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https://www.readbyqxmd.com/read/28435450/exome-sequencing-of-oral-squamous-cell-carcinoma-reveals-molecular-subgroups-and-novel-therapeutic-opportunities
#1
Shih-Chi Su, Chiao-Wen Lin, Yu-Fan Liu, Wen-Lang Fan, Mu-Kuan Chen, Chun-Ping Yu, Wei-En Yang, Chun-Wen Su, Chun-Yi Chuang, Wen-Hsiung Li, Wen-Hung Chung, Shun-Fa Yang
Oral squamous cell carcinoma (OSCC), an epithelial malignancy affecting a variety of subsites in the oral cavity, is prevalent in Asia. The survival rate of OSCC patients has not improved over the past decades due to its heterogeneous etiology, genetic aberrations, and treatment outcomes. Improvement in therapeutic strategies and tailored treatment options is an unmet need. To unveil the mutational spectrum, whole-exome sequencing of 120 OSCC from male individuals in Taiwan was conducted. Analyzing the contributions of the five mutational signatures extracted from the dataset of somatic variations identified four groups of tumors that were significantly associated with demographic and clinical features...
2017: Theranostics
https://www.readbyqxmd.com/read/28431166/landscape-genetics-of-aedes-mcintoshi-diptera-culicidae-an-important-vector-of-rift-valley-fever-virus-in-northeastern-kenya
#2
Lindsay P Campbell, Alana M Alexander
Rift Valley fever virus (RVFV) is a vector-borne, zoonotic disease that affects humans, wild ungulates, and domesticated livestock in Africa and the Arabian Peninsula. Rift Valley fever virus exhibits interepizootic and epizootic phases, the latter defined by widespread virus occurrence in domesticated livestock. Kenya appears to be particularly vulnerable to epizootics, with 11 outbreaks occurring between 1951 and 2007. The mosquito species Aedes mcintoshi (subgenus Neomelaniconion) is an important primary vector for RVFV in Kenya...
April 18, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28429724/clonal-evolution-in-myelodysplastic-syndromes
#3
Pedro da Silva-Coelho, Leonie I Kroeze, Kenichi Yoshida, Theresia N Koorenhof-Scheele, Ruth Knops, Louis T van de Locht, Aniek O de Graaf, Marion Massop, Sarah Sandmann, Martin Dugas, Marian J Stevens-Kroef, Jaroslav Cermak, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Theo de Witte, Nicole M A Blijlevens, Petra Muus, Gerwin Huls, Bert A van der Reijden, Seishi Ogawa, Joop H Jansen
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5-11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28428842/incipient-ecological-speciation-between-successional-varieties-of-a-dominant-tree-involves-intrinsic-postzygotic-isolating-barriers
#4
Elizabeth A Stacy, Bhama Paritosh, Melissa A Johnson, Donald K Price
Whereas disruptive selection imposed by heterogeneous environments can lead to the evolution of extrinsic isolating barriers between diverging populations, the evolution of intrinsic postzygotic barriers through divergent selection is less certain. Long-lived species such as trees may be especially slow to evolve intrinsic isolating barriers. We examined postpollination reproductive isolating barriers below the species boundary, in an ephemeral hybrid zone between two successional varieties of the landscape-dominant Hawaiian tree, Metrosideros polymorpha, on volcanically active Hawai'i Island...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28424728/landscape-population-genomics-of-forsythia-forsythia-suspensa-reveal-that-ecological-habitats-determine-the-adaptive-evolution-of-species
#5
Jie Yang, Cai-Yun Miao, Run-Li Mao, Yong Li
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424246/enteropathy-associated-t-cell-lymphoma-subtypes-are-characterized-by-loss-of-function-of-setd2
#6
Andrea B Moffitt, Sarah L Ondrejka, Matthew McKinney, Rachel E Rempel, John R Goodlad, Chun Huat Teh, Sirpa Leppa, Susanna Mannisto, Panu E Kovanen, Eric Tse, Rex K H Au-Yeung, Yok-Lam Kwong, Gopesh Srivastava, Javeed Iqbal, Jiayu Yu, Kikkeri Naresh, Diego Villa, Randy D Gascoyne, Jonathan Said, Magdalena B Czader, Amy Chadburn, Kristy L Richards, Deepthi Rajagopalan, Nicholas S Davis, Eileen C Smith, Brooke C Palus, Tiffany J Tzeng, Jane A Healy, Patricia L Lugar, Jyotishka Datta, Cassandra Love, Shawn Levy, David B Dunson, Yuan Zhuang, Eric D Hsi, Sandeep S Dave
Enteropathy-associated T cell lymphoma (EATL) is a lethal, and the most common, neoplastic complication of celiac disease. Here, we defined the genetic landscape of EATL through whole-exome sequencing of 69 EATL tumors. SETD2 was the most frequently silenced gene in EATL (32% of cases). The JAK-STAT pathway was the most frequently mutated pathway, with frequent mutations in STAT5B as well as JAK1, JAK3, STAT3, and SOCS1 We also identified mutations in KRAS, TP53, and TERT Type I EATL and type II EATL (monomorphic epitheliotropic intestinal T cell lymphoma) had highly overlapping genetic alterations indicating shared mechanisms underlying their pathogenesis...
