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https://www.readbyqxmd.com/read/28926153/comparative-and-population-genomics-landscape-of-phellinus-noxius-a-hypervariable-fungus-causing-root-rot-in-trees
#1
Chia-Lin Chung, Tracy J Lee, Mitsuteru Akiba, Hsin-Han Lee, Tzu-Hao Kuo, Dang Liu, Huei-Mien Ke, Toshiro Yokoi, Marylette B Roa, Meiyeh J Lu, Ya-Yun Chang, Pao-Jen Ann, Jyh-Nong Tsai, Chien-Yu Chen, Shean-Shong Tzean, Yuko Ota, Tsutomu Hattori, Norio Sahashi, Ruey-Fen Liou, Taisei Kikuchi, Isheng J Tsai
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28925066/beyond-the-androgen-receptor-ii-new-approaches-to-understanding-and-treating-metastatic-prostate-cancer-report-from-the-2017-coffey-holden-prostate-cancer-academy-meeting
#2
REVIEW
Andrea K Miyahira, Heather H Cheng, Wassim Abida, Leigh Ellis, Lauren C Harshman, Daniel E Spratt, Jonathan W Simons, Kenneth J Pienta, Howard R Soule
INTRODUCTION: The 2017 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Beyond the Androgen Receptor II: New Approaches to Understanding and Treating Metastatic Prostate Cancer," was held in Carlsbad, California from June 14-17, 2017. METHODS: The CHPCA is an annual scientific conference hosted by the Prostate Cancer Foundation (PCF) that is uniquely designed to produce extensive and constructive discussions on the most urgent and impactful topics concerning research into the biology and treatment of metastatic prostate cancer...
September 18, 2017: Prostate
https://www.readbyqxmd.com/read/28924451/phenotypic-landscape-of-non-conventional-yeast-species-for-different-stress-tolerance-traits-desirable-in-bioethanol-fermentation
#3
Vaskar Mukherjee, Dorota Radecka, Guido Aerts, Kevin J Verstrepen, Bart Lievens, Johan M Thevelein
BACKGROUND: Non-conventional yeasts present a huge, yet barely exploited, resource of yeast biodiversity for industrial applications. This presents a great opportunity to explore alternative ethanol-fermenting yeasts that are more adapted to some of the stress factors present in the harsh environmental conditions in second-generation (2G) bioethanol fermentation. Extremely tolerant yeast species are interesting candidates to investigate the underlying tolerance mechanisms and to identify genes that when transferred to existing industrial strains could help to design more stress-tolerant cell factories...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28923541/interpreting-the-genomic-landscape-of-introgression
#4
REVIEW
Simon H Martin, Chris D Jiggins
Introgression, the transfer of genetic material between species through hybridisation, occurs in many taxa and has important consequences. Genomic studies allow us to characterise the landscape of introgression across the genome, shedding light on both its adaptive benefits and the incompatibilities that help to maintain species barriers. Studies taking a genome-wide view suggest that adaptive introgression may be common, but that introgressed variation between many species is selected against throughout much of the genome...
September 15, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28915487/genetic-backgrounds-and-hidden-trait-complexity-in-natural-populations
#5
REVIEW
Téo Fournier, Joseph Schacherer
Dissecting the genetic basis of natural phenotypic variation is a major goal in biology. We know that most traits are strongly heritable. However, their genetic architecture is a long-standing question, which is unfortunately confounded by the lack of complete knowledge of the genetic components as well as their phenotypic effect in a specific genetic background. Many genetic variants are known to affect phenotypes but the same functional variant can have a different effect on the phenotype in different individuals of the same species...
September 12, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28914620/new-developments-in-the-molecular-mechanisms-of-pancreatic-tumorigenesis
#6
Matthäus Felsenstein, Ralph H Hruban, Laura D Wood
Pancreatic cancer is an aggressive disease with a dismal prognosis in dire need of novel diagnostic and therapeutic approaches. The past decade has witnessed an explosion of data on the genetic alterations that occur in pancreatic cancer, as comprehensive next-generation sequencing analyses have been performed on samples from large cohorts of patients. These studies have defined the genomic landscape of this disease and identified novel candidates whose mutations contribute to pancreatic tumorigenesis. They have also clarified the genetic alterations that underlie multistep tumorigenesis in precursor lesions and provided insights into clonal evolution in pancreatic neoplasia...
