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https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#1
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#2
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920388/human-drivers-of-ecological-and-evolutionary-dynamics-in-emerging-and-disappearing-infectious-disease-systems
#3
REVIEW
Mary A Rogalski, Camden D Gowler, Clara L Shaw, Ruth A Hufbauer, Meghan A Duffy
Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920386/does-eutrophication-driven-evolution-change-aquatic-ecosystems
#4
REVIEW
Timothy J Alexander, Pascal Vonlanthen, Ole Seehausen
Eutrophication increases primary production and changes the relative abundance, taxonomic composition and spatial distribution of primary producers within an aquatic ecosystem. The changes in composition and location of resources alter the distribution and flow of energy and biomass throughout the food web. Changes in productivity also alter the physico-chemical environment, which has further effects on the biota. Such ecological changes influence the direction and strength of natural and sexual selection experienced by populations...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920382/adaptation-to-fragmentation-evolutionary-dynamics-driven-by-human-influences
#5
REVIEW
Pierre-Olivier Cheptou, Anna L Hargreaves, Dries Bonte, Hans Jacquemyn
Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920381/harvest-induced-evolution-insights-from-aquatic-and-terrestrial-systems
#6
REVIEW
Anna Kuparinen, Marco Festa-Bianchet
Commercial and recreational harvests create selection pressures for fitness-related phenotypic traits that are partly under genetic control. Consequently, harvesting can drive evolution in targeted traits. However, the quantification of harvest-induced evolutionary life history and phenotypic changes is challenging, because both density-dependent feedback and environmental changes may also affect these changes through phenotypic plasticity. Here, we synthesize current knowledge and uncertainties on six key points: (i) whether or not harvest-induced evolution is happening, (ii) whether or not it is beneficial, (iii) how it shapes biological systems, (iv) how it could be avoided, (v) its importance relative to other drivers of phenotypic changes, and (vi) whether or not it should be explicitly accounted for in management...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920380/genetic-architecture-of-age-at-maturity-can-generate-divergent-and-disruptive-harvest-induced-evolution
#7
Anna Kuparinen, Jeffrey A Hutchings
Life-history traits are generally assumed to be inherited quantitatively. Fishing that targets large, old individuals is expected to decrease age at maturity. In Atlantic salmon (Salmo salar), it has recently been discovered that sea age at maturity is under strong control by a single locus with sexually dimorphic expression of heterozygotes, which makes it less intuitive to predict how life histories respond to selective fishing. We explore evolutionary responses to fishing in Atlantic salmon, using eco-evolutionary simulations with two alternative scenarios for the genetic architecture of age at maturity: (i) control by multiple loci with additive effects and (ii) control by one locus with sexually dimorphic expression...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920377/phenological-shifts-of-native-and-invasive-species-under-climate-change-insights-from-the-boechera-lythrum-model
#8
REVIEW
Robert I Colautti, Jon Ågren, Jill T Anderson
Warmer and drier climates have shifted phenologies of many species. However, the magnitude and direction of phenological shifts vary widely among taxa, and it is often unclear when shifts are adaptive or how they affect long-term viability. Here, we model evolution of flowering phenology based on our long-term research of two species exhibiting opposite shifts in floral phenology: Lythrum salicaria, which is invasive in North America, and the sparse Rocky Mountain native Boechera stricta Genetic constraints are similar in both species, but differences in the timing of environmental conditions that favour growth lead to opposite phenological shifts under climate change...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920376/invasions-and-extinctions-through-the-looking-glass-of-evolutionary-ecology
#9
REVIEW
Robert I Colautti, Jake M Alexander, Katrina M Dlugosch, Stephen R Keller, Sonia E Sultan
Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920375/eco-evolutionary-dynamics-in-urbanized-landscapes-evolution-species-sorting-and-the-change-in-zooplankton-body-size-along-urbanization-gradients
#10
Kristien I Brans, Lynn Govaert, Jessie M T Engelen, Andros T Gianuca, Caroline Souffreau, Luc De Meester
Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50-3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920374/urban-driven-phenotypic-changes-empirical-observations-and-theoretical-implications-for-eco-evolutionary-feedback
#11
REVIEW
Marina Alberti, John Marzluff, Victoria M Hunt
Emerging evidence that cities drive micro-evolution raises the question of whether rapid urbanization of Earth might impact ecosystems by causing systemic changes in functional traits that regulate urban ecosystems' productivity and stability. Intraspecific trait variation-variation in organisms' morphological, physiological or behavioural characteristics stemming from genetic variability and phenotypic plasticity-has significant implications for ecological functions such as nutrient cycling and primary productivity...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920373/human-influences-on-evolution-and-the-ecological-and-societal-consequences
#12
Andrew P Hendry, Kiyoko M Gotanda, Erik I Svensson
Humans have dramatic, diverse and far-reaching influences on the evolution of other organisms. Numerous examples of this human-induced contemporary evolution have been reported in a number of 'contexts', including hunting, harvesting, fishing, agriculture, medicine, climate change, pollution, eutrophication, urbanization, habitat fragmentation, biological invasions and emerging/disappearing diseases. Although numerous papers, journal special issues and books have addressed each of these contexts individually, the time has come to consider them together and thereby seek important similarities and differences...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27918537/the-genome-and-transcriptome-of-japanese-flounder-provide-insights-into-flatfish-asymmetry
#13
Changwei Shao, Baolong Bao, Zhiyuan Xie, Xinye Chen, Bo Li, Xiaodong Jia, Qiulin Yao, Guillermo Ortí, Wenhui Li, Xihong Li, Kristin Hamre, Juan Xu, Lei Wang, Fangyuan Chen, Yongsheng Tian, Alex M Schreiber, Na Wang, Fen Wei, Jilin Zhang, Zhongdian Dong, Lei Gao, Junwei Gai, Takashi Sakamoto, Sudong Mo, Wenjun Chen, Qiong Shi, Hui Li, Yunji Xiu, Yangzhen Li, Wenteng Xu, Zhiyi Shi, Guojie Zhang, Deborah M Power, Qingyin Wang, Manfred Schartl, Songlin Chen
Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation. The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways...
