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https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#1
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28427536/health-risks-of-food-oxidation
#2
Mario Estévez, Zhuqing Li, Olugbenga P Soladoye, Thomas Van-Hecke
The impact of dietary habits on our health is indisputable. Consumer's concern on aging and age-related diseases challenges scientists to underline the potential role of food on the extension and guarantee of lifespan and healthspan. While some dietary components and habits are generally regarded as beneficial for our health, some others are being found to exert potential toxic effects and hence, contribute to the onset of particular health disorders. Among the latter, lipid and protein oxidation products formed during food production, storage, processing, and culinary preparation have been recently identified as potentially harmful to humans...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28427468/learning-from-biomedical-linked-data-to-suggest-valid-pharmacogenes
#3
Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye, Adrien Coulet
BACKGROUND: A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, computational approaches based on the use of background knowledge have been proposed. Until now, only molecular networks or the biomedical literature were used, whereas many other resources are available. METHOD: We propose here to consume a diverse and larger set of resources using linked data related either to genes, drugs or diseases...
April 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28423569/accurate-prediction-of-protein-protein-interactions-by-integrating-potential-evolutionary-information-embedded-in-pssm-profile-and-discriminative-vector-machine-classifier
#4
Zheng-Wei Li, Zhu-Hong You, Xing Chen, Li-Ping Li, De-Shuang Huang, Gui-Ying Yan, Ru Nie, Yu-An Huang
Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421095/exploiting-wild-relatives-for-genomics-assisted-breeding-of-perennial-crops
#5
REVIEW
Zoë Migicovsky, Sean Myles
Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28415132/genetic-alterations-in-mesiodens-as-revealed-by-targeted-ngs-and-gene-co-occurrence-network-analysis
#6
Young Youn Kim, Jihye Hwang, Hye-Sung Kim, Hee Jun Kwon, Sanguk Kim, Ji Hyun Lee, Jae Hoon Lee
OBJECTIVE: Mesiodens is the most common type of supernumerary tooth which includes a population prevalence of 0.15-1.9%. Alongside evidence that the condition is heritable, mutations in single genes have been reported in few human supernumerary tooth cases. Gene sequencing methods in tradition way are time-consuming and labor-intensive, whereas next generation sequencing and bioinformatics are cost-effective for large samples and target sizes. MATERIALS AND METHODS: We describe the application of a targeted next generation sequencing (NGS) and bioinformatics approach to samples from 17 mesiodens patients...
April 17, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28413948/some-remarks-on-prediction-of-drug-target-interaction-with-network-models
#7
Shao-Wu Zhang, Xiao-Ying Yan
System-level understanding of the relationships between drugs and targets is very important for enhancing drug research, especially for drug function repositioning. The experimental methods used to determine drug-target interactions are usually time-consuming, tedious and expensive, and sometimes lack reproducibility. Thus, it is highly desired to develop computational methods for efficiently and effectively analyzing and detecting new drug-target interaction pairs. With the explosive growth of different types of omics data, such as genome, pharmacology, phenotypic, and other kinds of molecular networks, numerous computational approaches have been developed to predict drug-target interactions (DTI)...
April 14, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28409383/functional-analysis-of-arabinofuranosidases-and-a-xylanase-of-corynebacterium-alkanolyticum-for-arabinoxylan-utilization-in-corynebacterium-glutamicum
#8
Takayuki Kuge, Akira Watanabe, Satoshi Hasegawa, Haruhiko Teramoto, Masayuki Inui
Xylooligosaccharides (XOSs) and arabinoxylooligosaccharides (AXOSs) are major oligosaccharides derived from arabinoxylan. In our previous report, Corynebacterium glutamicum was engineered to utilize XOSs by introducing Corynebacterium alkanolyticum xyloside transporter and β-xylosidase. However, this strain was unable to consume AXOSs due to the absence of α-L-arabinofuranosidase activity. In this study, to confer AXOS utilization ability on C. glutamicum, two putative arabinofuranosidase genes (abf51A and abf51B) were isolated from C...
April 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28406170/identification-of-proteins-involved-in-the-anti-inflammatory-properties-of-propionibacterium-freudenreichii-by-means-of-a-multi-strain-study
#9
Stéphanie-Marie Deutsch, Mahendra Mariadassou, Pierre Nicolas, Sandrine Parayre, Rozenn Le Guellec, Victoria Chuat, Vincent Peton, Caroline Le Maréchal, Julien Burati, Valentin Loux, Valérie Briard-Bion, Julien Jardin, Coline Plé, Benoît Foligné, Gwénaël Jan, Hélène Falentin
Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 10(9) propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We selected 23 strains with varied anti-inflammatory potentials in order to identify the protein(s) involved. After comparative genomic analysis, 12 of these strains were further analysed by surface proteomics, eight of them being further submitted to transcriptomics...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28401315/improving-the-tool-box-for-robust-industrial-enzymes
#10
REVIEW
J A Littlechild
The speed of sequencing of microbial genomes and metagenomes is providing an ever increasing resource for the identification of new robust biocatalysts with industrial applications for many different aspects of industrial biotechnology. Using 'natures catalysts' provides a sustainable approach to chemical synthesis of fine chemicals, general chemicals such as surfactants and new consumer-based materials such as biodegradable plastics. This provides a sustainable and 'green chemistry' route to chemical synthesis which generates no toxic waste and is environmentally friendly...
