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https://www.readbyqxmd.com/read/28548230/molecular-basis-of-social-competence-in-medaka-fish
#1
REVIEW
Teruhiro Okuyama, Saori Yokoi, Hideaki Takeuchi
Oryzias latipes (Medaka) is an established vertebrate model for studying developmental genetics, genomics, and evolutionary biology. The physiology, embryology, and genetics of this species have been extensively investigated for centuries. Medaka fish recently attracted attention in the field of social neuroscience. This review introduces recent advances in medaka behavioral studies, focusing on female mating preferences and male mate-guarding behaviors. The medaka female has the ability to discriminate male individuals and prefers to mate with socially familiar males (female mating preference)...
May 26, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/28547179/telomere-length-measurement-by-qpcr-in-birds-is-affected-by-storage-method-of-blood-samples
#2
Sophie Reichert, Hannah Froy, Winnie Boner, Theresa M Burg, Francis Daunt, Robert Gillespie, Kate Griffiths, Sue Lewis, Richard A Phillips, Dan H Nussey, Pat Monaghan
Given the potential role of telomeres as biomarkers of individual health and ageing, there is an increasing interest in studying telomere dynamics in a wider range of taxa in the fields of ecology and evolutionary biology. Measuring telomere length across the lifespan in wild animal systems is essential for testing these hypotheses, and may be aided by archived blood samples collected as part of longitudinal field studies. However, sample collection, storage, and DNA extraction methods may influence telomere length measurement, and it may, therefore, be difficult to balance consistency in sampling protocol with making the most of available samples...
May 25, 2017: Oecologia
https://www.readbyqxmd.com/read/28545395/characterizing-the-roles-of-changing-population-size-and-selection-on-the-evolution-of-flux-control-in-metabolic-pathways
#3
Alena Orlenko, Peter B Chi, David A Liberles
BACKGROUND: Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance...
May 25, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28544874/the-relative-safety-of-paternal-maternal-and-traditional-foster-care-placements
#4
Jesse J Helton, Brian B Boutwell, Michael DiBernardo
When children are placed into foster care the caseworker must give preference to an adult relative, many of whom are grandparents, over an unrelated caregiver. This kinship preference is based in evolutionary biology, which suggests that the imperative to care for a child should be greater for kin versus non-kin. However, not all kin are related to a child in the same way, and level of paternity uncertainty may influence level of care provided. For instance, maternal grandparents can be assured that they share genetic material with their grandchild, while paternal grandparents may not have the same level of certainty...
May 22, 2017: Child Abuse & Neglect
https://www.readbyqxmd.com/read/28543226/interactions-within-and-between-clades-shaped-the-diversification-of-terrestrial-carnivores
#5
Mathias M Pires, Daniele Silvestro, Tiago B Quental
A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within-clade diversity dependence suppressing speciation rates and detected between-clade effects increasing extinction rates in six instances...
May 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28542786/digest-strengthening-the-link-between-sexual-selection-and-color-polymorphism
#6
Thomas E White
Heritable variation is the fuel for adaptive evolution, and the processes that generate and maintain it have been the focus of intense interest since the inception of modern evolutionary biology. The level at which variation is expressed determines, in large part, the processes that maintain it. Neutral and nearly-neutral molecular variation (e.g. silent nucleotide substitutions), for example, are seldom exposed to selection, and largely evolve via genetic drift (Kimura 1984). An enduring puzzle, however, is presented by extreme variation that is exposed to and persists in the face of selection...
May 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28542462/a-human-monocytic-nf-%C3%AE%C2%BAb-fluorescent-reporter-cell-line-for-detection-of-microbial-contaminants-in-biological-samples
#7
Claire Battin, Annika Hennig, Patrick Mayrhofer, Renate Kunert, Gerhard J Zlabinger, Peter Steinberger, Wolfgang Paster
Sensing of pathogens by innate immune cells is essential for the initiation of appropriate immune responses. Toll-like receptors (TLRs), which are highly sensitive for various structurally and evolutionary conserved molecules derived from microbes have a prominent role in this process. TLR engagement results in the activation of the transcription factor NF-κB, which induces the expression of cytokines and other inflammatory mediators. The exquisite sensitivity of TLR signalling can be exploited for the detection of bacteria and microbial contaminants in tissue cultures and in protein preparations...
2017: PloS One
https://www.readbyqxmd.com/read/28542163/two-extended-haplotype-blocks-are-associated-with-adaptation-to-high-altitude-habitats-in-east-african-honey-bees
#8
Andreas Wallberg, Caspar Schöning, Matthew T Webster, Martin Hasselmann
Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28541223/efficient-algorithms-for-genomic-duplication-models
#9
Jaroslaw Paszek, Pawel Gorecki
An important issue in evolutionary molecular biology is to discover genomic duplication episodes and their correspondence to the species tree. Existing approaches vary in the two fundamental aspects: the choice of evolutionary scenarios that model allowed locations of duplications in the species tree, and the rules of clustering gene duplications from gene trees into a single multiple duplication event. Here we study the method of clustering called minimum episodes for several models of allowed evolutionary scenarios with a focus on interval models in which every gene duplication has an interval consisting of allowed locations in the species tree...
