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Structural bioinformatics

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https://www.readbyqxmd.com/read/27914980/cloning-and-characterization-of-adipogenin-and-its-overexpression-enhances-fat-accumulation-of-bovine-myosatellite-cells
#1
Yang Liu, Bijie Jiang, Changzhen Fu, Ruijie Hao
Adipogenin (ADIG) is an adipocyte-specific membrane protein highly expressed in adipose tissues and is increased during the adipocyte differentiation. However, the roles and mechanisms of ADIG on fat accumulation and adipocyte differentiation in ex vivo still largely unknown. In this study, we isolated bovine myosatellite cells based on adhesion characteristics to investigate whether ADIG overexpression could promote trans-differentiation and increase fat accumulation in myosatellite cells. Immunofluorescence labeling was then used for the phenotypic characteristics of myosatellite...
November 30, 2016: Gene
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#2
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27904835/a-novel-dominant-d109a-cryab-mutation-in-a-family-with-myofibrillar-myopathy-affects-%C3%AE-b-crystallin-structure
#3
Jakub P Fichna, Anna Potulska-Chromik, Przemysław Miszta, Maria Jolanta Redowicz, Anna M Kaminska, Cezary Zekanowski, Sławomir Filipek
Myofibrillar myopathy (MFM) is a group of inherited muscular disorders characterized by myofibrils dissolution and abnormal accumulation of degradation products. So far causative mutations have been identified in nine genes encoding Z-disk proteins, including αB-crystallin (CRYAB), a small heat shock protein (also called HSPB5). Here, we report a case study of a 63-year-old Polish female with a progressive lower limb weakness and muscle biopsy suggesting a myofibrillar myopathy, and extra-muscular multisystemic involvement, including cataract and cardiomiopathy...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/27902792/rascaf-improving-genome-assembly-with-rna-sequencing-data
#4
Li Song, Dhruv S Shankar, Liliana Florea
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27900321/genome-wide-transcriptional-regulation-and-chromosome-structural-arrangement-by-galr-in-e-coli
#5
Zhong Qian, Andrei Trostel, Dale E A Lewis, Sang Jun Lee, Ximiao He, Anne M Stringer, Joseph T Wade, Thomas D Schneider, Tim Durfee, Sankar Adhya
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27899926/bioinformatic-analyses-of-subgroup-a-members-of-the-wheat-bzip-transcription-factor-family-and-functional-identification-of-tabzip174-involved-in-drought-stress-response
#6
Xueyin Li, Biane Feng, Fengjie Zhang, Yimiao Tang, Liping Zhang, Lingjian Ma, Changping Zhao, Shiqing Gao
Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27898073/proteomic-analysis-of-the-postsynaptic-density-implicates-synaptic-function-and-energy-pathways-in-bipolar-disorder
#7
M Föcking, P Dicker, L M Lopez, M Hryniewiecka, K Wynne, J A English, G Cagney, D R Cotter
The postsynaptic density (PSD) contains a complex set of proteins of known relevance to neuropsychiatric disorders such as schizophrenia and bipolar disorder. We enriched for this anatomical structure in the anterior cingulate cortex of 16 bipolar disorder samples and 20 controls from the Stanley Medical Research Institute. Unbiased shotgun proteomics incorporating label-free quantitation was used to identify differentially expressed proteins. Quantitative investigation of the PSD identified 2033 proteins, among which 288 were found to be differentially expressed...
November 29, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27897122/bioinformatics-analysis-of-chicken-mirnas-associated-with-monocyte-to-macrophage-differentiation-and-subsequent-ifng-stimulated-activation
#8
Kristopher Jl Irizarry, Adam Chan, Derek Kettle, Steven Kezian, Dominic Ma, Louis Palacios, Qingshun Li, Calvin L Keeler, Yvonne Drechsler
The goal of this project was to characterize the molecular and cellular roles of various gene targets regulated by 8 miRNAs in differentiating macrophages. Among a number of miRNAs that are found to be expressed in avian macrophages, we focused on eight specific miRNAs (miR-1618, miR-1586, miR-1633, miR-1627, miR-1646, miR-1649, miR-1610, miR-1647) associated with macrophage activation through Wnt signaling, ubiquitination, PPAR mediated macrophage function, vesicle mediated cytokine trafficking, and WD40 domain proteins in macrophage differentiation...
