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landscape genetics

Xiangfeng Wang, Hu Fang, Yong Cheng, Lin Li, Xiaohui Sun, Tao Fu, Peide Huang, Anping Zhang, Zhimin Feng, Chunxue Li, Xuanlin Huang, Guangyan Li, Peina Du, Huanming Yang, Xiaodong Fang, Fan Li, Qiang Gao, Baohua Liu
Synchronous colorectal cancers (syCRCs), which present two or more lesions at diagnosis, are rare and pose a great challenge for clinical management. Although some predisposing factors associated with syCRCs have been studied with limited accession, the full repertoire of genomic events among the lesions within an individual and the causes of syCRCs remain unclear. We performed whole-exome sequencing of 40 surgical tumour samples of paired lesions from 20 patients to characterize the genetic alterations. Lesions from same patient showed distinct landscapes of somatic aberrations and shared few mutations, which suggests that they originate and develop independently although they shared the similar genetic background...
March 13, 2018: Carcinogenesis
Nathan H Schumaker, Allen Brookes
Context: Simulation models are increasingly used in both theoretical and applied studies to explore system responses to natural and anthropogenic forcing functions, develop defensible predictions of future conditions, challenge simplifying assumptions that facilitated past research, and to train students in scientific concepts and technology. Researcher's increased use of simulation models has created a demand for new platforms that balance performance, utility, and flexibility. Objectives: We describe HexSim, a powerful new spatially-explicit, individual-based modeling framework that will have applications spanning diverse landscape settings, species, stressors, and disciplines (e...
February 1, 2018: Landscape Ecology
Holger Winkels, Erik Ehinger, Melanie Vassallo, Konrad Buscher, Huy Dinh, Kouji Kobiyama, Anouk Hamers, Clément Cochain, Ehsan Vafadarnejad, Antoine-Emmanuel Saliba, Alma Zernecke, Akula Pramod, Amlan Ghosh, Nathaly Anto Michel, Natalie Hoppe, Ingo Hilgendorf, Andreas Zirlik, Catherine Hedrick, Klaus Ley, Dennis Wolf
<u>Rationale:</u> Atherosclerosis is a chronic inflammatory disease that is driven by the interplay of pro- and anti-inflammatory leukocytes in the aorta. Yet, the phenotypic and transcriptional diversity of aortic leukocytes is only poorly understood. <u>Objective:</u> We characterized leukocytes from healthy and atherosclerotic mouse aortas in-depth by single cell RNA-sequencing (scRNAseq) and mass cytometry (CyTOF) to define an atlas of the immune cell landscape in atherosclerosis...
March 15, 2018: Circulation Research
Weicheng Ren, Xiaofei Ye, Hong Su, Wei Li, Dongbing Liu, Mohammad Pirmoradian, Xianhuo Wang, Bo Zhang, Qiang Zhang, Longyun Chen, Man Nie, Yao Liu, Bin Meng, Huiqiang Huang, Wenqi Jiang, Yixin Zeng, Wenyu Li, Kui Wu, Yong Hou, Klas G Wiman, Zhiming Li, Huilai Zhang, Roujun Peng, Shida Zhu, Qiang Pan-Hammarström
Hepatitis B virus (HBV) infection is endemic in some parts of Asia, Africa and South America and remains to be a significant public health problem in these areas. It is known as a leading risk factor for the development of hepatocellular carcinoma, but epidemiological studies have also shown that the infection may increase the incidence of several types B-cell lymphoma. Here, by characterizing altogether 275 Chinese diffuse large B-cell lymphoma (DLBCL) patients, we showed that patients with concomitant HBV infection (surface antigen positive, HBsAg+ ) are characterized by a younger age, a more advanced disease stage at diagnosis and a reduced overall survival...
March 15, 2018: Blood
Warren Winick-Ng, R Jane Rylett
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by synapse dysfunction and cognitive impairment. Understanding the development and progression of AD is challenging, as the disease is highly complex and multifactorial. Both environmental and genetic factors play a role in AD pathogenesis, highlighted by observations of complex DNA modifications at the single gene level, and by new evidence that also implicates changes in genome architecture in AD patients. The four-dimensional structure of chromatin in space and time is essential for context-dependent regulation of gene expression in post-mitotic neurons...
