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Structural bioinformatics

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https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#1
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#2
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327552/probing-medin-monomer-structure-and-its-amyloid-nucleation-using-13-c-direct-detection-nmr-in-combination-with-structural-bioinformatics
#3
Hannah A Davies, Daniel J Rigden, Marie M Phelan, Jillian Madine
Aortic medial amyloid is the most prevalent amyloid found to date, but remarkably little is known about it. It is characterised by aberrant deposition of a 5.4 kDa protein called medin within the medial layer of large arteries. Here we employ a combined approach of ab initio protein modelling and (13)C-direct detection NMR to generate a model for soluble monomeric medin comprising a stable core of three β-strands and shorter more labile strands at the termini. Molecular dynamics simulations suggested that detachment of the short, C-terminal β-strand from the soluble fold exposes key amyloidogenic regions as a potential site of nucleation enabling dimerisation and subsequent fibril formation...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323918/elucidating-the-role-of-the-desmosome-protein-p53-apoptosis-effector-related-to-pmp-22-perp-in-growth-hormone-tumors
#4
Katja Kiseljak-Vassiliades, Taylor S Mills, Yu Zhang, Mei Xu, Kevin O Lillehei, B K Kleinschmidt-DeMasters, Margaret E Wierman
Purpose: Densely granulated (DG) and sparsely granulated (SG) growth hormone (GH) pituitary adenomas differ in biological behavior which may be correlated with their known differences in cytoplasmic keratin distribution and E-cadherin expression. We desired to explore candidate genes which might further explain this behavior. Methods: Exon expression microarray was performed on 21 GH tumors (10 SG and 11 DG) and 20 normal control pituitaries from autopsy. Results: Bioinformatic analyses confirmed a differential molecular signature between normal pituitary and GH tumors as well as between the GH tumor subtypes...
February 9, 2017: Endocrinology
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#5
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28320624/improved-prediction-of-protein-protein-interactions-using-novel-negative-samples-features-and-an-ensemble-classifier
#6
Leyi Wei, Pengwei Xing, Jiancang Zeng, JinXiu Chen, Ran Su, Fei Guo
Computational methods are employed in bioinformatics to predict protein-protein interactions (PPIs). PPIs and protein-protein non-interactions (PPNIs) display different levels of development, and the number of PPIs is considerably greater than that of PPNIs. This significant difference in the number of PPIs and PPNIs increases the cost of constructing a balanced dataset. PPIs can be classified as either physical or genetic. However, ready-made PPNI databases were proven only to have no physical interactions and were not proven to have no genetic interactions...
March 4, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28319645/the-atypical-genesis-and-bioavailability-of-the-plant-based-small-rna-mir2911-bulking-up-while-breaking-down
#7
Jian Yang, Natee Kongchan, Cecilia Primo Planta, Joel R Neilson, Kendal D Hirschi
SCOPE: The uptake of dietary plant small RNAs (sRNAs) in consumers remains controversial, which is mainly due to low dietary content in combination with poor fractional absorption. MIR2911, among all the plant sRNAs including microRNAs, has been shown to be one of the most robustly absorbed sRNAs. Here we analyze the unusual abundance and unique genesis of MIR2911 during vegetable processing. METHODS AND RESULTS: Using qRT-PCR, the abundance of MIR2911 increased dramatically in macerated tissues while other microRNAs degraded...
March 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#8
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28315679/charged-groups-at-binding-interfaces-of-the-psbo-subunit-of-photosystem-ii-a-combined-bioinformatics-and-simulation-study
#9
Coral Del Val, Ana-Nicoleta Bondar
PsbO is an extrinsic subunit of photosystem II engaged in complex binding interactions within photosystem II. At the interface between PsbO, D1 and D2 subunits of photosystem II, a cluster of charged and polar groups of PsbO is part of an extended hydrogen-bond network thought to participate in proton transfer. The precise role of specific amino acid residues at this complex binding interface remains a key open question. Here, we address this question by carrying out extensive bioinformatics analyses and molecular dynamics simulations of PsbO proteins with mutations at the binding interface...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28315353/crystal-structure-of-the-extracellular-domain-of-the-human-dendritic-cell-surface-marker-cd83
#10
Christiane S Heilingloh, Stefan Klingl, Claudia Egerer-Sieber, Benedikt Schmid, Sigrid Weiler, Petra Mühl-Zürbes, Jörg Hofmann, Joachim D Stump, Heinrich Sticht, Mirko Kummer, Alexander Steinkasserer, Yves A Muller
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain, only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts is function on dendritic cells and additional immune cells...
March 14, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28314937/phylogenetic-analysis-of-idd-gene-family-and-characterization-of-its-expression-in-response-to-flower-induction-in-malus
#11
Sheng Fan, Dong Zhang, Libo Xing, Siyan Qi, Lisha Du, Haiqin Wu, Hongxia Shao, Youmei Li, Juanjuan Ma, Mingyu Han
Although INDETERMINATE DOMAIN (IDD) genes encoding specific plant transcription factors have important roles in plant growth and development, little is known about apple IDD (MdIDD) genes and their potential functions in the flower induction. In this study, we identified 20 putative IDD genes in apple and named them according to their chromosomal locations. All identified MdIDD genes shared a conserved IDD domain. A phylogenetic analysis separated MdIDDs and other plant IDD genes into four groups. Bioinformatic analysis of chemical characteristics, gene structure, and prediction of protein-protein interactions demonstrated the functional and structural diversity of MdIDD genes...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28314774/the-rare-sugar-n-acetylated-viosamine-is-a-major-component-of-mimivirus-fibers
#12
Francesco Piacente, Cristina De Castro, Sandra Jeudy, Matteo Gaglianone, Maria Elena Laugieri, Anna Notaro, Annalisa Salis, Gianluca Damonte, Chantal Abergel, Michela G Tonetti
The giant virus Mimivirus encodes an autonomous glycosylation system, which is thought to be responsible for the formation of complex and unusual glycans composing the fibers surrounding its icosahedral capsid, including the dideoxyhexose viosamine. Previous studies have identified a gene cluster in the virus genome, encoding enzymes involved in nucleotide-sugar production and glycan formation, but the functional characterization of these enzymes and the full identification of the glycans found in viral fibers remains incomplete...
