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Genetic evolution

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https://www.readbyqxmd.com/read/29457793/identifying-the-favored-mutation-in-a-positive-selective-sweep
#1
Ali Akbari, Joseph J Vitti, Arya Iranmehr, Mehrdad Bakhtiari, Pardis C Sabeti, Siavash Mirarab, Vineet Bafna
Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for "integrated selection of allele favored by evolution"), a method that enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations...
February 19, 2018: Nature Methods
https://www.readbyqxmd.com/read/29457640/application-of-adaptive-laboratory-evolution-to-overcome-a-flux-limitation-in-an-escherichia-coli-production-strain
#2
Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu
Gene deletion strategies using flux balance analysis (FBA) have improved the growth-coupled production of various compounds. However, the productivities were often below the expectation because the cells failed to adapt to these genetic perturbations. Here, we demonstrate the productivity of the succinate of the designed gene deletion strain was improved by adaptive laboratory evolution (ALE). Although FBA predicted deletions of adhE-pykAF-gldA-pflB lead to produce succinate from glycerol with a yield of 0...
February 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29456544/inheritance-of-mesotrione-resistance-in-an-amaranthus-tuberculatus-var-rudis-population-from-nebraska-usa
#3
Maxwel C Oliveira, Todd A Gaines, Amit J Jhala, Stevan Z Knezevic
A population of Amaranthus tuberculatus (var. rudis ) evolved resistance to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicides (mesotrione, tembotrione, and topramezone) in Nebraska. The level of resistance was the highest to mesotrione, and the mechanism of resistance in this population is metabolism-based likely via cytochrome P450 enzymes. The increasing number of weeds resistant to herbicides warrants studies on the ecology and evolutionary factors contributing for resistance evolution, including inheritance of resistance traits...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29456241/ecology-and-evolution-of-mycobacterium-tuberculosis
#4
REVIEW
Sebastien Gagneux
Tuberculosis (TB) is the number one cause of human death due to an infectious disease. The causative agents of TB are a group of closely related bacteria known as the Mycobacterium tuberculosis complex (MTBC). As the MTBC exhibits a clonal population structure with low DNA sequence diversity, methods (such as multilocus sequence typing) that are applied to more genetically diverse bacteria are uninformative, and much of the ecology and evolution of the MTBC has therefore remained unknown. Owing to recent advances in whole-genome sequencing and analyses of large collections of MTBC clinical isolates from around the world, many new insights have been gained, including a better understanding of the origin of the MTBC as an obligate pathogen and its molecular evolution and population genetic characteristics both within and between hosts, as well as many aspects related to antibiotic resistance...
February 19, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29455706/review-the-potential-of-seminal-fluid-mediated-paternal-maternal-communication-to-optimise-pregnancy-success
#5
J J Bromfield
Artificial insemination has been a landmark procedure in improving animal agriculture over the past 150 years. The utility of artificial insemination has facilitated a rapid improvement in animal genetics across agricultural species, leading to improvements of growth, health and productivity in poultry, swine, equine and cattle species. The utility of artificial insemination, as with all assisted reproductive technologies side-steps thousands of years of evolution that has led to the development of physiological systems to ensure the transmission of genetics from generation to generation...
February 19, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29455279/divergent-selection-of-pattern-recognition-receptors-in-mammals-with-different-ecological-characteristics
#6
Ran Tian, Meixiu Chen, Simin Chai, Xinghua Rong, Bingyao Chen, Wenhua Ren, Shixia Xu, Guang Yang
Pattern recognition receptors (PRRs) are specialized receptors that represent a key component of the host innate immune system. Whether molecular evolutionary history of different PRR classes have involved different genetic mechanisms underlying diverse pathogen environment in mammals, and whether distinct ecology of mammals may have imposed divergent selective pressures on the evolution of the PRRs, remained unknown. To test these hypotheses, we investigated the characterization of 20 genes belonging to four PRR classes in mammals...