2018: Frontiers in Molecular Neuroscience
Jonuelle Acosta, Walter Wang, David M Feldser
Tumor suppressor genes play critical roles orchestrating anti-cancer programs that are both context dependent and mechanistically diverse. Beyond canonical tumor suppressive programs that control cell division, cell death, and genome stability, unexpected tumor suppressor gene activities that regulate metabolism, immune surveillance, the epigenetic landscape, and others have recently emerged. This diversity underscores the important roles these genes play in maintaining cellular homeostasis to suppress cancer initiation and progression, but also highlights a tremendous challenge in discerning precise context-specific programs of tumor suppression controlled by a given tumor suppressor...
March 15, 2018: Oncogene
Changguo Ma, Chunjie Gu, Yongxia Huo, Xiaoyan Li, Xiong-Jian Luo
Genome-wide association studies (GWAS) have identified more than 100 loci that show robust association with schizophrenia risk. However, due to the complexity of linkage disequilibrium and gene regulatory, it is challenging to pinpoint the causal genes at the risk loci and translate the genetic findings from GWAS into disease mechanism and clinical treatment. Here we systematically predicted the plausible candidate causal genes for schizophrenia at genome-wide level. We utilized different approaches and strategies to predict causal genes for schizophrenia, including Sherlock, SMR, DAPPLE, Prix Fixe, NetWAS, and DEPICT...
March 15, 2018: Translational Psychiatry
Vadim I Agol, Anatoly P Gmyl
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements...
June 2018: Microbiology and Molecular Biology Reviews: MMBR
Ioana Rusu, Alessandra Modi, Stefania Vai, Elena Pilli, Cristina Mircea, Claudia Radu, Claudia Urduzia, Zeno Karl Pinter, Vitalie Bodolică, Cătălin Dobrinescu, Montserrat Hervella, Octavian Popescu, Martina Lari, David Caramelli, Beatrice Kelemen
Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period...
2018: PloS One
Wen Ye, Shaoping Ling, Ran-Yi Liu, Zhi-Zhong Pan, Gaoyuan Wang, Shijuan Gao, Jiangxue Wu, Lihua Cao, Lili Dong, Yingchang Li, Yi Zhou, Wuying Du, Xiangqi Meng, Jinna Chen, Xinyuan Guan, Yulong He, Changchuan Pan, X F Steven Zheng, Xuemei Lu, Shuai Chen, Wenlin Huang
Colorectal cancer (CRC) is the third most common cancer worldwide, with more than 1.3 million new cases and 690,000 deaths each year. In China, the incidence of CRC has increased dramatically due to dietary and lifestyle changes, to become the fifth leading cause of cancer-related death. Here, we performed whole-exome sequencing in 50rectal cancer cases among the Chinese population as part of the International Cancer Genome Consortium research project. Frequently-mutated genes and enriched pathways were identified...
March 14, 2018: Journal of Pathology
Heng Xu, Yang Shu
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine...
2018: Methods in Molecular Biology
Stephen C Heinsch, Siba R Das, Michael J Smanski
Increasing the final titer of a multi-gene metabolic pathway can be viewed as a multivariate optimization problem. While numerous multivariate optimization algorithms exist, few are specifically designed to accommodate the constraints posed by genetic engineering workflows. We present a strategy for optimizing expression levels across an arbitrary number of genes that requires few design-build-test iterations. We compare the performance of several optimization algorithms on a series of simulated expression landscapes...
2018: Frontiers in Microbiology
Haitham Mirghani, Ludovic Lacroix, Caroline Rossoni, Roger Sun, Anne Aupérin, Odile Casiraghi, Aude Villepelet, Roger Lacave, Gladwys Faucher, Virginie Marty, Charles Ferté, Jean Charles Soria, Caroline Even
BACKGROUND: Human papillomavirus (HPV)-driven oropharyngeal cancer (OPC) patients are characterised by a better prognosis than their HPV-negative counterparts. However, this significant survival advantage is not homogeneous and among HPV-positive patients those with a smoking history have a significantly increased risk of oncologic failure. The reason why tobacco consumption impacts negatively the prognosis is still elusive. Tobacco might induce additional genetic alterations leading to a more aggressive phenotype...