April 11, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28400784/high-throughput-phenotyping-of-sorghum-plant-height-using-an-unmanned-aerial-vehicle-and-its-application-to-genomic-prediction-modeling
#11
Kakeru Watanabe, Wei Guo, Keigo Arai, Hideki Takanashi, Hiromi Kajiya-Kanegae, Masaaki Kobayashi, Kentaro Yano, Tsuyoshi Tokunaga, Toru Fujiwara, Nobuhiro Tsutsumi, Hiroyoshi Iwata
Genomics-assisted breeding methods have been rapidly developed with novel technologies such as next-generation sequencing, genomic selection and genome-wide association study. However, phenotyping is still time consuming and is a serious bottleneck in genomics-assisted breeding. In this study, we established a high-throughput phenotyping system for sorghum plant height and its response to nitrogen availability; this system relies on the use of unmanned aerial vehicle (UAV) remote sensing with either an RGB or near-infrared, green and blue (NIR-GB) camera...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28397319/damold-a-data-mining-platform-for-variant-annotation-and-visualization-in-molecular-diagnostics-research
#12
Ram Vinay Pandey, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel
Next-Generation Sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization...
April 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28396505/genetic-characterisation-of-dog-personality-traits
#13
Joanna Ilska, Marie J Haskell, Sarah C Blott, Enrique Sánchez-Molano, Zita Polgar, Sarah E Lofgren, Dylan N Clements, Pam Wiener
The genetic architecture of behavioural traits in dogs is of great interest to owners, breeders and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behaviour. The genetic component of dog behaviour is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behaviour, which are both time-consuming and logistically difficult to measure, and known to be influenced by non-genetic factors...
April 10, 2017: Genetics
https://www.readbyqxmd.com/read/28391895/identification-of-a-novel-lmf1-nonsense-mutation-responsible-for-severe-hypertriglyceridemia-by-targeted-next-generation-sequencing
#14
Angelo B Cefalù, Rossella Spina, Davide Noto, Valeria Ingrassia, Vincenza Valenti, Antonina Giammanco, Francesca Fayer, Gabriella Misiano, Gianfranco Cocorullo, Chiara Scrimali, Ornella Palesano, Grazia I Altieri, Antonina Ganci, Carlo M Barbagallo, Maurizio R Averna
BACKGROUND: Severe hypertriglyceridemia (HTG) may result from mutations in genes affecting the intravascular lipolysis of triglyceride (TG)-rich lipoproteins. OBJECTIVE: The aim of this study was to develop a targeted next-generation sequencing panel for the molecular diagnosis of disorders characterized by severe HTG. METHODS: We developed a targeted customized panel for next-generation sequencing Ion Torrent Personal Genome Machine to capture the coding exons and intron/exon boundaries of 18 genes affecting the main pathways of TG synthesis and metabolism...
January 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/28388918/tea-camellia-sinensis-infusions-ameliorate-cancer-in-4ti-metastatic-breast-cancer-model
#15
Karori S Mbuthia, Paul O Mireji, Raphael M Ngure, Francesca Stomeo, Martina Kyallo, Chalo Muoki, Francis N Wachira
BACKGROUND: Tea (Camellia sinensis) infusions are widely consumed beverages with numerous health benefits. However, physiological and molecular responses mediating these activities are poorly understood. METHOD: Three replicates of 4TI cancer cell suspension (2.0 × 10(5) cells/ml) were challenged in vitro with various concentrations of green, black and purple tea infusions to asseses their cytoxicity and associated differentially expressed genes in the cells...
April 7, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28383679/ezmap-a-simple-pipeline-for-reproducible-analysis-of-the-human-virome
#16
Patrick Czeczko, Steven C Greenway, A P Jason de Koning
Summary: In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully-automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome...
April 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28380601/genome-wide-association-study-in-an-f2-duroc-x-pietrain-resource-population-for-economically-important-meat-quality-and-carcass-traits
#17
S Casiró, D Velez-Irizarry, C W Ernst, N E Raney, R O Bates, M G Charles, J P Steibel
Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0...
February 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28379292/kart-a-divide-and-conquer-algorithm-for-ngs-read-alignment
#18
Hsin-Nan Lin, Wen-Lian Hsu
Motivation: Next-generation sequencing (NGS) provides a great opportunity to investigate genome-wide variation at nucleotide resolution. Due to the huge amount of data, NGS applications require very fast and accurate alignment algorithms. Most existing algorithms for read mapping basically adopt seed-and-extend strategy, which is sequential in nature and takes much longer time on longer reads. Results: We develop a divide-and-conquer algorithm, called Kart, which can process long reads as fast as short reads by dividing a read into small fragments that can be aligned independently...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28377746/genome-guided-insights-into-the-plant-growth-promotion-capabilities-of-the-physiologically-versatile-bacillus-aryabhattai-strain-ab211
#19
Chandrima Bhattacharyya, Utpal Bakshi, Ivy Mallick, Shayantan Mukherji, Biswajit Bera, Abhrajyoti Ghosh
Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It's genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28371421/hepatitis-e-virus-in-wild-rabbits-and-european-brown-hares-in-germany
#20
F Hammerschmidt, K Schwaiger, L Dähnert, A Vina-Rodriguez, D Höper, M Gareis, M H Groschup, M Eiden
Recently, a change of hepatitis E from being a typical travel-associated disease to an autochthonous zoonosis in Germany was observed. An increasing number of autochthonous infections with the hepatitis E Virus (HEV) have been recognized in developed countries. Venison from wild boar is already known to be a potential source of infection, if not prepared properly by the consumer. In Germany, certain wild animals are known to be a reservoir for HEV. However, current information is missing about European brown hares (Lepus europaeus) and wild rabbits (Oryctolagus cuniculus)...
March 28, 2017: Zoonoses and Public Health
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