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Network protein function prediction

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https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#1
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27913149/mutations-at-protein-protein-interfaces-small-changes-over-big-surfaces-have-large-impacts-on-human-health
#2
REVIEW
Harry C Jubb, Arun P Pandurangan, Meghan A Turner, Bernardo Ochoa-Montaño, Tom L Blundell, David B Ascher
Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance...
November 29, 2016: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/27908912/a-deep-proteome-analysis-identifies-the-complete-secretome-as-the-functional-unit-of-human-cardiac-progenitor-cells
#3
Sudhish Sharma, Rachana Mishra, Grace E Bigham, Brody Wehman, Mohd M Khan, Huichun Xu, Progyaparamita Saha, Young Ah Goo, Srinivisa R Datla, Ling Chen, Mohan E Tulapurkar, Bradley S Taylor, Peixin Yang, Sotirios K Karathanasis, David R Goodlett, Sunjay Kaushal
RATIONALE: Cardiac progenitor cells are an attractive cell type for tissue regeneration but their mechanism for myocardial remodeling is still unclear. OBJECTIVE: This investigation determines how chronological age influences the phenotypic characteristics and the secretome of human cardiac progenitor cells (CPCs), as well as their potential to recover injured myocardium. METHODS AND RESULTS: Adult (aCPCs) and neonatal (nCPCs) cells were derived from patients more than 40 years or less than one month of age, respectively, and their functional potential was determined in a rodent myocardial infarction (MI) model...
December 1, 2016: Circulation Research
https://www.readbyqxmd.com/read/27903896/img-abc-new-features-for-bacterial-secondary-metabolism-analysis-and-targeted-biosynthetic-gene-cluster-discovery-in-thousands-of-microbial-genomes
#4
Michalis Hadjithomas, I-Min A Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor Markowitz, Nikos C Kyrpides, Natalia N Ivanova
Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900601/rna-seq-expression-analysis-of-enteric-neuron-cells-with-rotenone-treatment-and-prediction-of-regulated-pathways
#5
Qiang Guan, Xijin Wang, Yanyan Jiang, Lijuan Zhao, Zhiyu Nie, Lingjing Jin
The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson's disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes...
November 30, 2016: Neurochemical Research
https://www.readbyqxmd.com/read/27899679/atpid-a-genome-scale-resource-for-genotype-phenotype-associations-in-arabidopsis
#6
Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype-phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899596/chitars-3-1-the-enhanced-chimeric-transcripts-and-rna-seq-database-matched-with-protein-protein-interactions
#7
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896959/prosnet-integrating-homology-with-molecular-networks-for-protein-function-prediction
#8
Sheng Wang, Meng Qu, Jian Peng
Automated annotation of protein function has become a critical task in the post-genomic era. Network-based approaches and homology-based approaches have been widely used and recently tested in large-scale community-wide assessment experiments. It is natural to integrate network data with homology information to further improve the predictive performance. However, integrating these two heterogeneous, high-dimensional and noisy datasets is non-trivial. In this work, we introduce a novel protein function prediction algorithm ProSNet...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27893735/computational-discovery-of-putative-leads-for-drug-repositioning-through-drug-target-interaction-prediction
#9
Edgar D Coelho, Joel P Arrais, José Luís Oliveira
De novo experimental drug discovery is an expensive and time-consuming task. It requires the identification of drug-target interactions (DTIs) towards targets of biological interest, either to inhibit or enhance a specific molecular function. Dedicated computational models for protein simulation and DTI prediction are crucial for speed and to reduce the costs associated with DTI identification. In this paper we present a computational pipeline that enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27891682/robust-min-system-oscillation-in-the-presence-of-internal-photosynthetic-membranes-in-cyanobacteria
#10
Joshua S MacCready, Jory Schossau, Katherine W Osteryoung, Daniel C Ducat
The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ-ring formation and represents one of the best-understood examples of emergent protein self-organization in nature. The oscillatory patterns of the Min-system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self-organization by sterically occluding or sequestering MinCDE from the plasma membrane...
November 5, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27889536/compact-integration-of-multi-network-topology-for-functional-analysis-of-genes
#11
Hyunghoon Cho, Bonnie Berger, Jian Peng
The topological landscape of molecular or functional interaction networks provides a rich source of information for inferring functional patterns of genes or proteins. However, a pressing yet-unsolved challenge is how to combine multiple heterogeneous networks, each having different connectivity patterns, to achieve more accurate inference. Here, we describe the Mashup framework for scalable and robust network integration. In Mashup, the diffusion in each network is first analyzed to characterize the topological context of each node...
November 22, 2016: Cell Systems
https://www.readbyqxmd.com/read/27889153/metagenomics-reveals-flavour-metabolic-network-of-cereal-vinegar-microbiota
#12
Lin-Huan Wu, Zhen-Ming Lu, Xiao-Juan Zhang, Zong-Min Wang, Yong-Jian Yu, Jin-Song Shi, Zheng-Hong Xu
Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27881001/pathway-crosstalk-analysis-in-prostate-cancer-based-on-protein-protein-network-data
#13
H Y Li, N Jin, Y P Han, X F Jin
Prostate cancer (PCa) is one of the major leading cause in men and no effective biomarkers or therapy have been approved for it to date. This study aimed to explore the molecular mechanisms and identify the potential molecular biomarkers of PCa. The microarray profile GSE38241 including 18 prostate cancer metastasis and 21 normal prostate samples was retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by Limma. DEGs functions were investigated by Gene Ontology (GO) and pathway enrichment analysis...
