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Genetic evolution

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https://www.readbyqxmd.com/read/28107061/the-evolution-of-reproductive-phenology-in-broadcast-spawners-and-the-maintenance-of-sexually-antagonistic-polymorphism
#1
Colin Olito, Dustin J Marshall, Tim Connallon
Reproductive phenology is a crucial life-history trait that evolves in response to external environmental conditions and frequency- and density-dependent interactions within species. Broadcast spawners-which represent a large fraction of aquatic biodiversity-evolve phenologies that balance strong density-dependent fertilization success against abiotic environmental conditions that are required for successful reproduction. The overall balance between these processes may be particularly complex in dioecious species, where selection on reproductive timing potentially differs between the sexes...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106948/genetic-differentiation-associated-with-host-plants-and-geography-among-six-widespread-species-of-south-american-blepharoneura-fruit-flies-tephritidae
#2
Kristina Ottens, Isaac S Winkler, Matthew L Lewis, Sonja J Scheffer, Géssica A Gomes-Costa, Marty A Condon, Andrew A Forbes
Tropical herbivorous insects are astonishingly diverse and many are highly host-specific. Much evidence suggests that herbivorous insect diversity is a function of host-plant diversity; yet, the diversity of some lineages exceeds the diversity of plants. Although most species of herbivorous fruit flies in the Neotropical genus Blepharoneura are strongly host-specific (they deposit their eggs in a single host plant species and flower sex), some species are collected from multiple hosts or flowers and these may represent examples of lineages that are diversifying via changes in host use...
January 20, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28106467/follicular-lymphoma-a-b-cell-malignancy-addicted-to-epigenetic-mutations
#3
Koorosh Korfi, Sara Ali, James A Heward, Jude Fitzgibbon
While follicular lymphoma (FL) is exquisitely responsive to immuno-chemotherapy, many patients follow a relapsing remitting clinical course driven in part by a common precursor cell (CPC) population. Advances in next generation sequencing have provided valuable insights into the genetic landscape of FL and its clonal evolution in response to therapy, implicating perturbations of epigenetic regulators as a hallmark of the disease. Recurrent mutations of histone modifiers KMT2D, CREBBP, EP300, EZH2, ARIDIA, and linker histones are likely early events arising in the CPC pool, rendering epigenetic based therapies conceptually attractive for treatment of indolent and transformed FL...
January 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28106288/nuclear-inositide-signaling-via-phospholipase-c
#4
Stefano Ratti, Sara Mongiorgi, Giulia Ramazzotti, Matilde Y Follo, Giulia A Mariani, Pann-Ghill Suh, James A McCubrey, Lucio Cocco, Lucia Manzoli
The existence of an independent nuclear inositide pathway distinct from the cytoplasmic one has been demonstrated in different physiological systems and in diseases. In this prospect we analyze the role of PI-PLCβ1 nuclear isoform in relation to the cell cycle regulation, the cell differentiation and different physiopathological pathways focusing on the importance of the nuclear localization from both molecular and clinical point of view. PI-PLCβ1 is essential for G1/S transition through DAG and Cyclin D3 and plays also a central role in G2/M progression through Cyclin B1 and PKCα...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28106055/rapid-adaptive-phenotypic-change-following-colonization-of-a-newly-restored-habitat
#5
Camilla Lo Cascio Sætre, Charles Coleiro, Martin Austad, Mark Gauci, Glenn-Peter Sætre, Kjetil Lysne Voje, Fabrice Eroukhmanoff
Real-time observation of adaptive evolution in the wild is rare and limited to cases of marked, often anthropogenic, environmental change. Here we present the case of a small population of reed warblers (Acrocephalus scirpaceus) over a period of 19 years (1996-2014) after colonizing a restored wetland habitat in Malta. Our data show a population decrease in body mass, following a trajectory consistent with a population ascending an adaptive peak, a so-called Ornstein-Uhlenbeck process. We corroborate these findings with genetic and ecological data, revealing that individual survival is correlated with body mass, and more than half of the variation in mean population fitness is explained by variation in body mass...
