154,111 results match your criteria Evolutionary Bioinformatics [Journal]


Bacteriome-associated Wolbachia of the parthenogenetic termite Cavitermes tuberosus.

FEMS Microbiol Ecol 2018 Dec 14. Epub 2018 Dec 14.

Evolutionary Biology & Ecology, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium.

Wolbachia has deeply shaped the ecology and evolution of many arthropods, and interactions between the two partners are a continuum ranging from parasitism to mutualism. Non-dispersing queens of the termite Cavitermes tuberosus are parthenogenetically produced through gamete duplication, a mode of ploidy restoration generally induced by Wolbachia. These queens display a bacteriome-like structure in the anterior part of the mesenteron. Read More

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December 2018

Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish.

J Proteomics 2018 Dec 11. Epub 2018 Dec 11.

Laboratory of Evolutionary and Adaptive Physiology - Institute of Life, Earth and Environment - University of Namur, 61 Rue de Bruxelles, B5000 Namur, Belgium.

Early-life represents a critically sensitive window to endocrine disrupting chemicals, potentially leading to long-term repercussions on the phenotype later in life. The mechanisms underlying this phenomenon, referred to as the Developmental Origins of Health and Disease (DOHaD), are still poorly understood. To gain molecular understanding of these effects, we exposed mangrove rivulus (Kryptolebias marmoratus) for 28 days post hatching (dph) to 4 and 120 ng/L 17-α-ethinylestradiol, a model xenoestrogen. Read More

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December 2018

Molecular systematics of the Triplophysa robusta (Cobitoidea) complex: extensive gene flow in a depauperate lineage.

Mol Phylogenet Evol 2018 Dec 11. Epub 2018 Dec 11.

Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China. Electronic address:

Gene flow between populations assumed to be isolated frequently leads to incorrect inferences of evolutionary history. Understanding gene flow and its causes has long been a key topic in evolutionary biology. In this study, we explored the evolutionary history of the Triplophysa robusta complex, using a combination of multilocus analyses and coalescent simulation. Read More

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December 2018

Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure.

Genomics 2018 Dec 11. Epub 2018 Dec 11.

College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China. Electronic address:

The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning methods to predict potential drug-target interactions has attracted widespread attention. This paper presents a novel drug-target interactions prediction method called LRF-DTIs. Read More

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December 2018

Strategies in scheduling marine protected area establishment in a network system.

Ecol Appl 2018 Dec 14. Epub 2018 Dec 14.

ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.

Instantaneous implementation of systematic conservation plans at regional scales is rare. More typically, planned actions are applied incrementally over periods of years or decades. During protracted implementation, the character of the connected ecological system will change as a function of external anthropogenic pressures, local metapopulation processes, and environmental fluctuations. Read More

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December 2018

Evolutionary analysis of the Chikungunya virus epidemic in Mexico reveals intra-host mutational hotspots in the E1 protein.

PLoS One 2018 14;13(12):e0209292. Epub 2018 Dec 14.

División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico.

The epidemic potential of Chikungunya virus (CHIKV) was recently made evident by its introduction and rapid expansion in the Caribbean and the Americas. We sought to gain a detailed understanding of the dynamics of the epidemic in Mexico, the country with the highest number of confirmed CHIKV cases in the Americas, and to characterise viral evolution at the population and intra-host level. Analysis of the spatiotemporal distribution of 2,739 diagnosed cases in Mexico from December 2014 to December 2015 showed a rapid nationwide expansion of the epidemic with focalisation in the South West of the country. Read More

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December 2018

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.

PLoS Comput Biol 2018 Dec 14;14(12):e1006258. Epub 2018 Dec 14.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. Read More

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December 2018
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Influence of pathway topology and functional class on the molecular evolution of human metabolic genes.

PLoS One 2018 14;13(12):e0208782. Epub 2018 Dec 14.

Institute of Systems Biology, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain.

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. Read More

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December 2018

Structural deciphering of the NG2/CSPG4 proteoglycan multifunctionality.

FASEB J 2018 Dec 14:fj201801670R. Epub 2018 Dec 14.

Centre for Molecular and Translational Oncology (COMT), University of Parma, Parma, Italy.

