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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/28731829/pattern-and-process-in-the-comparative-study-of-convergent-evolution
#1
D Luke Mahler, Marjorie G Weber, Catherine E Wagner, Travis Ingram
Understanding processes that have shaped broad-scale biodiversity patterns is a fundamental goal in evolutionary biology. The development of phylogenetic comparative methods has yielded a tool kit for analyzing contemporary patterns by explicitly modeling processes of change in the past, providing neontologists tools for asking questions previously accessible only for select taxa via the fossil record or laboratory experimentation. The comparative approach, however, differs operationally from alternative approaches to studying convergence in that, for studies of only extant species, convergence must be inferred using evolutionary process models rather than being directly measured...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28723516/the-molecular-evolution-of-castration-resistant-prostate-cancer
#2
REVIEW
Yvonne Ceder, Anders Bjartell, Zoran Culig, Mark A Rubin, Scott Tomlins, Tapio Visakorpi
CONTEXT: Androgen deprivation therapy (ADT) is the backbone of treatment for advanced prostate cancer. However, castration-resistant prostate cancer (CRPC) nearly invariably develops through a range of different molecular mechanisms accompanied by progression to a more aggressive phenotype. OBJECTIVE: To understand the key molecular mechanisms leading to CRPC and the functional implications of this progression. Understanding molecular evolutionary mechanisms in CRPC is essential for the development of novel curative therapeutic approaches...
December 2016: European Urology Focus
https://www.readbyqxmd.com/read/28708860/charged-amino-acid-variability-related-to-n-glyco-sylation-and-epitopes-in-a-h3n2-influenza-hem-agglutinin-and-neuraminidase
#3
Zhong-Zhou Huang, Liang Yu, Ping Huang, Li-Jun Liang, Qing Guo
BACKGROUND: The A/H3N2 influenza viruses circulated in humans have been shown to undergo antigenic drift, a process in which amino acid mutations result from nucleotide substitutions. There are few reports regarding the charged amino acid mutations. The purpose of this paper is to explore the relations between charged amino acids, N-glycosylation and epitopes in hemagglutinin (HA) and neuraminidase (NA). METHODS: A total of 700 HA genes (691 NA genes) of A/H3N2 viruses were chronologically analyzed for the mutational variants in amino acid features, N-glycosylation sites and epitopes since its emergence in 1968...
2017: PloS One
https://www.readbyqxmd.com/read/28694796/evolutionary-diversification-of-alanine-transaminases-in-yeast-catabolic-specialization-and-biosynthetic-redundancy
#4
Ximena Escalera-Fanjul, Carlos Campero-Basaldua, Maritrini Colón, James González, Dariel Márquez, Alicia González
Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28687759/emerging-patterns-of-plasmid-host-coevolution-that-stabilize-antibiotic-resistance
#5
Thibault Stalder, Linda M Rogers, Chris Renfrow, Hirokazu Yano, Zachary Smith, Eva M Top
Multidrug resistant bacterial pathogens have become a serious global human health threat, and conjugative plasmids are important drivers of the rapid spread of resistance to last-resort antibiotics. Whereas antibiotics have been shown to select for adaptation of resistance plasmids to their new bacterial hosts, or vice versa, a general evolutionary mechanism has not yet emerged. Here we conducted an experimental evolution study aimed at determining general patterns of plasmid-bacteria evolution. Specifically, we found that a large conjugative resistance plasmid follows the same evolutionary trajectories as its non-conjugative mini-replicon in the same and other species...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28674689/allosteric-control-of-substrate-specificity-of-the-escherichia-coli-adp-glucose-pyrophosphorylase
#6
Ana C Ebrecht, Ligin Solamen, Benjamin L Hill, Alberto A Iglesias, Kenneth W Olsen, Miguel A Ballicora
The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28662086/abscisic-acid-pathway-involved-in-the-regulation-of-watermelon-fruit-ripening-and-quality-trait-evolution
#7
Yanping Wang, Shaogui Guo, Shouwei Tian, Jie Zhang, Yi Ren, Honghe Sun, Guoyi Gong, Haiying Zhang, Yong Xu
Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is a non-climacteric fruit. The modern sweet-dessert watermelon is the result of years of cultivation and selection for fruits with desirable qualities. To date, the mechanisms of watermelon fruit ripening, and the role of abscisic acid (ABA) in this process, has not been well understood. We quantified levels of free and conjugated ABA contents in the fruits of cultivated watermelon (97103; C. lanatus subsp. vulgaris), semi-wild germplasm (PI179878; C...
2017: PloS One
https://www.readbyqxmd.com/read/28655863/evolution-of-biosynthetic-diversity
#8
REVIEW
Anthony J Michael
Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life...
June 27, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28651991/ribosome-inactivating-proteins-from-an-evolutionary-perspective
#9
Walter Jesús Lapadula, Maximiliano Juri Ayub
Ribosome Inactivating Proteins (RIPs) are rRNA N-glycosidases that inhibit protein synthesis through the elimination of a single adenine residue from 28S rRNA. Many of these toxins have been characterized in depth from a biochemical and molecular point of view. In addition, their potential use in medicine as highly selective toxins is being explored. In contrast, the evolutionary history of RIP encoding genes has remained traditionally underexplored. In recent years, accumulation of large genomic data has fueled research on this issue and revealed unexpected information about the origin and evolution of RIP toxins...
