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Parallel evolution

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https://www.readbyqxmd.com/read/28429828/genomic-clustering-of-adaptive-loci-during-parallel-evolution-of-an-australian-wildflower
#1
Federico Roda, Greg M Walter, Rick Nipper, Daniel Ortiz-Barrientos
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#2
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28419895/electrochemical-oxidation-of-iron-and-alkalinity-generation-for-efficient-sulfide-control-in-sewers
#3
Hui-Wen Lin, Caroline Kustermans, Eleni Vaiopoulou, Antonin Prévoteau, Korneel Rabaey, Zhiguo Yuan, Ilje Pikaar
The addition of iron salts is one of the most commonly used dosing strategies for sulfide control in sewers. However, iron salts decrease the sewage pH which not only reduces the effectiveness of sulfide precipitation but also enhances the release of residual sulfide to the sewer atmosphere. Equally important, concentrated iron salt solutions are corrosive and their frequent transport, handling, and on-site storage often come with Occupational Health and Safety (OH&S) concerns. Here, we experimentally demonstrated a novel sulfide control approach using electrochemical systems with parallel placed iron electrodes...
April 15, 2017: Water Research
https://www.readbyqxmd.com/read/28419565/evolution-of-silent-myocardial-ischaemia-prevalence-and-cardiovascular-disease-risk-factor-management-in-type-2-diabetes-over-a-10-year-period-an-observational-study
#4
A Sultan, F Perriard, V Macioce, D Mariano-Goulart, C Boegner, J-P Daures, A Avignon
AIMS: To assess the evolution of silent myocardial ischaemia prevalence and of cardiovascular disease risk factor management over 10 years in people with Type 2 diabetes. METHODS: This repeated cross-sectional study prospectively included 770 people with Type 2 diabetes who presented at our centre in the period 1999-2009. All had at least one additional cardiovascular disease risk factor, no history of coronary disease and were screened for silent myocardial ischaemia using myocardial perfusion imaging...
April 18, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
https://www.readbyqxmd.com/read/28417598/genetic-analysis-of-a-morphologically-heterogeneous-ovarian-endometrioid-carcinoma
#5
Felipe C Geyer, Fresia Pareja, Kathleen A Burke, Anne M Schultheis, Yaser R Hussein, Jiqing Ye, Maria R De Filippo, Caterina Marchio, Gabriel S Macedo, Salvatore Piscuoglio, Raymond S Lim, Eugene Toy, Rajmohan Murali, Achim A Jungbluth, Jorge S Reis-Filho, Robert A Soslow, Britta Weigelt
AIMS: Low-grade ovarian endometrioid carcinomas may be associated with high-grade components. Whether the latter are clonally-related to and originate from the low-grade endometrioid carcinoma remains unclear. Here we employed massively parallel sequencing to characterize the genomic landscape and clonal relatedness of an ovarian endometrioid carcinoma containing low- and high-grade components. METHODS AND RESULTS: DNA samples extracted from each tumor component (low-grade endometrioid, high-grade anaplastic, high-grade squamous) and matched normal tissue were subjected to targeted massively parallel sequencing using the 410 gene Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay...
April 18, 2017: Histopathology
https://www.readbyqxmd.com/read/28415220/multistage-modeling-of-protein-dynamics-with-monomeric-myc-oncoprotein-as-an-example
#6
Jiaojiao Liu, Jin Dai, Jianfeng He, Antti J Niemi, Nevena Ilieva
We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#7
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28401753/self-assembly-of-complex-multi-metal-nanostructures-from-perforated-lamellar-block-copolymer-thin-films
#8
Seung Keun Cha, Gil Yong Lee, Jeong Ho Mun, Hyeong Min Jin, Chang Yun Moon, Jun Soo Kim, Kwang Ho Kim, Seong-Jun Jeong, Sang Ouk Kim
We introduce a facile and effective fabrication of complex multi-metallic nanostructures by means of block copolymer self-assembly. Two- and three-dimensional complex nanostructures, such as 'nanomesh', and 'double layered nanomeshes', and 'surface parallel cylinders on nanomesh', can be achieved by employing the self-assembly of perforated lamellar morphology in block copolymer thin films. Simultaneous integration of various metallic elements, including Pt, Au, and Co, into the self-assembled morphologies generates multi-metal complex nanostructures with highly interconnected morphology and large surface...
