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Structural bioinformatics

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https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#1
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149813/structural-analysis-of-cd59-of-chinese-tree-shrew-a-new-reference-molecule-for-human-immune-system-specific-cd59-drug-discovery
#2
Subhamay Panda, Leena Kumari, Santamay Panda
BACKGROUND: Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquires shared common as well as unique characteristics, and hence offers a genetic basis for employing this animal as a prospective model for biomedical research...
November 17, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/29143663/dirofilaria-immitis-jyd-34-isolate-whole-genome-analysis
#3
Catherine Bourguinat, Francois Lefebvre, Johanna Sandoval, Brenda Bondesen, Yovany Moreno, Roger K Prichard
BACKGROUND: Macrocyclic lactone (ML) anthelmintics are used for chemoprophylaxis for heartworm infection in dogs and cats. Cases of dogs becoming infected with heartworms, despite apparent compliance to recommended chemoprophylaxis with approved preventives, has led to such cases being considered as suspected lack of efficacy (LOE). Recently, microfilariae collected from a small number of LOE isolates were used as a source of infection of new host dogs and confirmed to have reduced susceptibility to ML in controlled efficacy studies using L3 challenge in dogs...
November 9, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29142235/proteomic-study-revealed-cellular-assembly-and-lipid-metabolism-dysregulation-in-sepsis-secondary-to-community-acquired-pneumonia
#4
Narendra Kumar Sharma, Alexandre Keiji Tashima, Milena Karina Colo Brunialti, Eden Ramalho Ferreira, Ricardo Jose Soares Torquato, Renato Arruda Mortara, Flavia Ribeiro Machado, Murillo Assuncao, Otelo Rigato, Reinaldo Salomao
Sepsis is a life-threatening disorder characterized by organ dysfunction and a major cause of mortality worldwide. The major challenge in studying sepsis is its diversity in such factors as age, source of infection and etiology. Recently, genomic and proteomic approaches have improved our understanding of its complex pathogenesis. In the present study, we use quantitative proteomics to evaluate the host proteome response in septic patients secondary to community-acquired pneumonia (CAP). Samples obtained at admission and after 7 days of follow-up were analyzed according to the outcomes of septic patients...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29139344/aeropyrum-pernix-membrane-topology-of-protein-vkor-promotes-protein-disulfide-bond-formation-in-two-subcellular-compartments
#5
Stijntje Hibender, Cristina Landeta, Mehmet Berkmen, Jon Beckwith, Dana Boyd
Disulfide bonds confer stability and activity to proteins. Bioinformatic approaches allow predictions of which organisms make protein disulfide bonds and in which subcellular compartments disulfide bond formation takes place. Such an analysis, along with biochemical and protein structural data, suggests that many of the extremophile Crenarachaea make protein disulfide bonds in both the cytoplasm and the cell envelope. We have sought to determine the oxidative folding pathways in the sequenced genomes of the Crenarchaea, by seeking homologues of the enzymes known to be involved in disulfide bond formation in bacteria...
November 15, 2017: Microbiology
https://www.readbyqxmd.com/read/29138239/expanding-the-chondroitin-glycoproteome-of-caenorhabditis-elegans
#6
Fredrik Noborn, Alejandro Gomez Toledo, Waqas Nasir, Jonas Nilsson, Tabea Dierker, Lena Kjellén, Göran Larson
Chondroitin sulfate proteoglycans (CSPGs) are important structural components of connective tissues in essentially all metazoan organisms. In vertebrates, CSPGs are involved also in more specialized processes such as neurogenesis and growth factor signaling. In invertebrates, however, knowledge of CSPGs core proteins and proteoglycan-related functions is relatively limited, even for Caenorhabditis elegans. This nematode produces large amounts of non-sulfated chondroitin in addition to low-sulfated chondroitin sulfate chains...