November 29, 2016: MicroRNA
https://www.readbyqxmd.com/read/27896753/information-visualization-for-biological-data
#9
Tobias Czauderna, Falk Schreiber
Visualization is a powerful method to present and explore a large amount of data. It is increasingly important in the life sciences and is used for analyzing different types of biological data, such as structural information, high-throughput data, and biochemical networks. This chapter gives a brief introduction to visualization methods for bioinformatics, presents two commonly used techniques in detail, and discusses a graphical standard for biological networks and cellular processes.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896720/working-with-ontologies
#10
Frank Kramer, Tim Beißbarth
Ontologies are powerful and popular tools to encode data in a structured format and manage knowledge. A large variety of existing ontologies offer users access to biomedical knowledge. This chapter contains a short theoretical background of ontologies and introduces two notable examples: The Gene Ontology and the ontology for Biological Pathways Exchange. For both ontologies a short overview and working bioinformatic applications, i.e., Gene Ontology enrichment analyses and pathway data visualization, are provided...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896718/managing-sequence-data
#11
Christopher O'Sullivan, Benjamin Busby, Ilene Karsch Mizrachi
Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSDC (International Nucleotide Sequence Database-DDBJ/ENA/GenBank + SRA) is an international, centralized primary sequence resource that is freely available on the Internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter discusses the structure and history of the nucleotide sequence database resources built at NCBI, provides information on how to submit sequences to the databases, and explains how to access the sequence data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27894019/elucidating-a-chemical-defense-mechanism-of-antarctic-sponges-a-computational-study
#12
Sai Lakshmana Vankayala, Fiona L Kearns, Bill J Baker, Joseph D Larkin, H Lee Woodcock
In 2000, a novel secondary metabolite (erebusinone, Ereb) was isolated from the Antarctic sea sponge, Isodictya erinacea. The bioactivity of Ereb was investigated, and it was found to inhibit molting when fed to the arthropod species Orchomene plebs. Xanthurenic acid (XA) is a known endogenous molt regulator present in arthropods. Experimental studies have confirmed that XA inhibits molting by binding to either (or both) of two P450 enzymes (CYP315a1 or CYP314a1) that are responsible for the final two hydroxylations in the production of the molt-inducing hormone, 20-hydroxyecdysone (20E)...
November 10, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27893399/enumerating-substituted-benzene-isomers-of-tree-like-chemical-graphs
#13
Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu
Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph G with no other cycles than benzene rings is called tree-like, and becomes a tree T possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation T are called the substituted benzene isomers of T. When we replace each virtual atom in T with a benzene ring to obtain a substituted benzene isomer, distinct isomers of T are caused by the difference in arrangements of atom groups around a benzene ring...
November 15, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27890593/evaluation-of-the-crystal-structure-of-a-fimbrillin-fima-from-porphyromonas-gingivalis-as-a-therapeutic-target-for-photo-activated-disinfection-with-toluidine-blue-o
#14
Maryam Pourhajibagher, Abbas Bahador
BACKGROUND: Porphyromonas gingivalis is one of the etiological agents in the initiation of combined periodontal-endodontic (perio-endo) lesions. Successful treatment of perio-endo lesions with photo-activated disinfection (PAD) as a novel therapeutic approach depends on the selection of an appropriate target site, specific photosensitizer (PS), and wavelength of light. Since the fimbrillin (FimA) is the most important pathogenic agent in P. gingivalis it was evaluated as a target site against PAD with toluidine blue O (TBO) as a PS...
November 23, 2016: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/27890086/multiple-isoforms-for-the-catalytic-subunit-of-pka-in-the-basal-fungal-lineage-mucor-circinelloides
#15
Lucas Fernández Núñez, Josefina Ocampo, Alexandra M Gottlieb, Silvia Rossi, Silvia Moreno
Protein kinase A (PKA) activity is involved in dimorphism of the basal fungal lineage Mucor. From the recently sequenced genome of Mucor circinelloides we could predict ten catalytic subunits of PKA. From sequence alignment and structural prediction we conclude that the catalytic core of the isoforms is conserved, and the difference between them resides in their amino termini. This high number of isoforms is maintained in the subdivision Mucoromycotina. Each paralogue, when compared to the ones form other fungi is more homologous to one of its orthologs than to its paralogs...
