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Selection signature

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https://www.readbyqxmd.com/read/28729732/evidence-of-selection-on-splicing-associated-loci-in-human-populations-and-relevance-to-disease-loci-mapping
#1
Eric R Gamazon, Anuar Konkashbaev, Eske M Derks, Nancy J Cox, Younghee Lee
We performed a whole-genome scan of genetic variants in splicing regulatory elements (SREs) and evaluated the extent to which natural selection has shaped extant patterns of variation in SREs. We investigated the degree of differentiation of single nucleotide polymorphisms (SNPs) in SREs among human populations and applied long-range haplotype- and multilocus allelic differentiation-based methods to detect selection signatures. We describe an approach, sampling a large number of loci across the genome from functional classes and using the consensus from multiple tests, for identifying candidates for selection signals...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729721/plasma-derived-exosome-characterization-reveals-a-distinct-microrna-signature-in-long-duration-type-1-diabetes
#2
Marta Garcia-Contreras, Sanket H Shah, Alejandro Tamayo, Paul D Robbins, Ronald B Golberg, Armando J Mendez, Camillo Ricordi
Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing ß cells which leads to chronic hyperglycemia. Exosomes are lipid vesicles derived from cellular multivesicular bodies that are enriched in specific miRNAs, potentially providing a disease-specific diagnostic signature. To assess the value of exosome miRNAs as biomarkers for T1DM, miRNA expression in plasma-derived exosomes was measured. Nanoparticle tracking analysis and transmission electron microscopy confirmed the presence of plasma-derived exosomes (EXOs) isolated by differential centrifugation...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728135/prostate-cancer-risk-and-dna-methylation-signatures-in-aging-rats-following-developmental-bpa-exposure-a-dose-response-analysis
#3
Gail S Prins, Shu-Hua Ye, Lynn Birch, Xiang Zhang, Ana Cheong, Han Lin, Esther Calderon-Gierszal, Jacob Groen, Wen-Yang Hu, Shuk-Mei Ho, Richard B van Breemen
BACKGROUND: Previous studies have uncovered heightened prostatic susceptibility to hormone-induced neoplasia from early-life exposure to low-dose bisphenol A (BPA). However, significant data gaps remain that are essential to address for biological relevance and necessary risk assessment. OBJECTIVES: A complete BPA dose-response analysis of prostate lesions across multiple prostatic lobes was conducted that included internal BPA dosimetry, progression to adenocarcinoma with aging and mechanistic connections to epigenetically reprogramed genes...
July 11, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28727830/the-receptor-tyrosine-kinase-axl-promotes-migration-and-invasion-in-colorectal-cancer
#4
Diana J Uribe, Edward K Mandell, Adam Watson, Jesse D Martinez, Jonathan A Leighton, Sourav Ghosh, Carla V Rothlin
The receptor tyrosine kinases (RTKs) TYRO3, AXL and MERTK (TAM) have well-described oncogenic functions in a number of cancers. Notwithstanding, TAM RTKs are also potent and indispensable inhibitors of inflammation. The combined deletion of Axl and Mertk in mice enhances chronic inflammation and autoimmunity, including increased inflammation in the gut and colitis-associated cancer. On the other hand, deletion of Tyro3 increases the risk of allergic responses. Therefore, the indiscriminate inhibition of these TAM RTKs could result in undesirable immunological diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28725416/contrasting-patterns-of-selection-between-mhc-i-and-ii-across-populations-of-humboldt-and-magellanic-penguins
#5
Nicole Sallaberry-Pincheira, Daniel González-Acuña, Pamela Padilla, Gisele P M Dantas, Guillermo Luna-Jorquera, Esteban Frere, Armando Valdés-Velásquez, Juliana A Vianna
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28725414/snps-across-time-and-space-population-genomic-signatures-of-founder-events-and-epizootics-in-the-house-finch-haemorhous-mexicanus
#6
Allison J Shultz, Allan J Baker, Geoffrey E Hill, Paul M Nolan, Scott V Edwards
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28724663/pd-l1-expression-and-immune-escape-in-melanoma-resistanceto-mapk-inhibitors
#7
Hojabr Kakavand, Robert V Rawson, Gulietta M Pupo, Jean Y H Yang, Alexander M Menzies, Matteo S Carlino, Richard F Kefford, Julie R Howle, Robyn Saw, John F Thompson, James S Wilmott, Georgina V Long, Richard A Scolyer, Helen Rizos
Purpose: To examine the relationship between immune activity, PD-L1 expression and tumor cell signaling, in metastatic melanomas prior to and during treatment with targeted MAPK inhibitors. <p>Experimental design: Thirty-eight tumors from 17 patients treated with BRAF inhibitor (n=12) or combination BRAF/MEK inhibitors (n=5) with known PD-L1 expression were analyzed. RNA expression arrays were performed on all pre-treatment (PRE, n=17), early during treatment (EDT, n=8) and progression (PROG, n=13) biopsies...
