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Biological evolution

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https://www.readbyqxmd.com/read/29356321/toward-a-mechanistic-explanation-of-phenotypic-evolution-the-need-for-a-theory-of-theory-integration
#1
Manfred D Laubichler, Sonja J Prohaska, Peter F Stadler
Reconciling different underlying ontologies and explanatory contexts has been one of the main challenges and impediments for theory integration in biology. Here, we analyze the challenge of developing an inclusive and integrative theory of phenotypic evolution as an example for the broader challenge of developing a theory of theory integration within the life sciences and suggest a number of necessary formal steps toward the resolution of often incompatible (hidden) assumptions. Theory integration in biology requires a better formal understanding of the structure of biological theories The strategy for integrating theories crucially depends on the relationships of the underlying ontologies...
January 22, 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/29355136/evolution-of-technology-for-molecular-genotyping-in-blood-group-systems
#2
REVIEW
Ajit Gorakshakar, Harita Gogri, Kanjaksha Ghosh
The molecular basis of the blood group antigens was identified first in the 1980s and 1990s. Since then the importance of molecular biology in transfusion medicine has been described extensively by several investigators. Molecular genotyping of blood group antigens is one of the important aspects and is successfully making its way into transfusion medicine. Low-, medium- and high-throughput techniques have been developed for this purpose. Depending on the requirement of the centre like screening for high- or low-prevalence antigens where antisera are not available, correct typing of multiple transfused patients, screening for antigen-negative donor units to reduce the rate of alloimmunization, etc...
September 2017: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/29354281/3d-printing-materials-and-their-use-in-medical-education-a-review-of-current-technology-and-trends-for-the-future
#3
Justine Garcia, ZhiLin Yang, Rosaire Mongrain, Richard L Leask, Kevin Lachapelle
3D printing is a new technology in constant evolution. It has rapidly expanded and is now being used in health education. Patient-specific models with anatomical fidelity created from imaging dataset have the potential to significantly improve the knowledge and skills of a new generation of surgeons. This review outlines five technical steps required to complete a printed model: They include (1) selecting the anatomical area of interest, (2) the creation of the 3D geometry, (3) the optimisation of the file for the printing and the appropriate selection of (4) the 3D printer and (5) materials...
January 2018: BMJ Simul Technol Enhanc Learn
https://www.readbyqxmd.com/read/29352153/biology-culture-co-evolution-in-finite-populations
#4
Bart de Boer, Bill Thompson
Language is the result of two concurrent evolutionary processes: biological and cultural inheritance. An influential evolutionary hypothesis known as the moving target problem implies inherent limitations on the interactions between our two inheritance streams that result from a difference in pace: the speed of cultural evolution is thought to rule out cognitive adaptation to culturally evolving aspects of language. We examine this hypothesis formally by casting it as as a problem of adaptation in time-varying environments...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351890/evolutionary-mechanisms-studied-through-protein-fitness-landscapes
#5
REVIEW
Aneth S Canale, Pamela A Cote-Hammarlof, Julia M Flynn, Daniel Na Bolon
Biology has, and continues to be, shaped by evolutionary mechanisms. Within the past decade, local fitness landscapes have become experimentally tractable and are providing new perspectives on evolutionary mechanisms. Powered by next-generation sequencing, the impacts of all individual amino acid substitutions on function have been quantified for dozens of proteins. These fitness maps have been utilized to investigate the biophysical underpinnings of existing protein function as well as the appearance and enhancement of new protein functions...
January 16, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29351590/characteristics-and-evolution-of-the-ecosystem-of-software-tools-supporting-research-in-molecular-biology
#6
Florencio Pazos, Monica Chagoyen
Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model...