April 12, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28397488/towards-lateral-length-standards-at-the-nanoscale-based-on-diblock-copolymers
#9
Giulia Aprile, Federico Ferrarese Lupi, Matteo Fretto, Emanuele Enrico, Natascia De Leo, Luca Boarino, Flavio Giovanni Volpe, Gabriele Seguini, Katia Sparnacci, Valentina Gianotti, Michele Laus, Jørgen Garnaes, Michele Perego
The self-assembly (SA) of DiBlock Copolymers (DBCs) based on the phase separation into different morphologies of small size and high-density features is widely investigated as patterning and nanofabrication technique. The integration of the conventional top-down approaches with the bottom-up SA of DBCs discloses the possibility to address the gap in nano-structured lateral length standards for nano-metrology, consequently supporting the miniaturization processes in device fabrication. In this frame, we studied the pattern characteristic dimensions (i...
April 11, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28396681/evolution-of-nucleotide-punctuation-marks-from-structural-to-linear-signals
#10
Nawal El Houmami, Hervé Seligmann
We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28396411/mechanosensation-is-evolutionarily-tuned-to-locomotor-mechanics
#11
Brett R Aiello, Mark W Westneat, Melina E Hale
The biomechanics of animal limbs has evolved to meet the functional demands for movement associated with different behaviors and environments. Effective movement relies not only on limb mechanics but also on appropriate mechanosensory feedback. By comparing sensory ability and mechanics within a phylogenetic framework, we show that peripheral mechanosensation has evolved with limb biomechanics, evolutionarily tuning the neuromechanical system to its functional demands. We examined sensory physiology and mechanics of the pectoral fins, forelimb homologs, in the fish family Labridae...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28392623/yuhania-a-unique-angiosperm-from-the-middle-jurassic-of-inner-mongolia-china
#12
Zhong-Jian Liu, Xin Wang
Despite increasing claims of pre-Cretaceous angiosperms, whether there really are angiosperms in the Jurassic is apparently still an open question for many people before further evidence is available. This question can only be answered by studying more Jurassic plant fossils. Here we report a fossil angiosperm, Yuhania daohugouensis gen. et sp. nov, from the Middle Jurassic of Inner Mongolia, China. The plant includes connected stem, leaves, flowers, aggregate fruits, fruitlets, and seeds within fruitlets. The leaves are helically arranged along the curving stem, linear in shape, with 5-6 parallel veins...
May 19, 2017: Historical Biology
https://www.readbyqxmd.com/read/28389569/parallel-adaptive-evolution-of-geographically-distant-herring-populations-on-both-sides-of-the-north-atlantic-ocean
#13
Sangeet Lamichhaney, Angela P Fuentes-Pardo, Nima Rafati, Nils Ryman, Gregory R McCracken, Christina Bourne, Rabindra Singh, Daniel E Ruzzante, Leif Andersson
Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean...
April 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28379935/simulation-fellowship-programs-an-international-survey-of-program-directors
#14
Brenda Natal, Demian Szyld, Scott Pasichow, Zia Bismilla, Jonathan Pirie, Adam Cheng
PURPOSE: To report on the evolution of simulation-based training (SBT) by identifying the composition and infrastructure of existing simulation fellowship programs, describing the current training practices, disclosing existing program barriers, and highlighting opportunities for standardization. METHOD: Investigators conducted a cross-sectional survey study among English-speaking simulation fellowship program directors (September 2014-September 2015). They identified fellowships through academic/institutional Web sites, peer-reviewed literature, Web-based search engines, and snowball sampling...