November 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29137181/structure-and-functional-analysis-of-promoters-from-two-liver-isoforms-of-cpt-i-in-grass-carp-ctenopharyngodon-idella
#7
Yi-Huan Xu, Zhi Luo, Kun Wu, Yao-Fang Fan, Wen-Jing You, Li-Han Zhang
Carnitine palmitoyltransferase I (CPT I) is a key enzyme involved in the regulation of lipid metabolism and fatty acid β-oxidation. To understand the transcriptional mechanism of CPT Iα1b and CPT Iα2a genes, we cloned the 2695-bp and 2631-bp regions of CPT Iα1b and CPT Iα2a promoters of grass carp (Ctenopharyngodon idella), respectively, and explored the structure and functional characteristics of these promoters. CPT Iα1b had two transcription start sites (TSSs), while CPT Iα2a had only one TSS. DNase I foot printing showed that the CPT Iα1b promoter was AT-rich and TATA-less, and mediated basal transcription through an initiator (INR)-independent mechanism...
November 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29136098/sequential-search-leads-to-faster-more-efficient-fragment-based-de-novo-protein-structure-prediction
#8
Saulo H P de Oliveira, Eleanor C Law, Jiye Shi, Charlotte M Deane
Motivation: Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. Results: We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29136092/microrpm-a-microrna-prediction-model-based-only-on-plant-small-rna-sequencing-data
#9
Kuan-Chien Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Chi-Nga Chow, Shu-Chuan Lee, Han-Qin Zheng, Po-Li Kuo, Guan-Zhen Li, Yu-Cheng Hung, Na-Sheng Lin, Wen-Chi Chang
Motivation: MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29136084/predicting-loop-conformational-ensembles
#10
Claire Marks, Jiye Shi, Charlotte M Deane
Motivation: Protein function is often facilitated by the existence of multiple stable conformations. Structure prediction algorithms need to be able to model these different conformations accurately, and produce an ensemble of structures that represent a target's conformational diversity rather than just a single state. Here, we investigate whether current loop prediction algorithms are capable of this. We use the algorithms to predict the structures of loops with multiple experimentally-determined conformations, and the structures of loops with only one conformation, and assess their ability to generate and select decoys that are close to any, or all, of the observed structures...
November 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29134779/crochelins-siderophores-with-a-novel-iron-chelating-moiety-from-the-nitrogen-fixing-bacterium-azotobacter-chroococcum
#11
Oliver Baars, Xinning Zhang, Marcus I Gibson, Alan T Stone, Francois M M Morel, Mohammad R Seyedsayamdost
Microbes utilize siderophores to access essential iron resources. Over 500 siderophores are known, but they utilize a small set of common moieties to bind iron. Azotobacter chroococcum expresses iron-rich nitrogenases with which it reduces N2. Though an important agricultural inoculant, the structures of its iron-binding molecules remain unknown. Herein, we examine the 'chelome' of A. chroococcum using a small molecule discovery and bioinformatics approach. We find that it produces vibrioferrin and amphibactins as well as a novel family of siderophores, the crochelins...
November 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29134140/genome-wide-identification-and-characterization-of-gras-transcription-factors-in-tomato-solanum-lycopersicum
#12
Yiling Niu, Tingting Zhao, Xiangyang Xu, Jingfu Li
Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time...
2017: PeerJ
https://www.readbyqxmd.com/read/29133510/single-cell-immuno-laser-microdissection-coupled-to-label-free-proteomics-to-reveal-the-proteotypes-of-human-brain-cells-after-ischemia
#13
Teresa García-Berrocoso, Víctor Llombart, Laura Colàs-Campàs, Alexandre Hainard, Virginie Licker, Anna Penalba, Laura Ramiro, Alba Simats, Alejandro Bustamante, Elena Martínez-Saez, Francesc Canals, Jean-Charles Sanchez, Joan Montaner
Cerebral ischemia entails rapid tissue damage in the affected brain area causing devastating neurological dysfunction. How each component of the neurovascular unit contributes or responds to the ischemic insult in the context of the human brain has not been solved yet. Thus, the analysis of the proteome is a straightforward approach to unraveling these cell proteotypes.In this study, post-mortem brain slices from ischemic stroke patients were obtained corresponding to infarcted (IC) and contralateral (CL) areas...