May 23, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28541174/enhancing-a-person-enhancing-a-civilization-a-research-program-at-the-intersection-of-bioethics-future-studies-and-astrobiology
#10
Milan M Ćirković
There are manifold intriguing issues located within largely unexplored borderlands of bioethics, future studies (including global risk analysis), and astrobiology. Human enhancement has for quite some time been among the foci of bioethical debates, but the same cannot be said about its global, transgenerational, and even cosmological consequences. In recent years, discussions of posthuman and, in general terms, postbiological civilization(s) have slowly gained a measure of academic respect, in parallel with the renewed interest in the entire field of future studies and the great strides made in understanding of the origin and evolution of life and intelligence in their widest, cosmic context...
July 2017: Cambridge Quarterly of Healthcare Ethics: CQ: the International Journal of Healthcare Ethics Committees
https://www.readbyqxmd.com/read/28540680/computational-prediction-of-microrna-target-genes-target-prediction-databases-and-web-resources
#11
Justin T Roberts, Glen M Borchert
MicroRNA (miRNA) mediated silencing and repression of mRNA molecules requires complementary base pairing between the "seed" region of the miRNA and the "seed match" region of target mRNAs. While this mechanism is fairly well understood, accurate prediction of valid miRNA targets remains challenging due to factors such as imperfect sequence specificity, target site availability, and the thermodynamic stability of the mRNA structure itself. As knowledge of what genes are being targeted by each miRNA is arguably the most important facet of miRNA biology, many approaches have been developed to address the need for reliable prediction and ranking of putative targets, with most using a combination of various strategies such as evolutionary conservation, statistical inference, and distinct features of the target sequences themselves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540040/dna-secondary-structure-formation-by-dna-shuffling-of-the-conserved-domains-of-the-cry-protein-of-bacillus-thuringiensis
#12
Efrain H Pinzon, Daniel A Sierra, Miguel O Suarez, Sergio Orduz, Alvaro M Florez
BACKGROUND: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an in silico analysis using different experimental DNA shuffling scenarios...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28539126/knowledge-driven-binning-approach-for-rare-variant-association-analysis-application-to-neuroimaging-biomarkers-in-alzheimer-s-disease
#13
Dokyoon Kim, Anna O Basile, Lisa Bang, Emrin Horgusluoglu, Seunggeun Lee, Marylyn D Ritchie, Andrew J Saykin, Kwangsik Nho
BACKGROUND: Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer's disease (LOAD)...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28538166/an-evolutionary-perspective-on-plasmid-lifestyle-modes
#14
REVIEW
Nils Hülter, Judith Ilhan, Tanita Wein, A Samer Kadibalban, Katrin Hammerschmidt, Tal Dagan
Plasmids are extra-chromosomal genetic elements whose ecology and evolution depend on their genetic repertoire and interaction with the host. We review the events that lead to transitions between plasmid lifestyle modes - invasion, host range, plasmid persistence and adaptation - from a plasmid perspective. Plasmid lifestyle is determined by various traits, including mobility, stability and indispensability that vary in their magnitude. Transitions between the plasmid lifestyles, invasion, host range, plasmid persistence and adpatation, are caused by the interplay between plasmid traits and host biology...
May 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28536196/physicochemical-code-for-quinary-protein-interactions-in-escherichia-coli
#15
Xin Mu, Seongil Choi, Lisa Lang, David Mowray, Nikolay V Dokholyan, Jens Danielsson, Mikael Oliveberg
How proteins sense and navigate the cellular interior to find their functional partners remains poorly understood. An intriguing aspect of this search is that it relies on diffusive encounters with the crowded cellular background, made up of protein surfaces that are largely nonconserved. The question is then if/how this protein search is amenable to selection and biological control. To shed light on this issue, we examined the motions of three evolutionary divergent proteins in the Escherichia coli cytoplasm by in-cell NMR...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28535292/adaptive-radiation-of-p-fluorescens-sbw25-in-experimental-microcosms-provides-an-understanding-of-the-evolutionary-ecology-and-molecular-biology-of-a-l-interface-biofilm-formation
#16
Anna Koza, Anna Kusmierska, Kimberley McLaughlin, Olena Moshynets, Andrew J Spiers
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader. In these microcosms, the ecosystem engineering of the early wild-type colonists establish the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that de-regulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface...
May 23, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28534784/incorporation-of-solvent-effect-into-multi-objective-evolutionary-algorithm-for-improved-protein-structure-prediction
#17
Shangce Gao, Jiujun Cheng, Yuki Todo, Mengchu Zhou
The problem of predicting the three-dimensional structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534314/rapid-molecular-sexing-of-three-spined-sticklebacks-gasterosteus-aculeatus-l-based-on-large-y-chromosomal-insertions
#18
Theo C M Bakker, Thomas Giger, Joachim G Frommen, Carlo R Largiadèr
There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences...
May 22, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28533897/introduction-to-the-special-issue-tree-invasions-towards-a-better-understanding-of-their-complex-evolutionary-dynamics
#19
Heidi Hirsch, David M Richardson, Johannes J Le Roux
Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28533660/genes-emotions-and-gut-microbiota-the-next-frontier-for-the-gastroenterologist
#20
REVIEW
Arturo Panduro, Ingrid Rivera-Iñiguez, Maricruz Sepulveda-Villegas, Sonia Roman
Most medical specialties including the field of gastroenterology are mainly aimed at treating diseases rather than preventing them. Genomic medicine studies the health/disease process based on the interaction of the human genes with the environment. The gastrointestinal (GI) system is an ideal model to analyze the interaction between our genes, emotions and the gut microbiota. Based on the current knowledge, this mini-review aims to provide an integrated synopsis of this interaction to achieve a better understanding of the GI disorders related to bad eating habits and stress-related disease...
May 7, 2017: World Journal of Gastroenterology: WJG
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