February 17, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29454983/old-and-new-glycopeptide-antibiotics-from-product-to-gene-and-back-in-the-post-genomic-era
#7
REVIEW
Giorgia Letizia Marcone, Elisa Binda, Francesca Berini, Flavia Marinelli
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics...
February 15, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29454026/adaptation-of-escherichia-coli-to-long-term-batch-culture-in-various-rich-media
#8
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee, Haixu Tang, Steven E Finkel, Karin E Kram
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms...
February 14, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29453822/full-genome-sequencing-of-porcine-circovirus-3-field-strains-from-denmark-italy-and-spain-demonstrates-a-high-within-europe-genetic-heterogeneity
#9
G Franzo, M Legnardi, C K Hjulsager, F Klaumann, L E Larsen, J Segales, M Drigo
Porcine circovirus 3 (PCV3) is a new species of the Circovirus genus, which has recently been associated with different clinical syndromes. Its presence has been reported in different countries of North and South America, Asia and recently also Europe (Poland). However, different from the other continents, no European PCV3 sequence is currently available in public databases. There is a strong need of epidemiological data and full-genome sequences from Europe because of its relevance in the understanding of PCV3 molecular epidemiology and control...
February 16, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29453424/genetic-control-and-evolutionary-potential-of-a-constitutive-resistance-mechanism-against-the-spruce-budworm-choristoneura-fumiferana-in-white-spruce-picea-glauca
#10
Claudia Méndez-Espinoza, Geneviève J Parent, Patrick Lenz, André Rainville, Laurence Tremblay, Greg Adams, Andrew McCartney, Éric Bauce, John MacKay
Insect herbivory may drive evolution by selecting for trees with heritable resistance against defoliation. The spruce budworm (Choristoneura fumiferana, SBW) is a highly damaging forest insect pest that can affect population structure of white spruce (Picea glauca) in North America. Resistance against SBW was recently described in white spruce and was linked to three constitutive resistance biomarkers: the phenolic compounds piceol and pungenol, and expression of a beta-glucosidase encoding gene (Pgβglu-1)...
February 17, 2018: Heredity
https://www.readbyqxmd.com/read/29453274/select-and-resequence-reveals-relative-fitness-of-bacteria-in-symbiotic-and-free-living-environments
#11
Liana T Burghardt, Brendan Epstein, Joseph Guhlin, Matt S Nelson, Margaret R Taylor, Nevin D Young, Michael J Sadowsky, Peter Tiffin
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti We find ( i ) selection that hosts exert on rhizobial communities depends on competition among strains, ( ii ) selection is stronger inside hosts than in either free-living environment, and ( iii ) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments...
February 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29453058/antigenic-and-genetic-evolution-of-contemporary-swine-h1-influenza-viruses-in-the-united-states
#12
Daniela S Rajao, Tavis K Anderson, Pravina Kitikoon, Jered Stratton, Nicola S Lewis, Amy L Vincent
Several lineages of influenza A viruses (IAV) currently circulate in North American pigs. Genetic diversity is further increased by transmission of IAV between swine and humans and subsequent evolution. Here, we characterized the genetic and antigenic evolution of contemporary swine H1N1 and H1N2 viruses representing clusters H1-α (1A.1), H1-β (1A.2), H1pdm (1A.3.3.2), H1-γ (1A.3.3.3), H1-δ1 (1B.2.2), and H1-δ2 (1B.2.1) currently circulating in pigs in the United States. The δ1-viruses diversified into two new genetic clades, H1-δ1a (1B...
February 13, 2018: Virology
https://www.readbyqxmd.com/read/29452359/convergent-amino-acid-signatures-in-polyphyletic-campylobacter-jejuni-sub-populations-suggest-human-niche-tropism
#13
Guillaume Méric, Alan McNally, Alberto Pessia, Evangelos Mourkas, Ben Pascoe, Leonardos Mageiros, Minna Vehkala, Jukka Corander, Samuel K Sheppard
Human infection with the gastrointestinal pathogen C. jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analysed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multi-host (ecological generalist) ST-21 and ST-45 clonal complexes (CCs)...