January 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28105956/vrn1-genes-variability-in-tetraploid-wheat-species-with-a-spring-growth-habit
#6
Irina Konopatskaia, Valeriya Vavilova, Elena Ya Kondratenko, Alexandr Blinov, Nikolay P Goncharov
BACKGROUND: Vernalization genes VRN1 play a major role in the transition from vegetative to reproductive growth in wheat. In di-, tetra- and hexaploid wheats the presence of a dominant allele of at least one VRN1 gene homologue (Vrn-A1, Vrn-B1, Vrn-G1 or Vrn-D1) determines the spring growth habit. Allelic variation between the Vrn-1 and vrn-1 alleles relies on mutations in the promoter region or the first intron. The origin and variability of the dominant VRN1 alleles, determining the spring growth habit in tetraploid wheat species have been poorly studied...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105722/charting-the-neglected-west-the-social-system-of-guinea-baboons
#7
Julia Fischer, Gisela H Kopp, Federica Dal Pesco, Adeelia Goffe, Kurt Hammerschmidt, Urs Kalbitzer, Matthias Klapproth, Peter Maciej, Ibrahima Ndao, Annika Patzelt, Dietmar Zinner
OBJECTIVES: Primate social systems are remarkably diverse, and thus play a central role in understanding social evolution, including the biological origin of human societies. Although baboons have been prominently featured in this context, historically little was known about the westernmost member of the genus, the Guinea baboon (Papio papio). MATERIAL AND METHODS: Here, we summarize the findings from the first years of observations at the field site CRP Simenti in the Niokolo Koba National Park in Senegal...
January 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28103823/stepwise-addition-of-genetic-changes-correlated-with-histological-change-from-well-differentiated-to-sarcomatoid-phenotypes-a-case-report
#8
Taichiro Goto, Yosuke Hirotsu, Hitoshi Mochizuki, Takahiro Nakagomi, Toshio Oyama, Kenji Amemiya, Masao Omata
BACKGROUND: Sarcomatoid cancer is defined by the World Health Organization as a category of non-small cell lung cancers with sarcoma or sarcoma-like differentiation. They are characterized by poor prognosis and resistance to conventional chemotherapy. However, the mutational profile of sarcomatoid cancer remains yet to be elucidated. Sarcomatoid cancers are usually biphasic tumors composed of carcinomatous and sarcomatous components, but the evolutional development of sarcomatoid cancer is controversial...
January 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28103805/evolutionary-history-of-podarcis-tiliguerta-on-corsica-and-sardinia
#9
V Rodríguez, J M Buades, R P Brown, B Terrasa, V Pérez-Mellado, C Corti, M Delaugerre, J A Castro, A Picornell, M M Ramon
BACKGROUND: Podarcis tiliguerta is a wall lizard endemic to the Mediterranean islands of Corsica and Sardinia. Previous findings of high mtDNA and morphological diversity have led to the suggestion that it may represent a species complex. Here, we analysed mitochondrial and nuclear markers (mtDNA, 3110 bp; 6 nDNA loci, 3961 bp) in P. tiliguerta sampled from thirty-two localities across Corsica and Sardinia. RESULTS: We find much greater intraspecific genetic divergence than between sister species of other Mediterranean island Podarcis, i...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#10
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103791/high-virulence-does-not-necessarily-impede-viral-adaptation-to-a-new-host-a-case-study-using-a-plant-rna-virus
#11
Anouk Willemsen, Mark P Zwart, Santiago F Elena
BACKGROUND: Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103613/tissue-based-next-generation-sequencing-application-in-a-universal-healthcare-system
#12
REVIEW
Seán O Hynes, Brendan Pang, Jacqueline A James, Perry Maxwell, Manuel Salto-Tellez
In the context of solid tumours, the evolution of cancer therapies to more targeted and nuanced approaches has led to the impetus for personalised medicine. The targets for these therapies are largely based on the driving genetic mutations of the tumours. To track these multiple driving mutations the use of next generation sequencing (NGS) coupled with a morphomolecular approach to tumours, has the potential to deliver on the promises of personalised medicine. A review of NGS and its application in a universal healthcare (UHC) setting is undertaken as the technology has a wide appeal and utility in diagnostic, clinical trial and research paradigms...
