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Structural bioinformatics

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https://www.readbyqxmd.com/read/28222234/transcriptome-analysis-of-the-brassica-napus-leptosphaeria-maculans-pathosystem-identifies-receptor-signalling-and-structural-genes-underlying-plant-resistance
#1
Michael G Becker, Xuehua Zhang, Philip L Walker, Joey C Wan, Jenna L Millar, Deirdre Khan, Matthew J Granger, Jacob D Cavers, Ainsley C Chan, Dilantha W G Fernando, Mark F Belmonte
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant yield loss worldwide. While genetic resistance has been used to mitigate the disease using traditional breeding strategies, there is little knowledge about the genes contributing to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L...
February 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28221002/computational-biology-and-chemistry-in-mti-emphasis-on-the-prediction-of-some-admet-properties
#2
REVIEW
Maria A Miteva, Bruno O Villoutreix
Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas...
February 21, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28212810/chromosomal-instability-analysis-and-regional-tumor-heterogeneity-in-colon-cancer
#3
Vincenza Barresi, Sergio Castorina, Nicolò Musso, Carmela Capizzi, Tonia Luca, Giovanna Privitera, Daniele Filippo Condorelli
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively)...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212420/transcriptome-using-illumina-sequencing-reveals-the-traits-of-spermatogenesis-and-developing-testes-in-eriocheir-sinensis
#4
Gen-Liang Li, Hui Qian
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145...
2017: PloS One
https://www.readbyqxmd.com/read/28209127/repo-an-r-package-for-data-centered-management-of-bioinformatic-pipelines
#5
Francesco Napolitano
BACKGROUND: Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and planning effort, which may become impractical in rapidly changing development environments...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28208072/identification-of-triosephosphate-isomerase-as-a-novel-allergen-in-octopus-fangsiao
#6
Yang Yang, Zhong-Wei Chen, Barry K Hurlburt, Gui-Ling Li, Yong-Xia Zhang, Dan-Xia Fei, Hai-Wang Shen, Min-Jie Cao, Guang-Ming Liu
Octopus is an important mollusk in human dietary for its nutritional value, however it also causes allergic reactions in humans. Major allergens from octopus have been identified, while the knowledge of novel allergens remains poor. In the present study, a novel allergen with molecular weight of 28kDa protein was purified from octopus (Octopus fangsiao) and identified as triosephosphate isomerase (TIM) by mass spectrometry. TIM aggregated beyond 45°C, and its IgE-binding activity was affected under extreme pH conditions due to the altered secondary structure...
February 13, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28198674/sequence-specific-bias-correction-for-rna-seq-data-using-recurrent-neural-networks
#7
Yao-Zhong Zhang, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
BACKGROUND: The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196451/phenotypic-and-genetic-analysis-of-dysprothrombinemia-due-to-a-novel-homozygous-mutation
#8
Kankan Su, Yanhui Jin, Zhihai Miao, Xiaoli Cheng, Lihong Yang, Mingshan Wang
OBJECTIVE: We study the phenotype and genotype of a novel gene mutation of factor II (FII) that leads to dysprothrombinemia, and do the meta-analysis to illuminate its molecular pathogenesis. It will further contribute to our comprehension of the pathogenesis of this type of disease. METHODS: The prothrombin time (PT), activated partial thromboplastin time (APTT) and the activities of other factors were determined by the one-stage clotting method. The prothrombin antigen was measured with enzyme-linked immunosorbent assay (ELISA)...
February 14, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28193903/structural-analysis-of-mycobacterium-tuberculosis-homologues-of-the-eukaryotic-proteasome-assembly-chaperone-2-pac2
#9
Lin Bai, Jordan B Jastrab, Marta Isasa, Kuan Hu, Hongjun Yu, Steven P Gygi, K Heran Darwin, Huilin Li
A previous bioinformatics analysis identified the Mycobacterium tuberculosis (M. tuberculosis) proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 could function in proteasome assembly. We solved the crystal structure of Rv2125 at 3.0 Å resolution, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2...
February 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28191780/cancer-stem-cells-therapeutic-target-database-the-first-comprehensive-database-for-therapeutic-targets-of-cancer-stem-cells
#10
Xiaoqing Hu, Ye Cong, Huizhe Howard Luo, Sijin Wu, Liyuan Eric Zhao, Quentin Liu, Yongliang Yang
Cancer stem cells (CSCs) are a subpopulation of tumor cells that have strong self-renewal capabilities and may contribute to the failure of conventional cancer therapies. Hence, therapeutics homing in on CSCs represent a novel and promising approach that may eradicate malignant tumors. However, the lack of information on validated targets of CSCs has greatly hindered the development of CSC-directed therapeutics. Herein, we describe the Cancer Stem Cells Therapeutic Target Database (CSCTT), the first online database to provide a rich bioinformatics resource for the display, search, and analysis of structure, function, and related annotation for therapeutic targets of cancer stem cells...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28191711/bioinformatic-screening-and-detection-of-allergen-cross-reactive-ige-binding-epitopes
#11
Scott McClain
Protein allergens can be related by cross-reactivity. Allergens that share relevant sequence can cross-react, those lacking similarity in their IgE antibody-binding epitopes do not cross-react. Cross-reactivity is based on shared epitopes which is due to shared sequence and higher level structure (charge and shape). Epitopes can be important in predicting cross-reactivity potential and may provide the potential to establish criteria that identify homology among allergens. Selected allergen's IgE binding epitope sequences were used to determine how the FASTA algorithm could be used to identify a threshold of significance...
