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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/29142125/emergence-of-double-and-triple-gene-reassortant-g1p-8-rotaviruses-possessing-a-ds-1-like-backbone-post-rotavirus-vaccine-introduction-in-malawi
#1
Khuzwayo C Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E Tate, Umesh D Parashar, Robert S Heyderman, Neil French, Nigel A Cunliffe, Iturriza-Gomara Miren
To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunisation programmes. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix™) into its immunisation schedule in 2012. Utilising a surveillance platform of hospitalised rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 - 2012) and after (2013 - 2014) vaccine introduction. Analysis of whole genomes obtained through next generation sequencing revealed that all randomly-selected pre-vaccine G1P[8] strains sequenced (n=32) possessed a Wa-like genetic constellation, whereas post-vaccine G1P[8] strains (n=18) had a DS-1-like constellation...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29134627/the-evolution-of-genital-shape-variation-in-female-cetaceans
#2
Dara N Orbach, Brandon Hedrick, Bernd Würsig, Sarah L Mesnick, Patricia Lr Brennan
Male genital diversification is likely the result of sexual selection. Female genital diversification may also result from sexual selection, although it is less well studied and understood. Female genitalia are complex among whales, dolphins, and porpoises, especially compared to other vertebrates. The evolutionary factors affecting the diversity of vaginal complexity could include ontogeny, allometry, phylogeny, sexual selection, and natural selection. We quantified shape variation in female genitalia using 2-D geometric morphometric analysis, and validated the application of this method to study soft tissues...
November 14, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29126189/comparative-genome-analysis-reveals-adaptation-to-the-ectophytic-lifestyle-of-sooty-blotch-and-flyspeck-fungi
#3
Chao Xu, Rong Zhang, Guangyu Sun, Mark L Gleason
Sooty blotch and flyspeck (SBFS) fungi are a distinctive group of plant pathogens which, although phylogenetically diverse, occupy an exclusively surface-dwelling niche. They cause economic losses by superficially blemishing the fruit of several tree crops, principally apple, in moist temperate regions worldwide. In this study, we performed genome-wide comparative analyses separately within three pairs of species of ascomycete pathogens; each pair contained an SBFS species as well as a closely related but plant-penetrating parasite (PPP) species...
November 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29124392/tracking-the-evolutionary-pathway-of-sex-chromosomes-among-fishes-characterizing-the-unique-xx-xy1y2-system-in-hoplias-malabaricus-teleostei-characiformes
#4
Ezequiel Aguiar de Oliveira, Alexandr Sember, Luiz Antonio Carlos Bertollo, Cassia Fernanda Yano, Tariq Ezaz, Orlando Moreira-Filho, Terumi Hatanaka, Vladimir Trifonov, Thomas Liehr, Ahmed Basheer Hamid Al-Rikabi, Petr Ráb, Hugmar Pains, Marcelo de Bello Cioffi
The Neotropical fish, Hoplias malabaricus, is one of the most cytogenetically studied fish taxon with seven distinct karyomorphs (A-G) comprising varying degrees of sex chromosome differentiation, ranging from homomorphic to highly differentiated simple and multiple sex chromosomes. Therefore, this fish offers a unique opportunity to track evolutionary mechanisms standing behind the sex chromosome evolution and differentiation. Here, we focused on a high-resolution cytogenetic characterization of the unique XX/XY1Y2 multiple sex chromosome system found in one of its karyomorphs (G)...
November 9, 2017: Chromosoma
https://www.readbyqxmd.com/read/29112837/vertical-observation-and-analysis-on-rapid-formation-and-evolutionary-mechanisms-of-a-prolonged-haze-episode-over-central-eastern-china
#5
Su-Qin Han, Tian-Yi Hao, Yu-Fen Zhang, Jing-le Liu, Pei-Yan Li, Zi-Ying Cai, Min Zhang, Qin-Liang Wang, Hao Zhang
To clarify the rapid formation and evolutionary mechanisms of an extremely severe and persistent haze and fog (HF) episode that occurred in central-eastern China from Dec 20 to 25, 2015, a novel campaign was conducted and vertical profiles of wind, temperature, light extinction coefficient (LEC) and PM2.5 concentration were used to analyze the rapid formation and evolutionary mechanisms of this HF episode. The substantial downward transportation of regional pollution from high layers and stagnant weather conditions favorable for the local pollution accumulation were the two main causes of the rapid increase in pollutant concentration...