June 24, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28648886/revisiting-pivotal-differential-genome-evolution-in-wheat
#10
REVIEW
Ghader Mirzaghaderi, Annaliese S Mason
An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as 'pivotal-differential' genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved...
June 22, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28642457/human-mediated-secondary-contact-of-two-tortoise-lineages-results-in-sex-biased-introgression
#11
Eva Graciá, Roberto C Rodríguez-Caro, Ana C Andreu, Uwe Fritz, Andrés Giménez, Francisco Botella
Human-mediated secondary contact of recently diverged taxa offers valuable opportunities for studying the evolutionary mechanisms involved in the establishment and maintenance of genetic boundaries between taxa. We used mitochondrial and microsatellite markers to examine a recently introduced population of the spur-thighed tortoise (Testudo graeca) of mixed origin in the Doñana National Park (SW Spain). The earliest records of tortoises in Doñana trace back to the 18th century, but several population reinforcements in the 20th century with animals from Morocco are well-documented...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634295/population-genomic-inference-of-the-strength-and-timing-of-selection-against-gene-flow
#12
Simon Aeschbacher, Jessica P Selby, John H Willis, Graham Coop
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630745/correlation-between-hox-code-and-vertebral-morphology-in-the-mouse-towards-a-universal-model-for-synapsida
#13
Christine Böhmer
BACKGROUND: The importance of the cervical vertebrae as part of the skull-neck system in facilitating the success and diversity of tetrapods is clear. The reconstruction of its evolution, however, is problematic because of the variation in the number of vertebrae, making it difficult to identify homologous elements. Quantification of the morphological differentiation in the neck of diverse archosaurs established homologous units of vertebrae (i.e. modules) resulting from Hox gene expression patterns within the cervical vertebral column...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28611746/adaptations-to-high-salt-in-a-halophilic-protist-differential-expression-and-gene-acquisitions-through-duplications-and-gene-transfers
#14
Tommy Harding, Andrew J Roger, Alastair G B Simpson
The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28592544/time-sampled-population-sequencing-reveals-the-interplay-of-selection-and-genetic-drift-in-experimental-evolution-of-potato-virus-y
#15
Denis Kutnjak, Santiago F Elena, Maja Ravnikar
RNA viruses are one of the fastest evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus...
June 7, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28591676/evolution-of-commensal-bacteria-in-the-intestinal-tract-of-mice
#16
REVIEW
Ana Sousa, Nelson Frazão, Ricardo S Ramiro, Isabel Gordo
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced...
June 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28578268/carbon-emission-allowance-allocation-with-a-mixed-mechanism-in-air-passenger-transport
#17
Rui Qiu, Jiuping Xu, Ziqiang Zeng
Air passenger transport carbon emissions have become a great challenge for both governments and airlines because of rapid developments in the aviation industry in recent decades. In this paper, a mixed mechanism composed of a cap-and-trade mechanism and a carbon tax mechanism is developed to assist governments in allocating carbon emission allowances to airlines operating on the routes. Combined this mixed mechanism with an equilibrium strategy, a bi-level multi-objective model is proposed for an air passenger transport carbon emission allowance allocation problem, in which a government is considered as a leader and the airlines as the followers...
June 1, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28576775/cold-fusion-massive-karyotype-evolution-in-the-antarctic-bullhead-notothen-notothenia-coriiceps
#18
Angel Amores, Catherine A Wilson, Corey A H Allard, H William Detrich, John H Postlethwait
Half of all vertebrate species share a series of chromosome fusions that preceded the teleost genome duplication (TGD), but we do not understand the causative evolutionary mechanisms. The "Robertsonian-translocation hypothesis" suggests a regular fusion of each ancestral acro- or telocentric chromosome to just one other by centromere fusions, thus halving the karyotype. An alternative "genome-stirring hypothesis" posits haphazard and repeated fusions, inversions, and reciprocal and nonreciprocal translocations...
July 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28559354/rna-seq-reveals-conservation-of-function-among-the-yolk-sacs-of-human-mouse-and-chicken
#19
Tereza Cindrova-Davies, Eric Jauniaux, Michael G Elliot, Sungsam Gong, Graham J Burton, D Stephen Charnock-Jones
The yolk sac is phylogenetically the oldest of the extraembryonic membranes. The human embryo retains a yolk sac, which goes through primary and secondary phases of development, but its importance is controversial. Although it is known to synthesize proteins, its transport functions are widely considered vestigial. Here, we report RNA-sequencing (RNA-seq) data for the human and murine yolk sacs and compare those data with data for the chicken. We also relate the human RNA-seq data to proteomic data for the coelomic fluid bathing the yolk sac...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28554837/identification-polymorphism-and-expression-of-mhc-class-i%C3%AE-in-golden-pompano-trachinotus-ovatus
#20
Zhenjie Cao, Mingwang He, Xiaojuan Chen, Shifeng Wang, Yan Cai, Zhenyu Xie, Yun Sun, Yongcan Zhou
The classical major histocompatibility complex class I (MHC I) plays a vital role in the immune system. In this study, we cloned and identified golden pompano (Trachinotus ovatus) MHC Iα (Trov-MHC Iα), which encodes 351 amino acid residues including a leader peptide, α1, α2, α3 domain, a transmembrane region and a cytoplasmic domain. Twenty six different sequences, which encoded various numbers of amino acid residues ranging from 348 to 354, were obtained from 12 individuals. Highly genetic polymorphism was found in the Trov-MHC Iα, especially in the α1 and α2 domains...
August 2017: Fish & Shellfish Immunology
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