the database such as on allergens in rice microbes (712 records), animals (617 records) and plants (1,105 records). Furthermore, this database provides bioinformatics tools for allergenicity prediction. Users can search for specific allergens by various methods and can run tools for allergenicity prediction using three different methods. AVAILABILITY: The database is available for free at htt... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742149 Sat, 29 Aug 2009 04:38:03 +0100 2742149 http://www.medworm.com/index.php?rid=2742148&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707298%26dopt%3DAbstract Authors: Ying X, Kim YJ, Mao Y, Liu M, Hou Y, Li H, Wang X, Zhao Y, Zhao D, Patel JM, Li W An increasing number of small RNAs have been discovered in mammals. However, their primary transcripts and upstream regulatory networks remain largely to be determined. Genomic analysis of small RNAs facilitates identification of their primary transcripts, and hence contributes to researches of their upstream regulatory networks. We here report a batch platform, BatchGenAna, which is specifically designed for large-scale genomic analysis of mammalian small RNAs. It can map and annotate for as many as 1000 small RNAs or 10,000 genomic loci of small RNAs at a time. It provides genomic features including RefSeq genes, mRNAs, ESTs and repeat elements in tabular and graphical results. It also allows e... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742148 Sat, 29 Aug 2009 04:38:03 +0100 2742148 http://www.medworm.com/index.php?rid=2742147&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707299%26dopt%3DAbstract Authors: Peng T, Du P, Li Y The software tool PBEAM provides a parallel implementation of the BEAM, which is the first algorithm for large scale epistatic interaction mapping, including genome-wide studies with hundreds of thousands of markers. BEAM describes markers and their interactions with a Bayesian partitioning model and computes the posterior probability of each marker sets via Markov Chain Monte Carlo (MCMC). PBEAM takes the advantage of simulating multiple Markov chains simultaneously. This design can efficiently reduce ~n-fold execution time in the circumstance of n CPUs. The implementation of PBEAM is based on MPI libraries. AVAILABILITY: PBEAM is available for download at http://bioinfo.au.tsinghua.edu.cn/pbeam/ PMID: 19707299 [PubMed - in process] (Source: Bioinformat... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742147 Sat, 29 Aug 2009 04:38:03 +0100 2742147 http://www.medworm.com/index.php?rid=2742146&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707300%26dopt%3DAbstract Authors: Arias RS, Ballard LL, Scheffler BE We introduce here the concept of Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers. After the first screening of SSR-markers tested on a subset of DNA samples, the user can apply UPIC to find marker combinations that maximize the genetic information obtained by a minimum or desirable number of markers. This allows a cost-effective planning of future experiments. We have developed Perl scripts to calculate all possible subset combinations of SSR markers, and determine based on unique patterns or alleles, which combinations can discriminate among all DNA samples included in a test. This makes UPIC an ess... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742146 Sat, 29 Aug 2009 04:38:03 +0100 2742146 http://www.medworm.com/index.php?rid=2742145&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707301%26dopt%3DAbstract Authors: Banky D, Ordog R, Grolmusz V Large quantity of reliable protein interaction data are available for model organisms in public depositories (e.g., MINT, DIP, HPRD, INTERACT). Most data correspond to experiments with the proteins of Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli and Mus musculus. For other important organisms the data availability is poor or non-existent. Here we present NASCENT, a completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein interaction network modeling through gene-name mapping, and outputs the resulting network in graphical form and also in computer-readab... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742145 Sat, 29 Aug 2009 04:38:03 +0100 2742145 http://www.medworm.com/index.php?rid=2742144&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707302%26dopt%3DAbstract Authors: Cao Y, Zhao Y, Cha L, Ying X, Wang L, Shao N, Li W In bacteria, there exist some small non-coding RNAs (sRNAs) with 40-500 nucleotides in length. Most of them function as posttranscriptional regulation of gene expression through binding to their target mRNAs, in which Hfq protein acts as RNA chaperone. With the increase of identified sRNA genes in the bacterium, prediction of sRNA targets plays a more important role in determining sRNA functions. However, there are few available computational tools for predicting sRNA targets at present. Here we introduced a web server, sRNATarget, for genome-scale prediction of bacterial sRNA targets. The server is based on a recently published model which uses Naive Bayes method as the supervised method and take RNA secondary structure profi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742144 Sat, 29 Aug 2009 04:38:03 +0100 2742144 http://www.medworm.com/index.php?rid=2742143&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707563%26dopt%3DAbstract Authors: Mishra H, Singh N, Lahiri T, Misra K Screening of " drug-like" molecule from the molecular database produced through high throughput techniques and their large repositories requires robust classification. In our work, a set of heuristically chosen nine molecular descriptors including four from Lipinski's rule, were used as classification parameter for screening "drug-like" molecules. The robustness of classification was compared with four fundamental descriptors of Lipinski. Back propagation neural network based classifier was applied on a database of 60000 molecules for classification of, " drug-like" and "non drug-like" molecules. Classification result using nine descriptors showed high classification accuracy of 96.1% in comparison to that using four Lipinski's descriptors ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2742143 Sat, 29 Aug 2009 04:38:03 +0100 2742143 http://www.medworm.com/index.php?rid=2284270&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293991%26dopt%3DAbstract Authors: Shankar R, Kataria B, Mukerji M Repetitive sequences occupy more than 40% of the human genome which is much larger compared to the 2% occupied by the coding DNA. Amongst these Alu elements are the second largest class of repeats, occupying nearly 10% of the whole genome. Alus have been implicated in many genomic processes, sometimes giving rise to aberrations while many times playing as silent player in genomic and regulatory evolution. Here we present a web server, AF1, exclusively developed for finding Alu like elements. Besides alignment based methodology, this server utilizes probabilistic scanning to find more diverged elements and employs a more precise way of element classification based on unequal weighting of sequence through sequence encoding. AVAILABILITY: AF1 is fr... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284270 Mon, 23 Mar 2009 10:12:36 +0100 2284270 http://www.medworm.com/index.php?rid=2284269&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293992%26dopt%3DAbstract Authors: Telefont M, Asaithambi A Scientific reference management has become crucial in rapidly expanding fields of biology. Many of the reference management systems currently employed are reference centric and not object/process focused. BrainSnail is a reference management/knowledge representation application that tries to bridge disconnect between subject and reference in the fields of neuropharmacology, neuroanatomy and neurophysiology. BrainSnail has been developed with considering both individual researcher and research group efforts. PMID: 19293992 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284269 Mon, 23 Mar 2009 10:12:36 +0100 2284269 http://www.medworm.com/index.php?rid=2284268&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293993%26dopt%3DAbstract Authors: Yang CH, Shih1 TM, Hung YC, Chang HW, Chuang LY Serial analysis of gene expression (SAGE) is a powerful quantification technique for gene expression data. The huge amount of tag data in SAGE libraries of samples is difficult to analyze with current SAGE analysis tools. Data is often not provided in a biologically significant way for cross-analysis and -comparison, thus limiting its application. Hence, an integrated software platform that can perform such a complex task is required. Here, we implement set theory for cross-analyzing gene expression data among different SAGE libraries of tissue sources; up- or down-regulated tissue-specific tags can be identified computationally. Extract-SAGE employs a genetic algorithm (GA) to reduce the number of genes among the SAGE libraries.... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284268 Mon, 23 Mar 2009 10:12:36 +0100 2284268 http://www.medworm.com/index.php?rid=2284267&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293994%26dopt%3DAbstract Authors: Massey SE ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the prese... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284267 Mon, 23 Mar 2009 10:12:36 +0100 2284267 http://www.medworm.com/index.php?rid=2284266&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293995%26dopt%3DAbstract Authors: Durden C, Dong Q Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. We have developed a web server, RICHness ESTimator (RICHEST), which implements three non-parametric statistical methods for richness estimation. Its user-friendly web interface allows users to analyze and compare their data conveniently over the web. AVAILABILITY: A web server hosting RICHEST is accessible at http://richest.cgb.indiana.edu/cgi-bin/index.cgi and the software is freely available for local installations. PMID: 19293995 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284266 Mon, 23 Mar 2009 10:12:36 +0100 2284266 http://www.medworm.com/index.php?rid=2284265&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293996%26dopt%3DAbstract We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools. AVAILABILITY: The database is freely available at http://chpvdb.biomedinformri.org/. PMID: 19293996 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284265 Mon, 23 Mar 2009 10:12:36 +0100 2284265 http://www.medworm.com/index.php?rid=2284264&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293997%26dopt%3DAbstract Authors: Salisbury JP, Williams JC Virtual high throughput screening (VHTS) was performed to assess possible interactions which might occur between commercially available triphenylphosphonium (TPP) cations and estrogen receptor alpha (ERalpha) that could be exploited to design novel ERalpha modulators. One application of TPP cations is for delivering bioactive molecules to targets in mitochondria as the large membrane potential of mitochondria leads cations to accumulate inside them. The estrogen receptors (ERs) alpha and beta, normally activated by the endogenous hormone 17beta-estradiol, are responsible for controlling transcription of nuclear DNA necessary for human development and reproduction. ERs are also associated with the plasma membrane and have been found in the mitochondria... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284264 Mon, 23 Mar 2009 10:12:36 +0100 2284264 http://www.medworm.com/index.php?rid=2284263&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293998%26dopt%3DAbstract Authors: Mulakayala C, Banaganapalli BN, Anuradha C, Chitta SK Streptococcus pneumonia is the common cause of sepsis and meningitis. Emergence of multiple antibiotic resistant strains in the community-acquired bacterium is catastrophic. Glucose kinase (GLK) is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression (CCR) system. Therefore, it is important to establish the structure-function relation of GLK in S. pneumoniae. However, a solved structure for S. pneumoniae GLK is not available at the protein data bank (PDB). Therefore, we created a model of GLK from S. pnemoniae using the X-ray structure of Glk from E. faecalis as template with MODELLER ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284263 Mon, 23 Mar 2009 10:12:36 +0100 2284263 http://www.medworm.com/index.php?rid=2284262&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19293999%26dopt%3DAbstract Authors: Kiezun A, Lee IT, Shomron N Logistic regression is often used to help make medical decisions with binary outcomes. Here we evaluate the use of several methods for selection of variables in logistic regression. We use a large dataset to predict the diagnosis of myocardial infarction in patients reporting to an emergency room with chest pain. Our results indicate that some of the examined methods are well suited for variable selection in logistic regression and that our model, and our myocardial infarction risk calculator, can be an additional tool to aid physicians in myocardial infarction diagnosis. PMID: 19293999 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284262 Mon, 23 Mar 2009 10:12:36 +0100 2284262 http://www.medworm.com/index.php?rid=2284261&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19294000%26dopt%3DAbstract Authors: Prasad P, Tandon V, Biswal D, Goswami L, Chatterjee A Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prev... