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https://www.readbyqxmd.com/read/29165848/ecological-disturbance-influences-adaptive-divergence-despite-high-gene-flow-in-golden-perch-macquaria-ambigua-implications-for-management-and-resilience-to-climate-change
#1
Catherine R M Attard, Chris J Brauer, Jonathan Sandoval-Castillo, Leanne K Faulks, Peter Unmack, Dean M Gilligan, Luciano B Beheregaray
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia using a genome-wide SNP dataset...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165844/oral-microbiomes-from-hunter-gatherers-and-traditional-farmers-reveal-shifts-in-commensal-balance-and-pathogen-load-linked-to-diet
#2
Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G Thomas, Andrea Bamberg Migliano, Francois Balloux
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165718/a-phi-class-glutathione-s-transferase-gene-for-verticillium-wilt-resistance-in-gossypium-arboreum-identified-in-a-genome-wide-association-study
#3
Qian Gong, Zhaoen Yang, Eryong Chen, Gaofei Sun, Shoupu He, Hamama Islam Butt, Chaojun Zhang, Xueyan Zhang, Zuoren Yang, Xiongming Du, Fuguang Li
Verticillium wilt disease is one of the most destructive biotic stresses faced by cotton plants. Here, we performed a genome-wide association study (GWAS) in 215 Chinese Gossypium arboreum accessions inoculated as seedlings with Verticillium dahliae to identify candidate loci involved in wilt resistance. We identified 309 loci that had a significant association with Verticillium wilt resistance and Log (P) values greater than 5.0; the highest signal appeared on Ca3 in a 74 Kb haplotype block. Five genes were also located within this haplotype block...
November 20, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29165618/human-specific-mutations-and-positively-selected-sites-in-marco-confer-functional-changes
#4
Kyle E Novakowski, Nicholas V L Yap, Charles Yin, Kaori Sakamoto, Bryan Heit, G Brian Golding, Dawn M E Bowdish
Macrophage Receptor with COllagenous structure (MARCO) is a class A scavenger receptor that binds, phagocytoses, and modifies inflammatory responses to bacterial pathogens. Multiple candidate gene approach studies have shown that polymorphisms in MARCO are associated with susceptibility or resistance to Mycobacterium tuberculosis infection, but how these variants alter function is not known. To complement candidate gene approach studies, we previously used phylogenetic analyses to identify a residue, glutamine 452 (Q452), within the ligand-binding Scavenger Receptor Cysteine Rich (SRCR) domain as undergoing positive selection in humans...
November 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29165578/clues-for-polygenic-inheritance-of-pituitary-stalk-interruption-syndrome-by-exome-sequencing-in-20-patients
#5
Nitash Zwaveling-Soonawala, Marielle Alders, Aldo Jongejan, Lidija Kovacic, Floor A Duijkers, Saskia M Maas, Eric Fliers, A S Paul van Trotsenburg, Raoul C Hennekam
Context: Pituitary stalk interruption syndrome (PSIS) consists of a small/absent anterior pituitary lobe, interrupted/absent pituitary stalk, and an ectopic posterior pituitary lobe. Mendelian forms of PSIS are detected infrequently (< 5%), and a polygenic etiology has been suggested. GLI2 variants have been reported in a relatively high frequency in PSIS. Objective: To provide further evidence for a non-Mendelian, polygenic etiology of PSIS. Methods: Exome sequencing (trio approach) in 20 patients with isolated PSIS...
November 20, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29165314/towards-natural-mimetics-of-metformin-and-rapamycin
#6
Alexander Aliper, Leslie Jellen, Franco Cortese, Artem Artemov, Darla Karpinsky-Semper, Alexey Moskalev, Andrew G Swick, Alex Zhavoronkov
Aging is now at the forefront of major challenges faced globally, creating an immediate need for safe, widescale interventions to reduce the burden of chronic disease and extend human healthspan. Metformin and rapamycin are two FDA-approved mTOR inhibitors proposed for this purpose, exhibiting significant anti-cancer and anti-aging properties beyond their current clinical applications. However, each faces issues with approval for off-label, prophylactic use due to adverse effects. Here, we initiate an effort to identify nutraceuticals-safer, naturally-occurring compounds-that mimic the anti-aging effects of metformin and rapamycin without adverse effects...
