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Structural bioinformatics

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https://www.readbyqxmd.com/read/29331591/brochosomins-and-other-novel-proteins-from-brochosomes-of-leafhoppers-insecta-hemiptera-cicadellidae
#1
Roman Rakitov, Alexander A Moysa, Arthur T Kopylov, Sergei A Moshkovskii, Ralph S Peters, Karen Meusemann, Bernhard Misof, Christopher H Dietrich, Kevin P Johnson, Lars Podsiadlowski, Kimberly K O Walden
Brochosomes (BS) are secretory granules resembling buckyballs, produced intracellularly in specialized glandular segments of the Malpighian tubules and forming superhydrophobic coatings on the integuments of leafhoppers (Hemiptera, Cicadellidae). Their composition is poorly known. Using a combination of SDS-PAGE, LC-MS/MS, next-generation sequencing (RNAseq) and bioinformatics we demonstrate that the major structural component of BS of the leafhopper Graphocephala fennahi Young is a novel family of 21-40-kDa secretory proteins, referred to herein as brochosomins (BSM), apparently cross-linked by disulfide bonds...
January 10, 2018: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29331478/comprehensive-analysis-of-lncrnas-and-mrnas-with-associated-co-expression-and-cerna-networks-in-c2c12-myoblasts-and-myotubes
#2
Rui Chen, Ting Jiang, Yanling She, Sidong Xie, Shanyao Zhou, Cheng Li, Jun Ou, Yulin Liu
Long non-coding RNAs (lncRNAs) are emerging as important regulators in the modulation of muscle development and muscle-related diseases. To explore potential regulators of muscle differentiation, we determined the expression profiles of lncRNAs and mRNAs in C2C12 mouse myoblast cell line using microarray analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to explore their function. We also constructed co-expression, cis/trans-regulation, and competing endogenous RNA (ceRNA) networks with bioinformatics methods...
January 10, 2018: Gene
https://www.readbyqxmd.com/read/29329380/circulating-micrornas-as-potential-biomarkers-of-disease-activity-and-structural-damage-in-ankylosing-spondylitis-patients
#3
Carlos Perez-Sanchez, Pilar Font-Ugalde, Patricia Ruiz-Limon, Chary Lopez-Pedrera, Maria C Castro-Villegas, Maria C Abalos-Aguilera, Nuria Barbarroja, Ivan Arias-de la Rosa, Maria D Lopez-Montilla, Alejandro Escudero-Contreras, Clementina Lopez-Medina, Eduardo Collantes-Estevez, Yolanda Jimenez-Gomez
Ankylosing spondylitis (AS) remains difficult to diagnose before irreversible damage to sacroiliac joint is noticeable. Circulating microRNAs have demonstrated to serve as diagnostic tools for several human diseases. Here, we analyzed plasma microRNAs to identify potential AS biomarkers. Higher expression levels of microRNA (miR)-146a-5p, miR-125a-5p, miR-151-3p, and miR-22-3p, and lower of miR-150-5p, and miR-451a were found in AS versus healthy donors. Interestingly, higher miR-146a-5p, miR-125a-5p, miR-151-3p, miR-22-3p, and miR-451a expression was also observed in AS than psoriatic arthritis patients...
January 10, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29329368/discovering-personalized-driver-mutation-profiles-of-single-samples-in-cancer-by-network-control-strategy
#4
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328375/the-role-of-il%C3%A2-16-gene-polymorphisms-in-endometriosis
#5
Michail Matalliotakis, Maria I Zervou, Elias Eliopoulos, Charoula Matalliotaki, Nilufer Rahmioglu, Ioannis Kalogiannidis, Krina Zondervan, Demetrios A Spandidos, Ioannis Matalliotakis, George N Goulielmos
Endometriosis is one of the most common gynecological diseases affecting up to 10% of the female population of childbearing age and a major cause of pain and infertility. It is influenced by multiple genetic, epigenetic and environmental factors. Interleukin‑16 (IL‑16) is a proinflammatory cytokine playing a pivotal role in many inflammatory and autoimmune diseases as well as in the pathogenesis of endometriosis. The aim of the present study was to evaluate the association of two IL‑16 gene single nucleotide polymorphisms (SNPs), rs4072111 and rs11556218, with the risk of endometriosis in women from Greece as well as to gain insight about the structural consequences of these two exonic SNPs regarding development of the disease...