April 19, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28424200/whole-exome-sequencing-of-metaplastic-breast-carcinoma-indicates-monoclonality-with-associated-ductal-carcinoma-component
#7
Bracha Avigdor, Katie Beierl, Christopher D Gocke, Daniel Zabransky, Karen Cravero, Kelly Kyker-Snowman, Berry Button, David Chu, Sarah Croessmann, Rory L Cochran, Roisin Connolly, Ben Ho Park, Ashley Cimino-Mathews, Sarah J Wheelan
Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma, a rare but aggressive cancer with a heterogenous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER-2) amplification/overexpression...
April 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28423717/non-homologous-end-joining-induced-alterations-in-dna-methylation-a-source-of-permanent-epigenetic-change
#8
Brittany Allen, Antonio Pezone, Antonio Porcellini, Mark T Muller, Michal M Masternak
In addition to genetic mutations, epigenetic revision plays a major role in the development and progression of cancer; specifically, inappropriate DNA methylation or demethylation of CpG residues may alter the expression of genes that promote tumorigenesis. We hypothesize that DNA repair, specifically the repair of DNA double strand breaks (DSB) by Non-Homologous End Joining (NHEJ) may play a role in this process. Using a GFP reporter system inserted into the genome of HeLa cells, we are able to induce targeted DNA damage that enables the cells, after successfully undergoing NHEJ repair, to express WT GFP...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423062/filamentous-fungal-carbon-catabolite-repression-supports-metabolic-plasticity-and-stress-responses-essential-for-disease-progression
#9
Sarah R Beattie, Kenneth M K Mark, Arsa Thammahong, Laure Nicolas Annick Ries, Sourabh Dhingra, Alayna K Caffrey-Carr, Chao Cheng, Candice C Black, Paul Bowyer, Michael J Bromley, Joshua J Obar, Gustavo H Goldman, Robert A Cramer
Aspergillus fumigatus is responsible for a disproportionate number of invasive mycosis cases relative to other common filamentous fungi. While many fungal factors critical for infection establishment are known, genes essential for disease persistence and progression are ill defined. We propose that fungal factors that promote navigation of the rapidly changing nutrient and structural landscape characteristic of disease progression represent untapped clinically relevant therapeutic targets. To this end, we find that A...
April 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28423033/can-soda-ash-dumping-grounds-provide-replacement-habitats-for-digger-wasps-hymenoptera-apoidea-spheciformes
#10
Lucyna Twerd, Maciej Krzyżyński, Barbara Waldon-Rudzionek, Piotr Olszewski
BACKGROUND: Published sources document a loss of biodiversity at an extreme rate, mainly because natural and semi-natural ecosystems are becoming fragmented and isolated, thus losing their biological functions. These changes significantly influence biological diversity, which is a complex phenomenon that changes over time. Contemporary ecologists must therefore draw attention to anthropogenic replacement habitats and increase their conservation status. In our studies we show the positive role of soda ash dumping grounds as an alternative habitat for digger wasps, especially the thermophilic species...