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2284261 Mon, 23 Mar 2009 10:12:36 +0100 2284261 http://www.medworm.com/index.php?rid=2235415&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255642%26dopt%3DAbstract In this study, phosphoryl thymidine kinase (thi E), a terminal enzyme in the thiamine biosynthesis pathway in the pathogen has been modeled to be used in future as a potential drug target by the design of suitable inhibitors. PMID: 19255642 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235415 Thu, 05 Mar 2009 13:25:50 +0100 2235415 http://www.medworm.com/index.php?rid=2235414&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255643%26dopt%3DAbstract Authors: Sundaramurthy P, Gakkhar S, Sowdhamini R The classical concept of linear pathways is being increasingly challenged by network representations, which emphasize the importance of interactions between components of a biological system, and motivates for adopting a system-level approach in biology. We have developed a dynamical system that integrates quantitative, dynamic and topological representation of network of ERK5 (Extracellular signal-regulated kinases 5), JNK(c-Jun N-terminal kinases) and P38 kinase cascades. We have observered that, the transient activation of ERK5, JNK1 and P38beta kinase, and the persistent activation of JNK2, JNK3 and P38 delta kinase does not get affected due to the cross-talks between ERK5, JNK and P38 kinase cascades. But it is due to the cross - t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235414 Thu, 05 Mar 2009 13:25:50 +0100 2235414 http://www.medworm.com/index.php?rid=2235413&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255644%26dopt%3DAbstract Authors: Sundaramurthy P, Gakkhar S, Sowdhamini R Signal transduction is a complex protein signaling process with a rich network of multifunctional interactions that occur in a non-linear fashion. Mitogen-activated protein kinase (MAPK) signal transduction pathways regulate diverse cellular processes ranging from proliferation and differentiation to apoptosis. In mammals, out of five, there are three well characterized subfamilies of MAPKs - ERKs (Extracellular signal-regulated kinases), JNKs (c-Jun N-terminal kinases), and P38 kinases, and their activators, are implicated in human diseases and are targets for drug development. Kinase cascades in MAPK pathways mediate the sensing and processing of stimuli. To understand how cells makes decisions, the dynamic interactions of components ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235413 Thu, 05 Mar 2009 13:25:50 +0100 2235413 http://www.medworm.com/index.php?rid=2235412&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255645%26dopt%3DAbstract Authors: Singh N, Misra K Histone acetyltransferase (HAT) is an enzyme required for chromatin remodeling and transcriptional activation. Sarcoendoplasmic reticulum Ca(2+) ATPase (SERCA) is an ATP coupled Ca(2+) ion pump involved in metabolic arrest. Both these enzymes are present in Plasmodia and have been selected as molecular targets for in silico studies of some new non-resistant antimalarial drugs like artemisinin, curcumin and diarylheptanoids along with some other inhibitors reported in literature. Ten top inhibitors have also been generated based on common pharmacophore from ZINC database. The HAT enzyme was modeled with the help of the Modeller software and the SERCA enzyme pdb file was obtained from the protein data bank. Ligbuilder was used for structure based drug designing,... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235412 Thu, 05 Mar 2009 13:25:50 +0100 2235412 http://www.medworm.com/index.php?rid=2235411&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255646%26dopt%3DAbstract Authors: Rayan A Comparative modelling is utilized to predict the 3-dimensional conformation of a given protein (target) based on its sequence alignment to experimentally determined protein structure (template). The use of such technique is already rewarding and increasingly widespread in biological research and drug development. The accuracy of the predictions as commonly accepted depends on the score of sequence identity of the target protein to the template. To assess the relationship between sequence identity and model quality, we carried out an analysis of a set of 4753 sequence and structure alignments. Throughout this research, the model accuracy was measured by root mean square deviations of Calpha atoms of the target-template structures. Surprisingly, the results show that seq... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235411 Thu, 05 Mar 2009 13:25:50 +0100 2235411 http://www.medworm.com/index.php?rid=2235410&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255647%26dopt%3DAbstract Authors: Varadwaj PK, Lahiri T Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235410 Thu, 05 Mar 2009 13:25:50 +0100 2235410 http://www.medworm.com/index.php?rid=2235409&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255648%26dopt%3DAbstract Authors: Vanhoutte K, de Asmundis C, Francesconi A, Figys1 J, Steurs G, Boussy T, Roos M, Mueller A, Massimo L, Paparella G, Van Caelenberg K, Chierchia GB, Sarkozy A, Y Terradellas PB, Zizi M Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235409 Thu, 05 Mar 2009 13:25:50 +0100 2235409 http://www.medworm.com/index.php?rid=2235408&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255649%26dopt%3DAbstract Authors: Suryapriya P, Snehalatha A, Kayalvili U, Krishna R, Singh S, Ulaganathan K Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles. Intensive data mining of literature resulted in the identification 861 root development QTLs and associated micr... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235408 Thu, 05 Mar 2009 13:25:50 +0100 2235408 http://www.medworm.com/index.php?rid=2235407&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255650%26dopt%3DAbstract Authors: Martins WS, Soares Lucas DC, de Souza Neves KF, Bertioli DJ Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the develo... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235407 Thu, 05 Mar 2009 13:25:50 +0100 2235407 http://www.medworm.com/index.php?rid=2235406&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19255651%26dopt%3DAbstract Authors: Akula SP, Miriyala RN, Thota H, Rao AA, Gedela S The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XM... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2235406 Thu, 05 Mar 2009 13:25:50 +0100 2235406 http://www.medworm.com/index.php?rid=2019048&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052658%26dopt%3DAbstract Authors: Sahoo GC, Dikhit MR, Das P Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane,... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019048 Sun, 07 Dec 2008 17:18:35 +0100 2019048 http://www.medworm.com/index.php?rid=2019047&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052659%26dopt%3DAbstract Authors: Suman S, Seth RK, Chandna S Previous studies on various insect cell lines have displayed very high radioresistance in Lepidoptera (butterflies and moths) as compared to mammals as well as other orders of Insecta including Diptera. Since NOS is known to modulate cellular radiation sensitivity, we carried out in silico analysis of Lepidopteran NOS and compared its structural and functional features including the sequence homology, predicted tertiary structure, post-translational phosphorylation and intracellular localization with the other species. Our study demonstrates that Lepidopteran NOS, while carrying significant sequence homology with mammalian nNOS, has structural/ functional features that may enhance resistance to radiation and other stress agents. A higher phosphoryla... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019047 Sun, 07 Dec 2008 17:18:35 +0100 2019047 http://www.medworm.com/index.php?rid=2019046&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052660%26dopt%3DAbstract This article discusses some of the important considerations that are imperative for designing a successful vHTS experiment. PMID: 19052660 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019046 Sun, 07 Dec 2008 17:18:35 +0100 2019046 http://www.medworm.com/index.php?rid=2019045&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052661%26dopt%3DAbstract Authors: Sahoo GC, Dikhit MR, Sahoo GC, Das P Alpha (alpha)-enolase (e), a glycolytic enzyme, has an alternative role as a surface receptor of several bacteria mediating plasminogen (pg) binding. It is also recognized as a virulence factor of some pathogenic bacteria facilitating plasminogen activation and host cell invasion. A mycoplasmal alpha-enolase is also a plasminogen binding protein. Molecular interactions of enolase from Mycoplasma pneumoniae with host plasminogen would be useful for exploring the pathogen-host interaction. In an attempt to identify plasminogen binding sites of M. pneumoniae enolase, homology modeling and docking studies were conducted to obtain modeled structures of the M. pneumoniae enolase-plasminogen complex. The refined model was validated further by stan... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019045 Sun, 07 Dec 2008 17:18:35 +0100 2019045 http://www.medworm.com/index.php?rid=2019044&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052662%26dopt%3DAbstract Authors: Selvaraj D, Sarma RK, Sathishkumar R MaturaseK gene (MatK) of chloroplast is highly conserved in plant systematics which is involved in Group II intron splicing. The size of the gene is 1500 bp in length, located with in the intron of trnK. In the present study, matK gene from Zingiberaceae was taken for the analysis of variants, parsimony site, patterns, transition/tranversion rates and phylogeny. The family of Zingiberaceae comprises 47 genera with medicinal values. The matK gene sequence have been obtained from genbank and used for the analysis. The sequence alignments were performed by Clustal X, transition/transversion rates were predicted by MEGA and phylogenetic analyses were carried out by PHYLIP package. The result indicates that the Zingiberaceae genus Afromonum, Alp... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019044 Sun, 07 Dec 2008 17:18:35 +0100 2019044 http://www.medworm.com/index.php?rid=2019043&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052663%26dopt%3DAbstract Authors: Banerjee N, Sarani R, Ranjani CV, Sowmiya G, Michael D, Balakrishnan N, Sekar K Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019043 Sun, 07 Dec 2008 17:18:35 +0100 2019043 http://www.medworm.com/index.php?rid=2019042&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052664%26dopt%3DAbstract Authors: Marcet-Houben M, Cabré M, Paternáin JL, Romeu A The first two steps of aflatoxin biosynthesis are catalyzed by the HexA/B and by the Pks protein. The phylogenetic analysis clearly distinguished fungal HexA/B from FAS subunits and from other homologous proteins. The phylogenetic trees of the HexA and HexB set of proteins share the same clustering. Proteins involved in the synthesis of fatty acids or in the aflatoxin or sterigmatocystin biosynthesis cluster separately. The Pks phylogenetic tree also differentiates the aflatoxin-related polypeptide sequences from those of other kinds of secondary metabolism. The function of some of the A. flavus Pks homologues may be deduced from the phylogenetic analysis. The conserved sequence motifs of protein domains shared by HexA/... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019042 Sun, 07 Dec 2008 17:18:35 +0100 2019042 http://www.medworm.com/index.php?rid=2019041&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052665%26dopt%3DAbstract Authors: Danishuddin , Khan AU Influenza A viruses of subtype H9N2 are wide spread among poultry and other mammalian species. Crossing the species barrier from poultry to human occurred in recent years creating a pandemic of H9N2 virus. It is known that the pathogenicity of H9N2 is lower than H5N1. Nonetheless, it is important to establish the molecular functions of H9N2 viral proteins. We studied mutations in the polymerase protein PB2 of H9N2 from different strains and compared it with the highly pathogenic H5N1. The mutation M294T was found to be important in the N-myristoylation domain of Ck/UP/2573/India/04(H9N2) isolate. Prediction of secondary structures and PROSITE motif assignments were performed for PB2 to gain functional insight. Subsequently, the effect of mutations in seco... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019041 Sun, 07 Dec 2008 17:18:35 +0100 2019041 http://www.medworm.com/index.php?rid=2019040&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052666%26dopt%3DAbstract We describe current and ongoing studies aimed to apply these overlapping areas of research, CARR and RISC, to a novel understanding of the immuno-neuropathology of HIV-1 infection, as an example. Taken together, the arguments presented here lead to a novel working hypothesis of molecular immune epigenetics as it pertains to HIV/AIDS, and the immunopathology of HIV-1-infected CD4+ cells. Specifically, we discuss these views in the context of the structure-function relationship of chromatin, the cdDNA/ncdDNA ratio, and possible nucleotide divergence in the untranslated regions (UTRs) of mature mRNA intronic and intergenic DNA sequences, and putative catastrophic consequences for immune surveillance and the preservation of health in HIV/AIDS. Here, we discuss the immunopathology of HIV Infect... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019040 Sun, 07 Dec 2008 17:18:35 +0100 2019040 http://www.medworm.com/index.php?rid=2019039&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19052667%26dopt%3DAbstract We describe current research that applies epigenetics to a novel understanding of the immuno-neuropathogenesis of HIV-1 viral infection and NeuroAIDS. We propose the hypothesis that HIV-1 alters the structure-function relationship of chromatin, coding DNA and non-coding DNA, including RNA transcribed from these regions resulting in pathogenesis in AIDS, drug abuse, and NeuroAIDS. We discuss the general implications of molecular epigenetics with special emphasis on drug abuse, bar-codes, pyknons, and miRNAs for translational and clinical research. We discuss the application of the recent recursive algorithm of biology to this field and propose to synthesize the Genomic and Epigenomic views into a holistic approach of HoloGenomics. PMID: 19052667 [PubMed - in process] (Source: Bioinforma... Bioinformation journals http://www.medworm.com/rss/comments.php?id=2019039 Sun, 07 Dec 2008 17:18:35 +0100 2019039 http://www.medworm.com/index.php?rid=1863678&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841236%26dopt%3DAbstract Authors: Biswas S, Guharoy M, Chakrabarti P The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs), made up of stretches of helix, strand and non-regular (NR) regions. On average 10-11 segments define the protein interface in protein-protein (PP) and protein-DNA (PD) complexes, while the number is higher (14) for protein-RNA (PR) complexes. While the length of helical segments in PP interaction increases with the interface area, this is not the case in PD and PR complexes. The propensities of residues to occur in the three types of secondary structural elements (SSEs) in the interface relative to the corresponding elements in the protein tertiary structures ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863678 Thu, 09 Oct 2008 20:10:04 +0100 1863678 http://www.medworm.com/index.php?rid=1863677&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841237%26dopt%3DAbstract Authors: Huang da W, Sherman BT, Stephens R, Baseler MW, Lane HC, Lempicki RA Our current biological knowledge is spread over many independent bioinformatics databases where many different types of gene and protein identifiers are used. The heterogeneous and redundant nature of these identifiers limits data analysis across different bioinformatics resources. It is an even more serious bottleneck of data analysis for larger datasets, such as gene lists derived from microarray and proteomic experiments. The DAVID Gene ID Conversion Tool (DICT), a web-based application, is able to convert user's input gene or gene product identifiers from one type to another in a more comprehensive and high-throughput manner with a uniquely enhanced ID-ID mapping database. AVAILABILITY: http://david.abcc.... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863677 Thu, 09 Oct 2008 20:10:04 +0100 1863677 http://www.medworm.com/index.php?rid=1863676&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841238%26dopt%3DAbstract Authors: Sundar AS, Varghese SM, Shameer K, Karaba N, Udayakumar M, Sowdhamini R The expressions of proteins in the cell are carefully regulated by transcription factors that interact with their downstream targets in specific signal transduction cascades. Our understanding of the regulation of functional genes responsive to stress signals is still nascent. Plants like Arabidopsis thaliana, are convenient model systems to study fundamental questions related to regulation of the stress transcriptome in response to stress challenges. Microarray results of the Arabidopsis transcriptome indicate that several genes could be upregulated during multiple stresses, such as cold, salinity, drought etc. Experimental biochemical validations have proved the involvement of several transcription facto... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863676 Thu, 09 Oct 2008 20:10:04 +0100 1863676 http://www.medworm.com/index.php?rid=1863675&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841239%26dopt%3DAbstract Authors: Telefont M, Liu Y The display of ontological information has become a crucial factor over the last decade in systems biology. The possibility to compare different ontological systems in a single application has however not been answered with an appropriate application. OntoSlug is an easy to use application that tries to fill this need. OntoSlug has been developed for use in classroom settings and scientific laboratory environment. PMID: 18841239 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863675 Thu, 09 Oct 2008 20:10:04 +0100 1863675 http://www.medworm.com/index.php?rid=1863674&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841240%26dopt%3DAbstract This article describes a method developed for predicting anticancer/non-anticancer drugs using artificial neural network (ANN). The ANN used in this study is a feed-forward neural network with a standard back-propagation training algorithm. Using 30 'inductive' QSAR descriptors alone, we have been able to achieve 84.28% accuracy for correct separation of compounds with- and without anticancer activity. For the complete set of 30 inductive QSAR descriptors, ANN based method reveals a superior model (accuracy = 84.28%, Q(pred) = 74.28%, sensitivity = 0.9285, specificity = 0.7857, Matthews correlation coefficient (MCC) = 0.6998). The method was trained and tested on a non redundant data set of 380 drugs (122 anticancer and 258 non-anticancer). The elaborated QSAR model based on the Artificial... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863674 Thu, 09 Oct 2008 20:10:04 +0100 1863674 http://www.medworm.com/index.php?rid=1863673&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841241%26dopt%3DAbstract Authors: Essoussi N, Boujenfa K, Limam M Multiple sequence alignment (MSA) is essential in phylogenetic, evolutionary and functional analysis. Several MSA tools are available in the literature. Here, we use several MSA tools such as ClustalX, Align-m, T-Coffee, SAGA, ProbCons, MAFFT, MUSCLE and DIALIGN to illustrate comparative phylogenetic trees analysis for two datasets. Results show that there is no single MSA tool that consistently outperforms the rest in producing reliable phylogenetic trees. PMID: 18841241 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863673 Thu, 09 Oct 2008 20:10:04 +0100 1863673 http://www.medworm.com/index.php?rid=1863672&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841242%26dopt%3DAbstract CONCLUSIONS: Near sequence identity of ITS2 regions of the members in a particular clade indicate that this region is undergoing parallel evolution to perform clade specific RNA biogenesis. The divergence of certain isolates of An. culicifacies from main clades in phylogenetic analyses suggests the possible existence of camouflaged sub-species within the complex of culicifacies. Using the fixed nucleotide differences, we estimate that these two clades have diverged nearly 3.3 million years ago, while the sibling species in clade 2 are under less evolutionary pressure, which may have evolved much later than the members in clade 1. PMID: 18841242 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863672 Thu, 09 Oct 2008 20:10:04 +0100 1863672 http://www.medworm.com/index.php?rid=1863671&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841243%26dopt%3DAbstract Authors: Reddy DM, Aspatwar A, Dholakia BB, Gupta VS The spindle checkpoint delays sister chromatid separation until all chromosomes have undergone bipolar spindle attachment. Previous studies have revealed BUB3, as an essential spindle checkpoint protein and its extensive sequence similarity with Rae1 (Gle2), a highly conserved member of WD40 repeat protein family throughout their length which was first shown to be involved in mRNA export. However, the recent discovery of Rae1 as an essential mitotic checkpoint protein, based on the studies from mouse and drosophila, has renewed the interest in its function during cell division. Study of evolution of proteins involved in checkpoint might throw light on evolution of eukaryotic cell cycle regulation. Here we report the evolutionary rela... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863671 Thu, 09 Oct 2008 20:10:04 +0100 1863671 http://www.medworm.com/index.php?rid=1863670&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841244%26dopt%3DAbstract Authors: Duan S, Zhang W, Bleibel WK, Cox NJ, Dolan ME The Affymetrix GeneChip(R) Human Exon 1.0 ST array (exon array) is designed to measure both gene-level and exon-level expression in human samples. This exon array contains ~1.4 million probesets consisting of ~5.4 million probes and profiles over 17,000 well-annotated gene transcripts in the human genome. As with all expression arrays, the exon array is vulnerable to SNPs within probes, because these SNPs can affect the hybridization of the probes and thus produce misleading expression values. In some cases, this could result in dramatic fluctuations of the exon-level expression. For this reason, we performed a genome-wide search for SNPs within regions that hybridize to probes by evaluating approximately 18 million SNPs in dbSNP (... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863670 Thu, 09 Oct 2008 20:10:04 +0100 1863670 http://www.medworm.com/index.php?rid=1863669&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18841245%26dopt%3DAbstract Authors: Anbazhagan P, Purushottam M, Kumar HB, Kubendran S, Mukherjee O, Brahmachari SK, Jain S, Sowdhamini R The chromosome 18q22-23 region has been shown to be implicated in bipolar disorder (BPAD) by several studies. PHLPP1 gene, in the locus (chromosome 18q22-23), is involved in circadian pathways and bears modules like 'PH domain and leucine rich repeat protein phosphatase'. This gene also contains a polyglutamine (CAG or PolyQ) repeat motif at the carboxyl terminal end. A comparative analysis of the PolyQ repeats of the PHLPP1 gene in humans, non-human primates and other species has been attempted in order to investigate the possible significance of repeat length as seen in other triplet-repeat associated diseases. Sequencing of the CAG repeat in humans and in non-human primates... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1863669 Thu, 09 Oct 2008 20:10:04 +0100 1863669 http://www.medworm.com/index.php?rid=1799244&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795104%26dopt%3DAbstract We describe an analytical two-stage framework with a multi-parallel data analysis method named wavelet-based generalized singular value decomposition and shaving method (WGSVD-shaving). This method is proposed for de-noising and dimension-reduction during early stage prognosis modeling. We also applied a supervised gene clustering technique with penalized logistic regression with Cox-model on an integrated data. We show the accuracy of the method using a simulated dataset with a case study on Hepatocelluar Carcinoma (HCC) cDNA and CGH data. The method shows improved results from GSVD-shaving and has application in the discovery of candidate genes associated with cancer. PMID: 18795104 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799244 Wed, 17 Sep 2008 17:10:46 +0100 1799244 http://www.medworm.com/index.php?rid=1799243&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795108%26dopt%3DAbstract We describe the design of a laccase with broader substrate spectrum in bioremediation. The application of evolutionary trace (ET) analysis of laccase at the ligand binding site for optimal design of the enzyme is described. In this attempt, class specific sites from ET analysis were mapped onto known crystal structure of laccase. The analysis revealed 162PHE as a critical residue in structure function relationship studies. PMID: 18795108 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799243 Wed, 17 Sep 2008 17:10:46 +0100 1799243 http://www.medworm.com/index.php?rid=1799242&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795109%26dopt%3DAbstract We describe a promoter recognition method named PCA-HPR to locate eukaryotic promoter regions and predict transcription start sites (TSSs). We computed codon (3-mer) and pentamer (5-mer) frequencies and created codon and pentamer frequency feature matrices to extract informative and discriminative features for effective classification. Principal component analysis (PCA) is applied to the feature matrices and a subset of principal components (PCs) are selected for classification. Our system uses three neural network classifiers to distinguish promoters versus exons, promoters versus introns, and promoters versus 3' un-translated region (3'UTR). We compared PCA-HPR with three well-known existing promoter prediction systems such as DragonGSF, Eponine and FirstEF. Validation shows that PCA-HPR... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799242 Wed, 17 Sep 2008 17:10:46 +0100 1799242 http://www.medworm.com/index.php?rid=1799241&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795110%26dopt%3DAbstract Authors: Lahiri T, Mishra H, Sarkar S, Misra K Multi-fractal property of heat-denatured protein aggregates (HDPA) is characteristic of its individual form. The visual similarity between digitally generated microscopic images of HDPA with that of surface-image of its individual X-ray structures in protein databank (PDB) displayed using Visual Molecular Dynamics (VMD) viewer is the basis of the study. We deigned experiments to view the fractal nature of proteins at different aggregate scales. Intensity based multi-fractal dimensions (ILMFD) extracted from various planes of digital microscopic images of protein aggregates were used to characterize HDPA into different classes. Moreover, the ILMFD parameters extracted from aggregates show similar classification pattern to digital images of ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799241 Wed, 17 Sep 2008 17:10:46 +0100 1799241 http://www.medworm.com/index.php?rid=1799240&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795111%26dopt%3DAbstract This study suggests that the highly electropositive substituents with low steric tolerance are required at 5 position of the pteridine ring and bulky electronegatve substituents are required at the meta-position of the phenyl ring. The information obtained from CoMFA and CoMSIA 3-D contour maps can be used for the design of deazapteridine-based analogs as anticancer agents. PMID: 18795111 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799240 Wed, 17 Sep 2008 17:10:46 +0100 1799240 http://www.medworm.com/index.php?rid=1799239&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795112%26dopt%3DAbstract Authors: Ramazzotti M, Monsellier E, Degl'innocenti D The correct display of data is often a key point for interpreting the results of experimental procedures. Multivariate data sets suffer from the problem of representation, since a dimensionality above 3 is beyond the capability of plotting programs. Moreover, non numerical variables such as protein annotations are usually fundamental for a full comprehension of biological data. Here we present a novel interactive XY plotter designed to take the full control of large datasets containing mixed-type variables, provided with an intuitive data management, a powerful labelling system and other features aimed at facilitating data interpretation and sub-setting. AVAILABILITY: XYLab program, test dataset and manual is available at www4.unifi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799239 Wed, 17 Sep 2008 17:10:46 +0100 1799239 http://www.medworm.com/index.php?rid=1799238&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795113%26dopt%3DAbstract Authors: Khan SN, Khan AU Binding modalities of doxorubicin (DOX), a widely used antineoplastic anthracyline antibiotic with hemoglobin (Hb) have been studied. The protein and the ligand were prepared using CORINA and protonated with insight II. The best conformation was sought by employing GOLDV. Molecular modeling calculations showed that DOX binds Hb to a non-classical drug binding site. The alpha subunit of Hb has been assigned to posses the binding site for DOX with a binding affinity (Ka) = 16.98 x10(3) mol(-1). The interaction was found to be thermodynamically favorable (DeltaG degrees = -66.23 KJmol(-1)). The analysis of DOX binding site to Hb suggested that the types of interactions that contribute in this binding are hydrophobic contacts, hydrogen bonding and electrostatic in... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799238 Wed, 17 Sep 2008 17:10:46 +0100 1799238 http://www.medworm.com/index.php?rid=1799237&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795114%26dopt%3DAbstract Authors: Rouchka EC, Phatak AW, Singh AV Microarrays provide a means of studying expression level of tens of thousands of genes by providing one or more oligonucleotide probe(s) for each transcript studied. Affymetrix(R) GeneChiptrade mark platforms historically pair each 25-base perfect match (PM) probe with a mismatch probe (MM) differing by a complementary base located in the 13(th) position to quantify and deflate effects of cross-hybridization. Analytical routines for analyzing these arrays take into account difference in expression levels of MM and PM probes to determine which ones are useful for further study. If a single nucleotide polymorphism (SNP) occurs at the 13(th) base, a probe with a higher MM expression level may be incorrectly omitted. In order to examine SNP affects ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799237 Wed, 17 Sep 2008 17:10:46 +0100 1799237 http://www.medworm.com/index.php?rid=1799236&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795115%26dopt%3DAbstract Authors: Wu CP, Law NF, Siu WC Current DNA compression algorithms work by finding similar repeated regions within the DNA sequence and then encoding these regions together to achieve compression. Our study on chromosome sequence similarity reveals that the length of similar repeated regions within one chromosome is about 4.5% of the total sequence length. The compression gain is often not high because of these short lengths. It is well known that similarity exist among different regions of chromosome sequences. This implies that similar repeated sequences are found among different regions of chromosome sequences. Here, we study cross-chromosomal similarity for DNA sequence compression. The length and location of similar repeated regions among the sixteen chromosomes of S. cerevisiae ar... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799236 Wed, 17 Sep 2008 17:10:46 +0100 1799236 http://www.medworm.com/index.php?rid=1799235&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18795116%26dopt%3DAbstract Authors: Imai K, Asakawa N, Tsuji T, Akazawa F, Ino A, Sonoyama M, Mitaku S A predictive software system, SOSUI-GramN, was developed for assessing the subcellular localization of proteins in Gram-negative bacteria. The system does not require the sequence homology data of any known sequences; instead, it uses only physicochemical parameters of the N- and C-terminal signal sequences, and the total sequence. The precision of the prediction system for subcellular localization to extracellular, outer membrane, periplasm, inner membrane and cytoplasmic medium was 92.3%, 89.4%, 86.4%, 97.5% and 93.5%, respectively, with corresponding recall rates of 70.3%, 87.5%, 76.0%, 97.5% and 88.4%, respectively. The overall performance for precision and recall obtained using this method was 92.9% and 86... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1799235 Wed, 17 Sep 2008 17:10:46 +0100 1799235 http://www.medworm.com/index.php?rid=1690178&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685717%26dopt%3DAbstract Authors: Zhang W, Duan S, Dolan ME The International HapMap Project provides a resource of genotypic data on single nucleotide polymorphisms (SNPs), which can be used in various association studies to identify the genetic determinants for phenotypic variations. Prior to the association studies, the HapMap dataset should be preprocessed in order to reduce the computation time and control the multiple testing problem. The less informative SNPs including those with very low genotyping rate and SNPs with rare minor allele frequencies to some extent in one or more population are removed. Some research designs only use SNPs in a subset of HapMap cell lines. Although the HapMap website and other association software packages have provided some basic tools for optimizing these datasets, a fast... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690178 Fri, 08 Aug 2008 18:24:38 +0100 1690178 http://www.medworm.com/index.php?rid=1690177&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685718%26dopt%3DAbstract Authors: Sudha KN, Shakira M, Prasanthi P, Sarika N, Kumar ChN, Babu PA Cyclooxygenase-2 (COX-2) enzyme binds to arachidonic acid and releases metabolites that are used to induce pain and inflammation. COX-2 selective inhibitors such as celecoxib, rofecoxib and valdecoxib are currently used to reduce inflammatory response. However, they lack anti-thrombotic activity and hence lead to cardiovascular and renal liabilities apart from gastrointestinal irritation. Therefore, there is still a need to develop more potent COX-2 inhibitors. In this paper, we report the screening of various compounds from the ZINC database (contains 4.6 million small molecule compounds) using the eHiTS (electronic High Throughput Screening) software tool against the COX-2 protein. The strategy employed can be co... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690177 Fri, 08 Aug 2008 18:24:38 +0100 1690177 http://www.medworm.com/index.php?rid=1690176&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685719%26dopt%3DAbstract Authors: Manikandan J, Aarthi JJ, Kumar SD, Pushparaj PN MicroRNAs (miRNAs) are members of a family of non-coding RNAs of 8-24 nucleotide RNA molecules that regulate target mRNAs. The first miRNAs, lin-4 and let-7, were first discovered in the year 1993 by Ambros, Ruvkun, and co-workers while studying development in Caenorhabditis elegans. miRNAs can play vital functions form C. elegans to higher vertebrates by typical Watson-Crick base pairing to specific mRNAs to regulate the expression of a specific gene. It has been well established that multicellular eukaryotes utilize miRNAs to regulate many biological processes such as embryonic development, proliferation, differentiation, and cell death. Recent studies have shown that miRNAs may provide new insight in cancer research. A recent ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690176 Fri, 08 Aug 2008 18:24:38 +0100 1690176 http://www.medworm.com/index.php?rid=1690175&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685720%26dopt%3DAbstract We present a new algorithm for detecting CGIs, called CpG Island Finder (CpGIF), which combines the best features in the most commonly used algorithms and avoids their disadvantages as much as possible. Five public tools for CpG island searching are used to compare with CpGIF for the assessment of accuracy and computational efficiency. The results reveal that CpGIF has higher performance coefficient and correlation coefficient than these previous methods, which indicates that CpGIF is able to provide high sensitivity and specificity at the same time. CpGIF is also faster than those methods with comparable prediction accuracy. PMID: 18685720 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690175 Fri, 08 Aug 2008 18:24:38 +0100 1690175 http://www.medworm.com/index.php?rid=1690174&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685721%26dopt%3DAbstract Authors: Arul L, Benita G, Balasubramanian P Glycosyl hydrolases hydrolyze the glycosidic bond either in carbohydrates or between carbohydrate and non-carbohydrate moiety. The beta-glucuronidase (beta D-glucuronoside glucuronosohydrolase; EC 3.2.1.31) enzyme belongs to the family-2 glycosyl hydrolase. The E. coli borne beta-glucuronidase gene (uidA) was devised as a gene fusion marker in plant genetic transformation experiments. Recent plant transformation vectors contain a novel beta-glucuronidase (gusA) derived from Staphylococcus sp. RLH1 for E. coli uidA. It is known to have a ten fold higher sensitivity compared to E. coli beta-glucuronidase. The functional superiority of Staphylococcus (gusA) over E. coli (uidA) activity is not fully known. The comparison of secondary structural ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690174 Fri, 08 Aug 2008 18:24:38 +0100 1690174 http://www.medworm.com/index.php?rid=1690173&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685722%26dopt%3DAbstract Authors: Kim CK, Choi JW, Park D, Kang MJ, Seol YJ, Hyun do Y, Hahn JH The Plant Gene Index (PlantGI) database is developed as a web-based search system with search capabilities for keywords to provide information on gene indices specifically for agricultural plants. The database contains specific Gene Index information for ten agricultural species, namely, rice, Chinese cabbage, wheat, maize, soybean, barley, mushroom, Arabidopsis, hot pepper and tomato. PlantGI differs from other Gene Index databases in being specific to agricultural plant species and thus complements services from similar other developments. The database includes options for interactive mining of EST CONTIGS and assembled EST data for user specific keyword queries. The current version of PlantGI contains a total of ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690173 Fri, 08 Aug 2008 18:24:38 +0100 1690173 http://www.medworm.com/index.php?rid=1690172&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685723%26dopt%3DAbstract Authors: Ordog R The fast growing Protein Data Bank (PDB) contains a vast amount of 3-dimensional data on proteins, and nucleic-acid structures obtained by X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. PyDeT is a PyMOL (molecular visualization software system) plug-in that visualize tessellations derived from the protein structure along with the source protein. PyDeT is released under a GNU General Public License (GPL) and is available from the authors. PMID: 18685723 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690172 Fri, 08 Aug 2008 18:24:38 +0100 1690172 http://www.medworm.com/index.php?rid=1690171&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685724%26dopt%3DAbstract Authors: Shapshak P, Rodriguez HE, Kayathri R, Levine A, Chiappelli F, Minagar A Alzheimer's disease (AD), the most common cause of dementia, has few clinical similarities to HIV-1-associated dementia (HAD). However, genes were identified related among these dementias. Discovering correlations between gene function, expression, and structure in the human genome continues to aid in understanding the similarities between pathogenesis of these two dementing disorders. The current work attempts to identify relationships between these dementias in spite of their clinical differences, based on genomic structure, function, and expression. In this comparative study, the NCBI Entrez Genome Database is used to detect these relationships. This approach serves as a model for future diagnosis and t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690171 Fri, 08 Aug 2008 18:24:38 +0100 1690171 http://www.medworm.com/index.php?rid=1690170&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685725%26dopt%3DAbstract Authors: Valdivia-Granda W