March 10, 2018: European Journal of Cancer
Aaron Parkhurst
In light of increasingly high rates of diabetes, heart disease, and obesity among citizens of the Arabian Gulf, popular health discourse in the region has emphasised the emergent Arab genome as the primary etiological basis of major health conditions. However, after many years of public dissemination of genomic knowledge in the region, and widespread acceptance of this knowledge among Gulf Arab citizens, the rates of chronic illness continue to increase. This paper briefly explores the clash between indigenous Islamic knowledge systems and biomedical knowledge systems imported into the United Arab Emirates...
April 2018: Anthropology & Medicine
Krishna R Veeramah, Andreas Rott, Melanie Groß, Lucy van Dorp, Saioa López, Karola Kirsanow, Christian Sell, Jens Blöcher, Daniel Wegmann, Vivian Link, Zuzana Hofmanová, Joris Peters, Bernd Trautmann, Anja Gairhos, Jochen Haberstroh, Bernd Päffgen, Garrett Hellenthal, Brigitte Haas-Gebhard, Michaela Harbeck, Joachim Burger
Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent. Therefore, we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Tatsuya Nobori, André C Velásquez, Jingni Wu, Brian H Kvitko, James M Kremer, Yiming Wang, Sheng Yang He, Kenichi Tsuda
Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Julian A Gingold, Dandan Zhu, Dung-Fang Lee, Ahmed Kaseb, Jian Chen
Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), the two most common primary liver cancers, represent the second most common cancer-related cause of death worldwide, with most cases being diagnosed at an advanced stage. Recent genome-wide studies have helped to elucidate the molecular pathogenesis and genetic heterogeneity of liver cancers. This review of the genetic landscape of HCC and iCCA discusses the most recent findings from genomic profiling and the current understanding of the pathways involved in the initiation and progression of liver cancer...
March 9, 2018: Trends in Molecular Medicine
Colton O'Brien, Arathi H S
Intensive agricultural practices resulting in large scale habitat loss ranks as the top contributing factors in the global bee decline. Growing Genetically Modified Herbicide Tolerant (GMHT) crops as large monocultures has resulted extensive applications of herbicides leading to the degradation of natural habitats surrounding farmlands. Herbicide tolerance trait is beneficial for crops such as Canola (Brassica napus) that are extremely vulnerable to weed competition. While the trait in itself does not harm pollinators, growing genetically modified herbicide tolerant cultivars indirectly contributes towards pollinator declines through habitat loss...
March 12, 2018: GM Crops & Food
Diana Bellavia, Rocco Palermo, Maria Pia Felli, Isabella Screpanti, Saula Checquolo
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy. Although the therapy of ALL has significantly improved, the heterogeneous genetic landscape of the disease often causes relapse, which is difficult to treat. Achieving a positive outcome for patients with relapsed or refractory ALL remains a challenging issue. The high prevalence of NOTCH-activating mutations in T-cell acute lymphoblastic leukemia (T-ALL) and the central role of NOTCH signaling in regulating cell survival and growth of ALL provide a rationale for the development of Notch signaling-targeted strategies in this disease...
March 12, 2018: Expert Opinion on Therapeutic Targets
Rosemary G Gillespie, Suresh P Benjamin, Michael S Brewer, Malia Ana J Rivera, George K Roderick
Insular adaptive radiations in which repeated bouts of diversification lead to phenotypically similar sets of taxa serve to highlight predictability in the evolutionary process [1]. However, examples of such replicated events are rare. Cross-clade comparisons of adaptive radiations are much needed to determine whether similar ecological opportunities can lead to the same outcomes. Here, we report a heretofore uncovered adaptive radiation of Hawaiian stick spiders (Theridiidae, Ariamnes) in which different species exhibit a set of discrete ecomorphs associated with different microhabitats...
February 27, 2018: Current Biology: CB
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