February 13, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28191466/prediction-and-analysis-of-key-genes-in-glioblastoma-based-on-bioinformatics
#12
Hao Long, Chaofeng Liang, Xi'an Zhang, Luxiong Fang, Gang Wang, Songtao Qi, Haizhong Huo, Ye Song
Understanding the mechanisms of glioblastoma at the molecular and structural level is not only interesting for basic science but also valuable for biotechnological application, such as the clinical treatment. In the present study, bioinformatics analysis was performed to reveal and identify the key genes of glioblastoma multiforme (GBM). The results obtained in the present study signified the importance of some genes, such as COL3A1, FN1, and MMP9, for glioblastoma. Based on the selected genes, a prediction model was built, which achieved 94...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28188552/enhanced-biodegradation-of-low-and-high-density-polyethylene-by-novel-bacterial-consortia-formulated-from-plastic-contaminated-cow-dung-under-thermophilic-conditions
#13
Sinosh Skariyachan, Anagha Shamsundar Setlur, Sujay Yashwant Naik, Ashwini Amaresh Naik, Makam Usharani, Kiran S Vasist
The current study aimed to devise eco-friendly, safe, and cost-effective strategies for enhanced degradation of low- and high-density polyethylene (LDPE and HDPE) using newly formulated thermophilic microbial consortia from cow dung and to assess the biodegradation end products. The plastic-degrading bacteria from cow dung samples gathered from highly plastic-acclimated environments were enriched by standard protocols. The degradation ability was comprehended by zone of clearance method, and the percentage of degradation was monitored by weight reduction process...
February 10, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#14
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28185571/hippi-highly-accurate-protein-family-classification-with-ensembles-of-hmms
#15
Nam-Phuong Nguyen, Michael Nute, Siavash Mirarab, Tandy Warnow
BACKGROUND: Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. RESULTS: We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification)...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28173761/a-novel-complex-runx2-gene-mutation-causes-cleidocranial-dysplasia
#16
Wen'an Xu, Qiuyue Chen, Cuixian Liu, Jiajing Chen, Fu Xiong, Buling Wu
BACKGROUND: Haploinsufficiency of the runt-related transcription factor 2 (RUNX2) gene is known to cause cleidocranial dysplasia (CCD). Here, we investigated a complex, heterozygous RUNX2 gene mutation in a Chinese family with CCD and the pathogenesis associated with the variations. METHODS: Genomic DNA extracted from peripheral venous blood was taken from the proband, her parents and 3 siblings, and 150 normal controls. Analysis of their respective RUNX2 gene sequences was performed by PCR amplification and Sanger sequencing...
February 7, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28168755/palbociclib-can-overcome-mutations-in-cyclin-dependent-kinase-6-that-break-hydrogen-bonds-between-the-drug-and-the-protein
#17
Stella Hernandez Maganhi, Patrizia Jensen, Ignez Caracelli, Julio Zukerman Schpector, Stefan Fröhling, Ran Friedman
Inhibition of cyclin dependent kinases (CDKs) 4 and 6 prevent cells from entering the synthesis phase of the cell cycle. CDK4 and 6 are therefore important drug targets in various cancers. The selective CDK4/6 inhibitor palbociclib is approved for the treatment of breast cancer and has shown activity in a cellular model of mixed lineage leukaemia (MLL)-rearranged acute myeloid leukaemia (AML). We studied the interactions of palbociclib and CDK6 using molecular dynamics simulations. Analysis of the simulations suggested several interactions that stabilised the drug in its binding site and that were not observed in the crystal structure of the protein-drug complex...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168746/perspectives-and-expectations-in-structural-bioinformatics-of-metalloproteins
#18
EDITORIAL
Sen Yao, Robert M Flight, Eric C Rouchka, Hunter N B Moseley
Recent papers highlight the presence of large numbers of compressed angles in metal ion coordination geometries for metalloprotein entries in the worldwide Protein Data Bank, due mainly to multidentate coordination. The prevalence of these compressed angles has raised the controversial idea that significantly populated aberrant or even novel coordination geometries may exist. Some of these papers have undergone severe criticism, apparently due to views held that only canonical coordination geometries exist in significant numbers...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28167213/metagenomics-approach-to-the-study-of-the-gut-microbiome-structure-and-function-in-zebrafish-danio-rerio-fed-with-gluten-formulated-diet
#19
Hyunmin Koo, Joseph A Hakim, Mickie L Powell, Ranjit Kumar, Peter G Eipers, Casey D Morrow, Michael Crowley, Elliot J Lefkowitz, Stephen A Watts, Asim K Bej
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine...
February 3, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28164791/characterization-and-distinction-of-two-flagellar-systems-in-extraintestinal-pathogenic-escherichia-coli-pcn033
#20
Feng Liu, Jiyang Fu, Canying Liu, Jing Chen, Minhua Sun, Huanchun Chen, Chen Tan, Xiangru Wang
Extraintestinal pathogenic Escherichia coli (ExPEC) can invade and colonize multiple extraintestinal tissues and can cause a wide range of infections; however the mechanisms of its pathogenicity are not well understood. Flagella contribute to the infection of E. coli strains by mediating adhesion and invasion. Our previous bioinformatic analysis revealed two flagella gene clusters in the genome of an ExPEC isolate, PCN033. One encodes the conventional flagellum system (Flag-1) and the other encodes the Flag-2 system, whose function is uncharacterized...
March 2017: Microbiological Research
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