January 9, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29328069/inhibition-of-muc1-biosynthesis-via-threonyl-trna-synthetase-suppresses-pancreatic-cancer-cell-migration
#6
Seung Jae Jeong, Jong Hyun Kim, Beom Jin Lim, Ina Yoon, Ji-Ae Song, Hee-Sun Moon, Doyeun Kim, Dong Ki Lee, Sunghoon Kim
Mucin1 (MUC1), a heterodimeric oncoprotein, containing tandem repeat structures with a high proportion of threonine, is aberrantly overexpressed in many human cancers including pancreatic cancer. Since the overall survival rate of pancreatic cancer patients has remained low for several decades, novel therapeutic approaches are highly needed. Intestinal mucin has been known to be affected by dietary threonine supply since de novo synthesis of mucin proteins is sensitive to luminal threonine concentration. However, it is unknown whether biosynthesis of MUC1 is regulated by threonine in human cancers...
January 12, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29325877/dmcatd-a-cathepsin-d-like-peptidase-of-the-hematophagous-insect-dipetalogaster-maxima-hemiptera-reduviidae-purification-bioinformatic-analyses-and-the-significance-of-its-interaction-with-lipophorin-in-the-internalization-by-developing-oocytes
#7
Jimena Leyria, Leonardo L Fruttero, Rodrigo Ligabue-Braun, Marina S Defferrari, Estela L Arrese, José L Soulages, Beatriz P Settembrini, Celia R Carlini, Lilián E Canavoso
DmCatD, a cathepsin D-like peptidase of the hematophagous insect Dipetalogaster maxima, is synthesized by the fat body and the ovary and functions as yolk protein precursor. Functionally, DmCatD is involved in vitellin proteolysis. In this work, we purified and sequenced DmCatD, performed bioinformatic analyses and investigated the events involved in its targeting and storage in developing oocytes. By ion exchange and gel filtration chromatography, DmCatD was purified from egg homogenates and its identity was confirmed by mass spectrometry...
January 8, 2018: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#8
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324327/elucidating-the-interfaces-involved-in-card-card-interactions-mediated-by-nlrp1-and-caspase-1-using-molecular-dynamics-simulation
#9
Jitendra Maharana
Inflammasomes are the multi-protein caspase-activating complexes mainly assembled by the sensor proteins (NLRs/ALRs), adaptor molecule (ASC) and effector molecule pro-caspase-1 for the production and release of proinflammatory cytokines, IL-1β and IL-18. NLRP1 is the first NLR known to assemble the multi-protein complex. Unlike NLRP3, NLRP1 has an additional effector binding domain (CARD) at the carboxyl-terminal, which is reported to interact with pro-caspase-1 (precluding the recruitment of ASC) for the transmission of danger signals...
December 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29323384/tracking-iron-associated-proteomes-in-pathogens-by-a-fluorescence-approach
#10
Nan Jiang, Tianfan Cheng, Minji Wang, Godfrey Chi-Fung Chan, Lijian Jin, Hongyan Li, Hongzhe Sun
Porphyromonas gingivalis is a key oral anaerobic bacterium involved in human periodontitis, which may affect up to 15% adults worldwide. Using the membrane permeable fluorescent probe Fe-TRACER, we identified 17 iron-associated proteins in Porphyromonas gingivalis. We demonstrated the specific binding of the probe towards iron-associated proteins using transferrin as an example and provided an X-ray structure of the fluorescent probe-bound transferrin. Our study provides a basis for the understanding of iron homeostasis in pathogens, and our approach based on the integration of fluorescence imaging with proteomics and bioinformatics can be readily extended to mine other metalloproteomes in microbials...