July 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28723948/integrative-functional-analyses-using-rainbow-trout-selected-for-tolerance-to-plant-diets-reveal-nutrigenomic-signatures-for-soy-utilization-without-the-concurrence-of-enteritis
#8
Jason Abernathy, Andreas Brezas, Kevin R Snekvik, Ronald W Hardy, Ken Overturf
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation...
2017: PloS One
https://www.readbyqxmd.com/read/28723667/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#9
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
June 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722210/plasma-microrna-based-signatures-to-predict-3-year-postoperative-recurrence-risk-for-stage-ii-and-iii-gastric-cancer
#10
Xinyang Liu, Xiaowei Zhang, Zhe Zhang, Jinjia Chang, Zhichao Wang, Zheng Wu, Chenchen Wang, Zuojun Sun, Xiaoxiao Ge, Ruixuan Geng, Wenbo Tang, Congqi Dai, Ying Lin, Fengjuan Lin, Menghong Sun, Weihua Jia, Wenqiong Xue, Jiafu Ji, Ying Hu, Guoyou Qin, Jin Li
Our aim was to identify plasma microRNA (miRNA)-based signatures to predict 3-year postoperative recurrence risk for patients with stage II and III gastric cancer (GC) so as to provide insights for individualized adjuvant therapy. Plasma miRNA expression was investigated in three phases, involving 407 patients recruited from three centers. ABI miRNA microarray and TaqMan Low Density Array were adopted in the discovery phase to identify potential miRNAs. Quantitative reverse-transcriptase polymerase chain reaction was used to assess the expression of selected miRNAs...
July 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28722011/accumulating-the-hydride-state-in-the-catalytic-cycle-of-fefe-hydrogenases
#11
Martin Winkler, Moritz Senger, Jifu Duan, Julian Esselborn, Florian Wittkamp, Eckhard Hofmann, Ulf-Peter Apfel, Sven Timo Stripp, Thomas Happe
H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28720782/dysregulated-mirnas-and-their-pathogenic-implications-for-the-neurometabolic-disease-propionic-acidemia
#12
Ana Rivera-Barahona, Alejandro Fulgencio-Covián, Celia Pérez-Cerdá, Ricardo Ramos, Michael A Barry, Magdalena Ugarte, Belén Pérez, Eva Richard, Lourdes R Desviat
miRNome expression profiling was performed in a mouse model of propionic acidemia (PA) and in patients' plasma samples to investigate the role of miRNAs in the pathophysiology of the disease and to identify novel biomarkers and therapeutic targets. PA is a potentially lethal neurometabolic disease with patients developing neurological deficits and cardiomyopathy in the long-term, among other complications. In the PA mouse liver we identified 14 significantly dysregulated miRNAs. Three selected miRNAs, miR-34a-5p, miR-338-3p and miR-350, were found upregulated in brain and heart tissues...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716966/hierarchically-organized-medial-frontal-cortex-basal-ganglia-loops-selectively-control-task-and-response-selection
#13
Franziska M Korb, Jiefeng Jiang, Joseph A King, Tobias Egner
Adaptive behavior requires context-sensitive configuration of task-sets that specify time-varying stimulus-response mappings. Intriguingly, response time costs associated with changing task-sets and motor responses are known to be strongly interactive: switch costs at the task-level are small in the presence of a response-switch but large when accompanied by a response-repetition, and vice versa for response-switch costs. The reasons behind this well-known inter-dependence between task- and response-level control processes are currently not well understood...