November 4, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29108008/insights-into-the-molecular-evolution-of-peptidase-inhibitors-in-arthropods
#6
Joaquin Alonso, Manuel Martinez
Peptidase inhibitors are key proteins involved in the control of peptidases. In arthropods, peptidase inhibitors modulate the activity of peptidases involved in endogenous physiological processes and peptidases of the organisms with which they interact. Exploring available arthropod genomic sequences is a powerful way to obtain the repertoire of peptidase inhibitors in every arthropod species and to understand the evolutionary mechanisms involved in the diversification of this kind of proteins. A genomic comparative analysis of peptidase inhibitors in species belonging to different arthropod taxonomic groups was performed...
2017: PloS One
https://www.readbyqxmd.com/read/29096001/hybrids-and-horizontal-transfer-introgression-allows-adaptive-allele-discovery
#7
Roswitha Schmickl, Sarah Marburger, Sian Bray, Levi Yant
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally...
October 31, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29061902/non-adaptive-origins-of-evolutionary-innovations-increase-network-complexity-in-interacting-digital-organisms
#8
Miguel A Fortuna, Luis Zaman, Andreas Wagner, Jordi Bascompte
The origin of evolutionary innovations is a central problem in evolutionary biology. To what extent such innovations have adaptive or non-adaptive origins is hard to assess in real organisms. This limitation, however, can be overcome using digital organisms, i.e. self-replicating computer programs that mutate, evolve and coevolve within a user-defined computational environment. Here, we quantify the role of the non-adaptive origins of host resistance traits in determining the evolution of ecological interactions among host and parasite digital organisms...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29055057/sperm-competition-but-not-major-histocompatibility-divergence-drive-differential-fertilization-success-between-alternative-reproductive-tactics-in-chinook-salmon
#9
S J Lehnert, L Helou, T E Pitcher, J W Heath, D D Heath
Post-copulatory sexual selection processes, including sperm competition and cryptic female choice (CFC), can operate based on major histocompatibility (MH) genes. We investigated sperm competition between male alternative reproductive tactics (jack (sneaker) and hooknose (guard)) of Chinook salmon (Oncorhynchus tshawytscha). Using a full factorial design, we examined in vitro competitive fertilization success of paired jack and hooknose males at three time points after sperm activation (0, 15 and 60 seconds) to test for male competition, CFC and time effects on male fertilization success...
October 20, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29052098/comparative-transcriptome-analysis-reveals-whole-genome-duplications-and-gene-selection-patterns-in-cultivated-and-wild-chrysanthemum-species
#10
So Youn Won, Soo-Jin Kwon, Tae-Ho Lee, Jae-A Jung, Jung Sun Kim, Sang-Ho Kang, Seong-Han Sohn
Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C...
October 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29049306/protein-structural-disorder-of-the-envelope-v3-loop-contributes-to-the-switch-in-human-immunodeficiency-virus-type-1-cell-tropism
#11
Xiaowei Jiang, Felix Feyertag, David L Robertson
Human immunodeficiency virus type 1 (HIV-1) envelope gp120 is partly an intrinsically disordered (unstructured/disordered) protein as it contains regions that do not fold into well-defined protein structures. These disordered regions play important roles in HIV's life cycle, particularly, V3 loop-dependent cell entry, which determines how the virus uses two coreceptors on immune cells, the chemokine receptors CCR5 (R5), CXCR4 (X4) or both (R5X4 virus). Most infecting HIV-1 variants utilise CCR5, while a switch to CXCR4-use occurs in the majority of infections...
2017: PloS One
https://www.readbyqxmd.com/read/29046540/compensatory-mutations-improve-general-permissiveness-to-antibiotic-resistance-plasmids
#12
Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K Thomason, Houra Merrikh, Jose M Ponciano, Eva M Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multidrug resistance plasmid RP4, determined plasmid persistence and cost using a joint experimental-modelling approach, resequenced evolved clones, and reconstructed key mutations...
September 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29045561/structural-variability-across-the-primate-brain-a-cross-species-comparison
#13
Paula L Croxson, Stephanie J Forkel, Leonardo Cerliani, Michel Thiebaut de Schotten
A large amount of variability exists across human brains; revealed initially on a small scale by postmortem studies and, more recently, on a larger scale with the advent of neuroimaging. Here we compared structural variability between human and macaque monkey brains using grey and white matter magnetic resonance imaging measures. The monkey brain was overall structurally as variable as the human brain, but variability had a distinct distribution pattern, with some key areas showing high variability. We also report the first evidence of a relationship between anatomical variability and evolutionary expansion in the primate brain...
October 13, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29035570/a-median-solver-and-phylogenetic-inference-based-on-double-cut-and-join-sorting
#14
Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang
Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing availability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: small parsimony problem (SPP) and big parsimony problem (BPP). Maximum parsimony is a popular approach for SPP and BPP, which relies on iteratively solving an NP-hard problem, the median problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29032444/modulating-signaling-networks-by-crispr-cas9-mediated-transposable-element-insertion
#15
REVIEW
Luis María Vaschetto
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it...
