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conservation genetics

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https://www.readbyqxmd.com/read/28550058/whole-genome-and-core-genome-multilocus-sequence-typing-and-single-nucleotide-polymorphism-analyses-of-listeria-monocytogenes-associated-with-an-outbreak-linked-to-cheese-united-states-2013
#1
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28550046/genome-instability-a-conserved-mechanism-of-ageing
#2
REVIEW
Jan Vijg, Xiao Dong, Brandon Milholland, Lei Zhang
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals...
May 26, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28550013/an-essential-regulatory-system-originating-from-polygenic-transcriptional-rewiring-of-phop-phoq-of-xanthomonas-campestris
#3
Bao-Yu Peng, Yue Pan, Ru-Jiao Li, Jin-Wei Wei, Fang Liang, Li Wang, Fang-Fang Wang, Wei Qian
How essential, regulatory genes originate and evolve is intriguing because mutations of these genes not only lead to lethality in organisms, but also have pleiotropic effects since they control the expression of multiple downstream genes. Therefore, the evolution of essential, regulatory genes is not only determined by genetic variations of their own sequences, but also by the biological function of downstream genes and molecular mechanisms of regulation. To understand the origin of essential, regulatory genes, experimental dissection of the complete regulatory cascade is needed...
May 26, 2017: Genetics
https://www.readbyqxmd.com/read/28549824/the-hsp90-chaperone-network-modulates-candida-virulence-traits
#4
REVIEW
Teresa R O'Meara, Nicole Robbins, Leah E Cowen
Hsp90 is a conserved molecular chaperone that facilitates the folding and function of client proteins. Hsp90 function is dynamically regulated by interactions with co-chaperones and by post-translational modifications. In the fungal pathogen Candida albicans, Hsp90 enables drug resistance and virulence by stabilizing diverse signal transducers. Here, we review studies that have unveiled regulators of Hsp90 function, as well as downstream effectors that govern the key virulence traits of morphogenesis and drug resistance...
May 23, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28549194/disentangling-timing-of-admixture-patterns-of-introgression-and-phenotypic-indicators-in-a-hybridizing-wolf-population
#5
M Galaverni, R Caniglia, L Pagani, E Fabbri, A Boattini, E Randi
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favouring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analysed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture...
May 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28547737/08sg2-osbak1-regulates-grain-size-and-number-and-functions-differently-in-indica-and-japonica-backgrounds-in-rice
#6
Hua Yuan, Shijun Fan, Juan Huang, Shijie Zhan, Shifu Wang, Peng Gao, Weilan Chen, Bin Tu, Bingtian Ma, Yuping Wang, Peng Qin, Shigui Li
BACKGROUND: Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous. RESULTS: We identified a rice small grain (sg2) mutant in an EMS mutant library generated from an indica variety, Shuhui498. Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F2 population...
December 2017: Rice
https://www.readbyqxmd.com/read/28547520/small-scale-intraspecific-patterns-of-adaptive-immunogenetic-polymorphisms-and-neutral-variation-in-lake-superior-lake-trout
#7
Shauna M Baillie, Riley R Hemstock, Andrew M Muir, Charles C Krueger, Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake...
May 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28546999/a-birth-of-bipartite-exon-by-intragenic-deletion
#8
Kandai Nozu, Kazumoto Iijima, Toru Igarashi, Shiro Yamada, Jana Kralovicova, Yoshimi Nozu, Tomohiko Yamamura, Shogo Minamikawa, Ichiro Morioka, Takeshi Ninchoji, Hiroshi Kaito, Koichi Nakanishi, Igor Vorechovsky
BACKGROUND: Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS: We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS: The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28545349/exploring-different-mutations-at-a-single-amino-acid-position-of-cucumber-green-mottle-mosaic-virus-replicase-to-attain-stable-symptom-attenuation
#9
Liming Liu, Bin Peng, Zhenwei Zhang, Yang Wu, Manuel Miras, Miguel A Aranda, Qinsheng Gu
Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus (family Virgaviridae) which causes serious economic losses in cucurbit crops. A possibility for CGMMV control is the use of cross-protection, for which stable attenuated isolates are required. In this study, an infectious clone was constructed for the hn isolate of CGMMV. Unexpectedly, this clone carried a non-conserved mutation involving a single nucleotide change resulting in the replacement of Arg to Cys at residue 284 of the replicase protein; this mutation correlated with delayed symptom induction and RNA accumulation, as shown in time course experiments...