January 16, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29351242/-vessels-in-the-storm-searching-for-prognostic-and-predictive-angiogenic-factors-in-colorectal-cancer
#7
REVIEW
Adriano Angelucci, Simona Delle Monache, Alessio Cortellini, Monica Di Padova, Ficorella Corrado
High expectations are placed upon anti-angiogenic compounds for metastatic colorectal cancer (mCRC), the first malignancy for which such type of treatment has been approved. Indeed, clinical trials have confirmed that targeting the formation of new vessels can improve in many cases clinical outcomes of mCRC patients. However, current anti-angiogenic drugs are far from obtaining the desirable or expected curative results. Many are the factors probably involved in such disappointing results, but particular attention is currently focused on the validation of biomarkers able to improve the direction of treatment protocols...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29349635/the-diving-reflex-and-asphyxia-working-across-species-in-physiological-ecology
#8
Joel B Hagen
Beginning in the mid-1930s the comparative physiologists Laurence Irving and Per Fredrik (Pete) Scholander pioneered the study of diving mammals, particularly harbor seals. Although resting on earlier work dating back to the late nineteenth century, their research was distinctive in several ways. In contrast to medically oriented physiology, the approaches of Irving and Scholander were strongly influenced by natural history, zoology, ecology, and evolutionary biology. Diving mammals, they argued, shared the cardiopulmonary physiology of terrestrial mammals, but evolution had modified these basic adaptive processes in extreme ways...
January 18, 2018: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/29349600/beneficial-mutations-from-evolution-experiments-increase-rates-of-growth-and-fermentation
#9
Aysha L Sezmis, Martino E Malerba, Dustin J Marshall, Michael J McDonald
A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at the cost of reduced yield (K). We show that for some of these mutants, high R coincides with higher rates of ethanol secretion, suggesting that higher growth rates are due to an increased preference to utilize glucose through the fermentation pathway, instead of respiration...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#10
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29348864/the-macro-evolutionary-events-in-esophageal-squamous-cell-carcinoma
#11
Bin Yang, Ting Yan, Heyang Cui, Enwei Xu, Yanchun Ma, Caixia Cheng, Ling Zhang, Pengzhou Kong, Fang Wang, Yu Qian, Jian Yang, Yaoping Li, Hongyi Li, Yanghui Bi, Xiaoling Hu, Juan Wang, Bin Song, Jie Yang, Wei Gao, Jing Liu, Binbin Zou, Ruyi Shi, Yanyan Zhang, Haiyan Liu, Yiqian Liu, Yuanfang Zhai, Lu Chang, Yi Wang, Yingchun Zhang, Zhiwu Jia, Xing Chen, Yanfeng Xi, Guodong Li, Jianfang Liang, Jiansheng Guo, Shiping Guo, Rongsheng Zhang, Xiaolong Cheng, Yongping Cui
Understanding the evolutionary processes operative in cancer genome may provide insights into clinical outcome and drug-resistance. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. Here, we integrated published genomic sequencing data to investigate underlying evolutionary characteristics in ESCC. We found most of ESCC genomes were polyploidy with high genomic instability. Whole genome doubling that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348641/refined-control-of-cell-stemness-allowed-animal-evolution-in-the-oxic-realm
#12
REVIEW
Emma U Hammarlund, Kristoffer von Stedingk, Sven Påhlman
Animal diversification on Earth has long been presumed to be associated with the increasing extent of oxic niches. Here, we challenge that view. We start with the fact that hypoxia (<1-3% O2) maintains cellular immaturity (stemness), whereas adult stem cells continuously-and paradoxically-regenerate animal tissue in oxygenated settings. Novel insights from tumour biology illuminate how cell stemness nevertheless can be achieved through the action of oxygen-sensing transcription factors in oxygenated, regenerating tissue...