November 15, 2017: Aging
https://www.readbyqxmd.com/read/29165068/identifying-candidates-for-breast-cancer-using-interactions-of-chemicals-and-proteins
#7
Jing Lu, Kangle Shang, Yi Bi
Breast cancer is one of the major cause of cancer death in women worldwide. Therefore, it is urgent to discovery novel drugs or design effective treatments for this disease. However, the research and development of drugs by using only experimental methods is always time-consuming and expensive. With the development of computer science, some advanced computational methods can make full use of known knowledge to design candidate drugs, thereby reducing the cost and time of experimental testing. In this study, a computational method was proposed to identify novel candidates for breast cancer...
November 20, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/29165046/phytophthora-parasitica-effector-pprxlr2-suppresses-nicotiana-benthamiana-immunity
#8
Ronaldo J D Dalio, Heros José Máximo, Tiago Silva Oliveira, Renata Dias, Michele Breton, Henrique Leme Felizatti, Marcos Antonio Antonio Machado
Phytophthora species secrete several classes of effector proteins during interaction with their hosts. These proteins can have multiple functions including modulation of host physiology and immunity. The RxLR effectors have the ability to enter plant cells using the plant machinery. Some of these effectors have been characterized as immunity suppressors; however, very little is known about their functions in the interaction between Phytophthora parasitica and its hosts. Using a bioinformatics pipeline, we have identified 172 candidate RxLR effectors (CREs) in the isolate IAC 01_95 of P...
November 22, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29164621/determining-candidate-single-nucleotide-polymorphisms-in-acquired-laryngotracheal-stenosis
#9
Mursalin M Anis, Natalia Krynetskaia, Zhigen Zhao, Evgeny Krynetskiy, Ahmed M S Soliman
OBJECTIVES/HYPOTHESIS: Despite wide adoption of strategies to prevent injury from prolonged intubation and tracheotomy, acquired laryngotracheal stenosis (ALTS) has not disappeared. ALTS' persistence may be due to patient factors that confer unique susceptibility for some. We sought to identify genetic markers in genes associated with wound healing that could be associated with ALTS. STUDY DESIGN: Case-control study. METHODS: One hundred thirty-eight patients were recruited, 53 patients with ALTS and 85 control patients who underwent intubation or tracheotomy without evidence of ALTS...
November 22, 2017: Laryngoscope
https://www.readbyqxmd.com/read/29164594/rna-sequencing-study-of-peripheral-blood-mononuclear-cells-in-sporadic-meniere-s-disease-patients-possible-contribution-of-immunologic-dysfunction-to-the-development-of-this-disorder
#10
Ying Sun, Daogong Zhang, Gaoying Sun, Yafeng Lv, Yawei Li, Xiaofei Li, Yongdong Song, Jianfeng Li, Zhaomin Fan, Haibo Wang
To date, the pathogenesis of Meniere's disease (MD) remains unclear. This study aims to investigate the possible relationship between potential immune system related genes and sporadic Meniere's disease. The whole RNA-sequencing (RNA-seq) technology was used to analyze the transcriptome of peripheral blood mononuclear cells of 3 MD patients and 3 control individuals. Of 366 differentially expressed genes (DEGs), 154 genes were up-regulated and 212 genes were down-regulated (|log2Foldchange| >1 and p <0...
November 22, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/29164578/mir-590-3p-promotes-colon-cancer-cell-proliferation-via-wnt-%C3%AE-catenin-signaling-pathway-by-inhibiting-wif1-and-dkk1
#11
Z-Y Feng, X-H Xu, D-Z Cen, C-Y Luo, S-B Wu
OBJECTIVE: Colon cancer is one of the most common and deadly types of gastrointestinal tumor. Despite progressive treatments, the patient prognosis has not been improved effectively. MATERIALS AND METHODS: Expression of miRNA and mRNA were tested by Realtime PCR. Cell cycle was detected by flow cytometry. Cell viability was evaluated by MTT assay. Cell spheroid formation was determined by colony assay. Wnt signaling pathway activity was evaluated by TOP/FOP ratio...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29164273/mapping-and-characterization-of-wheat-stem-rust%C3%A2-resistance-genes-srtm5-and-sr60-from-triticum-monococcum
#12
Shisheng Chen, Yan Guo, Jordan Briggs, Felix Dubach, Shiaoman Chao, Wenjun Zhang, Matthew N Rouse, Jorge Dubcovsky
The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5A(m)S, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7A(m)L, completely linked to Sr22...
