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landscape genetics

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https://www.readbyqxmd.com/read/28214357/nesting-habits-influence-population-genetic-structure-of-a-bee-living-in-anthropogenic-disturbance
#1
J L Vickruck, M H Richards
While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in human made wooden structures, linking their geographic distribution and population structure to human activities and disturbance...
February 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28213331/mitochondrial-metabolism-and-energy-sensing-in-tumor-progression
#2
REVIEW
Luisa Iommarini, Anna Ghelli, Giuseppe Gasparre, Anna Maria Porcelli
Energy homeostasis is pivotal for cell fate since metabolic regulation, cell proliferation and death are strongly dependent on the balance between catabolic and anabolic pathways. In particular, metabolic and energetic changes have been observed in cancer cells even before the discovery of oncogenes and tumor suppressors, but has been neglected for a long time. Instead, during the past 20years a renaissance of the study of tumor metabolism has led to a revised and more accurate sight of the metabolic landscape of cancer cells...
February 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28212305/epigenetic-landscape-during-coronavirus-infection
#3
Alexandra Schäfer, Ralph S Baric
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus-host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#4
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28211463/ecological-and-genetic-basis-of-metapopulation-persistence-of-the-glanville-fritillary-butterfly-in-fragmented-landscapes
#5
Ilkka Hanski, Torsti Schulz, Swee Chong Wong, Virpi Ahola, Annukka Ruokolainen, Sami P Ojanen
Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28210865/the-impact-of-melanoma-genetics-on-treatment-response-and-resistance-in-clinical-and-experimental-studies
#6
M Kunz, M Hölzel
Recent attempts to characterize the melanoma mutational landscape using high-throughput sequencing technologies have identified new genes and pathways involved in the molecular pathogenesis of melanoma. Apart from mutated BRAF, NRAS, and KIT, a series of new recurrently mutated candidate genes with impact on signaling pathways have been identified such as NF1, PTEN, IDH1, RAC1, ARID2, and TP53. Under targeted treatment using BRAF and MEK1/2 inhibitors either alone or in combination, a majority of patients experience recurrences, which are due to different genetic mechanisms such as gene amplifications of BRAF or NRAS, MEK1/2 and PI3K mutations...
February 16, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28209969/solution-of-the-spatial-neutral-model-yields-new-bounds-on-the-amazonian-species-richness
#7
Yahav Shem-Tov, Matan Danino, Nadav M Shnerb
Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed or mainland-island scenarios. Here we combine analytic results and numerics to obtain an approximate solution for the species abundance distribution and the species richness for the neutral model on continuous landscape...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209761/genetic-adaptation-of-the-schizothoracine-fishes-to-the-phased-uplifting-of-qinghai-tibetan-plateau
#8
Dongsheng Zhang, Mengchao Yu, Peng Hu, Sihua Peng, Yimeng Liu, Weiwen Li, Congcong Wang, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen
Many species of Schizothoracine, a sub-family of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion in high-altitudes, we sequenced tissue transcriptomes of two highland and two sub-highland Schizothoracines, and analyzed gene evolution patterns by comparing to lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fishes lived around 32...
February 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28209157/stakeholder-perspectives-on-the-implementation-of-genetic-carrier-screening-in-a-changing-landscape
#9
Kim C A Holtkamp, Evelien M Vos, Tessel Rigter, Phillis Lakeman, Lidewij Henneman, Martina C Cornel
BACKGROUND: In most countries, genetic carrier screening is neither offered, nor embedded in mainstream healthcare. Technological developments have triggered a two-fold transition in carrier screening: the expansion from screening one single disorder to many disorders simultaneously, and offering screening universally, regardless of ancestry. This study aims to identify general and population-specific barriers and needs reflected by stakeholders regarding the implementation of carrier screening in a changing landscape...
February 16, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28202815/covariation-in-levels-of-nucleotide-diversity-in-homologous-regions-of-the-avian-genome-long-after-completion-of-lineage-sorting
#10
Ludovic Dutoit, Nagarjun Vijay, Carina F Mugal, Christen M Bossu, Reto Burri, Jochen Wolf, Hans Ellegren
Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome)...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28202665/neuronal-death-signaling-pathways-triggered-by-mutant-lrrk2
#11
REVIEW
Hardy J Rideout
Autosomal dominantly inherited mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease. While considerable progress has been made in understanding its function and the many different cellular activities in which it participates, a clear understanding of the mechanism(s) of the induction of neuronal death by mutant forms of LRRK2 remains elusive. Although several in vivo models have documented the progressive loss of dopaminergic neurons of the substantia nigra, more complete interrogations of the modality of neuronal death have been gained from cellular models...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28198816/low-genetic-diversity-and-strong-population-structure-shaped-by-anthropogenic-habitat-fragmentation-in-a-critically-endangered-primate-trachypithecus-leucocephalus
#12
W Wang, Y Qiao, S Li, W Pan, M Yao
Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure...
