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Selection signature

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https://www.readbyqxmd.com/read/28637314/dna-methylation-signatures-and-coagulation-factors-in-the-peripheral-blood-leucocytes-of-epithelial-ovarian-cancer
#1
Lian Li, Hong Zheng, Yubei Huang, Caiyun Huang, Shuang Zhang, Jing Tian, Pei Li, Anil K Sood, Wei Zhang, Kexin Chen
Solid tumors are increasingly recognized as a systemic disease that is manifested by changes in DNA, RNA, proteins, and metabolites in the blood. Whereas many studies have reported gene mutation events in the circulation, few studies have focused on epigenetic DNA methylation markers. To identify DNA methylation biomarkers in peripheral blood for ovarian cancer, we performed a two-stage epigenome-wide association study. In the discovery stage, we measured genome wide DNA methylation for 485,000 CpG sites in peripheral blood in 24 epithelial ovarian cancer cases and 24 age-matched healthy controls...
June 16, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28636618/de-novo-transcriptome-of-the-mayfly-cloeon-viridulum-and-transcriptional-signatures-of-prometabola
#2
Qin Si, Juan-Yan Luo, Ze Hu, Wei Zhang, Chang-Fa Zhou
Mayflies (Ephemeroptera) display many primitive characters and a unique type of metamorphosis (Prometabola). However, information on the genomes and transcriptomes of this insect group is limited. The RNA sequencing study presented here generated the first de novo transcriptome assembly of Cloeon viridulum (Ephemeroptera: Baetidae), and compared gene expression signatures among the young larva (YL), mature larva (ML), subimago (SI), and imago (IM) stages of this mayfly. The transcriptome, based on 88 Gb of sequence data, comprised a set of 81,185 high quality transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28633351/data-compression-can-discriminate-broilers-by-selection-line-detect-haplotypes-and-estimate-genetic-potential-for-complex-phenotypes
#3
N J Hudson, R J Hawken, R Okimoto, R L Sapp, A Reverter
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers...
June 15, 2017: Poultry Science
https://www.readbyqxmd.com/read/28632432/serum-micrornas-as-early-indicators-for-estimation-of-exposure-degree-in-response-to-ionizing-irradiation
#4
Wenjun Wei, Jinpeng He, Jufang Wang, Nan Ding, Bing Wang, Sulan Lin, Xurui Zhang, Junrui Hua, He Li, Burong Hu
Exposure to ionizing radiation from nuclear devices, spaceflights or terrorist attacks represents a major threat to human health and public security. After a radiological incident, noninvasive biomarkers that can facilitate rapid assessment of exposure risk in the early stages are urgently needed for optimal medical treatment. Serum microRNAs (miRNAs) are ideal biomarkers because they are stable in response to environmental changes, they are common among different species and are easily collected. Here, we performed miRNA PCR arrays to analyze miRNA expression profiles at 24 h postirradiation...
June 20, 2017: Radiation Research
https://www.readbyqxmd.com/read/28631230/sequence-analysis-of-chromosome-1-revealed-different-selection-patterns-between-chinese-wild-mice-and-laboratory-strains
#5
Fuyi Xu, Shixian Hu, Tianzhu Chao, Maochun Wang, Kai Li, Yuxun Zhou, Hongyan Xu, Junhua Xiao
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1...
June 19, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28630252/alpha-band-brain-oscillations-shape-the-processing-of-perceptible-as-well-as-imperceptible-somatosensory-stimuli-during-selective-attention
#6
Norman Forschack, Till Nierhaus, Matthias M Müller, Arno Villringer
Attention filters and weights sensory information according to behavioral demands. Stimulus-related neural responses are increased for the attended stimulus. Does alpha-band activity mediate this effect and is it restricted to conscious sensory events (suprathreshold), or does it also extend to unconscious stimuli (subthreshold)? To address these questions, we recorded EEG in healthy male and female volunteers undergoing subthreshold and suprathreshold somatosensory electrical stimulation to the left or right index finger...
June 19, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28629560/ct-based-radiomics-signature-for-differentiating-borrmann-type-iv-gastric-cancer-from-primary-gastric-lymphoma
#7
Zelan Ma, Mengjie Fang, Yanqi Huang, Lan He, Xin Chen, Cuishan Liang, Xiaomei Huang, Zixuan Cheng, Di Dong, Changhong Liang, Jiajun Xie, Jie Tian, Zaiyi Liu
PURPOSE: To evaluate the value of CT-based radiomics signature for differentiating Borrmann type IV gastric cancer (GC) from primary gastric lymphoma (PGL). MATERIALS AND METHODS: 40 patients with Borrmann type IV GC and 30 patients with PGL were retrospectively recruited. 485 radiomics features were extracted and selected from the portal venous CT images to build a radiomics signature. Subjective CT findings, including gastric wall peristalsis, perigastric fat infiltration, lymphadenopathy below the renal hila and enhancement pattern, were assessed to construct a subjective findings model...