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28314354/structural-bioinformatics-tools-for-drug-design
#13
(no author information available yet)
No abstract text is available yet for this article.
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28306751/peptidomic-and-transcriptomic-profiling-of-four-distinct-spider-venoms
#14
Vera Oldrati, Dominique Koua, Pierre-Marie Allard, Nicolas Hulo, Miriam Arrell, Wolfgang Nentwig, Frédérique Lisacek, Jean-Luc Wolfender, Lucia Kuhn-Nentwig, Reto Stöcklin
Venom based research is exploited to find novel candidates for the development of innovative pharmacological tools, drug candidates and new ingredients for cosmetic and agrochemical industries. Moreover, venomics, as a well-established approach in systems biology, helps to elucidate the genetic mechanisms of the production of such a great molecular biodiversity. Today the advances made in the proteomics, transcriptomics and bioinformatics fields, favor venomics, allowing the in depth study of complex matrices and the elucidation even of minor compounds present in minute biological samples...
2017: PloS One
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#15
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28301509/genome-wide-association-mapping-in-winter-barley-for-grain-yield-and-culm-cell-wall-polymer-content-using-the-high-throughput-compp-technique
#16
Andrea Bellucci, Alessandro Tondelli, Jonatan U Fangel, Anna Maria Torp, Xin Xu, William G T Willats, Andrew Flavell, Luigi Cattivelli, Søren K Rasmussen
A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0...
2017: PloS One
https://www.readbyqxmd.com/read/28298518/evidence-for-ancient-origins-of-bowman-birk-inhibitors-from-selaginella-moellendorffii
#17
Amy Midori James, Achala S Jayasena, Jingjing Zhang, Oliver Berkowitz, David Secco, Gavin J Knott, James Whelan, Charles Bond, Joshua S Mylne
Bowman-Birk Inhibitors (BBIs) are a well-known family of plant protease inhibitors first described 70 years ago. BBIs are known only in the legume (Fabaceae) and cereal (Poaceae) families, but peptides that mimic their trypsin inhibitory loops exist in sunflowers and frogs. The disparate biosynthetic origins and distant phylogenetic distribution implies these loops evolved independently, but their structural similarity suggests a common ancestor. Targeted bioinformatic searches for the BBI inhibitory loop discovered highly divergent BBI like sequences in the seedless, vascular spikemoss Selaginella moellendorffii...
March 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28298157/conserved-charged-amino-acids-are-key-determinants-for-fatty-acid-binding-proteins-fabps-membrane-interactions-a-multi-methodological-computational-approach
#18
Fernando Zamarreño, Alejandro Giorgetti, María Julia Amundarain, Juan Francisco Viso, Betina Córsico, Marcelo D Costabel
Based on the analysis of the mechanism of ligand transfer to membranes employing in vitro methods, Fatty Acid Binding Protein (FABP) family has been divided in two subgroups: collisional and diffusional FABPs. Although the collisional mechanism has been well characterized employing in vitro methods, the structural features responsible for the difference between collisional and diffusional mechanisms remain uncertain. In this work, we have identified the amino acids putatively responsible for the interaction with membranes of both, collisional and diffusional, subgroups of FABPs...
March 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28297664/coupling-between-protein-stability-and-catalytic-activity-determines-pathogenicity-of-g6pd-variants
#19
Anna D Cunningham, Alexandre Colavin, Kerwyn Casey Huang, Daria Mochly-Rosen
G6PD deficiency, an enzymopathy affecting 7% of the world population, is caused by over 160 identified amino acid variants in glucose-6-phosphate dehydrogenase (G6PD). The clinical presentation of G6PD deficiency is diverse, likely due to the broad distribution of variants across the protein and the potential for multidimensional biochemical effects. In this study, we use bioinformatic and biochemical analyses to interpret the relationship between G6PD variants and their clinical phenotype. Using structural information and statistical analyses of known G6PD variants, we predict the molecular phenotype of five uncharacterized variants from a reference population database...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28294226/insight-into-the-gastro-duodenal-digestion-resistance-of-soybean-proteins-and-potential-implications-for-residual-immunogenicity
#20
Elisabetta De Angelis, Rosa Pilolli, Simona L Bavaro, Linda Monaci
Soy is an important component of the human diet thanks to its nutritional value and high protein content; however, it also represents a risk for allergenic consumers due to its potential to trigger adverse reactions in sensitized individuals. The putative correlation between immunoreactivity and resistance to the human gastrointestinal (GI) digestion has drawn attention to investigating soybean proteins digestibility. In this work, we provided further insights into this field by performing in vitro simulated GI digestion experiments directly on ground soybean seeds, to provide more realistic results obtained from the digestion of the whole food matrix...
March 15, 2017: Food & Function
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