December 2016: Fungal Biology
https://www.readbyqxmd.com/read/27890013/in-silico-characterization-of-a-hypothetical-protein-rv1288-of-mycobacterium-tuberculosis-containing-an-esterase-signature-and-an-uncommon-lyte-domain
#16
Arbind Kumar, Pratibha Maan, Gurpreet Singh, Jagdeep Kaur
BACKGROUND: Death toll due to tuberculosis is still rising day by day. Whole genome sequence of Mycobacterium tuberculosis has provided a platform to conduct research in order to identify the probable drug target. OBJECTIVES: Out of 4000 gene products of M. tuberculosis, approximately 40% of proteins are annotated as hypothetical. Identifying and characterizing these proteins could provide a new prescriptive for developing new TB drugs. Rv1288, a protein of M. tuberculosis H37Rv has been annotated as a hypothetical protein in database...
November 24, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27888332/interaction-of-gut-microbiota-with-bile-acid-metabolism-and-its-influence-on-disease-states
#17
REVIEW
Christopher Staley, Alexa R Weingarden, Alexander Khoruts, Michael J Sadowsky
Primary bile acids serve important roles in cholesterol metabolism, lipid digestion, host-microbe interactions, and regulatory pathways in the human host. While most bile acids are reabsorbed and recycled via enterohepatic cycling, ∼5% serve as substrates for bacterial biotransformation in the colon. Enzymes involved in various transformations have been characterized from cultured gut bacteria and reveal taxa-specific distribution. More recently, bioinformatic approaches have revealed greater diversity in isoforms of these enzymes, and the microbial species in which they are found...
November 25, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27887025/design-and-expression-of-a-chimeric-vaccine-candidate-for-avian-necrotic-enteritis
#18
Amin Rostami, Fatemeh Goshadrou, Reza Pilehchian Langroudi, S Zahra Bathaie, Ali Riazi, Jafar Amani, Gholamreza Ahmadian
Necrotic enteritis is an economically important disease of poultry mainly caused by Clostridium perfringens The bacteria release multiple toxins of which NetB, alpha toxin and TpeL have been reported to play important roles in pathogenicity and/or severity of the disease. In this study, the sequence of clostridial toxins NetB, alpha toxin and TpeL were analyzed using bioinformatics tools to determine protein domains with high immunogenicity factor. Several chimeric trivalent proteins consisting of the immunogenic regions of the three toxins were designed and evaluated...
November 24, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27883265/genomic-approaches-to-the-assessment-of-human-spina-bifida-risk
#19
REVIEW
M Elizabeth Ross, Christopher E Mason, Richard H Finnell
Structural birth defects are a leading cause of mortality and morbidity in children world-wide, affecting as much as 6% of all live births. Among these conditions, neural tube defects (NTDs), including spina bifida and anencephaly, arise from a combination of complex gene and environment interactions that are as yet poorly understood within human populations. Rapid advances in massively parallel DNA sequencing and bioinformatics allow for analyses of the entire genome beyond the 2% of the genomic sequence covering protein coding regions...
November 24, 2016: Birth Defects Research. Part A, Clinical and Molecular Teratology
https://www.readbyqxmd.com/read/27882067/bioinformatic-identification-of-rare-codon-clusters-rccs-in-hbv-genome-and-evaluation-of-rccs-in-proteins-structure-of-hepatitis-b-virus
#20
Mojtaba Mortazavi, Mohammad Zarenezhad, Saeid Gholamzadeh, Seyed Moayed Alavian, Mohammad Ghorbani, Reza Dehghani, Abdorrasoul Malekpour, Mohammadhasan Meshkibaf, Ali Fakhrzad
BACKGROUND: Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES: The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS: For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families...
October 2016: Hepatitis Monthly
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