June 2017: European Journal of Radiology
https://www.readbyqxmd.com/read/28627602/molecular-profiling-of-locally-advanced-rectal-adenocarcinoma-using-microrna-expression-review
#8
Cory Pettit, Steve Walston, Patrick Wald, Amy Webb, Terence M Williams
Treatment for locally-advanced rectal cancer (LARC) typically consists of neoadjuvant chemoradiation followed by total mesorectal excision. Recently, there has been growing interest in non-operative management for patients who are medically-inoperable or wish to avoid surgical morbidity and permanent colostomy. Approximately 50% of patients who receive pre-operative neoadjuvant chemoradiation develop some degree of pathologic response. Approximately 10-20% of patients are found to have a complete pathologic response, a finding which has frequently been shown to predict better clinical outcomes, including local-regional control, distant metastasis and survival...
June 14, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28627128/signatures-of-soft-sweeps-across-the-dt1-locus-underlying-determinate-growth-habit-in-soybean-glycine-max-l-merr
#9
Limei Zhong, Qiaomei Yang, Xin Yan, Chao Yu, Liu Su, Xifeng Zhang, Youlin Zhu
Determinate growth habit is an agronomically important trait associated with domestication in soybean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four non-synonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb were identified, which constitute the soft sweeps for the adaptation...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28624625/a-formalin-fixed-paraffin-embedded-ffpe-based-prognostic-signature-to-predict-metastasis-in-clinically-low-risk-stage-i-ii-microsatellite-stable-colorectal-cancer
#10
Yee Syuen Low, Christopher Blöcker, John R McPherson, See Aik Tang, Ying Ying Cheng, Joyner Y S Wong, Clarinda Chua, Tony K H Lim, Choong Leong Tang, Min Hoe Chew, Patrick Tan, Iain B Tan, Steven G Rozen, Peh Yean Cheah
Approximately 20% early-stage (I/II) colorectal cancer (CRC) patients develop metastases despite curative surgery. We aim to develop a formalin-fixed and paraffin-embedded (FFPE)-based predictor of metastases in early-stage, clinically-defined low risk, microsatellite-stable (MSS) CRC patients. We considered genome-wide mRNA and miRNA expression and mutation status of 20 genes assayed in 150 fresh-frozen tumours with known metastasis status. We selected 193 genes for further analysis using NanoString nCounter arrays on corresponding FFPE tumours...
June 15, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28624575/intestinal-fungal-dysbiosis-associates-with-visceral-hypersensitivity-in-patients-with-irritable-bowel-syndrome-and-rats
#11
Sara Botschuijver, Guus Roeselers, Evgeni Levin, Daisy M Jonkers, Olaf Welting, Sigrid Em Heinsbroek, Heleen H de Weerd, Teun Boekhout, Matteo Fornai, Ad A Masclee, Frank H J Schuren, Wouter J de Jonge, Jurgen Seppen, Rene M van den Wijngaard
BACKGROUND & AIMS: Visceral hypersensitivity is one feature of irritable bowel syndrome (IBS). Bacterial dysbiosis might be involved in activation of nociceptive sensory pathways, but there have been few studies of the role of the mycobiome (the fungal microbiome) in development of IBS. We analyzed intestinal mycobiomes of patients with IBS and a rat model of visceral hypersensitivity. METHODS: We used internal transcribed spacer 1-based metabarcoding to compare fecal mycobiomes of 18 healthy volunteers with those of 39 patients with IBS (with visceral hypersensitivity or normal levels of sensitivity)...
June 14, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28623393/limited-mhc-class-i-intron-2-repertoire-variation-in-bonobos
#12
Natasja G de Groot, Corrine M C Heijmans, Philippe Helsen, Nel Otting, Zjef Pereboom, Jeroen M G Stevens, Ronald E Bontrop
Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2-3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1...
June 16, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28622586/outerwear-through-the-ages-evolutionary-cell-biology-of-vesicle-coats
#13
REVIEW
Joel B Dacks, Margaret S Robinson
Vesicular transport was key to the evolution of eukaryotes, and is essential for eukaryotic life today. All modern eukaryotes have a set of vesicle coat proteins, which couple cargo selection to vesicle budding in the secretory and endocytic pathways. Although these coats share common features (e.g. recruitment via small GTPases, β-propeller-α-solenoid proteins acting as scaffolds), the relationships between them are not always clear. Structural studies on the coats themselves, comparative genomics and cell biology in diverse eukaryotes, and the recent discovery of the Asgard archaea and their 'eukaryotic signature proteins' are helping us to piece together how coats may have evolved during the prokaryote-to-eukaryote transition...
June 13, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28620137/biological-specificity-of-cdk4-6-inhibitors-dose-response-relationship-in-vivo-signaling-and-composite-response-signature
#14
Erik S Knudsen, Jack Hutcheson, Paris Vail, Agnieszka K Witkiewicz
Recently developed potent and selective CDK4/6 inhibitors fall into two classes based on structure and toxicity profiles in clinical studies. One class, exemplified by palbociclib and ribociclib, exhibits neutropenia as a dose-limiting toxicity and requires discontinuous dosing. In contrast, the structurally distinct CDK4/6 inhibitor abemaciclib is dosed continuously, and has diarrhea and fatigue as dose-limiting toxicities. In preclinical models, palbociclib has been extensively studied and induces cell cycle inhibition in an RB-dependent manner...