January 19, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#13
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28102740/update-on-functional-and-genetic-laboratory-assays-for-the-detection-of-platelet-microvesicles
#14
Maxime Laroche, Claire Dunois, Anne Marie Vissac, Jean Amiral
Functional and genetic assays for measuring platelet microvesicles (PMVs) are presented and discussed. Functional assays concern two groups of methods: a) homogeneous assays using the cofactor activity of phospholipids (PPLs) contained in PMVs and present in assayed plasmas, and a coagulation or a thrombin generation assay (TGA) as "end points"; b) capture-based assays, in which PMVs bind to an immobilized ligand, such as Annexin V in the presence of calcium, or monoclonal antibodies (MoAbs) specific for membrane proteins...
January 19, 2017: Platelets
https://www.readbyqxmd.com/read/28102430/innate-and-intrinsic-antiviral-immunity-in-drosophila
#15
REVIEW
Assel Mussabekova, Laurent Daeffler, Jean-Luc Imler
The fruit fly Drosophila melanogaster has been a valuable model to investigate the genetic mechanisms of innate immunity. Initially focused on the resistance to bacteria and fungi, these studies have been extended to include antiviral immunity over the last decade. Like all living organisms, insects are continually exposed to viruses and have developed efficient defense mechanisms. We review here our current understanding on antiviral host defense in fruit flies. A major antiviral defense in Drosophila is RNA interference, in particular the small interfering (si) RNA pathway...
January 19, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28101896/adaptation-of-genetically-monomorphic-bacteria-evolution-of-copper-resistance-through-multiple-horizontal-gene-transfers-of-complex-and-versatile-mobile-genetic-elements
#16
D Richard, V Ravigné, A Rieux, B Facon, C Boyer, K Boyer, P Grygiel, S Javegny, M Terville, B I Canteros, I Robène, C Vernière, A Chabirand, O Pruvost, P Lefeuvre
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons...
January 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28101534/pathogenicity-determinants-of-the-human-malaria-parasite-plasmodium-falciparum-have-ancient-origins
#17
Andrew J Brazier, Marion Avril, Maria Bernabeu, Maxwell Benjamin, Joseph D Smith
Plasmodium falciparum, the most deadly of the human malaria parasites, is a member of the Laverania subgenus that also infects African Great Apes. The virulence of P. falciparum is related to cytoadhesion of infected erythrocytes in microvasculature, but the origin of dangerous parasite adhesion traits is poorly understood. To investigate the evolutionary history of the P. falciparum cytoadhesion pathogenicity determinant, we studied adhesion domains from the chimpanzee malaria parasite P. reichenowi. We demonstrate that the P...
January 2017: MSphere
https://www.readbyqxmd.com/read/28100708/the-origin-of-floral-organ-identity-quartets
#18
Philip Ruelens, Zhicheng Zhang, Hilda van Mourik, Steven Maere, Kerstin Kaufmann, Koen Geuten
The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting of phylogenetically related MADS-domain proteins...
January 18, 2017: Plant Cell
https://www.readbyqxmd.com/read/28100615/rhinovirus-c-asthma-and-cell-surface-expression-of-virus-receptor-cdhr3
#19
Ann C Palmenberg
Human rhinoviruses of the A, B, and C species are defined agents of the common cold. But more than that, the RV-A and RV-C are the dominant cause of hospitalization-category infections in young children, especially those with asthma. The RV-C use of cadherin-related family member 3 (CDHR3) as its cellular receptor, creates a direct phenotypic link between human genetics ("G" vs "A" alleles cause Cys529 vs Tyr529 protein variants) and the efficiency with which RV-C can infect cells. With a lower cell surface display density, the human-specific Cys529 variant apparently confers partial protection from the severest virus-induced asthma episodes...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100614/human-rhinovirus-diversity-and-evolution-how-strange-the-change-from-major-to-minor
#20
Nicole Lewis-Rogers, Jon Seger, Frederick R Adler
: Rhinoviruses are the most common cause of the common cold. Their many distinct lineages fall into "major" and "minor" groups that use different cell-surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino-acid substitution at exposed sites in the capsid proteins VP2, VP3 and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences...
January 18, 2017: Journal of Virology
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