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Genetic diversity

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https://www.readbyqxmd.com/read/28822770/regulation-of-autoimmune-myocarditis-by-host-responses-to-the-microbiome
#1
Jobert G Barin, Monica V Talor, Nicola L Diny, SuFey Ong, Julie A Schaub, Elizabeth Gebremariam, Djahida Bedja, Guobao Chen, Hee Sun Choi, Xuezhou Hou, Lei Wu, Ashley B Cardamone, Daniel A Peterson, Noel R Rose, Daniela Čiháková
The extensive, diverse communities that constitute the microbiome are increasingly appreciated as important regulators of human health and disease through inflammatory, immune, and metabolic pathways. We sought to elucidate pathways by which microbiota contribute to inflammatory, autoimmune cardiac disease. We employed an animal model of experimental autoimmune myocarditis (EAM), which results in inflammatory and autoimmune pathophysiology and subsequent maladaptive cardiac remodeling and heart failure. Antibiotic dysbiosis protected mice from EAM and fibrotic cardiac dysfunction...
August 16, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28822625/landscaping-crossover-interference-across-a-genome
#2
REVIEW
Lidan Sun, Jing Wang, Mengmeng Sang, Libo Jiang, Bingyu Zhao, Tangran Cheng, Qixiang Zhang, Rongling Wu
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations...
August 16, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28822276/exploiting-algal-mineralization-for-nanotechnology-bringing-coccoliths-to-the-fore
#3
REVIEW
Alastair W Skeffington, André Scheffel
Complex mineral structures are produced by many microalgal species. Pioneering work on diatom silica has demonstrated the potential of such structures in nanotechnology. The calcified scales of coccolithophores (coccoliths) have received less attention, but the large diversity of architectures make coccoliths attractive as parts for nano-devices. Currently coccolith calcite can be modified by the incorporation of metal ions or adsorption of enzymes to the surface, but genetic modification of coccolithophores may permit the production of coccoliths with customized architectures and surface properties...
August 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28822175/-application-of-plant-tissue-culture-in-field-of-chinese-medicine-resources
#4
REVIEW
Juan Wang, Jin-Xin Li, Jian-Li Li, Wen-Yuan Gao
Plant tissue culture technology has been widely used in the field of traditional Chinese medicine(TCM) resources with its unique advantages, playing an important role in the protection of TCM resources. In this review, some applications of plant tissue culture were summarized, including production of active compounds by using plant tissue culture, genetic diversity analysis, Dao-di herbs, elicitor application, biosynthesis and transgenic plants. Through the above researches will promote the further development of plant tissue culture technology, making it play a greater role in the field of TCM resources...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28822012/mtor-co-targeting-strategies-for-head-and-neck-cancer-therapy
#5
Zhiyong Wang, Juan Callejas Valera, Xuefeng Zhao, Qianming Chen, J Silvio Gutkind
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. There is an urgent need to develop effective therapeutic approaches to prevent and treat HNSCC. Recent deep sequencing of the HNSCC genomic landscape revealed a multiplicity and diversity of genetic alterations in this malignancy. Although a large variety of specific molecules were found altered in each individual tumor, they all participate in only a handful of driver signaling pathways. Among them, the PI3K/mTOR pathway is the most frequently activated, which plays a central role in cancer initiation and progression...
August 18, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28821592/global-analysis-of-gene-expression-in-response-to-whole-chromosome-aneuploidy-in-hexaploid-wheat
#6
Ai Zhang, Ning Li, Lei Gong, Xiaowan Gou, Bin Wang, Xin Deng, Changping Li, Qianli Dong, Huakun Zhang, Bao Liu
Aneuploidy, a condition of unbalanced chromosome content, represents a large-effect mutation that bears significant relevancy to human health and microbe adaptation. As such, extensive studies of aneuploidy have been conducted in unicellular model organisms and cancer cells. Aneuploidy also frequently is associated with plant polyploidization, but its impact on gene expression and relevance to polyploid genome evolution/functional innovation remain largely unknown. Here, we used a panel of diverse types of whole-chromosome aneuploidy of hexaploid wheat, all under the common genetic background of cv...
August 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#7
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28821255/the-whole-genomic-analysis-of-orf-virus-strain-hn3-12-isolated-from-henan-province-central-china
#8
Huiqin Chen, Wei Li, Zhenzhan Kuang, Daxiang Chen, Xiaoqing Liao, Ming Li, Shuhong Luo, Wenbo Hao
BACKGROUND: The Orf virus (ORFV) is the causative agent of orf, a globally-occurring, acute, pustular, contagious disease affecting sheep, goats and humans with a worldwide distribution. Currently, the genomic analysis of four ORFV strains from the Fujian province in southern China and a NA1/11 strain isolated from the Jilin province in northeast China have been reported. However, little is known about the genomic information of ORFV strains from central China. RESULTS: From a recent outbreak in a sheep herd in the Henan province of central China, a novel ORFV strain (HN3/12) was isolated and cultured in ovine fetal turbinate (OFTu) cells...
August 18, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28821241/genetic-diversity-and-virulence-potential-of-clinical-and-environmental-aeromonas-spp-isolates-from-a-diarrhea-outbreak
#9
Lívia Christina Alves da Silva, Tereza Cristina Leal-Balbino, Beatriz Souza Toscano de Melo, Carina Lucena Mendes-Marques, Antonio Mauro Rezende, Alzira Maria Paiva de Almeida, Nilma Cintra Leal
BACKGROUND: Aeromonas spp. are gram-negative bacteria that can cause a variety of infections in both humans and animals and play a controversial role in diarrhea outbreaks. Our aim was to identify clinical and environmental Aeromonas isolates associated with a cholera outbreak in a northeast county of Brazil at the species level. We also aimed to determine the genetic structure of the bacterial population and the virulence potential of the Aeromonas isolates. METHODS AND RESULTS: Analysis based on concatenated sequences of the 16S rRNA and gyrB genes suggested the classification of the 119 isolates studied into the following species: A...
