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Genomic selection

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https://www.readbyqxmd.com/read/28109190/qtl-mapping-and-candidate-genes-for-resistance-to-fusarium-ear-rot-and-fumonisin-contamination-in-maize
#1
Valentina Maschietto, Cinzia Colombi, Raul Pirona, Giorgio Pea, Francesco Strozzi, Adriano Marocco, Laura Rossini, Alessandra Lanubile
BACKGROUND: Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes...
January 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28108681/re-emergence-of-methicillin-susceptibility-in-a-resistant-lineage-of-staphylococcus-aureus
#2
Alice Ledda, James R Price, Kevin Cole, Martin J Llewelyn, Angela M Kearns, Derrick W Crook, John Paul, Xavier Didelot
OBJECTIVES: MRSA is a leading cause of hospital-associated infection. Acquired resistance is encoded by the mecA gene or its homologue mecC, but little is known about the evolutionary dynamics involved in gain and loss of resistance. The objective of this study was to obtain an expanded understanding of Staphylococcus aureus methicillin resistance microevolution in vivo, by focusing on a single lineage. METHODS: We compared the whole-genome sequences of 231 isolates from a single epidemic lineage [clonal complex 30 (CC30) and spa-type t018] of S...
January 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28108622/a-genome-wide-loss-of-function-screen-identifies-slc26a2-as-a-novel-mediator-of-trail-resistance
#3
Lina Dimberg, Christina G Towers, Kian Behbakht, Taylor Hotz, Jihye Kim, Susan P Fosmire, Christopher C Porter, Aik-Choon Tan, Andrew Thorburn, Heide L Ford
: TNF-related apoptosis inducing ligand (TRAIL) is a potent death-inducing ligand that mediates apoptosis through the extrinsic pathway and serves as an important endogenous tumor suppressor mechanism. Because tumor cells are often killed by TRAIL and normal cells are not, drugs that activate the TRAIL pathway have been thought to have potential clinical value. However, to date, most TRAIL-related clinical trials have largely failed due to the tumor cells having intrinsic or acquired resistance to TRAIL-induced apoptosis...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28108601/phylogenomics-using-target-restricted-assembly-resolves-intra-generic-relationships-of-parasitic-lice-phthiraptera-columbicola
#4
Bret M Boyd, Julie M Allen, Nam Nguyen, Andrew D Sweet, Tandy Warnow, Michael D Shapiro, Scott M Villa, Sarah E Bush, Dale H Clayton, Kevin P Johnson
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species...
January 19, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28108586/fluctuating-selection-in-the-moran
#5
Antony M Dean, Clarence Lehman, Xiao Yi
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large and the variance in selection is big...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108177/discriminating-between-adaptive-and-carcinogenic-liver-hypertrophy-in-rat-studies-using-logistic-ridge-regression-analysis-of-toxicogenomic-data-the-mode-of-action-and-predictive-models
#6
Shujie Liu, Taisuke Kawamoto, Osamu Morita, Kouichi Yoshinari, Hiroshi Honda
Chemical exposure often results in liver hypertrophy in animal tests, characterized by increased liver weight, hepatocellular hypertrophy, and/or cell proliferation. While most of these changes are considered adaptive responses, there is concern that they may be associated with carcinogenesis. In this study, we have employed a toxicogenomic approach using a logistic ridge regression model to identify genes responsible for liver hypertrophy and hypertrophic hepatocarcinogenesis and to develop a predictive model for assessing hypertrophy-inducing compounds...
January 17, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28107530/broad-scale-genetic-diversity-of-cannabis-for-forensic-applications
#7
Christophe Dufresnes, Catherine Jan, Friederike Bienert, Jérôme Goudet, Luca Fumagalli
Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs...