2017: PloS One
https://www.readbyqxmd.com/read/28422131/variants-in-cplx1-in-two-families-with-autosomal-recessive-severe-infantile-myoclonic-epilepsy-and-id
#11
Silke Redler, Tim M Strom, Thomas Wieland, Kirsten Cremer, Hartmut Engels, Felix Distelmaier, Jörg Schaper, Alma Küchler, Johannes R Lemke, Stephanie Jeschke, Nicole Schreyer, Heinrich Sticht, Margarete Koch, Hermann-Josef Lüdecke, Dagmar Wieczorek
For a large number of individuals with intellectual disability (ID), the molecular basis of the disorder is still unknown. However, whole-exome sequencing (WES) is providing more and more insights into the genetic landscape of ID. In the present study, we performed trio-based WES in 311 patients with unsolved ID and additional clinical features, and identified homozygous CPLX1 variants in three patients with ID from two unrelated families. All displayed marked developmental delay and migrating myoclonic epilepsy, and one showed a cerebellar cleft in addition...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28420341/genetic-sequence-based-prediction-of-long-range-chromatin-interactions-suggests-a-potential-role-of-short-tandem-repeat-sequences-in-genome-organization
#12
Sarvesh Nikumbh, Nico Pfeifer
BACKGROUND: Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions - the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28417598/genetic-analysis-of-a-morphologically-heterogeneous-ovarian-endometrioid-carcinoma
#13
Felipe C Geyer, Fresia Pareja, Kathleen A Burke, Anne M Schultheis, Yaser R Hussein, Jiqing Ye, Maria R De Filippo, Caterina Marchio, Gabriel S Macedo, Salvatore Piscuoglio, Raymond S Lim, Eugene Toy, Rajmohan Murali, Achim A Jungbluth, Jorge S Reis-Filho, Robert A Soslow, Britta Weigelt
AIMS: Low-grade ovarian endometrioid carcinomas may be associated with high-grade components. Whether the latter are clonally-related to and originate from the low-grade endometrioid carcinoma remains unclear. Here we employed massively parallel sequencing to characterize the genomic landscape and clonal relatedness of an ovarian endometrioid carcinoma containing low- and high-grade components. METHODS AND RESULTS: DNA samples extracted from each tumor component (low-grade endometrioid, high-grade anaplastic, high-grade squamous) and matched normal tissue were subjected to targeted massively parallel sequencing using the 410 gene Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay...
April 18, 2017: Histopathology
https://www.readbyqxmd.com/read/28416588/association-between-mutation-status-and-left-ventricular-reverse-remodelling-in-dilated-cardiomyopathy
#14
Matteo Dal Ferro, Davide Stolfo, Alessandro Altinier, Marta Gigli, Martina Perrieri, Federica Ramani, Giulia Barbati, Alberto Pivetta, Francesca Brun, Lorenzo Monserrat, Mauro Giacca, Luisa Mestroni, Marco Merlo, Gianfranco Sinagra
OBJECTIVE: To explore the genetic landscape of a well selected dilated cardiomyopathy (DCM) cohort, assessing the possible relation between different genotypes and left ventricular reverse remodelling (LVRR). METHODS: A cohort of 152 patients with DCM from the Heart Muscle Disease Registry of Trieste has been studied by next-generation sequencing (NGS). Patients were grouped into different 'gene-clusters' with functionally homogeneous genetic backgrounds. LVRR was defined by left ventricular ejection fraction normalisation or increase ≥10% associated with normalisation in indexed left ventricular end-diastolic diameter or relative decrease ≥10% at 24 months follow-up...
April 17, 2017: Heart: Official Journal of the British Cardiac Society
https://www.readbyqxmd.com/read/28413979/drug-resistance-of-enzalutamide-in-crpc
#15
Xuedong Chen, Jieyang Lu, Liqun Xia, Gonghui Li
Enzalutamide (MDV3100, XTANDI ) is a second generation androgen receptor inhibitor that is designed for the treatment of castration-resistant prostate cancer (CRPC) and has prolonged survival time. Although Enzalutamide was also associated with such significant benefits, The majority of treated patients, innate or acquired resistance invariably arises, but the mechanisms of mdv3100 resistance have not yet been clearly clarified. Nevertheless, because the better knowledge of the genetic landscape of MDV3100 is under way, resistance to MDV3100 could be basically divided in two distinct pathways, either dependent or independent of the androgen receptor activity...