The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes. This transformational field, known as metagenomics, is generating massive amounts of molecular information that can overwhelm the performance of conventional analysis and visualization algorithms. Here, I briefly highlight some of the emerging challenges this new discipline presents to the computational biology community and point some of the opportunities to develop applications that can translate metagenomic information into biomedical, agricultural, environmental, and industrial applications. PMID: 18685725 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690170 Fri, 08 Aug 2008 18:24:38 +0100 1690170 http://www.medworm.com/index.php?rid=1690169&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18685726%26dopt%3DAbstract Authors: Dwivedi N, Dwivedi SP, Kumar A, Katoch VM, Mishra S The availability of completely sequenced genomes allow the use of computational techniques to investigate cis-acting sequences controlling transcription regulation associated with groups of functionally related genes. Theoretical analysis was performed to assign functions to regulatory systems. The identification of such sites is relevant for locating a promoter at the 5' boundary of a gene. They also allow the prediction of specific gene-expression pattern and response to disturbances in a known signaling pathway. Here, we describe the identification of composite transcription factor (TF) binding sites over promoter regions in16s-rRNA gene for mycobacterium species strains ICC47, ICC67, ICC43 and CMVL700. It is established t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1690169 Fri, 08 Aug 2008 18:24:38 +0100 1690169 http://www.medworm.com/index.php?rid=1591350&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317570%26dopt%3DAbstract Authors: Pushparaj PN, Aarthi JJ, Kumar SD, Manikandan J RNA interference (RNAi) is a powerful technology with huge applications for functional genomics, target identification in drug discovery and elucidation of molecular signaling pathways. Current RNAi studies have demonstrated the clinical potential of small interfering RNAs (siRNAs) in metabolic diseases, cancer, AIDS, malaria, neurodegenerative disorders, dental diseases and other illnesses. Interestingly, recent studies have shown that the small RNA molecules, either indigenously produced as microRNAs (miRNAs) or exogenously administered synthetic dsRNAs could effectively activate a particular gene in a sequence specific manner instead of silencing it. This novel, but still uncharacterized, phenomenon has been termed as RNA acti... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591350 Mon, 07 Jul 2008 20:26:24 +0100 1591350 http://www.medworm.com/index.php?rid=1591349&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317571%26dopt%3DAbstract Authors: Zhang W, Dolan ME The International HapMap Project provides a key resource of genotypic data on human lymphoblastoid cell lines derived from four major world populations of European, African, Chinese and Japanese ancestry for researchers to associate with various phenotypic data to find genes affecting health, disease and response to drugs. Recently, the HapMap resource has significantly benefited research areas such as gene expression variation studies. Besides some intrinsic limitations, there are a few challenges that should be considered in the next wave of research using this tremendous resource. We suggest that overcoming these challenges or considering the confounding variables in the interpretation of results can provide more insights into the current views of the huma... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591349 Mon, 07 Jul 2008 20:26:24 +0100 1591349 http://www.medworm.com/index.php?rid=1591348&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317572%26dopt%3DAbstract Authors: Nandi T Human infection with avian influenza H5N1 is an emerging infectious disease characterized by respiratory symptoms and a high fatality rate. Hemagglutinin and neuraminidase are the two surface proteins responsible for infection by influenza virus. Till date, neuraminidase has been the major target for antiviral drugs. In the present study we chose hemagglutinin protein as it mediates the binding of the virus to target cells through sialic acid residues on the host cell-surface. Hemagglutinin of H5 avian influenza (PDB ID: 1JSN) was used as the receptor protein. Ligands were generated by structure-based de novo approach and virtual screening of ZINC database. A total of 11,104 conformers were generated and docked into the receptor binding site using 'High Throughput Virt... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591348 Mon, 07 Jul 2008 20:26:24 +0100 1591348 http://www.medworm.com/index.php?rid=1591347&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317573%26dopt%3DAbstract Authors: Gollery M PMID: 18317573 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591347 Mon, 07 Jul 2008 20:26:24 +0100 1591347 http://www.medworm.com/index.php?rid=1591346&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317574%26dopt%3DAbstract Authors: Yari A, Passo FS, Yari V, Sanni O, Yari M, Dovenou MZ, Traore R, Hounyet JP We design a "simple" and "low cost" model technology for monitoring HIV viral load in resource-poor settings: SMARThivVLmos. Cost and complexity are the major challenges to the developing world, in monitoring HIV patients viral load. We have previously demonstrated in our SMARThivPack model that cost and complexity of laboratory monitoring of HIV patients, may be reduced not only at a first technology development level, but also at a second technology implementation, and at a third global coordination levels. In our SMARThivPack model, the P24 HIV viral load monitoring system passed both the "cost" and the "complexity" tests. However, compared to other alternative viral monitoring systems such as the C... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591346 Mon, 07 Jul 2008 20:26:24 +0100 1591346 http://www.medworm.com/index.php?rid=1591345&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317575%26dopt%3DAbstract In conclusion, this pilot clinical study indicates that the combined administration of sesamin with schisandra extract could improve blood fluidity after 1 week of oral intake and this effect was sustained up to 2 weeks. PMID: 18317575 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591345 Mon, 07 Jul 2008 20:26:24 +0100 1591345 http://www.medworm.com/index.php?rid=1591344&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317576%26dopt%3DAbstract This study presents an allergenic protein prediction system that appears to be capable of producing high sensitivity and specificity. The proposed system is based on support vector machine (SVM) using evolutionary information in the form of an amino acid position specific scoring matrix (PSSM). The performance of this system is assessed by a 10-fold cross-validation experiment using a dataset consisting of 693 allergens and 1041 non-allergens obtained from Swiss-Prot and Structural Database of Allergenic Proteins (SDAP). The PSSM method produced an accuracy of 90.1% in comparison to the methods based on SVM using amino acid, dipeptide composition, pseudo (5-tier) amino acid composition that achieved an accuracy of 86.3, 86.5 and 82.1% respectively. The results show that evolutionary inform... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591344 Mon, 07 Jul 2008 20:26:24 +0100 1591344 http://www.medworm.com/index.php?rid=1591343&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317577%26dopt%3DAbstract Authors: Yari A, Passo FS, Yari V, Sanni O, Yari M, Dovenou MZ, Traore R, Hounyet JP We design a "simple" and "low cost" model technology for monitoring HIV patients CD4 number in resource-poor settings: SMARThivCD4mos. Cost and complexity are the major challenges to the developing world in transferring and implementing HIV surveillance technologies. We previously proposed a "three tests" combo kit model for improving HIV patients monitoring standards in resource-poor settings. From the pool of recommended alternative CD4 counting technologies, our "three tests" combo kit model retained the Capcellia technology for its "simplicity". However, compared to other CD4 counting technologies, such as Dynabeads, the Capcellia technology is "expensive". Here, we describe a cost reduction strate... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591343 Mon, 07 Jul 2008 20:26:24 +0100 1591343 http://www.medworm.com/index.php?rid=1591342&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317578%26dopt%3DAbstract Authors: Latheef SA, Prasad B, Bavaji M, Subramanyam G Medicinal plants play an important role in health care. The use of medicinal plants for treatment is growing in view of cost and non-compliance of modern medicine as in case of non-communicable diseases. Plants such as Boswellia, ovalifoliolata, Cycas beddomei, Pimpinella tirupatiensis, Pterocarpus santalinus, Shorea thumbuggaia, Syzygium alternifolium, Terminalia pallida are endemic to Tirumala hills of seshachalam range falling under the Eastern Ghats of India. These plants species have medicinal properties such as anti-tumorogenic, anti-microbial, purgative, hypoglycemic, abortificient, analgesic, anti-septic, anti-pyretic and anti-inflammatory. We created a database named DEPTH in an attempt to communicate data of these plants ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591342 Mon, 07 Jul 2008 20:26:24 +0100 1591342 http://www.medworm.com/index.php?rid=1591341&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18317579%26dopt%3DAbstract RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN. Bioinformation. 2008;2(6):263-70 Authors: Naik PK, Mittal VK, Gupta S The problem of predicting non-long terminal repeats (LTR) like long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) from the DNA sequence is still an open problem in bioinformatics. To elevate the quality of annotations of LINES and SINEs an automated tool "RetroPred" was developed. The pipeline allowed rapid and thorough annotation of non-LTR retrotransposons. The non-LTR retrotransposable elements were initially predicted by Pairwise Aligner for Long Sequences (PALS) and Parsimonious Inference of a Libr... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591341 Mon, 07 Jul 2008 20:26:24 +0100 1591341 http://www.medworm.com/index.php?rid=1591340&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478078%26dopt%3DAbstract Authors: Costantini S, Paladino A, Facchiano AM The center of mass of a protein is an artificial point useful for detecting important and simple features of proteins structure, shape and association.CALCOM is a software which calculates the center of mass of a protein, starting from PDB protein structure files. In the case of protein complexes and of protein-small ligand complexes, the position of protein residues or of ligand atoms respect to each protein subunit can be evaluated, as well as the distance among the center of mass of the protein subunits, in order to compare different conformations and evaluate the relative motion of subunits. AVAILABILITY: THE SERVICE IS AVAILABLE AT THE URL: http://bioinformatica.isa.cnr.it/CALCOM/. PMID: 18478078 [PubMed - in process] (Source: Bi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591340 Mon, 07 Jul 2008 20:26:24 +0100 1591340 http://www.medworm.com/index.php?rid=1591339&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478079%26dopt%3DAbstract Authors: Choong MK, Yan H This paper presents a new method for exon detection in DNA sequences based on multi-scale parametric spectral analysis. A forward-backward linear prediction (FBLP) with the singular value decomposition (SVD) algorithm FBLP-SVD is applied to the double-base curves (DB-curves) of a DNA sequence using a variable moving window sizes to estimate the signal spectrum at multiple scales. Simulations are done on short human genes in the range of 11bp to 2032bp and the results show that our proposed method out-performs the classical Fourier transform method. The multi-scale approach is shown to be more effective than using a single scale with a fixed window size. In addition, our method is flexible as it requires no training data. PMID: 18478079 [PubMed - in process... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591339 Mon, 07 Jul 2008 20:26:24 +0100 1591339 http://www.medworm.com/index.php?rid=1591338&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478080%26dopt%3DAbstract We present a library of protein functional templates (PFTs) designed to represent the compositional and evolutionary conservation patterns of functional sites at the molecular and biological function level. Subsequently we developed LIMACS (LInear MAtching of Conservation Scores), a software tool that uses the template library for the prediction of functionally important sites in a multiple sequence alignment, transferring the molecular function annotation from the most-similar functional site in the template library to a predicted site. AVAILABILITY: The PFT library, the LIMACS program and source code are available for PC, Mac and Linux operating systems from ftp://ftp.ncbi.nih.gov/pub/lanczyck/limacs. PMID: 18478080 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591338 Mon, 07 Jul 2008 20:26:24 +0100 1591338 http://www.medworm.com/index.php?rid=1591337&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478081%26dopt%3DAbstract This study also reports the possible regions of gene rearrangements in these two genomes and further characterization of such RNA regions could shed more light on their possible role in genome evolution. PMID: 18478081 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591337 Mon, 07 Jul 2008 20:26:24 +0100 1591337 http://www.medworm.com/index.php?rid=1591336&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478082%26dopt%3DAbstract Authors: Zhang H, Lu M, Zhang Y, Li Z Soluble guanylate cyclase (sGC) is an important heme sensor protein. Regulation of the status of heme in the heme binding domain (or HNOX domain) by various gaseous activators can increase the catalytic efficiency of the cyclase domain. Several studies have demonstrated that the full activation of sGC is directly related to the cleavage of the Fe-His bond of the HNOX domain. To expand the primary response of the sGC HNOX domain to the cleavage event, a structural model of the sGC HNOX domain was constructed using homology modeling and the Fe-His bond was released at 6 ns of a 10-ns molecular dynamics simulation. An instant increment of Calpha-RMSD over L2 (Loop2, residues 124-130) was found after the cleavage of the Fe-His bond, which was consisten... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591336 Mon, 07 Jul 2008 20:26:24 +0100 1591336 http://www.medworm.com/index.php?rid=1591335&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478083%26dopt%3DAbstract Authors: Xu W, Wang M, Zhang X, Wang L, Feng H Gene selection is to detect the most significantly expressed genes under different conditions expression data. The current challenge in gene selection is the comparison of a large number of genes with limited patient samples. Thus it is trivial task in simple statistical analysis. Various statistical measurements are adopted by filter methods applied in gene selection studies. Their ability to discriminate phenotypes is crucial in classification and selection. Here we describe the standard deviation error distribution (SDED) method for gene selection. It utilizes variations within-class and among-class in gene expression data. We tested the method using 4 leukemia datasets available in the public domain. The method was compared with the GS... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591335 Mon, 07 Jul 2008 20:26:24 +0100 1591335 http://www.medworm.com/index.php?rid=1591334&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478084%26dopt%3DAbstract Authors: Anandagopu P, Suhanya S, Jayaraj V, Rajasekaran E Distribution of thymine in protein coding mRNA sequences has been studied here. Our study suggest that thymine in protein coding sequences are not randomly distributed but with probability. Frame1 prefers to have definite amount of thymine. It is observed that the thymine content of frame 4 is also involved in protein coding. Frame 3 prefers to have least amount of thymine. However, frame 2 and frame 6 shows a variable degree of thymine content. The mRNA sequences of heterosexual animals, particularly, the human show a different distribution profile (less thymine in frame 1) compared to that of yeast and plants. PMID: 18478084 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591334 Mon, 07 Jul 2008 20:26:24 +0100 1591334 http://www.medworm.com/index.php?rid=1591333&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478085%26dopt%3DAbstract Authors: Koshy N, Ponnuvel KM, Sinha RK, Qadri S The domesticated silkworm, Bombyx mori serves as an ideal representative of lepidopteran species for a variety of scientific studies. As a result, databases have been created to organize information pertaining to the silkworm genome that is subject to constant updating. Of these, four main databases are important for store nucleotide information in the form of genomic data, ESTs and microsatelites. These databases also store data related to other lepidoptera and important insects, which help in insect biological research. Though a considerable amount of nucleotide data is currently available, there is a paucity of data related to silkworm and other lepidopteran proteins. Hence, the focus of this article is to present the current status o... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591333 Mon, 07 Jul 2008 20:26:24 +0100 1591333 http://www.medworm.com/index.php?rid=1591332&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478086%26dopt%3DAbstract Authors: Fantaccione S, Woodrow P, Pontecorvo G Genetic assessment was carried out on three Italian melon accessions by sequence and structural analysis of the internal transcribed spacer 1 (ITS1) from three populations belonging to two Cucumis melo L. varieties (madras and tendral). Alignment of the 18S-5.8S-26S sequences from three melon accessions showed that there were three single-nucleotide polymorphisms (SNPs) and one short insertion-deletion (indel) at the 5'end ITS1. An amplification refractory mutation system (ARMS)-PCR-based analysis was successfully applied to the SNP markers of the ITS1 sequences for the fingerprinting analysis of three melon populations. Secondary structure models for each ITS1 were derived. The prediction of ITS1 RNA secondary structure from each accessi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591332 Mon, 07 Jul 2008 20:26:24 +0100 1591332 http://www.medworm.com/index.php?rid=1591331&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18478087%26dopt%3DAbstract Authors: Lu J, Luo L The accurate identification of promoter regions and transcription start sites is a challenge to the construction of human transcription regulation networks. Thus, an efficient prediction method based on theoretical formulation is necessary for this purpose. We used the method of increment diversity with quadratic discriminant analysis (IDQD) to predict transcription start sites (TSS). The method produced sensitivity and positive predictive value of more than 65% with positives to negatives ratio of 1:58. The performance evaluation using Receiver Operator Characteristics (ROC) showed an auROC (area under ROC) of greater than 96%. The evaluation by Precision Recall Curves (PRC) showed an auPRC (area under PRC) of about 26% for positives to negatives ratio of 1:679 an... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591331 Mon, 07 Jul 2008 20:26:24 +0100 1591331 http://www.medworm.com/index.php?rid=1591412&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597917%26dopt%3DAbstract Authors: Annamala MK, Inampudi KK, Guruprasad L The Ag85 family enzymes are responsible for the synthesis of cell wall components in mycobacterial species. Inhibitors to these enzymes are potential antimycobacterial agents. We have carried out the docking of phoshonate and trehalose analog inhibitors into the three dimensional structure of mycolyltransferase enzyme, Ag85C of M. tuberculosis using the GOLD software. The inhibitor binding positions and affinity were evaluated using both the scoring fitness functions- GoldScore and ChemScore. We observed that the inhibitor binding position identified using the GoldScore was marginally better than the ChemScore. A qualitative agreement between the reported experimental biological activities (IC50) and the GoldScore was observed. We identif... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591412 Mon, 01 Jan 2007 05:00:00 +0100 1591412 http://www.medworm.com/index.php?rid=1591411&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597918%26dopt%3DAbstract Authors: Perrizo W PMID: 17597918 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591411 Mon, 01 Jan 2007 05:00:00 +0100 1591411 http://www.medworm.com/index.php?rid=1591410&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597919%26dopt%3DAbstract Authors: Gollery M PMID: 17597919 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591410 Mon, 01 Jan 2007 05:00:00 +0100 1591410 http://www.medworm.com/index.php?rid=1591409&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597920%26dopt%3DAbstract We present here a fine example which points out the interest of MED-SuMo approach for functional structural annotation. PMID: 17597920 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591409 Mon, 01 Jan 2007 05:00:00 +0100 1591409 http://www.medworm.com/index.php?rid=1591408&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597921%26dopt%3DAbstract Authors: Rak R, Kurgan L, Reformat M The GENIA ontology is a taxonomy that was developed as a result of manual annotation of a subset of MEDLINE, the GENIA corpus. Both the ontology and corpus have been used as a benchmark to test and develop biological information extraction tools. Recent work shows, however, that there is a demand for a more comprehensive ontology that would go along with the corpus. We propose a complete OWL ontology built on top of the GENIA ontology utilizing the GENIA corpus. The proposed ontology includes elements such as the original taxonomy of categories, biological entities as individuals, relations between individuals using verbs and verb nominalizations as object properties, and links to the UMLS Metathesaurus concepts. AVAILABILITY: http://www.ece.ualbert... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591408 Mon, 01 Jan 2007 05:00:00 +0100 1591408 http://www.medworm.com/index.php?rid=1591407&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597922%26dopt%3DAbstract Authors: Prolo P, Chiappelli F, Angeli A, Dovio A, Perotti P, Pautasso M, Sartori ML, Saba L, Mussino S, Fraccalini T, Fantó F, Mocellini C, Rosso MG, Grasso E Patients with Alzheimer's disease (AD) are characterized by an altered sensitivity to cortisol-mediated modulation of circulating lymphocytes. Longitudinal studies are needed to address the clinical applicability of these abnormalities as prognostic factors. Therefore, we designed a longitudinal study to address the clinical applicability of physiologic modulation of Natural Killer (NK) cell activity as a prognostic factor in AD. NK activity was assessed as baseline measurement and in response to modulation by cortisol at 10(-6)M. To verify the immunophysiological integrity of the NK cell population, we tested augmentation ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591407 Mon, 01 Jan 2007 05:00:00 +0100 1591407 http://www.medworm.com/index.php?rid=1591406&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597923%26dopt%3DAbstract Authors: Shanmughavel P The massive development of biodiversity related information systems over the WWW (World Wide Web) has created much excitement in recent years. These arrays of new data sources are counterbalanced by the difficulty in knowing their location and nature. However, biologists and computer scientists have started to pull together in a rising tide of coherence and organization to address this issue. The fledging field of biodiversity informatics is expected to deliver major advances that could turn the WWW into a giant global biodiversity information system. The present paper briefly reviews the databases in preserving the biodiversity data. PMID: 17597923 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591406 Mon, 01 Jan 2007 05:00:00 +0100 1591406 http://www.medworm.com/index.php?rid=1591405&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597924%26dopt%3DAbstract Authors: Reddy DM Haemoglobins are found ubiquitously in eukaryotes and many bacteria. In plants, haemoglobins were first identified in species, which can fix nitrogen via symbiosis with bacteria. Recent findings suggest that another class of haemoglobins termed as nonsymbiotic haemoglobins are present through out the plant kingdom and are expressed differentially during plant development. Limited data available suggests that non-symbiotic haemoglobins are involved in hypoxic stress and oversupply of nutrients. Due to lack of information on structurally conserved, functionally important residues in non-symbiotic haemoglobins, further studies to elucidate the molecular mechanisms underlying the biological role are hampered. To determine functionally important residues in non-symbiotic h... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591405 Mon, 01 Jan 2007 05:00:00 +0100 1591405 http://www.medworm.com/index.php?rid=1591404&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597925%26dopt%3DAbstract Authors: Sivashankari S, Shanmughavel P The rapidly emerging field of comparative genomics has yielded dramatic results. Comparative genome analysis has become feasible with the availability of a number of completely sequenced genomes. Comparison of complete genomes between organisms allow for global views on genome evolution and the availability of many completely sequenced genomes increases the predictive power in deciphering the hidden information in genome design, function and evolution. Thus, comparison of human genes with genes from other genomes in a genomic landscape could help assign novel functions for un-annotated genes. Here, we discuss the recently used techniques for comparative genomics and their derived inferences in genome biology. PMID: 17597925 [PubMed] (Source: ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591404 Mon, 01 Jan 2007 05:00:00 +0100 1591404 http://www.medworm.com/index.php?rid=1591403&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597926%26dopt%3DAbstract Authors: Johnson CD, Balagurunathan Y, Dougherty ER, Afshari CA, He Q, Ramos KS To understand the complex nature of the atherogenic response initiated by oxidative stress in vascular smooth muscle cells (vSMCs), computational prediction methodology was employed to define putative gene-gene and gene-environment interactions in vSMCs subjected to oxidative chemical stress. Computational relationships were derived from the global gene expression profiles of murine cells challenged with a chemical pro-oxidant to cause oxidative stress or cells treated with anti-oxidant prior to oxidative injury. Target clones were chosen based on their biological relevance within the context of the atherogenic response and included lysyl oxidase, matrix metalloproteinase 2, insulin like growth factor bindi... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591403 Mon, 01 Jan 2007 05:00:00 +0100 1591403 http://www.medworm.com/index.php?rid=1591402&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597927%26dopt%3DAbstract Authors: Brand JP, Chen L, Cui X, Bartolucci AA, Page GP, Kim K, Barnes S, Srinivasasainagendra V, Beasley MT, Allison DB The adaptive alpha-spending algorithm incorporates additional contextual evidence (including correlations among genes) about differential expression to adjust the initial p-values to yield the alpha-spending adjusted p-values. The alpha-spending algorithm is named so because of its similarity with the alpha-spending algorithm in interim analysis of clinical trials in which stage-specific significance levels are assigned to each stage of the clinical trial. We show that the Bonferroni correction applied to the alpha-spending adjusted p-values approximately controls the Family Wise Error Rate under the complete null hypothesis. Using simulations we also show that the ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591402 Mon, 01 Jan 2007 05:00:00 +0100 1591402 http://www.medworm.com/index.php?rid=1591401&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597928%26dopt%3DAbstract Authors: Logan DA, Koch AL, Dong W, Griffith J, Nilsen R, Case ME, Schüttler HB, Arnold J The products of five structural genes and two regulatory genes of the qa gene cluster of Neurospora crassa control the metabolism of quinic acid (QA) as a carbon source. A detailed genetic network model of this metabolic process has been reported. This investigation is designed to expand the current model of the QA reaction network. The ensemble method of network identification was used to model RNA profiling data on the qa gene cluster. Through microarray and cluster analysis, genome-wide identification of RNA transcripts associated with quinic acid metabolism in N. crassa is described and suggests a connection to other metabolic circuits. More than 100 genes whose products include carbon me... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591401 Mon, 01 Jan 2007 05:00:00 +0100 1591401 http://www.medworm.com/index.php?rid=1591400&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597929%26dopt%3DAbstract Authors: Boratyn GM, Datta S, Datta S In this paper we propose a data based algorithm to marry existing biological knowledge (e.g., functional annotations of genes) with experimental data (gene expression profiles) in creating an overall dissimilarity that can be used with any clustering algorithm that uses a general dissimilarity matrix. We explore this idea with two publicly available gene expression data sets and functional annotations where the results are compared with the clustering results that uses only the experimental data. Although more elaborate evaluations might be called for, the present paper makes a strong case for utilizing existing biological information in the clustering process. AVAILABILITY: Supplement is available at www.somnathdatta.org/Supp/Bioinformation/append... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591400 Mon, 01 Jan 2007 05:00:00 +0100 1591400 http://www.medworm.com/index.php?rid=1591399&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597930%26dopt%3DAbstract Authors: Singh AV, Knudsen KB, Knudsen TB Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591399 Mon, 01 Jan 2007 05:00:00 +0100 1591399 http://www.medworm.com/index.php?rid=1591398&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597931%26dopt%3DAbstract This article extends the order restricted inference approach for time-course or dose-response gene expression microarray data, introduced by Peddada and colleagues (2003) for the case when gene expression is heteroscedastic over time or dose. The new methodology uses an iterative algorithm to estimate mean expression at various times/doses when mean expression is subject to pre-defined patterns or profiles, known as order-restrictions. Simulation studies reveal that the resulting bootstrap-based methodology for gene selection maintains the false positive rate at the nominal level while competing well with ORIOGEN in terms of power. The proposed methodology is illustrated using a breast cancer cell-line data analyzed by Peddada and colleagues (2003). PMID: 17597931 [PubMed] (Source: Bio... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591398 Mon, 01 Jan 2007 05:00:00 +0100 1591398 http://www.medworm.com/index.php?rid=1591397&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597932%26dopt%3DAbstract Authors: Pirooznia M, Nagarajan V, Deng Y Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a Venn diagram. Venn diagrams are graphical ways of representing interactions among sets to display information that can be read easily. Here we propose a simple but effective web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI's Entrez Nucleotide database. AVAILABILITY: GeneVenn is available for free at http://mcbc.usm.edu/genevenn/ PMID: 17597932 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591397 Mon, 01 Jan 2007 05:00:00 +0100 1591397 http://www.medworm.com/index.php?rid=1591396&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597933%26dopt%3DAbstract Authors: Lee EK, Park T In microarray experiments many undesirable systematic variations are commonly observed. Often investigators analyzing microarray data need to make subjective decisions about the quality of the experiment, by examining its chip image and a simple scatter plot. Thus, a more rigorous but simple method is desirable to determine the quality of microarray data. We propose two exploratory methods to investigate the quality of microarray experiments with replicated chips. The first method is based on correlations among chips and the second on the actual intensity values for each gene. The proposed methods are illustrated using a real microarray data set. The methods provide an initial estimation for determining the quality of microarray experiments. PMID: 17597933 [... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591396 Mon, 01 Jan 2007 05:00:00 +0100 1591396 http://www.medworm.com/index.php?rid=1591395&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597934%26dopt%3DAbstract Authors: Klebanov L, Yakovlev A Our answer to the question posed in the title is negative. This intentionally provocative note discusses the issue of sample size in microarray studies from several angles. We suggest that the current view of microarrays as no more than a screening tool be changed and small sample studies no longer be considered appropriate. PMID: 17597934 [PubMed] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591395 Mon, 01 Jan 2007 05:00:00 +0100 1591395 http://www.medworm.com/index.php?rid=1591394&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597935%26dopt%3DAbstract Authors: Conde L, Montaner D, Burguet-Castell J, Tárraga J, Al-Shahrour F, Dopazo J Contrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of t... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591394 Mon, 01 Jan 2007 05:00:00 +0100 1591394 http://www.medworm.com/index.php?rid=1591393&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17597936%26dopt%3DAbstract Authors: Cheng C, Pounds S The microarray gene expression applications have greatly stimulated the statistical research on the massive multiple hypothesis tests problem. There is now a large body of literature in this area and basically five paradigms of massive multiple tests: control of the false discovery rate (FDR), estimation of FDR, significance threshold criteria, control of family-wise error rate (FWER) or generalized FWER (gFWER), and empirical Bayes approaches. This paper contains a technical survey of the developments of the FDR-related paradigms, emphasizing precise formulation of the problem, concepts of error measurements, and considerations in applications. The goal is not to do an exhaustive literature survey, but rather to review the current state of the field. PMI... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591393 Mon, 01 Jan 2007 05:00:00 +0100 1591393 http://www.medworm.com/index.php?rid=1591390&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084641%26dopt%3DAbstract Authors: Chiappelli F, Prolo P, D Cajulis K, Angeli A, Dovio A, Perotti P, Pautasso M, Luisa Sartori M, Saba L, Mussino S, Fraccalini T, Fanto F, Manfrini E, Mocellini C, Gabriella Rosso M, Grasso E The emerging domain of epigenetics in molecular medicine finds application for a variety of patient populations. Here, we present fundamental neuroendocrine immune evidence obtained in patients with senile dementia of the Alzheimer's type (sDAT), and discuss the implications of these data from the viewpoint of translational epigenetics of Alzheimer's disease. We followed 18 subjects with mild sDAT treated with acetylcholinesterase inhibitors, and 10 control subjects matched for age in a repeated measure design every six months for 18 months. We monitored psychosocial profile (Mini-Mental St... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591390 Mon, 01 Jan 2007 05:00:00 +0100 1591390 http://www.medworm.com/index.php?rid=1591389&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084642%26dopt%3DAbstract Authors: Kumar L, E Futschik M For the analysis of microarray data, clustering techniques are frequently used. Most of such methods are based on hard clustering of data wherein one gene (or sample) is assigned to exactly one cluster. Hard clustering, however, suffers from several drawbacks such as sensitivity to noise and information loss. In contrast, soft clustering methods can assign a gene to several clusters. They can overcome shortcomings of conventional hard clustering techniques and offer further advantages. Thus, we constructed an R package termed Mfuzz implementing soft clustering tools for microarray data analysis. The additional package Mfuzzgui provides a convenient TclTk based graphical user interface. AVAILABILITY: The R package Mfuzz and Mfuzzgui are available at http:/... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591389 Mon, 01 Jan 2007 05:00:00 +0100 1591389 http://www.medworm.com/index.php?rid=1591388&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084643%26dopt%3DAbstract Authors: Lakshmi PT At the turn of the millennium, cyanobacteria deserve attention to be reviewed to understand the past, present and future. The advent of post genomic research, which encompasses functional genomics, structural genomics, transcriptomics, pharmacogenomics, proteomics and metabolomics that allows a systematic wide approach for biological system studies. Thus by exploiting genomic and associated protein information through computational analyses, the fledging information that are generated by biotechnological analyses, could be well extrapolated to fill in the lacuna of scarce information on cyanobacteria and as an effort this paper attempts to highlights the perspectives available and awakens researcher to concentrate in the field of cyanobacterial informatics. PMID... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591388 Mon, 01 Jan 2007 05:00:00 +0100 1591388 http://www.medworm.com/index.php?rid=1591387&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084644%26dopt%3DAbstract Authors: Murthy VR, Raghuram DV, Murthy PN Studies pertaining to drug-DNA interactions in treating a disease efficiently have taken an important place in recent times. Murthy and colleagues were active in correlating the drug activity, with physical parameters like refractivity, susceptibility, molecular electron ionization cross-section and the dosage. The molecular polarizability, diamagnetic susceptibility and molecular electron ionization cross section Q have been evaluated. An analysis of Q in the light of the data available on plasma protein binding, bio availability, Log P and half-Life show semblance of regular dependence of Q on them and hence an effort is made to bring this dependence into a regular mathematical relationship. The dosage of each drug is calculated. A critical ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591387 Mon, 01 Jan 2007 05:00:00 +0100 1591387 http://www.medworm.com/index.php?rid=1591386&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084645%26dopt%3DAbstract Authors: Kashyap L, Tabish M, Ganesh G, Dubey D C. elegans C46H11.4 gene encodes a Let-23 fertility effector/regulator protein of the EGF-receptor class of the tyrosine kinase family. Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. C. elegans genome sequencing consortium has reported three alternatively spliced transcripts of C46H11.4 gene which encodes for three hypothetical proteins namely, C46H11.4a, C46H11.4b and C46H11.4c. Using a combination of various bioinformatics tools like gene or exon finding programmes, blast searches, alignment tools etc followed by experimental validation, we report the presence of three more alternatively spliced transcripts which encode for novel hypothetical proteins C46H11.4d, C46H11.4e and C46H11.4f. T... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591386 Mon, 01 Jan 2007 05:00:00 +0100 1591386 http://www.medworm.com/index.php?rid=1591385&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084646%26dopt%3DAbstract Authors: Arulrayan N, Rangasamy S, James E, Pitchai D Effective treatment of diabetes is increasingly dependent on active constituents of medicinal plants capable of controlling hyperglycemia as well as its secondary complications. Sensing the importance of documenting such medicinal plants, here we describe a web database containing information (name, literature citation, active compounds and few related full text articles) of the diabetes medicinal plants exhibiting hypoglycemic, antioxidant and antimicrobial effects. AVAILABILITY: http://www.autogeneralfilters.com/holycross/Home.html. PMID: 18084646 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591385 Mon, 01 Jan 2007 05:00:00 +0100 1591385 http://www.medworm.com/index.php?rid=1591384&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084647%26dopt%3DAbstract Authors: Prolo P, Chiappelli F, Grasso E, Rosso MG, Neagos N, Dovio A, Sartori ML, Perotti P, Fantò F, Civita M, Fiorucci A, Villanueva P, Angeli A Aluminium (Al) has been investigated as a neurotoxic substance. Al ranks among the potential environmental risk factors for Alzheimer's disease (AD). Epidemiological studies tested the relationship between Al in drinking water and AD, showing a significant correlation between elevated levels of monomeric Al in water and AD, although data to date remain inconclusive with respect to total Al. The aim of this study was to test whether or not Al exacerbates cellular toxicity mediated by the amyloid beta (Abeta) peptide. We evaluated the role of Al in modulating programmed cell death (apoptosis) in human cell cultures. We used the osteosarc... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591384 Mon, 01 Jan 2007 05:00:00 +0100 1591384 http://www.medworm.com/index.php?rid=1591383&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084648%26dopt%3DAbstract Authors: Tiwari A, Tiwari V HBNG is a graph theory based tool for visualization of hydrogen bond network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains and rings in protein structures. HBNG takes hydrogen bonds list files (output from HBAT, HBEXPLORE, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT and T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures. AVAILABILITY: Progra... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591383 Mon, 01 Jan 2007 05:00:00 +0100 1591383 http://www.medworm.com/index.php?rid=1591382&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084649%26dopt%3DAbstract Authors: Suravajhala P Genes with unknown function are called orphan genes while their transcripts and peptides are called hypothetical proteins. There are many genes and their associated proteins that remain uncharacterized in the human genome. A database of human hypothetical proteins with ascribed functions could be helpful for biologists to search for potential proteins of interest. In recent years, the rapid completion of genome sequences has created essential information to link genes to gene products. In order to better explain functions for un-annotated proteins we designed BioinformaTRICKS (an open source project) and used it to develop a database called HYPO. AVAILABILITY: The database is available for free at http://pc-dugong.ruc.dk:8080. PMID: 18084649 [PubMed - in proc... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591382 Mon, 01 Jan 2007 05:00:00 +0100 1591382 http://www.medworm.com/index.php?rid=1591381&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084650%26dopt%3DAbstract Authors: Surolia A, Dhar R Rudimentary studies on aspects of biochemistry in India date back to 1927. But, in the field of Immunology, such studies were started by scholars only during early 1970s at the All India Institute of Medical Sciences, New Delhi, India. Science and Technology was not an immediate priority until 1961 due to domestic and political conditions in the country. We were then 11 years old since independence and our focus was on economic and social developments. Gradually, improvements were made in the field and now we have 15 to 20 major groups (small in size) of immunologists in the country, who have made significant contribution in the field during the last 8 to 10 years. Hence, we anticipate improvements in manpower and infrastructure in the near future. PMID: ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591381 Mon, 01 Jan 2007 05:00:00 +0100 1591381 http://www.medworm.com/index.php?rid=1591380&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188418%26dopt%3DAbstract This study was aimed at identifying, in 203 patients with Alzheimer's disease followed during long-term treatment with Acetylcholinesterase inhibitors (ChEIs), the predictive factors of the clinical response among cognition (MMSE), functioning (BADL and IADL) measures and age and gender at the baseline (T0). The ANCOVA test showed a significant association between MMSE scores at time T0 and T3, and the variation T9 to T0, T15 to T0 and T21 to T0 of the MMSE scores, using also gender, age and drug as covariates. The significance was higher for the patients affected by mild dementia. Regarding functional activities, a significant relationship was detected, by the ANCOVA test, only between the scores at T3 and the variation T15 to T0 for BADL, and the variation T9 to T0, T15 to T0 for IADL, r... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591380 Mon, 01 Jan 2007 05:00:00 +0100 1591380 http://www.medworm.com/index.php?rid=1591379&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188419%26dopt%3DAbstract Authors: Kashyap L, Tabish M, Ganesh S, Dubey D Y95B8A.12 gene of C. elegans encodes RhoGEF domain, which is a novel module in the Guanine nucleotide exchange factors (GEFs). Alternative splicing increases transcriptome and proteome diversification. Y95B8A.12 gene has two reported alternatively spliced transcripts by the C. elegans genome sequencing consortium. In the work presented here, we report the presence of four new spliced transcripts of Y95B8A.12 arising as a result of alternative splicing in the pre-mRNA encoded by Y95B8A.12 gene. Our methodology involved the use of various gene or exon finding programmes and several other bioinformatics tools followed by experimental validation. We have also studied alternative splicing pattern in RhoGEF domain encoding orthologues gene from... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591379 Mon, 01 Jan 2007 05:00:00 +0100 1591379 http://www.medworm.com/index.php?rid=1591378&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188420%26dopt%3DAbstract Authors: Kashyap L, Tabish M Cadherins are calcium-dependent, homophilic, cell-cell adhesion receptors that regulate morphogenesis, pattern formation and cell migration. The C. elegans Genome Sequencing Consortium has reported 12 genes from C. elegansgenome encoding members of the cadherin superfamily. Alternative splicing of eukaryotic pre-mRNAs is a mechanism for generating potentially many transcript isoforms from a single gene. Here, using a combination of various gene or exon finding programmes and several other bioinformatics tools followed by experimental validation using RT-PCR, we have studied alternative splicing pattern in the cadherin encoding genes from C. elegansgenome. We have predicted that 7 of the 12 genes encoding the cadherin superfamily undergo extensive alternativ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591378 Mon, 01 Jan 2007 05:00:00 +0100 1591378 http://www.medworm.com/index.php?rid=1591377&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188421%26dopt%3DAbstract Authors: Anwar T, Khan AU Influenza virus causes febrile respiratory illness. The infection results in significant mortality, morbidity and economic disruption. In this bioinformatics study, we used the NS1 (the conserved nonstructural) protein of influenza A virus to demonstrate its role in infectivity. Our in silico study revealed a new Casein kinase II (CKII) phosphorylation domain at position 151-154. This domain was formed due to the mutation at position 151 (T151I). Moreover, considerable difference in the secondary structure of this protein due to mutation was also reported. It is also confirmed by contact residue analysis that the changes in secondary structure are due to mutations. PMID: 18188421 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591377 Mon, 01 Jan 2007 05:00:00 +0100 1591377 http://www.medworm.com/index.php?rid=1591376&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188422%26dopt%3DAbstract Authors: Vetrivel U, Arunkumar V, Dorairaj S Currently available codon usage analysis tools lack intuitive graphical user interface and are limited to inbuilt calculations. ACUA (Automated Codon Usage Tool) has been developed to perform high throughput sequence analysis aiding statistical profiling of codon usage. The results of ACUA are presented in a spreadsheet with all perquisite codon usage data required for statistical analysis, displayed in a graphical interface. The package is also capable of on-click sequence retrieval from the results interface, and this feature is unique to ACUA. AVAILABILITY: The package is available for non-commercial purposes and can be downloaded from: http://www.bioinsilico.com/acua. PMID: 18188422 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591376 Mon, 01 Jan 2007 05:00:00 +0100 1591376 http://www.medworm.com/index.php?rid=1591375&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188423%26dopt%3DAbstract Authors: Babu PA, Udyama J, Kumar RK, Boddepalli R, Mangala DS, Rao GN Molecular biology databases are an integral part of biological research. To date, many databases were established with varied options to access associated biological data. Depending on the data being annotated, some are architecturally similar while others are specialized. In order to provide a partial solution to data integration, we report Database of Databases (DoD2007), constructed using html and javascript. The database has a web-based user interface with simple global search, specific database search, keyword help as well as links to abstracts, full-text and database home pages. Majority of data were derived form Nucleic Acids Research database issue and other published resources. The current release includes ... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591375 Mon, 01 Jan 2007 05:00:00 +0100 1591375 http://www.medworm.com/index.php?rid=1591374&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188424%26dopt%3DAbstract This article focuses on the identification of drug targets by subjecting the Entamoeba genome to BLAST with the e-value inclusion threshold set to 0.005 and choke point analysis. A total of 86.9 percent of proposed drug targets with biological evidence are chokepoint reactions in Entamoeba genome database. PMID: 18188424 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591374 Mon, 01 Jan 2007 05:00:00 +0100 1591374 http://www.medworm.com/index.php?rid=1591373&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188425%26dopt%3DAbstract Authors: Gowthaman R, Krishnamoorthy S, Nandakumar RD, Ayyarappan V Telomeres and centromere are two essential features of all eukaryotic chromosomes. They provide function that is necessary for the stability of chromosomes. We developed a comprehensive database named TeCK, which covers a gamut of sequence and other related information about telomeric patterns, telomere repeat sequences, centromere sequences and centromeric patterns present in chromosomes. It also contains information about telomerase ribo-nucleoprotein complexes, centromere binding protein and centromere DNA-binding protein complexes. The database also includes a collection of all kinetochore-associated proteins including inner, outer and central kinetochore proteins. The database can be searched using a user-friendly... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591373 Mon, 01 Jan 2007 05:00:00 +0100 1591373 http://www.medworm.com/index.php?rid=1591372&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188426%26dopt%3DAbstract Authors: Saravanan V, Shanmughavel P A wide range of web based prediction and annotation tools are frequently used for determining protein function from sequence. However, parallel processing of sequences for annotation through web tools is not possible due to several constraints in functional programming for multiple queries. Here, we propose the development of APAF as an automated protein annotation filter to overcome some of these difficulties through an integrated approach. PMID: 18188426 [PubMed - in process] (Source: Bioinformation) Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591372 Mon, 01 Jan 2007 05:00:00 +0100 1591372 http://www.medworm.com/index.php?rid=1591371&cid=s_37594_79_f&fid=37594&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18188427%26dopt%3DAbstract Authors: Eapen BR Ultraviolet A photosensitivity is a debilitating symptom associated with the metabolic disorder Smith-Lemli-Opitz syndrome (SLOS). SLOS is a manifestation of the deficiency of 7-dehydrocholesterol reductase, an enzyme involved in the cholesterol biosynthesis. As a result several abnormal intermediary compounds are formed among which Cholesta 5, 7, 9(11)-trien-3beta-ol is the most likely cause of photosensitivity. The effect of various drugs acting on cholesterol biosynthetic pathway on SLOS is not clear as clinical trials are not available for this rare disorder. A Flux Balance Analysis (FBA) has been carried out using the software CellNetAnalyzer or FluxAnalyzer to gain insight into the probable effects of various drugs acting on cholesterol biosynthetic pathway on p... Bioinformation journals http://www.medworm.com/rss/comments.php?id=1591371 Mon, 01 Jan 2007 05:00:00 +0100 1591371