2017: PloS One
https://www.readbyqxmd.com/read/28107502/rnai-based-functional-genomics-identifies-new-virulence-determinants-in-mucormycosis
#8
Trung Anh Trieu, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Marta Sanchis, Javier Capilla, Patricia Navarro-Rodriguez, Loida Lopez-Fernandez, Santiago Torres-Martínez, Victoriano Garre, Rosa María Ruiz-Vázquez, Francisco E Nicolás
Mucorales are an emerging group of human pathogens that are responsible for the lethal disease mucormycosis. Unfortunately, functional studies on the genetic factors behind the virulence of these organisms are hampered by their limited genetic tractability, since they are reluctant to classical genetic tools like transposable elements or gene mapping. Here, we describe an RNAi-based functional genomic platform that allows the identification of new virulence factors through a forward genetic approach firstly described in Mucorales...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107441/fine-mapping-and-candidate-gene-analysis-of-the-tiller-suppression-gene-ts1-in-rice
#9
Lei Liu, Fen Meng, Yonggang He, Menghao Zhu, Yanhao Shen, Zhihong Zhang
Tiller number is one of the key factors that influences rice plant type and yield components. In this study, an EMS-induced rice tiller suppression mutant ts1 was characterized. Morphological and histological observations revealed that, in the ts1 plants, the tiller buds were abnormally formed and therefore cannot outgrow into tillers. With an F2 population derived from a cross between ts1 and an indica cultivar Wushansimiao, a major gene, tiller suppression 1 (ts1) was fine-mapped to a 108.5 kb genomic region between markers ID8378 and SSR6884 on the short arm of rice chromosome 2...
2017: PloS One
https://www.readbyqxmd.com/read/28107386/regulation-of-pi-2b-pilus-expression-in-hypervirulent-streptococcus-agalactiae-st-17-bm110
#10
Bruno Périchon, Noémi Szili, Laurence du Merle, Isabelle Rosinski-Chupin, Myriam Gominet, Samuel Bellais, Claire Poyart, Patrick Trieu-Cuot, Shaynoor Dramsi
The widely spread Streptococcus agalactiae (also known as Group B Streptococcus, GBS) "hypervirulent" ST17 clone is strongly associated with neonatal meningitis. The PI-2b locus is mainly found in ST17 strains but is also present in a few non ST17 human isolates such as the ST-7 prototype strain A909. Here, we analysed the expression of the PI-2b pilus in the ST17 strain BM110 as compared to the non ST17 A909. Comparative genome analyses revealed the presence of a 43-base pair (bp) hairpin-like structure in the upstream region of PI-2b operon in all 26 ST17 genomes, which was absent in the 8 non-ST17 strains carrying the PI-2b locus...
2017: PloS One
https://www.readbyqxmd.com/read/28106107/development-of-a-nested-pcr-assay-for-the-rapid-detection-of-pilidiella-granati-in-pomegranate-fruit
#11
Xue Yang, Uzma Hameed, Ai-Fang Zhang, Hao-Yu Zang, Chun-Yan Gu, Yu Chen, Yi-Liu Xu
Pilidiella granati, a causal agent of twig blight and crown rot of pomegranate, is an emerging threat that may cause severe risk to the pomegranate industry in the future. Development of a rapid assay for the timely and accurate detection of P. granati will be helpful in the active surveillance and management of the disease caused by this pathogen. In this study, a nested PCR method was established for the detection of P. granati. Comparative analysis of genetic diversity within 5.8S rDNA internal transcribed spacer (ITS) sequences of P...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105943/comprehensive-analysis-of-draft-genomes-of-two-closely-related-pseudomonas-syringae-phylogroup-2b-strains-infecting-mono-and-dicotyledon-host-plants
#12
Rinat I Sultanov, Georgij P Arapidi, Svetlana V Vinogradova, Vadim M Govorun, Duglas G Luster, Alexander N Ignatov
BACKGROUND: In recent years, the damage caused by bacterial pathogens to major crops has been increasing worldwide. Pseudomonas syringae is a widespread bacterial species that infects almost all major crops. Different P. syringae strains use a wide range of biochemical mechanisms, including phytotoxins and effectors of the type III and type IV secretion systems, which determine the specific nature of the pathogen virulence. RESULTS: Strains 1845 (isolated from dicots) and 2507 (isolated from monocots) were selected for sequencing because they specialize on different groups of plants...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105942/the-occurrence-of-spring-forms-in-tetraploid-timopheevi-wheat-is-associated-with-variation-in-the-first-intron-of-the-vrn-a1-gene
#13
Andrey Borisovich Shcherban, Aleksandra Aleksandrovna Schichkina, Elena Artemovna Salina