November 21, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29164142/pathogenesis-molecular-genetics-and-genomics-of-mycobacterium-avium-subsp-paratuberculosis-the-etiologic-agent-of-johne-s-disease
#13
REVIEW
Govardhan Rathnaiah, Denise K Zinniel, John P Bannantine, Judith R Stabel, Yrjö T Gröhn, Michael T Collins, Raúl G Barletta
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease in ruminants causing chronic diarrhea, malnutrition, and muscular wasting. Neonates and young animals are infected primarily by the fecal-oral route. MAP attaches to, translocates via the intestinal mucosa, and is phagocytosed by macrophages. The ensuing host cellular immune response leads to granulomatous enteritis characterized by a thick and corrugated intestinal wall. We review various tissue culture systems, ileal loops, and mice, goats, and cattle used to study MAP pathogenesis...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29163601/genome-wide-constitutively-expressed-gene-analysis-and-new-reference-gene-selection-based-on-transcriptome-data-a-case-study-from-poplar-canker-disease-interaction
#14
Jiaping Zhao, Fan Yang, Jinxia Feng, Yanli Wang, Barbara Lachenbruch, Jiange Wang, Xianchong Wan
A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163588/genome-wide-analysis-of-japonica-rice-performance-under-limited-water-and-permanent-flooding-conditions
#15
Andrea Volante, Francesca Desiderio, Alessandro Tondelli, Rosaria Perrini, Gabriele Orasen, Chiara Biselli, Paolo Riccardi, Alessandra Vattari, Daniela Cavalluzzo, Simona Urso, Manel Ben Hassen, Agostino Fricano, Pietro Piffanelli, Paolo Cozzi, Filippo Biscarini, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163563/genetic-dissection-of-the-major-quantitative-trait-locus-qse11-and-its-validation-as-the-major-influence-on-the-rate-of-stigma-exsertion-in-rice-oryza-sativa-l
#16
Md Habibur Rahman, Yingxing Zhang, Keqin Zhang, Md Sazzadur Rahman, Hirendra N Barman, Aamir Riaz, Yuyu Chen, Weixun Wu, Xiaodeng Zhan, Liyong Cao, Shihua Cheng
The rate of stigma exsertion (SE) is an important trait in rice breeding because the efficiency of hybrid rice seed production can be improved by increasing the percentage of stigmas that exsert. In this study, we developed a near isogenic line (NIL) from two parents, XieqingzaoB (XQZB) and Zhonghoi9308 (ZH9308), which have high and low SE rates in that order. In our previous study, we employed 75 chromosome segment substitution lines (CSSLs) and analyzed quantitative trait loci (QTLs) for their influence on SE rate...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163559/genome-wide-association-study-of-calcium-accumulation-in-grains-of-european-wheat-cultivars
#17
Dalia Z Alomari, Kai Eggert, Nicolaus von Wirén, Klaus Pillen, Marion S Röder
Mineral concentrations in cereals are important for human health, especially for people who depend mainly on consuming cereal diet. In this study, we carried out a genome-wide association study (GWAS) of calcium concentrations in wheat (Triticum aestivum L.) grains using a European wheat diversity panel of 353 varieties [339 winter wheat (WW) plus 14 of spring wheat (SW)] and phenotypic data based on two field seasons. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA chip and a 35k Affymetrix chip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163411/diversity-within-italian-cheesemaking-brine-associated-bacterial-communities-evidenced-by-massive-parallel-16s-rrna-gene-tag-sequencing
#18
Marilena Marino, Nadia Innocente, Michela Maifreni, Jérôme Mounier, José F Cobo-Díaz, Emmanuel Coton, Lisa Carraro, Barbara Cardazzo
This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163404/do-viruses-exchange-genes-across-superkingdoms-of-life
#19
Shahana S Malik, Syeda Azem-E-Zahra, Kyung Mo Kim, Gustavo Caetano-Anollés, Arshan Nasir
Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163390/comparative-genomics-reveals-specific-genetic-architectures-in-nicotine-metabolism-of-pseudomonas-sp-jy-q
#20
Jun Li, Shulan Qian, Lie Xiong, Chengyun Zhu, Ming Shu, Jie Wang, Yang Jiao, Houlong He, Fuming Zhang, Robert J Linhardt, Weihong Zhong
Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l(-1) nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l(-1)) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations...
2017: Frontiers in Microbiology
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