October 14, 2017: Current Genetics
https://www.readbyqxmd.com/read/29030885/phylogenetic-distribution-of-a-male-pheromone-that-may-exploit-a-nonsexual-preference-in-lampreys
#16
Tyler J Buchinger, Ugo Bussy, Ke Li, Huiyong Wang, Mar Huertas, Cindy F Baker, Liang Jia, Michael C Hayes, Weiming Li, Nicholas S Johnson
Pheromones are among the most important sexual signals used by organisms throughout the animal kingdom. However, few are identified in vertebrates, leaving the evolutionary mechanisms underlying vertebrate pheromones poorly understood. Pre-existing biases in receivers' perceptual systems shape visual and auditory signaling systems, but studies on how receiver biases influence the evolution of pheromone communication remain sparse. The lamprey Petromyzon marinus uses a relatively well-understood suite of pheromones and offers a unique opportunity to study the evolution of vertebrate pheromone communication...
October 14, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29030729/long-photoperiod-affects-the-maize-transition-from-vegetative-to-reproductive-stages-a-proteomic-comparison-between-photoperiod-sensitive-inbred-line-and-its-recurrent-parent
#17
Lei Tian, Shunxi Wang, Xiaoheng Song, Jun Zhang, Ping Liu, Zan Chen, Yanhui Chen, Liuji Wu
Maize (Zea mays L.) is a typical short-day plant that is produced as an important food product and industrial material. The photoperiod is one of the most important evolutionary mechanisms enabling the adaptation of plant developmental phases to changes in climate conditions. There are differences in the photoperiod sensitivity of maize inbred lines from tropical to temperate regions. In this study, to identify the maize proteins responsive to a long photoperiod (LP), the photoperiod-insensitive inbred line HZ4 and its near-isogenic line H496, which is sensitive to LP conditions, were analyzed under long-day conditions using isobaric tags for relative and absolute quantitation...
October 13, 2017: Amino Acids
https://www.readbyqxmd.com/read/29029188/an-analysis-of-the-epidemic-of-kpc-producing-klebsiella-pneumoniae-convergence-of-two-evolutionary-mechanisms-creates-the-perfect-storm
#18
Laura J Rojas, George M Weinstock, Elsa De La Cadena, Lorena Diaz, Rafael Rios, Blake M Hanson, Joseph S Brown, Purva Vats, Daniel S Phillips, Hoan Nguyen, Kristine M Hujer, Adriana Correa, Mark D Adams, Federico Perez, Erica Sodergren, Apurva Narechania, Paul J Planet, Maria V Villegas, Robert A Bonomo, Cesar A Arias
Background: Carbapenem resistance is a critical health care challenge worldwide. Particularly concerning is the widespread dissemination of Klebsiella pneumoniae carbapenemase (KPC). K. pneumoniae harboring blaKPC (KPC-Kpn) is endemic in many areas including United States, where the epidemic was primarily mediated by the clonal dissemination of Kpn ST258. We postulated that the spread of blaKPC in other regions occurs by different and more complex mechanisms. To test this, we investigated the evolution and dynamics of spread of KPC-Kpn in Colombia, where KPC became rapidly endemic after emerging in 2005...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28989790/mechanistic-insights-into-molecular-evolution-of-species-specific-differential-glycosaminoglycan-binding-surfaces-in-growth-related-oncogene-chemokines
#19
Khushboo Gulati, Minal Jamsandekar, Krishna Mohan Poluri
Chemokines are chemotactic cytokines involved in leucocyte trafficking to infected tissue. Growth-related oncogene (GRO) chemokines namely CXCL1, CXCL2 and CXCL3 are neutrophil activating chemokines sharing a conserved three-dimensional structure, but encompassing functional diversity due to gene duplication and evolutionary events. However, the evolutionary mechanisms including selection pressures involved in diversification of GRO genes have not yet been characterized. Here, we performed comprehensive evolutionary analysis of GRO genes among different mammalian species...
September 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28985206/clonal-evolution-in-leukemia
#20
REVIEW
Adolfo A Ferrando, Carlos López-Otín
Human leukemias are liquid malignancies characterized by diffuse infiltration of the bone marrow by transformed hematopoietic progenitors. The accessibility of tumor cells obtained from peripheral blood or through bone marrow aspirates, together with recent advances in cancer genomics and single-cell molecular analysis, have facilitated the study of clonal populations and their genetic and epigenetic evolution over time with unprecedented detail. The results of these analyses challenge the classic view of leukemia as a clonal homogeneous diffuse tumor and introduce a more complex and dynamic scenario...
October 6, 2017: Nature Medicine
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