November 24, 2016: Neoplasma
https://www.readbyqxmd.com/read/27879651/prediction-of-protein-protein-interactions-by-evidence-combining-methods
#14
REVIEW
Ji-Wei Chang, Yan-Qing Zhou, Muhammad Tahir Ul Qamar, Ling-Ling Chen, Yu-Duan Ding
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of cell functions. Several experimental techniques operating in vivo or in vitro have made significant contributions to screening a large number of protein interaction partners, especially high-throughput experimental methods. However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map sketching of PPIs...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27862697/zfp36l2-promotes-cancer-cell-aggressiveness-and-is-regulated-by-antitumor-microrna-375-in-pancreatic-ductal-adenocarcinoma
#15
Keiichi Yonemori, Naohiko Seki, Hiroshi Kurahara, Yusaku Osako, Tetsuya Idichi, Takayuki Arai, Keiichi Koshizuka, Yoshiaki Kita, Kosei Maemura, Shoji Natsugoe
Due to its aggressive nature, pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and hard-to-treat malignancies. Recently developed targeted molecular strategies have contributed to remarkable improvements in the treatment of several cancers. However, such therapies have not been applied to PDAC. Therefore, new treatment options are needed for PDAC based on current genomic approaches. Expression of microRNA-375 (miR-375) was significantly reduced in miRNA expression signatures of several types of cancers, including PDAC...
November 14, 2016: Cancer Science
https://www.readbyqxmd.com/read/27853459/immunosenescence-related-transcriptomic-and-immunologic-changes-in-older-individuals-following-influenza-vaccination
#16
Richard B Kennedy, Inna G Ovsyannikova, Iana H Haralambieva, Ann L Oberg, Michael T Zimmermann, Diane E Grill, Gregory A Poland
The goal of annual influenza vaccination is to reduce mortality and morbidity associated with this disease through the generation of protective immune responses. The objective of the current study was to examine markers of immunosenescence and identify immunosenescence-related differences in gene expression, gene regulation, cytokine secretion, and immunologic changes in an older study population receiving seasonal influenza A/H1N1 vaccination. Surprisingly, prior studies in this cohort revealed weak correlations between immunosenescence markers and humoral immune response to vaccination...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27852202/protein-structure-network-based-drug-design
#17
Zhongjie Liang, Guang Hu
Although structure-based drug design (SBDD) has become an indispensable tool in drug discovery for a long time, it continues to pose major challenges to date. With the advancement of "omics" techniques, systems biology has enriched SBDD into a new era, called polypharmacology, in which multi-targets drug or drug combination is designed to fight complex diseases. As a preliminary tool in systems biology, protein structure networks (PSNs) treat a protein as a set of residues linked by edges corresponding to the intramolecular interactions existing in folded structures between the residues...
2016: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/27849614/epipolymorphisms-associated-with-the-clinical-outcome-of-autoimmune-arthritis-affect-cd4-t-cell-activation-pathways
#18
Roberto Spreafico, Maura Rossetti, John W Whitaker, Wei Wang, Daniel J Lovell, Salvatore Albani
Multifactorial diseases, including autoimmune juvenile idiopathic arthritis (JIA), result from a complex interplay between genetics and environment. Epigenetic mechanisms are believed to integrate such gene-environment interactions, fine-tuning gene expression, and possibly contributing to immune system dysregulation. Although anti-TNF therapy has strongly increased JIA remission rates, it is not curative and up to 80% of patients flare upon treatment withdrawal. Thus, a crucial unmet medical and scientific need is to understand the immunological mechanisms associated with remission or flare to inform clinical decisions...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27849060/large-scale-identification-of-human-protein-function-using-topological-features-of-interaction-network
#19
Zhanchao Li, Zhiqing Liu, Wenqian Zhong, Menghua Huang, Na Wu, Yun Xie, Zong Dai, Xiaoyong Zou
The annotation of protein function is a vital step to elucidate the essence of life at a molecular level, and it is also meritorious in biomedical and pharmaceutical industry. Developments of sequencing technology result in constant expansion of the gap between the number of the known sequences and their functions. Therefore, it is indispensable to develop a computational method for the annotation of protein function. Herein, a novel method is proposed to identify protein function based on the weighted human protein-protein interaction network and graph theory...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27836980/proteome-profiling-outperforms-transcriptome-profiling-for-co-expression-based-gene-function-prediction
#20
Jing Wang, Zihao Ma, Steven A Carr, Philipp Mertins, Hui Zhang, Zhen Zhang, Daniel W Chan, Matthew J C Ellis, R Reid Townsend, Richard D Smith, Jason E McDermott, Xian Chen, Amanda G Paulovich, Emily S Boja, Mehdi Mesri, Christopher R Kinsinger, Henry Rodriguez, Karin D Rodland, Daniel C Liebler, Bing Zhang
Co-expression of mRNAs under multiple conditions is commonly used to infer co-functionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for co-expression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)...
November 11, 2016: Molecular & Cellular Proteomics: MCP
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