September 13, 2017: Advances in Anatomic Pathology
https://www.readbyqxmd.com/read/28914569/mutations-in-myeloproliferative-neoplasms-their-significance-and-clinical-use
#7
Fiorella Schischlik, Robert Kralovics
Clonal hematologic diseases of the blood such as polycythemia vera, essential thrombocythemia and primary myelofibrosis belong to the BCR-ABL negative Myeloproliferative Neoplasms (MPN). These diseases are characterized by clonal expansion of hematopoietic precursor cells followed by increased production of differentiated cells of the myeloid lineage. Initiation of clonal hematopoiesis, formation of a clinical phenotype as well as disease progression form part of MPN disease evolution. The disease is driven by acquired somatic mutations in critical pathways such as cytokine signaling, epigenetic regulation, RNA splicing, and transcription factor signaling...
September 15, 2017: Expert Review of Hematology
https://www.readbyqxmd.com/read/28912831/genome-sequencing-and-transcriptome-analysis-of-trichoderma-reesei-qm9978-strain-reveals-a-distal-chromosome-translocation-to-be-responsible-for-loss-of-vib1-expression-and-loss-of-cellulase-induction
#8
Christa Ivanova, Jonas Ramoni, Thiziri Aouam, Alexa Frischmann, Bernhard Seiboth, Scott E Baker, Stéphane Le Crom, Sophie Lemoine, Antoine Margeot, Frédérique Bidard
BACKGROUND: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28911151/expanding-the-phenotypic-and-genotypic-landscape-of-autoimmune-polyendocrine-syndrome-type-1
#9
Elizaveta M Orlova, Leila S Sozaeva, Maria A Kareva, Bergithe E Oftedal, Anette S B Wolff, Lars Breivik, Ekaterina Y Zakharova, Olga N Ivanova, Olle Kämpe, Ivan I Dedov, Per M Knappskog, Valentina A Peterkova, Eystein S Husebye
Context: Autoimmune polyendocrine syndrome type 1 (APS-1) is a rare monogenic autoimmune disease caused by mutations in the autoimmune regulator (AIRE) gene and characterized by chronic mucocutaneous candidiasis, hypoparathyroidism, and primary adrenal insufficiency. Comprehensive characterizations of large patient cohorts are rare. Objective: To perform an extensive clinical, immunological, and genetic characterization of a large nationwide Russian APS-1 cohort...
September 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28911083/multiregion-whole-exome-sequencing-of-matched-primary-and-metastatic-tumors-revealed-genomic-heterogeneity-and-suggested-polyclonal-seeding-in-colorectal-cancer-metastasis
#10
Q Wei, Z Ye, X Zhong, L Li, C Wang, R E Myers, J P Palazzo, D Fortuna, A Yan, S A Waldman, X Chen, J A Posey, A Basu-Mallick, B H Jiang, L Hou, J Shu, Y Sun, J Xing, B Li, H Yang
Background: Distant metastasis accounts for 90% of deaths from colorectal cancer (CRC). Genomic heterogeneity has been reported in various solid malignancies, but remains largely under-explored in metastatic CRC tumors, especially in primary to metastatic tumor evolution. Patients and methods: We conducted high-depth whole-exome sequencing in multiple regions of matched primary and metastatic CRC tumors. Using a total of 28 tumor, normal, and lymph node tissues, we analyzed inter- and intra-individual heterogeneity, inferred the tumor subclonal architectures, and depicted the subclonal evolutionary routes from primary to metastatic tumors...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28910638/the-landscape-of-type-vi-secretion-across-human-gut-microbiomes-reveals-its-role-in-community-composition
#11
Adrian J Verster, Benjamin D Ross, Matthew C Radey, Yiqiao Bao, Andrew L Goodman, Joseph D Mougous, Elhanan Borenstein
Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels...
September 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28910456/identification-of-alk-rearrangements-in-malignant-peritoneal-mesothelioma
#12
Yin P Hung, Fei Dong, Jaclyn C Watkins, Valentina Nardi, Raphael Bueno, Paola Dal Cin, John J Godleski, Christopher P Crum, Lucian R Chirieac
Importance: Malignant peritoneal mesothelioma is a rare, aggressive tumor arising from the peritoneal lining, induced by asbestos, therapeutic radiation, or germline mutations. Nevertheless, the molecular features remain largely unknown. Objective: To investigate anaplastic lymphoma kinase (ALK) rearrangements in a large series of peritoneal mesothelioma and characterize the mutational landscape of these tumors. Design, Setting, and Participants: We studied 88 consecutive patients (39 men, 49 women; median age 61, range 17-84 years) with peritoneal mesotheliomas diagnosed at a single institution between 2005 and 2015...