The chondroitin sulfate proteoglycan 4 ( CSPG4) gene encodes a transmembrane proteoglycan (PG) constituting the largest and most structurally complex macromolecule of the human surfaceome. Its transcript shows an extensive evolutionary conservation and, due to the elaborated intracellular processing of the translated protein, it generates an array of glycoforms with the potential to exert variant-specific functions. CSPG4-mediated molecular events are articulated through the interaction with more than 40 putative ligands and the concurrent involvement of the ectodomain and cytoplasmic tail. Read More

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December 2018

Identification of a germline-expression promoter for genome editing in Bombyx mori.

Insect Sci 2018 Dec 14. Epub 2018 Dec 14.

CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.

Identification of stage- and tissue-specific cis-regulatory elements will enable more precise genomic editing. In previous studies of the silkworm Bombyx mori, we identified and characterized several tissue and sex-specific cis-regulatory elements using transgenic technology, including a female- and fat body-specific promoter, vitellogenin; testis-specific promoters, Radial spoke head 1 (BmR1) and beta-tubulin 4 (Bmβ4). Here we reported a cis-regulatory element specific for a somatic and germ cell expressed promoter, nanos (Bmnos). Read More

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December 2018

Experimental trait mis-matches uncover specificity of evolutionary links between multiple signaling traits and their interactions in hummingbirds.

Evolution 2018 Dec 14. Epub 2018 Dec 14.

School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501.

Many animal signals co-occur, and these signals may co-evolve due to their interactive properties. Previous work has demonstrated ecological drivers of evolutionary relationships between signals and the environment, which leads to questions about why specific signal pairs evolved among species that possess multiple signals. We asked whether the coloration of different species was optimized for presentation with its natural behavioral display. Read More

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December 2018

Social cues affect quantitative genetic variation and covariation in animal personality traits.

Evolution 2018 Dec 14. Epub 2018 Dec 14.

Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley.

The social environment is expected to have substantial effects on behavior, and as a consequence its heritability and evolvability. We investigated these effects by exposing Australian field crickets (Teleogryllus oceanicus) to either silence or recordings of male acoustic sexual signals. We used a combined pedigree and full-sib/half-sib breeding design to estimate the repeatability, heritability, and evolvability of behaviors related to boldness, exploration, and activity. Read More

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December 2018

The omnivorous predator Macrolophus pygmaeus, a good candidate for the control of both greenhouse whitefly and poinsettia thrips on gerbera plants.

Insect Sci 2018 Dec 13. Epub 2018 Dec 13.

Wageningen University & Research, BU Greenhouse Horticulture, PO Box 20, 2265, ZG, Bleiswijk, The Netherlands.

The poinsettia thrips Echinothrips americanus Morgan is a relatively new pest that has spread rapidly worldwide and causes serious damage in both vegetable and ornamental plants. In this study, we investigated if and how effective this pest can be controlled in gerbera by the omnivorous predator Macrolophus pygmaeus (Rambur). Because herbivores on plants can interact through a shared predator, we also investigated how poinsettia thrips control is affected by the presence of the greenhouse whitefly Trialeurodes vaporariorum (Westwood), a pest that commonly co-exists with E. Read More

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December 2018

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation.

Anim Genet 2018 Dec 13. Epub 2018 Dec 13.

GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France.

After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNPs (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Read More

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December 2018

Evaluation of artificial heating sources for the thermoregulation of Aldabra giant tortoises (Aldabrachelys gigantea) in Zurich zoo.

Zoo Biol 2018 Nov 22;37(6):458-465. Epub 2018 Nov 22.

Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland.

We recorded the thermoregulatory patterns of five Aldabra giant tortoises (Aldabrachelys gigantea) (25-193 kg) during spring (ZRH spring trial), after the installation of a heating area (concrete heat pad and basking lamp) at Zurich Zoo, Switzerland. The measurements were compared to published results on the same tortoises observed prior to the installation of the heater (ZRH summer and winter trials), and on wild tortoises on Aldabra Atoll. The mean environmental temperature outside the heating area was 23. Read More

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November 2018

LC/MS detection of oligogalacturonic acids obtained from tragacanth degradation by pectinase producing bacteria.

J Basic Microbiol 2018 Dec 13. Epub 2018 Dec 13.

School of Chemical and Biological Engineering, Seoul National University, Gwanak-gu, Seoul, Republic of Korea.

Tragacanth, a highly branched carbohydrate polymer isolated from Astragalus, is one of the most commonly used gums in food industry. The primary structure of tragacanth is composed of galacturonic acid monomers connected with α 1-4 links, and it is very similar to the pectin. Tragacanth degradation by microorganisms is significant in two aspects: first, food preservation and microbial growth control due to too much use of tragacanth in the food industry, second, therapeutic and pharmaceutical potential of obtained oligosaccharides. Read More

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December 2018

ADAPTATIONS OF THE MARSUPIAL NEWBORN: BIRTH AS AN EXTREME ENVIRONMENT.