February 15, 2017: Heredity
https://www.readbyqxmd.com/read/28198375/haploinsufficiency-networks-identify-targetable-patterns-of-allelic-deficiency-in-low-mutation-ovarian-cancer
#13
Joe Ryan Delaney, Chandni B Patel, Katelyn McCabe Willis, Mina Haghighiabyaneh, Joshua Axelrod, Isabelle Tancioni, Dan Lu, Jaidev Bapat, Shanique Young, Octavia Cadassou, Alena Bartakova, Parthiv Sheth, Carley Haft, Sandra Hui, Cheryl Saenz, David D Schlaepfer, Olivier Harismendy, Dwayne G Stupack
Identification of specific oncogenic gene changes has enabled the modern generation of targeted cancer therapeutics. In high-grade serous ovarian cancer (OV), the bulk of genetic changes is not somatic point mutations, but rather somatic copy-number alterations (SCNAs). The impact of SCNAs on tumour biology remains poorly understood. Here we build haploinsufficiency network analyses to identify which SCNA patterns are most disruptive in OV. Of all KEGG pathways (N=187), autophagy is the most significantly disrupted by coincident gene deletions...
February 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28196625/-did-he-who-made-the-lamb-make-thee-new-developments-in-treating-the-fearful-symmetry-of-acute-myeloid-leukemia
#14
REVIEW
Gabriela Brumatti, Najoua Lalaoui, Andrew H Wei, John Silke
Malignant cells must circumvent endogenous cell death pathways to survive and develop into cancers. Acquired cell death resistance also sets up malignant cells to survive anticancer therapies. Acute Myeloid Leukemia (AML) is an aggressive blood cancer characterized by high relapse rate and resistance to cytotoxic therapies. Recent collaborative profiling projects have led to a greater understanding of the 'fearful symmetry' of the genomic landscape of AML, and point to the development of novel potential therapies that can overcome factors linked to chemoresistance...
February 11, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28193859/genetic-regulatory-signatures-underlying-islet-gene-expression-and-type-2-diabetes
#15
Arushi Varshney, Laura J Scott, Ryan P Welch, Michael R Erdos, Peter S Chines, Narisu Narisu, Ricardo D'O Albanus, Peter Orchard, Brooke N Wolford, Romy Kursawe, Swarooparani Vadlamudi, Maren E Cannon, John P Didion, John Hensley, Anthony Kirilusha, Lori L Bonnycastle, D Leland Taylor, Richard Watanabe, Karen L Mohlke, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193289/microgeographical-structure-in-the-major-neotropical-malaria-vector-anopheles-darlingi-using-microsatellites-and-snp-markers
#16
Melina Campos, Jan E Conn, Diego Peres Alonso, Joseph M Vinetz, Kevin J Emerson, Paulo Eduardo Martins Ribolla
BACKGROUND: In recent decades, throughout the Amazon Basin, landscape modification contributing to profound ecological change has proceeded at an unprecedented rate. Deforestation that accompanies human activities can significantly change aspects of anopheline biology, though this may be site-specific. Such local changes in anopheline biology could have a great impact on malaria transmission. The aim of this study was to investigate population genetics of the main malaria vector in Brazil, Anopheles darlingi, from a microgeographical perspective...
February 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28188333/use-of-modern-tomato-breeding-germplasm-for-deciphering-the-genetic-control-of-agronomical-traits-by-genome-wide-association-study
#17
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato...
February 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28188128/interaction-landscape-of-inherited-polymorphisms-with-somatic-events-in-cancer
#18
Hannah Carter, Rachel Marty, Matan Hofree, Andy Gross, James Jensen, Kathleen M Fisch, Xingyu Wu, Christopher DeBoever, Eric L Van Nostrand, Yan Song, Emily Wheeler, Jason F Kreisberg, Scott M Lippman, Gene Yeo, J Silvio Gutkind, Trey Ideker
Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5954 tumors to reveal and systematically validate 412 genetic interactions between germline polymorphisms and major somatic events, including tumor formation in specific tissues and alteration of specific cancer genes. Among germline-somatic interactions, we find germline variants in RBFOX1 that increase incidence of SF3B1 somatic mutation by eight-fold via functional alterations in RNA splicing...
February 10, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28183512/a-test-in-context-lipoprotein-a-diagnosis-prognosis-controversies-and-emerging-therapies
#19
REVIEW
Sotirios Tsimikas
Evidence that elevated lipoprotein(a) (Lp[a]) levels contribute to cardiovascular disease (CVD) and calcific aortic valve stenosis (CAVS) is substantial. Development of isoform-independent assays, in concert with genetic, epidemiological, translational, and pathophysiological insights, have established Lp(a) as an independent, genetic, and likely causal risk factor for CVD and CAVS. These observations are consistent across a broad spectrum of patients, risk factors, and concomitant therapies, including patients with low-density lipoprotein cholesterol <70 mg/dl...
February 14, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28182618/the-evolving-landscape-of-hiv-drug-resistance-diagnostics-for-expanding-testing-in-resource-limited-settings
#20
Seth C Inzaule, Raph L Hamers, Roger Paredes, Chunfu Yang, Rob Schuurman, Tobias F Rinke de Wit
Global scale-up of antiretroviral treatment (ART) has dramatically changed the prospects of HIV/AIDS disease rendering life-long chronic care and treatment a reality for millions of HIV-infected patients. Affordable technologies to monitor ART are needed to ensure long-term durability of limited available drug regimens. HIV drug resistance tests can complement existing strategies in optimizing clinical decision-making for patients with treatment failure, in addition to facilitating population-based surveillance of HIV drug resistance...
February 9, 2017: AIDS Reviews
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