July 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28714406/role-of-the-immune-component-of-tumor-microenvironment-in-the-efficiency-of-cancer-treatment-perspectives-for-the-personalized-therapy
#14
Marina Stakheyeva, Vladimir Riabov, Irina Mitrofanova, Nikolai Litviakov, Evgeny Choynzonov, Nadezhda Cherdyntseva, Julia Kzhyshkowska
Despite significant progress in cancer diagnostics and development of novel therapeutic regimens, successful treatment of advanced forms of cancer is still a challenge and may require personalized therapeutic approaches. In this review, we analyzed major mechanisms responsible for tumor cells chemoresistance and emphasized that intratumor heterogeneity is a critical factor that limits efficiency of cancer treatment. Intratumor heterogeneity is caused by genomic instability in cancer cells, resulting in the selection of resistant clones...
July 14, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28713819/differential-analysis-of-genetic-epigenetic-and-cytogenetic-abnormalities-in-aml
#15
Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Acute myeloid leukemia (AML) is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc) are found to be predominantly mutated...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28712948/when-pain-really-matters-a-vicarious-pain-brain-marker-tracks-empathy-for-pain-in-the-romantic-partner
#16
Marina López-Solà, Leonie Koban, Anjali Krishnan, Tor D Wager
In a previous study (Krishnan, 2016) we identified a whole-brain pattern, the Vicarious Pain Signature (VPS), which predicts vicarious pain when participants observe pictures of strangers in pain. Here, we test its generalization to observation of pain in a close significant other. Participants experienced painful heat (Self-pain) and observed their romantic partner in pain (Partner-Pain). We measured whether (i) the VPS would respond selectively to Partner-Pain and (ii) the Neurologic Pain Signature (NPS), a measure validated to track somatic pain, would selectively respond to Self-Pain, despite the high interpersonal closeness between partners...
July 13, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28708071/evolutionary-origins-of-cancer-driver-genes-and-implications-for-cancer-prognosis
#17
Xin-Yi Chu, Ling-Han Jiang, Xiong-Hui Zhou, Ze-Jia Cui, Hong-Yu Zhang
The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer...
July 14, 2017: Genes
https://www.readbyqxmd.com/read/28707606/evidence-of-positive-selection-towards-zebuine-haplotypes-in-the-bola-region-of-brangus-cattle
#18
D E Goszczynski, C M Corbi-Botto, H M Durand, A Rogberg-Muñoz, S Munilla, P Peral-Garcia, R J C Cantet, G Giovambattista
The Brangus breed was developed to combine the superior characteristics of both of its founder breeds, Angus and Brahman. It combines the high adaptability to tropical and subtropical environments, disease resistance, and overall hardiness of Zebu cattle with the reproductive potential and carcass quality of Angus. It is known that the major histocompatibility complex (MHC, also known as bovine leucocyte antigen: BoLA), located on chromosome 23, encodes several genes involved in the adaptive immune response and may be responsible for adaptation to harsh environments...
July 14, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28701938/improving-eeg-based-emotion-classification-using-conditional-transfer-learning
#19
Yuan-Pin Lin, Tzyy-Ping Jung
To overcome the individual differences, an accurate electroencephalogram (EEG)-based emotion-classification system requires a considerable amount of ecological calibration data for each individual, which is labor-intensive and time-consuming. Transfer learning (TL) has drawn increasing attention in the field of EEG signal mining in recent years. The TL leverages existing data collected from other people to build a model for a new individual with little calibration data. However, brute-force transfer to an individual (i...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28700901/hyperspectral-image-analysis-for-rapid-and-accurate-discrimination-of-bacterial-infections-a-benchmark-study
#20
Simone Arrigoni, Giovanni Turra, Alberto Signoroni
With the rapid diffusion of Full Laboratory Automation systems, Clinical Microbiology is currently experiencing a new digital revolution. The ability to capture and process large amounts of visual data from microbiological specimen processing enables the definition of completely new objectives. These include the direct identification of pathogens growing on culturing plates, with expected improvements in rapid definition of the right treatment for patients affected by bacterial infections. In this framework, the synergies between light spectroscopy and image analysis, offered by hyperspectral imaging, are of prominent interest...
June 21, 2017: Computers in Biology and Medicine
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