December 5, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27918528/origin-of-modern-syphilis-and-emergence-of-a-pandemic-treponema-pallidum-cluster
#14
Natasha Arora, Verena J Schuenemann, Günter Jäger, Alexander Peltzer, Alexander Seitz, Alexander Herbig, Michal Strouhal, Linda Grillová, Leonor Sánchez-Busó, Denise Kühnert, Kirsten I Bos, Leyla Rivero Davis, Lenka Mikalová, Sylvia Bruisten, Peter Komericki, Patrick French, Paul R Grant, María A Pando, Lucía Gallo Vaulet, Marcelo Rodríguez Fermepin, Antonio Martinez, Arturo Centurion Lara, Lorenzo Giacani, Steven J Norris, David Šmajs, Philipp P Bosshard, Fernando González-Candelas, Kay Nieselt, Johannes Krause, Homayoun C Bagheri
The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history(1). Surprisingly, despite the availability of effective antibiotic treatment since the mid-twentieth century, this bacterial infection, which is caused by Treponema pallidum subsp. pallidum (TPA), has been re-emerging globally in the last few decades with an estimated 10.6 million cases in 2008 (ref. 2). Although resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the second-line antibiotic azithromycin(3)...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27918435/piecemeal-buildup-of-the-genetic-code-ribosomes-and-genomes-from-primordial-trna-building-blocks
#15
Derek Caetano-Anollés, Gustavo Caetano-Anollés
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains...
December 2, 2016: Life
https://www.readbyqxmd.com/read/27917706/the-changes-of-positive-selection-within-env-gene-of-hiv-1-b-crf07_bc-and-crf08_bc-from-china-over-time
#16
Tingting Li, Binlian Sun, Yanyan Jiang, Haiyan Zeng, Yanpeng Li, Yan Wang, Rongge Yang
: It is not clear about the possible evolutionary changes of the three predominant strains of HIV-1 in China over the course of the epidemic. Envelope (env) gene of HIV-1 is a good target for this evolutionary pressure for its enriched epitopes. METHODS: We collected 159 full or part of env sequences sampled between 1997 and 2010 from database of China, we calculated the genetic distance, detected the positively selected sites by PAML suite and then compared the number using Fisher's exact test between the early period 1997 to 2003and the late period2004 to 2010...
December 5, 2016: Current HIV Research
https://www.readbyqxmd.com/read/27917480/evolutionary-processes-and-its-environmental-correlates-in-the-cranial-morphology-of-western-chipmunks-tamias
#17
Ana Paula A Assis, Daniela M Rossoni, James L Patton, Gabriel Marroig
The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members...
December 5, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27916633/characterization-of-the-tetraspan-junctional-complex-4jc-superfamily
#18
Amy Chou, Andre Lee, Kevin J Hendargo, Vamsee S Reddy, Maksim A Shlykov, Harikrishnan Kuppusamykrishnan, Arturo Medrano-Soto, Milton H Saier
Connexins or innexins form gap junctions, while claudins and occludins form tight junctions. In this study, statistical data, derived using novel software, indicate that these four junctional protein families and eleven other families of channel and channel auxiliary proteins are related by common descent and comprise the Tetraspan (4 TMS) Junctional Complex (4JC) Superfamily. These proteins all share similar 4 transmembrane α-helical (TMS) topologies. Evidence is presented that they arose via an intragenic duplication event, whereby a 2 TMS-encoding genetic element duplicated tandemly to give 4 TMS proteins...
December 1, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27916528/repeated-inactivation-of-the-first-committed-enzyme-underlies-the-loss-of-benzaldehyde-emission-after-the-selfing-transition-in-capsella
#19
Claudia Sas, Frank Müller, Christian Kappel, Tyler V Kent, Stephen I Wright, Monika Hilker, Michael Lenhard
The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]...
November 23, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27916524/gain-and-loss-of-floral-scent-production-through-changes-in-structural-genes-during-pollinator-mediated-speciation
#20
Avichai Amrad, Michel Moser, Therese Mandel, Michel de Vries, Robert C Schuurink, Loreta Freitas, Cris Kuhlemeier
The interactions of plants with their pollinators are thought to be a driving force in the evolution of angiosperms. Adaptation to a new pollinator involves coordinated changes in multiple floral traits controlled by multiple genes. Surprisingly, such complex genetic shifts have happened numerous times during evolution. Here we report on the genetic basis of the changes in one such trait, floral scent emission, in the genus Petunia (Solanaceae). The increase in the quantity and complexity of the volatiles during the shift from bee to hawkmoth pollination was due to de novo expression of the genes encoding benzoic acid/salicylic acid carboxyl methyltransferase (BSMT) and benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase (BPBT) together with moderately increased transcript levels for most enzymes of the phenylpropanoid/benzenoid pathway...
November 22, 2016: Current Biology: CB
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