January 11, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29322913/cell-type-discovery-and-representation-in-the-era-of-high-content-single-cell-phenotyping
#11
Trygve Bakken, Lindsay Cowell, Brian D Aevermann, Mark Novotny, Rebecca Hodge, Jeremy A Miller, Alexandra Lee, Ivan Chang, Jamison McCorrison, Bali Pulendran, Yu Qian, Nicholas J Schork, Roger S Lasken, Ed S Lein, Richard H Scheuermann
BACKGROUND: A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322437/deep-computational-circular-rna-analytics-from-rna-seq-data
#12
Tobias Jakobi, Christoph Dieterich
Circular RNAs (circRNAs) have been first described as "scrambled exons" in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29319890/two-novel-unstable-hemoglobin-variants-due-to-in-frame-deletions-of-key-amino-acids-in-the-%C3%AE-globin-chain
#13
Karen Gabriela Scheps, Marcia Anahí Hasenahuer, Gustavo Parisi, Héctor M Targovnik, Eliana García, Ernesto Samuel Veber, Renée Crisp, Graciela Elena, Viviana Varela, María Silvina Fornasari
Hemoglobinopathies are the most common autosomal recessive disorders and are mostly inherited in a recessive manner. However, certain mutations can affect the globin chain stability, leading to dominant forms of thalassemia. The aim of this work was the molecular and structural characterization of two heterozygous in-frame deletions, leading to β-globin variants in pediatric patients in Argentina. The HBB gene of the probands and their parents was sequenced, and other markers of globin chain imbalance were analyzed...
January 10, 2018: European Journal of Haematology
https://www.readbyqxmd.com/read/29317699/inflammatory-proteomic-network-analysis-of-statin-treated-and-lipopolysaccharide-activated-macrophages
#14
Abu Hena M Kamal, Jayanta K Chakrabarty, S M Nashir Udden, Md Hasan Zaki, Saiful M Chowdhury
A significant component of immune biology research is the investigation of protein encoding genes that play central roles in contributing inflammatory response. A gel-free quantitative bottom-up proteomics study was performed on immune cell macrophages after the combined treatment of lipopolysaccharide (LPS) and statin drugs using mass spectrometry and a detailed bioinformatics analyses were conducted. Systematic bioinformatics analysis was applied for discovering novel relationships among proteins and effects of statin and lipopolysaccharide in macrophage cells...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316486/exploring-the-association-of-rs10490924-polymorphism-with-age-related-macular-degeneration-an-in-silico-approach
#15
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. ARMS2 gene encodes a putative small (11 kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of A69S mutation, we performed a detailed analysis of an ARMS2 sequence with a broad set of bioinformatics tools...
January 4, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29316298/improving-the-safety-assessment-of-chemicals-and-drug-candidates-by-the-integration-of-bio-informatics-and-chemoinformatics-data
#16
Thomas Steger-Hartmann, Francois Pognan
The application of read-across and in silico tools for regulatory decision-making has been limited for pharmaceutical compounds to the assessment of genotoxic impurity. In contrast, the broad availability of toxicity data for industrial chemicals has triggered regulatory frameworks for read-across (e.g. ECHA read-across assessment framework), software tools and public databases for an automated process of gap filling for safety assessment framework. This MiniReview provides an overview of the currently existing in silico and read-across approaches for chemicals together with recent developments for pharmaceutical compounds in these areas...
January 7, 2018: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/29313734/special-issue-preface-the-9th-computational-structural-bioinformatics-workshop
#17
Jing He, Kamal Al Nasr, Weitao Sun, Yonggang Lu
No abstract text is available yet for this article.
January 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29311639/exploring-viral-diversity-in-a-unique-south-african-soil-habitat
#18
Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don Cowan
The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311112/dispersion-profiles-and-gene-associations-of-repetitive-dnas-in-the-euchromatin-of-the-beetle-tribolium-castaneum
#19
Josip Brajković, Željka Pezer, Branka Bruvo-Mađarić, Antonio Sermek, Isidoro Feliciello, Đurđica Ugarković
Satellite DNAs are tandemly repeated sequences clustered within heterochromatin. However, in some cases such as the major TCAST1 satellite DNA from the beetle Tribolium castaneum, they are found partially dispersed within euchromatin. Such organization together with transcriptional activity enables TCAST1 to modulate the activity of neighbouring genes. In order to explore if other T. castaneum repetitive families have features which could provide them with a possible gene-modulatory role we compare here the structure, organization, dispersion profiles and transcription activity of ten distinct TCAST repetitive families including TCAST1...
January 8, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29309510/mustguseal-a-server-for-multiple-structure-guided-sequence-alignment-of-protein-families
#20
D A Suplatov, K E Kopylov, N N Popova, V Voevodin, V K Švedas
Motivation: Comparative analysis of homologous proteins in a functionally diverse superfamily is a valuable tool at studying structure-function relationship, but represents a methodological challenge. Results: The Mustguseal web-server can automatically build large structure-guided sequence alignments of functionally diverse protein families that include thousands of proteins basing on all available information about their structures and sequences in public databases...
December 22, 2017: Bioinformatics
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