April 17, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28412737/whole-exome-sequencing-identifies-sgcd-and-acvrl1-mutations-associated-with-total-anomalous-pulmonary-venous-return-tapvr-in-chinese-population
#16
Jun Li, Shiwei Yang, Zhening Pu, Juncheng Dai, Tao Jiang, Fangzhi Du, Zhu Jiang, Yue Cheng, Genyin Dai, Jun Wang, Jirong Qi, Liming Cao, Xueying Cheng, Cong Ren, Xinli Li, Yuming Qin
As a rare type of Congenital Heart Defects (CHD), the genetic mechanism of Total Anomalous Pulmonary Venous Return (TAPVR) remains unknown, although previous studies have revealed potential disease-driving regions/genes. Blood samples collected from the 6 sporadic TAPVR cases and 81 non-TAPVR controls were subjected to whole exome sequencing. All detected variations were confirmed by direct Sanger sequencing. Here, we identified 2 non-synonymous missense mutations: c.C652T, p.R218W in activin A receptor type II-like 1 (ACVRL1), c...
February 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28411852/the-molecular-revolution-in-cutaneous-biology-era-of-molecular-diagnostics-for-inherited-skin%C3%A2-diseases
#17
REVIEW
John A McGrath
The discovery of pathogenic mutations in inherited skin diseases represents one of the major landmarks of late 20th century molecular genetics. Mutation data can provide accurate diagnoses, improve genetic counseling, help define disease mechanisms, establish disease models, and provide a basis for translational research and testing of novel therapeutics. The process of detecting disease mutations, however, has not always been straightforward. Traditional approaches using genetic linkage or candidate gene analysis have often been limited, costly, and slow to yield new insights, but the advent of next-generation sequencing (NGS) technologies has altered the landscape of current gene discovery and mutation detection approaches...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411319/fifty-year-spatiotemporal-analysis-of-landscape-changes-in-the-mont-saint-hilaire-unesco-biosphere-reserve-quebec-canada
#18
Marc Béliveau, Daniel Germain, Ana-Neli Ianăş
Diachronic analysis with a GIS-based classification of land-use changes based on aerial photographs, orthophotos, topographic maps, geotechnical reports, urban plans, and using landscape metrics has permitted insight into the driving forces responsible for landscape fragmentation in the Mont Saint-Hilaire (MSH) Biosphere Reserve over the period 1958-2015. Although the occurrence of exogenous factors, such as extreme weather and fires, can have a significant influence on the fragmentation of the territory in time and space, the accelerated development of the built environment (+470%) is nevertheless found to be primarily responsible for landscape fragmentation and the loss of areas formerly occupied by orchards, agriculture, and woodlands...
May 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28411160/life-on-the-rocks-multilocus-phylogeography-of-rock-hyrax-procavia-capensis-from-southern-africa
#19
K Amanda Maswanganye, Michael J Cunningham, Nigel C Bennett, Christian T Chimimba, Paulette Bloomer
Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28409725/genetic-landscape-of-sporadic-vestibular-schwannoma
#20
Aril Løge Håvik, Ove Bruland, Erling Myrseth, Hrvoje Miletic, Mads Aarhus, Per-Morten Knappskog, Morten Lund-Johansen
OBJECTIVE Vestibular schwannoma (VS) is a benign tumor with associated morbidities and reduced quality of life. Except for mutations in NF2, the genetic landscape of VS remains to be elucidated. Little is known about the effect of Gamma Knife radiosurgery (GKRS) on the VS genome. The aim of this study was to characterize mutations occurring in this tumor to identify new genes and signaling pathways important for the development of VS. In addition, the authors sought to evaluate whether GKRS resulted in an increase in the number of mutations...
April 14, 2017: Journal of Neurosurgery
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