May 25, 2017: Phytopathology
https://www.readbyqxmd.com/read/28545104/pkng-senses-amino-acid-availability-to-control-metabolism-and-virulence-of-mycobacterium-tuberculosis
#10
Barbara Rieck, Giulia Degiacomi, Michael Zimmermann, Alessandro Cascioferro, Francesca Boldrin, Natalie R Lazar-Adler, Andrew R Bottrill, Fabien le Chevalier, Wafa Frigui, Marco Bellinzoni, María-Natalia Lisa, Pedro M Alzari, Liem Nguyen, Roland Brosch, Uwe Sauer, Riccardo Manganelli, Helen M O'Hare
Sensing and response to changes in nutrient availability are essential for the lifestyle of environmental and pathogenic bacteria. Serine/threonine protein kinase G (PknG) is required for virulence of the human pathogen Mycobacterium tuberculosis, and its putative substrate GarA regulates the tricarboxylic acid cycle in M. tuberculosis and other Actinobacteria by protein-protein binding. We sought to understand the stimuli that lead to phosphorylation of GarA, and the roles of this regulatory system in pathogenic and non-pathogenic bacteria...
May 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28544664/to-reproduce-or-work-insect-castes-emerge-from-socially-induced-changes-in-nutrition-related-genes
#11
Amy L Toth
In social species, there is a fundamental trade-off between 'me' and 'we'; that is, should I reproduce, or should I work to help others to reproduce? In this issue of Molecular Ecology, Okada et al. () delve into the evolution and genetic mechanisms of this core question, focusing on social caste formation in insects. The authors take advantage of a unique ant in the genus Diacamma, which has secondarily lost the classic, highly different queens and workers found in many other ants, bees and wasps. Instead, Diacamma ant castes are decided via aggressive dominance interactions among adult females, similar to dominance hierarchies seen in primitively social insects and many social vertebrates...
June 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28544181/the-k-2-conundrum
#12
Jasmine K Janes, Joshua M Miller, Julian R Dupuis, René M Malenfant, Jamieson C Gorrell, Catherine I Cullingham, Rose L Andrew
Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow. STRUCTURE, the most highly cited of several clustering-based methods, was developed to provide robust estimates without the need for populations to be determined a priori. STRUCTURE introduces the problem of selecting the optimal number of clusters and as a result the ΔK method was proposed to assist in the identification of the 'true' number of clusters...
May 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543048/estimating-demographic-contributions-to-effective-population-size-in-an-age-structured-wild-population-experiencing-environmental-and-demographic-stochasticity
#13
Amanda E Trask, Eric M Bignal, Davy I McCracken, Stuart B Piertney, Jane M Reid
1.A population's effective size (Ne ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However estimating Ne , and identifying key demographic mechanisms that underlie the Ne to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. 2.A sophisticated demographic method of estimating Ne /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated...
May 24, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28542616/regulation-of-acetyl-coa-synthetase-transcription-by-the-crbs-r-two-component-system-is-conserved-in-genetically-diverse-environmental-pathogens
#14
Kristin Jacob, Anna Rasmussen, Paul Tyler, Mariah M Servos, Mariame Sylla, Cecilia Prado, Elizabeth Daniele, Josh S Sharp, Alexandra E Purdy
The CrbS/R two-component signal transduction system is a conserved regulatory mechanism through which specific Gram-negative bacteria control acetate flux into primary metabolic pathways. CrbS/R governs expression of acetyl-CoA synthase (acsA), an enzyme that converts acetate to acetyl-CoA, a metabolite at the nexus of the cell's most important energy-harvesting and biosynthetic reactions. During infection, bacteria can utilize this system to hijack host acetate metabolism and alter the course of colonization and pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28542435/development-and-evaluation-of-a-bioinformatics-approach-for-designing-molecular-assays-for-viral-detection
#15
Pierre H H Schneeberger, Joël F Pothier, Andreas Bühlmann, Brion Duffy, Christian Beuret, Jürg Utzinger, Jürg E Frey
BACKGROUND: Viruses belonging to the Flaviviridae and Bunyaviridae families show considerable genetic diversity. However, this diversity is not necessarily taken into account when developing diagnostic assays, which are often based on the pairwise alignment of a limited number of sequences. Our objective was to develop and evaluate a bioinformatics workflow addressing two recurrent issues of molecular assay design: (i) the high intraspecies genetic diversity in viruses and (ii) the potential for cross-reactivity with close relatives...