BACKGROUND: Triticum araraticum and Triticum timopheevii are tetraploid species of the Timopheevi group. The former includes both winter and spring forms with a predominance of winter forms, whereas T. timopheevii is considered a spring species. In order to clarify the origin of the spring growth habit in T. timopheevii, allelic variability of the VRN-1 gene was investigated in a set of accessions of both tetraploid species, together with the diploid species Ae. speltoides, presumed donor of the G genome to these tetraploids...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#14
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105933/haploid-yeast-cells-undergo-a-reversible-phenotypic-switch-associated-with-chromosome-ii-copy-number
#15
Polina Drozdova, Ludmila Mironova, Galina Zhouravleva
BACKGROUND: SUP35 and SUP45 are essential genes encoding polypeptide chain release factors. However, mutants for these genes may be viable but display pleiotropic phenotypes which include, but are not limited to, nonsense suppressor phenotype due to translation termination defect. [PSI (+)] prion formation is another Sup35p-associated mechanism leading to nonsense suppression through decreased availability of functional Sup35p. [PSI (+)] differs from genuine sup35 mutations by the possibility of its elimination and subsequent re-induction...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28105918/mirnacle-machine-learning-with-smote-and-random-forest-for-improving-selectivity-in-pre-mirna-ab-initio-prediction
#16
Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro Vasconcelos, Fabio Ribeiro Cerqueira
BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs)...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105916/gpcrs-from-fusarium-graminearum-detection-modeling-and-virtual-screening-the-search-for-new-routes-to-control-head-blight-disease
#17
Emmanuel Bresso, Roberto Togawa, Kim Hammond-Kosack, Martin Urban, Bernard Maigret, Natalia Florencio Martins
BACKGOUND: Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105610/antithyroid-drug-induced-agranulocytosis-state-of-the-art-on-diagnosis-and-management
#18
Nuno Vicente, Luís Cardoso, Luísa Barros, Francisco Carrilho
Agranulocytosis is a rare but serious complication of antithyroid drug therapy, and an up-to-date understanding of this topic is important. Both direct toxicity and immune-mediated responses have been described as possible mechanisms. Some major susceptibility loci have recently been identified, which may lead the diagnosis of agranulocytosis into a genomic era. Onset is acute and patients present with symptoms and signs of infection together with high fever. Clinical suspicion is pivotal and should prompt blood sampling...
January 19, 2017: Drugs in R&D
https://www.readbyqxmd.com/read/28104812/antibody-secreting-plasma-cells-persist-for-decades-in-human-intestine
#19
Ole J B Landsverk, Omri Snir, Raquel Bartolomé Casado, Lisa Richter, Jeff E Mold, Pedro Réu, Rune Horneland, Vemund Paulsen, Sheraz Yaqub, Einar Martin Aandahl, Ole M Øyen, Hildur Sif Thorarensen, Mehran Salehpour, Göran Possnert, Jonas Frisén, Ludvig M Sollid, Espen S Baekkevold, Frode L Jahnsen
Plasma cells (PCs) produce antibodies that mediate immunity after infection or vaccination. In contrast to PCs in the bone marrow, PCs in the gut have been considered short lived. In this study, we studied PC dynamics in the human small intestine by cell-turnover analysis in organ transplants and by retrospective cell birth dating measuring carbon-14 in genomic DNA. We identified three distinct PC subsets: a CD19(+) PC subset was dynamically exchanged, whereas of two CD19(-) PC subsets, CD45(+) PCs exhibited little and CD45(-) PCs no replacement and had a median age of 11 and 22 yr, respectively...
January 19, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28104771/circulating-noncoding-rnas-as-biomarkers-of-cardiovascular-disease-and-injury
#20
REVIEW
Janika Viereck, Thomas Thum
The discovery of thousands of noncoding RNAs (ncRNAs) has expanded our view on mammalian genomes and transcriptomes, as well as their organization and regulation. Accumulating evidence on aberrantly regulated ncRNAs, including short microRNAs, long ncRNAs and circular RNAs, across various heart diseases indicates that ncRNAs are critical contributors to cardiovascular pathophysiology. In addition, ncRNAs are released into the circulation where they are present in concentration levels that differ between healthy subjects and diseased patients...
January 20, 2017: Circulation Research
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