February 14, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29452133/some-properties-of-the-conditioned-reconstructed-process-with-bernoulli-sampling
#14
Carsten Wiuf
In many areas of genetics it is of relevance to consider a population of individuals that is founded by a single individual in the past. One model for such a scenario is the conditioned reconstructed process with Bernoulli sampling that describes the evolution of a population of individuals that originates from a single individual. Several aspects of this reconstructed process are studied, in particular the Markov structure of the process. It is shown that at any given time in the past, the conditioned reconstructed process behaves as the original conditioned reconstructed process after a suitable time-dependent change of the sampling probability...
February 13, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29452030/comparative-phylogenetic-and-expression-analysis-of-small-gtpases-families-in-legume-and-non-legume-plants
#15
Ana Claudia Flores, Virginia Dalla Via, Virginia Savy, Ulises Mancini Villagra, María Eugenia Zanetti, Flavio Blanco
BACKGROUND: Small monomeric GTPases act as molecular switches in several processes that involve polar cell growth, participating mainly in vesicle trafficking and cytoskeleton rearrangements. This gene superfamily has largely expanded in plants through evolution as compared with other Kingdoms, leading to the suggestion that members of each subfamily might have acquired new functions associated to plant-specific processes. Legume plants engage in a nitrogen-fixing symbiotic interaction with rhizobia in a process that involves polar growth processes associated with the infection throughout the root hair...
February 16, 2018: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29451715/transitions-in-sex-determination-and-sex-chromosomes-across-vertebrate-species
#16
Matthew W Pennell, Judith E Mank, Catherine L Peichel
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown if there are convergent trends in the directionality of turnover in sex determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles, and amphibians...
February 16, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29451433/populations-of-phytophthora-rubi-show-little-differentiation-and-high-rates-of-migration-among-states-in-the-western-united-states
#17
Javier F Tabima, Michael D Coffey, Inga Zasada, Niklaus J Grünwald
Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western U.S., where the majority of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the U...
February 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29450759/gene-expression-and-population-polymorphism-of-maize-iranian-mosaic-virus-in-zea-mays-and-intracellular-localization-and-interactions-of-viral-n-p-and-m-proteins-in-nicotiana-benthamiana
#18
Abozar Ghorbani, Keramatollah Izadpanah, Ralf G Dietzgen
Maize Iranian mosaic virus (MIMV; Mononegavirales, Rhabdoviridae, Nucleorhabdovirus) infects maize and several other poaceous plants. MIMV encodes six proteins, i.e., nucleocapsid protein (N), polymerase cofactor phosphoprotein (P), putative movement protein (P3), matrix protein (M), glycoprotein (G), and large RNA-dependent RNA polymerase (L). In the present study, MIMV gene expression and genetic polymorphism of an MIMV population in maize were determined. N, P, P3, and M protein genes were more highly expressed than the 5' terminal G and L genes...
February 15, 2018: Virus Genes
https://www.readbyqxmd.com/read/29450378/ocular-posterior-pole-pathological-modifications-related-to-complicated-pregnancy-a-review
#19
REVIEW
Vanessa Andrada Păun, Zamfir-Radu Ionescu, Liliana Voinea, Monica Cîrstoiu, Alexandru Baroș, Ștefan Pricopie, Radu Ciuluvică
Ocular posterior pole modification are a pathological manifestation in complicated pregnancies, especially when pregnancy induced hypertension is present (PIH), as well as in preeclampsia (PE) or eclampsia. Nonetheless, as the pregnancy evolves, the possibility for an aggravated evolution with HELLP syndrome, disseminated intravascular coagulation, and idiopathic thrombocytopenic purpura may have an ocular manifestation that, mainly, implies a loss of visual field or acuity, that, left unattended, may constitute a permanent impairment...
April 2017: Romanian Journal of Ophthalmology
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#20
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
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