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https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#1
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28534878/successive-range-expansion-promotes-diversity-and-accelerates-evolution-in-spatially-structured-microbial-populations
#2
Felix Goldschmidt, Roland R Regoes, David R Johnson
Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534829/variation-in-the-genetic-repertoire-of-viruses-infecting-micromonas-pusilla-reflects-horizontal-gene-transfer-and-links-to-their-environmental-distribution
#3
Jan F Finke, Danielle M Winget, Amy M Chan, Curtis A Suttle
Prasinophytes, a group of eukaryotic phytoplankton, has a global distribution and is infected by large double-stranded DNA viruses (prasinoviruses) in the family Phycodnaviridae. This study examines the genetic repertoire, phylogeny, and environmental distribution of phycodnaviruses infecting Micromonas pusilla, other prasinophytes and chlorophytes. Based on comparisons among the genomes of viruses infecting M. pusilla and other phycodnaviruses, as well as the genome from a host isolate of M. pusilla, viruses infecting M...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534786/evolutionary-computing-enriched-computer-aided-diagnosis-system-for-diabetic-retinopathy-a-survey
#4
Romany Mansour
The alterations caused due to diabetes mellitus results into significant micro-vasculature that eventually causes diabetic retinopathy (DR) that keeps on increasing as per time and eventually causes complete vision loss. Identifying subtle variations in morphological changes in retinal blood vessels, optic disk, exudates, micro-aneurysms, hemorrhage etc is complicate and requires robust computer aided diagnosis (CAD) system so as to enable earlier and efficient DR diagnosis practices. In majority of the existing CAD systems, the need of functional enhancement has been realized time by time to ensure accurate and time efficient DR...
May 17, 2017: IEEE Reviews in Biomedical Engineering
https://www.readbyqxmd.com/read/28534314/rapid-molecular-sexing-of-three-spined-sticklebacks-gasterosteus-aculeatus-l-based-on-large-y-chromosomal-insertions
#5
Theo C M Bakker, Thomas Giger, Joachim G Frommen, Carlo R Largiadèr
There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences...
May 22, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28533979/a-genome-wide-assessment-of-stages-of-elevational-parapatry-in-bornean-passerine-birds-reveals-no-introgression-implications-for-processes-and-patterns-of-speciation
#6
Robert G Moyle, Joseph D Manthey, Peter A Hosner, Mustafa Rahman, Maklarin Lakim, Frederick H Sheldon
Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo...
2017: PeerJ
https://www.readbyqxmd.com/read/28533660/genes-emotions-and-gut-microbiota-the-next-frontier-for-the-gastroenterologist
#7
REVIEW
Arturo Panduro, Ingrid Rivera-Iñiguez, Maricruz Sepulveda-Villegas, Sonia Roman
Most medical specialties including the field of gastroenterology are mainly aimed at treating diseases rather than preventing them. Genomic medicine studies the health/disease process based on the interaction of the human genes with the environment. The gastrointestinal (GI) system is an ideal model to analyze the interaction between our genes, emotions and the gut microbiota. Based on the current knowledge, this mini-review aims to provide an integrated synopsis of this interaction to achieve a better understanding of the GI disorders related to bad eating habits and stress-related disease...
May 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28533464/the-colours-of-humanity-the-evolution-of-pigmentation-in-the-human-lineage
#8
REVIEW
Nina G Jablonski, George Chaplin
Humans are a colourful species of primate, with human skin, hair and eye coloration having been influenced by a great variety of evolutionary forces throughout prehistory. Functionally naked skin has been the physical interface between the physical environment and the human body for most of the history of the genus Homo, and hence skin coloration has been under intense natural selection. From an original condition of protective, dark, eumelanin-enriched coloration in early tropical-dwelling Homo and Homo sapiens, loss of melanin pigmentation occurred under natural selection as Homo sapiens dispersed into non-tropical latitudes of Africa and Eurasia...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533463/signal-function-drives-phenotypic-and-genetic-diversity-the-effects-of-signalling-individual-identity-quality-or-behavioural-strategy
#9
REVIEW
Elizabeth A Tibbetts, Sean P Mullen, James Dale
Animal coloration is influenced by selection pressures associated with communication. During communication, signallers display traits that inform receivers and modify receiver behaviour in ways that benefit signallers. Here, we discuss how selection on signallers to convey different kinds of information influences animal phenotypes and genotypes. Specifically, we address the phenotypic and genetic consequences of communicating three different kinds of information: individual identity, behavioural strategy and quality...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533454/genomics-of-coloration-in-natural-animal-populations
#10
REVIEW
Luis M San-Jose, Alexandre Roulin