June 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28618201/targeted-quantification-of-functional-enzyme-dynamics-in-environmental-samples-for-microbially-mediated-biogeochemical-processes
#15
Minjing Li, Yuqian Gao, Wei-Jun Qian, Liang Shi, Yuanyuan Liu, William C Nelson, Carrie D Nicora, Charles T Resch, Christopher Thompson, Sen Yan, James K Fredrickson, John M Zachara, Chongxuan Liu
Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass, and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28615526/identifying-prognostic-signature-in-ovarian-cancer-using-dirgenerank
#16
Jian-Yong Wang, Ling-Ling Chen, Xiong-Hui Zhou
Identifying the prognostic genes in cancer is essential not only for the treatment of cancer patients, but also for drug discovery. However, it's still a big challenge to select the prognostic genes that can distinguish the risk of cancer patients across various data sets because of tumor heterogeneity. In this situation, the selected genes whose expression levels are statistically related to prognostic risks may be passengers. In this paper, based on gene expression data and prognostic data of ovarian cancer patients, we used conditional mutual information to construct gene dependency network in which the nodes (genes) with more out-degrees have more chances to be the modulators of cancer prognosis...
May 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28614715/phgdh-defines-a-metabolic-subtype-in-lung-adenocarcinomas-with-poor-prognosis
#17
Boxi Zhang, Adi Zheng, Per Hydbring, Gorbatchev Ambroise, Amanda Tomie Ouchida, Michel Goiny, Helin Vakifahmetoglu-Norberg, Erik Norberg
Molecular signatures are emerging determinants of choice of therapy for lung adenocarcinomas. An evolving therapeutic approach includes targeting metabolic dependencies in cancers. Here, using an integrative approach, we have dissected the metabolic fingerprints of lung adenocarcinomas, and we show that Phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in serine biosynthesis, is highly expressed in a adenocarcinoma subset with poor prognosis. This subset harbors a gene signature for DNA replication and proliferation...
June 13, 2017: Cell Reports
https://www.readbyqxmd.com/read/28612385/genetic-accommodation-in-the-wild-evolution-of-gene-expression-plasticity-during-character-displacement
#18
Nicholas A Levis, Antonio Serrato-Capuchina, David W Pfennig
Ecological character displacement is considered crucial in promoting diversification, yet relatively little is known of its underlying mechanisms. We examined whether evolutionary shifts in gene expression plasticity ('genetic accommodation') mediate character displacement in spadefoot toads. Where Spea bombifrons and S. multiplicata occur separately in allopatry (the ancestral condition), each produces alternative, diet-induced, larval ecomorphs: omnivores, which eat detritus, and carnivores, which specialize on shrimp...
June 14, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28611031/cpt1a-missense-mutation-associated-with-fatty-acid-metabolism-and-reduced-height-in-greenlanders
#19
Line Skotte, Anders Koch, Victor Yakimov, Sirui Zhou, Bolette Søborg, Mikael Andersson, Sascha W Michelsen, Johan E Navne, Jacqueline M Mistry, Patrick A Dion, Michael L Pedersen, Malene L Børresen, Guy A Rouleau, Frank Geller, Mads Melbye, Bjarke Feenstra
BACKGROUND: Inuit have lived for thousands of years in an extremely cold environment on a diet dominated by marine-derived fat. To investigate how this selective pressure has affected the genetic regulation of fatty acid metabolism, we assessed 233 serum metabolic phenotypes in a population-based sample of 1570 Greenlanders. METHODS AND RESULTS: Using array-based and targeted genotyping, we found that rs80356779, a p.Pro479Leu variant in CPT1A, was strongly associated with markers of n-3 fatty acid metabolism, including degree of unsaturation (P=1...
June 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28608831/france-s-state-of-the-art-distributed-optical-fibre-sensors-qualified-for-the-monitoring-of-the-french-underground-repository-for-high-level-and-intermediate-level-long-lived-radioactive-wastes
#20
REVIEW
Sylvie Delepine-Lesoille, Sylvain Girard, Marcel Landolt, Johan Bertrand, Isabelle Planes, Aziz Boukenter, Emmanuel Marin, Georges Humbert, Stéphanie Leparmentier, Jean-Louis Auguste, Youcef Ouerdane
This paper presents the state of the art distributed sensing systems, based on optical fibres, developed and qualified for the French Cigéo project, the underground repository for high level and intermediate level long-lived radioactive wastes. Four main parameters, namely strain, temperature, radiation and hydrogen concentration are currently investigated by optical fibre sensors, as well as the tolerances of selected technologies to the unique constraints of the Cigéo's severe environment. Using fluorine-doped silica optical fibre surrounded by a carbon layer and polyimide coating, it is possible to exploit its Raman, Brillouin and Rayleigh scattering signatures to achieve the distributed sensing of the temperature and the strain inside the repository cells of radioactive wastes...
June 13, 2017: Sensors
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