January 18, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29347596/generalized-fractional-diffusion-equations-for-subdiffusion-in-arbitrarily-growing-domains
#13
C N Angstmann, B I Henry, A V McGann
The ubiquity of subdiffusive transport in physical and biological systems has led to intensive efforts to provide robust theoretical models for this phenomena. These models often involve fractional derivatives. The important physical extension of this work to processes occurring in growing materials has proven highly nontrivial. Here we derive evolution equations for modeling subdiffusive transport in a growing medium. The derivation is based on a continuous-time random walk. The concise formulation of these evolution equations requires the introduction of a new, comoving, fractional derivative...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347028/continuous-time-random-walk-model-for-anomalous-diffusion-in-expanding-media
#14
F Le Vot, E Abad, S B Yuste
Expanding media are typical in many different fields, e.g., in biology and cosmology. In general, a medium expansion (contraction) brings about dramatic changes in the behavior of diffusive transport properties such as the set of positional moments and the Green's function. Here, we focus on the characterization of such effects when the diffusion process is described by the continuous-time random-walk (CTRW) model. As is well known, when the medium is static this model yields anomalous diffusion for a proper choice of the probability density function (pdf) for the jump length and the waiting time, but the behavior may change drastically if a medium expansion is superimposed on the intrinsic random motion of the diffusing particle...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346651/bipartite-network-analysis-of-gene-sharings-in-the-microbial-world
#15
Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O McInerney, Philippe Lopez, Eric Bapteste
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#16
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341020/mri-in-the-study-of-animal-models-of-stroke
#17
Pedro Ramos-Cabrer, Daniel Padro
Stroke consists of the loss of cerebral functions resulting from the interruption of blood supply to a region of the brain, and represents the second cause of death and the leading cause of major disability in adults in Europe. Stroke is a very active field of research at preclinical and clinical levels, and Magnetic Resonance Imaging (MRI) is one of the most powerful tools that scientist and clinicians have for the study of the onset, evolution and consequences of this devastating disease, as well as for the monitoring of the success of available treatments, or for the development of novel therapeutic strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29339745/genomic-and-transcriptomic-analysis-of-the-asian-honeybee-apis-cerana-provides-novel-insights-into-honeybee-biology
#18
Qingyun Diao, Liangxian Sun, Huajun Zheng, Zhijiang Zeng, Shengyue Wang, Shufa Xu, Huoqing Zheng, Yanping Chen, Yuanyuan Shi, Yuezhu Wang, Fei Meng, Qingliang Sang, Lianfei Cao, Fang Liu, Yongqiang Zhu, Wenfeng Li, Zhiguo Li, Congjie Dai, Minjun Yang, Shenglu Chen, Runsheng Chen, Shaowu Zhang, Jay D Evans, Qiang Huang, Jie Liu, Fuliang Hu, Songkun Su, Jie Wu
The Asian honeybee Apis cerana is one of two bee species that have been commercially kept with immense economic value. Here we present the analysis of genomic sequence and transcriptomic exploration for A. cerana as well as the comparative genomic analysis of the Asian honeybee and the European honeybee A. mellifera. The genome and RNA-seq data yield new insights into the behavioral and physiological resistance to the parasitic mite Varroa the evolution of antimicrobial peptides, and the genetic basis for labor division in A...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339505/nonenzymatic-release-of-n7-methylguanine-channels-repair-of-abasic-sites-into-an-ap-endonuclease-independent-pathway-in-arabidopsis
#19
Casimiro Barbado, Dolores Córdoba-Cañero, Rafael R Ariza, Teresa Roldán-Arjona
Abasic (apurinic/apyrimidinic, AP) sites in DNA arise from spontaneous base loss or by enzymatic removal during base excision repair. It is commonly accepted that both classes of AP site have analogous biochemical properties and are equivalent substrates for AP endonucleases and AP lyases, although the relative roles of these two types of enzymes are not well understood. We provide here genetic and biochemical evidence that, in Arabidopsis, AP sites generated by spontaneous loss of N7-methylguanine (N7-meG) are exclusively repaired through an AP endonuclease-independent pathway initiated by FPG, a bifunctional DNA glycosylase with AP lyase activity...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339418/an-evolutionary-biochemical-connection-between-promoter-and-primer-dependent-polymerases-revealed-by-selective-evolution-of-ligands-by-exponential-enrichment-selex
#20
Katherine J Fenstermacher, Vasudevan Achuthan, Thomas D Schneider, Jeffrey J DeStefano
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified Selective Evolution of Ligands by Exponential Enrichment (SELEX) approach...
January 16, 2018: Journal of Bacteriology
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