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533337/development-of-a-medium-density-combined-species-snp-array-for-pacific-and-european-oysters-crassostrea-gigas-and-ostrea-edulis
#11
Alejandro P Gutierrez, Frances Turner, Karim Gharbi, Richard Talbot, Natalie R Lowe, Carolina Peñaloza, Mark McCullough, Paulo A Prodöhl, Tim P Bean, Ross D Houston
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species medium density SNP array for Pacific oyster (C. gigas) and European flat oyster (O. edulis), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28532797/genetic-basis-for-loss-of-immuno-reactive-o-chain-in-salmonella-enterica-serovar-enteritidis-veterinary-isolates
#12
Istvan Szabo, Marianne Grafe, Nicole Kemper, Ernst Junker, Burkhard Malorny
Fifty-two rough Salmonella enterica serovar Enteritidis (S. Enteritidis) isolates from broilers and the environment were characterized for their serological and genotypic properties. Under routine diagnostic serotyping methods such isolates lack the immuno-reactivity of the O-chain of the lipopolysaccharide (LPS), and are referred to as non-typeable. Using a modified slide agglutination method, the isolates could be differentiated into three different serological variants. Twenty-six isolates (50%) were defined as semi-rough, nineteen isolates (37%) as deep-rough, four isolates (8%) as rough and three isolates could not be assigned...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532795/host-cell-tropism-genome-characterization-and-evolutionary-features-of-oapv4-a-novel-deltapapillomavirus-identified-in-sheep-fibropapilloma
#13
Gessica Tore, Carla Cacciotto, Antonio Giovanni Anfossi, Gian Mario Dore, Elisabetta Antuofermo, Alessandra Scagliarini, Giovanni Pietro Burrai, Salvatore Pau, Maria Teresa Zedda, Gerolamo Masala, Marco Pittau, Alberto Alberti
Investigating papillomavirus (PV) diversity is crucial to fully comprehend pathogenicity, genetic features, and evolution of taxa hosted by domestic and wild animal species. This study reports the identification of OaPV4, a novel ovine PV type within Deltapapillomaviruses 3. The study of OaPV4 genomic features combined to in situ hybridization and immunohistochemistry investigations allowed extrapolating several general biological features of ovine PVs, such as their cellular tropism, pathogenicity, and evolutionary history...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28531958/unique-postglacial-evolution-of-the-hornbeam-carpinus-betulus-l-in-the-carpathians-and-the-balkan-peninsula-revealed-by-chloroplast-dna
#14
Dragoş Postolache, Flaviu Popescu, Ladislav Paule, Dalibor Ballian, Peter Zhelev, Sorina Fărcaş, Juraj Paule, Ovidiu Badea
The Balkan Peninsula is one of the largest and most important European glacial refugia. However, the evolutionary history and phylogeographic pattern of temperate tree species that survived in the Balkans glacial refugia and their contribution to the genetic structure of the current population in the Carpathian Mountains remains poorly understood. Using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and extensive population sampling, we explored the phylogeographic pattern of Carpinus betulus in both the Balkan Peninsula and the Carpathian region...
May 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28531201/evolutionary-forces-affecting-synonymous-variations-in-plant-genomes
#15
Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#16
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28529975/phylogenetic-analyses-suggest-that-factors-other-than-the-capsid-protein-play-a-role-in-the-epidemic-potential-of-gii-2-norovirus
#17
Kentaro Tohma, Cara J Lepore, Lauren A Ford-Siltz, Gabriel I Parra
Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII...
May 2017: MSphere
https://www.readbyqxmd.com/read/28529652/de-novo-assembly-of-the-liver-transcriptome-of-the-european-starling-sturnus-vulgaris
#18
Mark F Richardson, William B Sherwin, Lee A Rollins
The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28529504/a-novel-avian-paramyxovirus-putative-serotype-15-isolated-from-wild-birds
#19
Hyun-Jeong Lee, Ji-Ye Kim, Youn-Jeong Lee, Eun-Kyung Lee, Byoung-Min Song, Hee-Soo Lee, Kang-Seuk Choi
In January 2014, a viral hemagglutinating agent named UPO216 was isolated from fecal droppings of wild birds at the UPO wetland in South Korea during an avian influenza surveillance program. Electron microscopy identified the UPO216 virus as an avian paramyxovirus (APMV). Pathogenicity tests and molecular pathotyping revealed that the virus was avirulent in chickens. The UPO216 virus was assigned to a serological group antigenically distinct from known serotypes of APMV (-1, -2, -3, -4, -6, -7, -8, and -9) by hemagglutination inhibition test, despite showing weak cross-reactivity with APMV-1 and APMV-9...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28529469/a-comparative-genomics-approach-revealed-evolutionary-dynamics-of-microsatellite-imperfection-and-conservation-in-genus-gossypium
#20
Muhammad Mahmood Ahmed, Chao Shen, Anam Qadir Khan, Muhammad Atif Wahid, Muhammad Shaban, Zhongxu Lin
BACKGROUND: Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. RESULTS: Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites...
2017: Hereditas
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