September 14, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28905227/genomics-for-all-in-the-21st-century
#13
Martina C Cornel, Vence L Bonham
As the field of genomics enters the second decade after the completion of the International Human Genome Project, human genomics research is still far from reflective of the ancestral diversity found in global populations. This special issue of the Journal of Community Genetics brings together a global perspective on the need for researchers and health care professionals to support achievable milestones that will enhance global ancestral diversity in genomic research for the 21st century, and integrate the resulting knowledge into health care that benefits everyone...
September 14, 2017: Journal of Community Genetics
https://www.readbyqxmd.com/read/28905157/landscape-genetics-in-the-subterranean-rodent-ctenomys-chasiquensis-associated-with-highly-disturbed-habitats-from-the-southeastern-pampas-region-argentina
#14
Matías Sebastián Mora, Fernando J Mapelli, Aldana López, María Jimena Gómez Fernández, Patricia M Mirol, Marcelo J Kittlein
Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci...
September 13, 2017: Genetica
https://www.readbyqxmd.com/read/28905131/exploring-evidence-of-positive-selection-signatures-in-cattle-breeds-selected-for-different-traits
#15
Mengistie Taye, Wonseok Lee, Soomin Jeon, Joon Yoon, Tadelle Dessie, Olivier Hanotte, Okeyo Ally Mwai, Stephen Kemp, Seoae Cho, Sung Jong Oh, Hak-Kyo Lee, Heebal Kim
Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N'Dama cattle breeds using Tajima's D, XP-CLR, and XP-EHH population statistical methods...
September 13, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28904767/genetic-differentiation-and-inferred-dynamics-of-a-hybrid-zone-between-northern-spotted-owls-strix-occidentalis-caurina-and-california-spotted-owls-s-%C3%A2-o-%C3%A2-occidentalis-in-northern-california
#16
Mark P Miller, Thomas D Mullins, Eric D Forsman, Susan M Haig
Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls (NSO: S. o. caurina) and California Spotted Owls (CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mtDNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28904763/winter-bait-stations-as-a-multispecies-survey-tool
#17
Lacy Robinson, Samuel A Cushman, Michael K Lucid
Winter bait stations are becoming a commonly used technique for multispecies inventory and monitoring but a technical evaluation of their effectiveness is lacking. Bait stations have three components: carcass attractant, remote camera, and hair snare. Our 22,975 km(2) mountainous study area was stratified with a 5 × 5 km sampling grid centered on northern Idaho and including portions of Washington, Montana, and British Columbia. From 2010-14, we conducted 563 sampling sessions at 497 bait stations in 453 5 × 5 km cells...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28903907/research-progress-on-genetic-heterogeneity-between-primary-and-paired-metastatic-colorectal-cancer
#18
You-Wang Lu, Kun-Hua Wang
Colorectal cancer (CRC) is one of the leading causes of cancer deaths in China. A standard practice in treating metastatic CRC (mCRC) is to predict benefits of the anti-EGFR monoclonal antibody treatment based on the somatic mutation spectrum. Because metastatic samples are difficult to obtain clinically, primary tumors are normally used instead. However, due to the genetic heterogeneity between primary and paired metastatic tumors, primary site biopsy always underrepresents the mutational landscape of metastatic sites...
June 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903454/precision-medicine-for-hepatocellular-carcinoma-driver-mutations-and-targeted-therapy
#19
REVIEW
Xiao-Xiao Ding, Qing-Ge Zhu, Shi-Ming Zhang, Lei Guan, Ting Li, Lei Zhang, Shi-Yang Wang, Wan-Li Ren, Xue-Mei Chen, Jing Zhao, Song Lin, Zhi-Zhen Liu, Yan-Xia Bai, Bing He, Hu-Qin Zhang
Hepatocellular carcinoma (HCC) is the third most frequent cause of tumor-related mortality and there are an estimated approximately 850,000 new cases annually. Most HCC patients are diagnosed at middle or advanced stage, losing the opportunity of surgery. The development of HCC is promoted by accumulated diverse genetic mutations, which confer selective growth advantages to tumor cells and are called "driver mutations". The discovery of driver mutations provides a novel precision medicine strategy for late stage HCC, called targeted therapy...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28902852/genome-wide-chromatin-mapping-with-size-resolution-reveals-a-dynamic-sub-nucleosomal-landscape-in-arabidopsis
#20
Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R Crawford, Konrad Paszkiewicz, Nicholas A Kent, James A H Murray
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes...
September 2017: PLoS Genetics
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