August 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28821238/genome-wide-analysis-of-ltr-retrotransposon-diversity-and-its-impact-on-the-evolution-of-the-genus-helianthus-l
#10
Flavia Mascagni, Tommaso Giordani, Marilena Ceccarelli, Andrea Cavallini, Lucia Natali
BACKGROUND: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28821229/mechanisms-of-peripheral-phylogeographic-divergence-in-the-indo-pacific-lessons-from-the-spiny-lobster-panulirus-homarus
#11
Ahmad Farhadi, Andrew G Jeffs, Hamid Farahmand, Thankappan Sarasam Rejiniemon, Greg Smith, Shane D Lavery
BACKGROUND: There is increasing recognition of the concordance between marine biogeographic and phylogeographic boundaries. However, it is still unclear how population-level divergence translates into species-level divergence, and what are the principal factors that first initiate that divergence, and then maintain reproductive isolation. This study examines the likely forces driving population and lineage divergences in the broadly-distributed Indo-Pacific spiny lobster Panulirus homarus, which has peripheral divergent lineages in the west and east...
August 18, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28821188/panmixia-and-limited-interspecific-introgression-in-coyotes-canis-latrans-from-west-virginia-and-virginia-usa
#12
Justin H Bohling, Lauren L Mastro, Jennifer R Adams, Eric M Gese, Sheldon F Owen, Lisette P Waits
The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#13
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820749/surgical-pathology-of-gastrointestinal-stromal-tumors-practical-implications-of-morphologic-and-molecular-heterogeneity-for-precision-medicine
#14
Gregory W Charville, Teri A Longacre
Gastrointestinal stromal tumor (GIST), the most common mesenchymal neoplasm of the gastrointestinal tract, exhibits diverse histologic and clinical manifestations. With its putative origin in the gastrointestinal pacemaker cell of Cajal, GIST can arise in association with any portion of the tubular gastrointestinal tract. Morphologically, GISTs are classified as spindled or epithelioid, though each of these subtypes encompasses a broad spectrum of microscopic appearances, many of which mimic other histologic entities...
August 17, 2017: Advances in Anatomic Pathology
https://www.readbyqxmd.com/read/28820456/deciphering-single-nucleotide-polymorphisms-and-evolutionary-trends-in-isolates-of-the-cydia-pomonella-granulovirus
#15
Jörg T Wennmann, Pit Radtke, Karolin E Eberle, Gianpiero Gueli Alletti, Johannes A Jehle
Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820343/population-structure-of-pseudocercospora-fijiensis-in-costa-rica-reveals-shared-haplotype-diversity-with-southeast-asian-populations
#16
Amanda Saville, Melodi Charles, Suchitra Chavan, Miguel Munoz, Luis Gomez-Alpizar, Jean B Ristaino
Pseudocercospora fijiensis Deighton is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20-80% yield loss in the absence of fungicides in bananas. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared to Honduran and global populations to better understand migration patterns and inform management strategies. One hundred and eighteen isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared to a previously published global dataset of populations of P...
August 18, 2017: Phytopathology
https://www.readbyqxmd.com/read/28818910/draft-genome-sequence-of-a-clinical-isolate-of-streptococcus-mutans-strain-hm
#17
Yoshio Kondo, Haruka Nishimata, Kiyoshi Hidaka, Tomoyuki Hasuwa, Hiroyuki Moriuchi, Taku Fujiwara, Tomonori Hoshino
We report the draft genome sequence of Streptococcus mutans strain HM isolated from a 4-year-old girl with infective endocarditis. The genomics information will provide information on the genetic diversity and virulence potential of S. mutans strain HM.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818902/draft-genome-sequence-of-ideonella-sp-strain-a-288-isolated-from-an-iron-precipitating-biofilm
#18
Burga Braun, Sven Künzel, Ulrich Szewzyk
Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain A_228. This isolate, obtained from a bog iron ore-containing floodplain area in Germany, provides valuable information about the genetic diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq technique was used to sequence the draft genome sequence of the strain.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818866/systematic-identification-of-determinants-for-single-strand-annealing-mediated-deletion-formation-in-saccharomyces-cerevisiae
#19
Maia Segura-Wang, Megumi Onishi-Seebacher, Adrian M Stütz, Balca R Mardin, Jan O Korbel
To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are the genomic structural variants (SVs). In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast), a highly tractable model organism, are not fully recognized. Here we developed and applied a genome-wide assay to identify yeast gene knock-out mutants associated with de novo deletion formation, in particular single strand annealing (SSA) -mediated deletion formation in a systematic manner...
August 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28818567/a-protein-chimera-including-pspa-in-fusion-with-potd-is-protective-against-invasive-pneumococcal-infection-and-reduces-nasopharyngeal-colonization-in-mice
#20
T R Converso, C Goulart, M Darrieux, L C C Leite
Despite the success of the available polysaccharide-based vaccines against Streptococcus pneumoniae in preventing invasive diseases, this bacterium remains a major cause of death in many parts of the world. New vaccine strategies are needed in order to increase protection. Thus, the utilization of fusion proteins is being investigated as an alternative to the current formulations. In the present work, we demonstrate that a chimeric protein, composed of PspA and PotD in fusion is able to maintain the protective characteristics of both parental proteins, providing protection against systemic infection while reducing nasal colonization...
August 14, 2017: Vaccine
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