April 4, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28378692/can-we-predict-disease-course-with-clinical-factors
#15
Zsuzsanna Vegh, Zsuzsanna Kurti, Petra Anna Golovics, Laszlo Lakatos
The disease phenotype at diagnosis and the disease course of Crohn's disease (CD) and ulcerative colitis (UC) show remarkable heterogeneity across patients. In recent population-based epidemiological and referral cohort studies, the evolution of disease phenotype of CD and UC varied significantly. Most CD and severe UC patients still requires hospitalization or surgery/colectomy during follow-up. A change in the natural history of IBD with improved outcomes in parallel with tailored positioning of aggressive immunomodulator and biological therapy has been suspected according to the recently available literature...
March 28, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28377604/mechanical-relaxation-to-rejuvenation-transition-in-a-zr-based-bulk-metallic-glass
#16
M Zhang, Y M Wang, F X Li, S Q Jiang, M Z Li, L Liu
The relaxation of amorphous materials, i.e., aging, would largely endanger their performances in service. Here we report a mechanical relaxation-to-rejuvenation transition of a Zr35Ti30Be27.5Cu7.5 bulk metallic glass (BMG) in elastostatic compression at ambient temperature, thus provide an accessible way to tailor the mechanical properties of amorphous materials. To unravel the structural evolution underlying the observed transition, atomistic simulations parallel with the experimental tests on a typical model glass system Zr60Cu40 were performed, which successfully reproduced and thus upheld the experimentally observed mechanical relaxation-to-rejuvenation transition...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28370611/diverse-genome-organization-following-13-independent-mesopolyploid-events-in-brassicaceae-contrasts-with-convergent-patterns-of-gene-retention
#17
Terezie Mandáková, Zheng Li, Michael S Barker, Martin A Lysak
Hybridization and polyploidy followed by genome-wide diploidization significantly impacted the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization impacted post-polyploid gene retention...
March 31, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28368455/tracking-a-cad-alk-gene-rearrangement-in-urine-and-blood-of-a-colorectal-cancer-patient-treated-with-an-alk-inhibitor
#18
G Siravegna, A Sartore-Bianchi, B Mussolin, A Cassingena, A Amatu, L Novara, M Buscarino, G Corti, G Crisafulli, A Bartolini, F Tosi, M Erlander, F Di Nicolantonio, S Siena, A Bardelli
Background: Monitoring response and resistance to kinase inhibitors is essential to precision cancer medicine, and is usually investigated by molecular profiling of a tissue biopsy obtained at progression. However, tumor heterogeneity and tissue sampling bias limit the effectiveness of this strategy. In addition, tissue biopsies are not always feasible and are associated with risks due to the invasiveness of the procedure. To overcome these limitations, blood-based liquid biopsy analysis has proven effective to non-invasively follow tumor's clonal evolution...
March 24, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28357814/before-hierarchy-the-rise-and-fall-of-stephen-jay-gould-s-first-macroevolutionary-synthesis
#19
Max W Dresow
Few of Stephen Jay Gould's accomplishments in evolutionary biology have received more attention than his hierarchical theory of evolution, which postulates a causal discontinuity between micro- and macroevolutionary events. But Gould's hierarchical theory was his second attempt to supply a theoretical framework for macroevolutionary studies-and one he did not inaugurate until the mid-1970s. In this paper, I examine Gould's first attempt: a proposed fusion of theoretical morphology, multivariate biometry and the experimental study of adaptation in fossils...
June 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/28348390/donor-cell-leukemia-evidence-for-multiple-pre-leukemic-clones-and-parallel-long-term-clonal-evolution-in-donor-and-recipient
#20
S Herold, M Kuhn, M V Bonin, T Stange, U Platzbecker, J Radke, T Lange, K Sockel, K Gutsche, J Schetelig, C Röllig, C Schuster, I Roeder, A Dahl, B Mohr, H Serve, C Brandts, G Ehninger, M Bornhäuser, C Thiede
Leukemia accepted article preview online, 28 March 2017. doi:10.1038/leu.2017.104.
March 28, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
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