November 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29131568/diisonitrile-natural-product-sf2768-functions-as-a-chalkophore-that-mediates-copper-acquisition-in-streptomyces-thioluteus
#14
Lijuan Wang, Mengyi Zhu, Qingbo Zhang, Xu Zhang, Panlei Yang, Zihui Liu, Yun Deng, Yiguang Zhu, Xueshi Huang, Li Han, Shengqing Li, Jing He
A non-ribosomal peptide synthetase (NRPS) gene cluster (sfa) was identified in Streptomyces thioluteus to direct the biosynthesis of the diisonitrile antibiotic SF2768. Its biosynthetic pathway was reasonably proposed based on bioinformatics analysis, metabolic profiles of mutants and the elucidation of the intermediate and shunt product structures. Bioinformatics-based alignment found a putative ATP-binding cassette (ABC) transporter related to iron import within the biosynthetic gene cluster, which implied that the product might be a siderophore...
November 13, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29131478/gene-isolation-using-degenerate-primers-targeting-protein-motif-a-laboratory-exercise
#15
Brandon Pei Hui Yeo, Lian Chee Foong, Sheh May Tam, Vivian Lee, Siaw San Hwang
Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29130500/purification-characterization-and-application-of-a-novel-antimicrobial-peptide-from-andrias-davidianus-blood
#16
Jinjin Pei, Zhenzhen Feng, Ting Ren, Haiyan Sun, Hao Han, Wengang Jin, Jun Dang
The Andrias davidianus has been known as a traditional Chinese medicine for a long time. Its blood is considered as a waste or by-product of the meat production industry. Although there are reports on isolation of the antimicrobial peptides from different resources, there are no reports of their isolation from Andrias davidianus blood. In this work, an antimicrobial peptide, andricin B, was isolated from the blood of Andrias davidianus by an innovative method in which the magnetic liposome adsorption was combined with reversed-phase high performance liquid chromatography...
November 11, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29130371/-lost-in-translation-seeing-the-forest-by-focusing-on-the-trees
#17
Kelly T Hughes, Fabienne F V Chevance
A complex process translates messenger RNA (mRNA) base sequence into protein amino acid sequence. Transfer RNAs must recognize 3-base codons in the mRNA to insert the correct amino acids into the growing protein. Codon degeneracy makes decoding complicated in that multiple (synonymous) triplets can encode a single amino acid and multiple tRNAs can have the same anticodon. Over the last twenty years, new developments in structural biology, genome sequencing and bioinformatics has elucidated the intricacies of the ribosome structure and the details of the translation process...
November 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29129969/statistical-contributions-to-bioinformatics-design-modeling-structure-learning-and-integration
#18
Jeffrey S Morris, Veerabhadran Baladandayuthapani
The advent of high-throughput multi-platform genomics technologies providing whole-genome molecular summaries of biological samples has revolutionalized biomedical research. These technologiees yield highly structured big data, whose analysis poses significant quantitative challenges. The field of Bioinformatics has emerged to deal with these challenges, and is comprised of many quantitative and biological scientists working together to effectively process these data and extract the treasure trove of information they contain...
2017: Statistical Modelling
https://www.readbyqxmd.com/read/29129631/binding-of-calcium-and-target-peptide-to-calmodulin-like-protein-cml19-the-centrin-2-of-arabidopsis-thaliana
#19
Valentina La Verde, Matteo Trande, Mariapina D'Onofrio, Paola Dominici, Alessandra Astegno
Calmodulin-like protein 19 (CML19) is an Arabidopsis centrin that modulates nucleotide excision repair (NER) by binding to RAD4 protein, the Arabidopsis homolog of human Xeroderma pigmentosum complementation group C protein. Although the necessity of CML19 as a part of the RAD4 plant recognition complex for functional NER is known at a cellular level, little is known at a molecular level. Herein, we used a combination of biophysical and biochemical approaches to investigate the structural and ion and target-peptide binding properties of CML19...
November 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29126724/dual-or-multi-targeting-inhibitors-the-next-generation-anticancer-agents
#20
REVIEW
Nulgumnalli Manjunathaiah Raghavendra, Divya Pingili, Sundeep Kadasi, Akhila Mettu, S V U M Prasad
Dual-targeting/Multi-targeting of oncoproteins by a single drug molecule represents an efficient, logical and alternative approach to drug combinations. An increasing interest in this approach is indicated by a steady upsurge in the number of articles on targeting dual/multi proteins published in the last 5 years. Combining different inhibitors that destiny specific single target is the standard treatment for cancer. A new generation of dual or multi-targeting drugs is emerging, where a single chemical entity can act on multiple molecular targets...
October 10, 2017: European Journal of Medicinal Chemistry
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