2017: PloS One
https://www.readbyqxmd.com/read/28542313/environmental-dna-edna-metabarcoding-assays-to-detect-invasive-invertebrate-species-in-the-great-lakes
#16
Katy E Klymus, Nathaniel T Marshall, Carol A Stepien
Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring...
2017: PloS One
https://www.readbyqxmd.com/read/28542261/considering-reefscape-configuration-and-composition-in-biophysical-models-advance-seascape-genetics
#17
Simon Van Wynsberge, Serge Andréfouët, Nabila Gaertner-Mazouni, Josina Tiavouane, Daphné Grulois, Jérôme Lefèvre, Malin L Pinsky, Cécile Fauvelot
Previous seascape genetics studies have emphasized the role of ocean currents and geographic distances to explain the genetic structure of marine species, but the role of benthic habitat has been more rarely considered. Here, we compared the population genetic structure observed in West Pacific giant clam populations against model simulations that accounted habitat composition and configuration, geographical distance, and oceanic currents. Dispersal determined by geographical distance provided a modelled genetic structure in better agreement with the observations than dispersal by oceanic currents, possibly due to insufficient spatial resolution of available oceanographic and coastal circulation models...
2017: PloS One
https://www.readbyqxmd.com/read/28541527/sleep-dependent-modulation-of-metabolic-rate-in-drosophila
#18
Bethany A Stahl, Melissa E Slocumb, Hersh Chaitin, Justin R Diangelo, Alex C Keene
Dysregulation of sleep is associated with metabolic diseases, and metabolic rate is acutely regulated by sleep-wake behavior. In humans and rodent models, sleep loss is associated with obesity, reduced metabolic rate, and negative energy balance, yet little is known about the neural mechanisms governing interactions between sleep and metabolism. We have developed a system to simultaneously measure sleep and metabolic rate in individual Drosophila, allowing for interrogation of neural systems governing interactions between sleep and metabolic rate...
May 25, 2017: Sleep
https://www.readbyqxmd.com/read/28541519/reduced-sleep-during-social-isolation-leads-to-cellular-stress-and-induction-of-the-unfolded-protein-response-upr
#19
Marishka K Brown, Ewa Strus, Nirinjini Naidoo
Study Objectives: Social isolation has a multitude of negative consequences on human health including the ability to endure challenges to the immune system, sleep amount and efficiency, and general morbidity and mortality. These adverse health outcomes are conserved in other social species. In the fruit fly Drosophila melanogaster, social isolation leads to increased aggression, impaired memory and reduced amounts of daytime sleep. There is a correlation between molecules affected by social isolation and those implicated in sleep in Drosophila...
May 25, 2017: Sleep
https://www.readbyqxmd.com/read/28541511/molecular-association-of-arabidopsis-rth-with-its-homolog-rte1-in-regulating-ethylene-signaling
#20
Fangfang Zheng, Xiankui Cui, Maximo Rivarola, Ting Gao, Caren Chang, Chun-Hai Dong
The plant hormone ethylene affects many biological processes during plant growth and development. Ethylene is perceived by ethylene receptors at the endoplasmic reticulum (ER) membrane. The ETR1 ethylene receptor is positively regulated by the transmembrane protein RTE1, which localizes to the ER and Golgi apparatus. The RTE1 gene family is conserved in animals, plants, and lower eukaryotes. In Arabidopsis, RTE1-HOMOLOG (RTH) is the only homolog of the Arabidopsis RTE1 gene family. The regulatory function of the Arabidopsis RTH in ethylene signaling and plant growth is largely unknown...
May 24, 2017: Journal of Experimental Botany
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