Anat Rec (Hoboken) 2018 Dec 12. Epub 2018 Dec 12.

Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, 10065.

At birth a mammalian neonate enters an extreme environment compared to the intrauterine environment in which it has grown. This transition may be particularly extreme in marsupials because they are born at an exceedingly altricial state, after an exceptionally short gestation. Their stage of development must be considered embryonic by almost any criteria. Read More

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December 2018

Scavenger birds exploiting rubbish dumps: Pathogens at the gates.

Transbound Emerg Dis 2018 Dec 13. Epub 2018 Dec 13.

Grupo de Investigaciones en Biología de la Conservación, Laboratorio Ecotono, INIBIOMA (Universidad Nacional Del Comahue - CONICET), Quintral 1250 (R8400FRF), San Carlos de Bariloche, Argentina.

Different bacteria are present in rubbish dumps used as food resources by various bird species. Birds may be good indicators of the presence of zoonotic diseases in these sites since they can be infected with zoonotic pathogens by foraging on organic waste, and can also act as carriers. We studied if foraging in rubbish dumps increases the occurrence of Salmonella spp. Read More

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December 2018

DENTAL SIGNATURES FOR EXUDATIVORY IN LIVING PRIMATES, WITH COMPARISONS TO OTHER GOUGING MAMMALS.

Anat Rec (Hoboken) 2018 Dec 12. Epub 2018 Dec 12.

Dept. of Anthropology, University of Toronto Scarborough, Toronto, CANADA.

Exudativory, the consumption of gums, is an obligate or a facultative dietary niche for some primates and marsupials. Exudativory has been cited as a dietary niche that may have been present in early primates, so finding a dental signature for exudativory is highly desirable. The present study combines exudativorous lorisoids (galagos and lorises) into one sample to compare to closely related, non-exudativorous lorisoids to search for a consistent dental signature of exudativory. Read More

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December 2018

Masticatory Apparatus Performance and Functional Morphology in the Extremely Large Mice from Gough Island.

Anat Rec (Hoboken) 2018 Dec 13. Epub 2018 Dec 13.

Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, 44272, USA.

Since their arrival approximately 200 years ago, the house mice (Mus musculus) on Gough Island (GI) rapidly increased in size to become the largest wild house mice on record. Along with this extreme increase in body size, GI mice adopted a predatory diet, consuming significant quantities of seabird chicks and eggs. We studied this natural experiment to determine how evolution of extreme size and a novel diet impacted masticatory apparatus performance and functional morphology in these mice. Read More

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December 2018

Meta synthetic biology: controlling the evolution of engineered living systems.

Microb Biotechnol 2018 Dec 12. Epub 2018 Dec 12.

Microbial Evolution and Synthetic Biology Group, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 , Kgs. Lyngby, Denmark.

A major aim of synthetic biology is the design of robust living systems for real-world applications. In seemingly contrast, evolution changes the living, exploring new survival strategies in response to environmental challenges. How do we cope with this paradox? Can we control or even exploit the molecular mechanisms of evolution for biotechnological and biosustainable innovation and will the principles of engineering lead to fundamental insights in evolutionary biology? A merger of synthetic biology with experimental evolution is occurring and it will radically accelerate the development of these scientific disciplines. Read More

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December 2018

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees.

Ecol Lett 2018 Dec 12. Epub 2018 Dec 12.

ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong National Station for Forest Ecosystem Research, East China Normal University, 200241, Shanghai.

Climate is widely recognised as an important determinant of the latitudinal diversity gradient. However, most existing studies make no distinction between direct and indirect effects of climate, which substantially hinders our understanding of how climate constrains biodiversity globally. Using data from 35 large forest plots, we test hypothesised relationships amongst climate, topography, forest structural attributes (stem abundance, tree size variation and stand basal area) and tree species richness to better understand drivers of latitudinal tree diversity patterns. Read More

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December 2018

Modelling inducible defences in predator-prey interactions: assumptions and dynamical consequences of three distinct approaches.

Ecol Lett 2018 Dec 12. Epub 2018 Dec 12.

Department of Ecology and Ecosystem Modelling, Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, Potsdam, 14469, Germany.

Inducible defences against predation are widespread in the natural world, allowing prey to economise on the costs of defence when predation risk varies over time or is spatially structured. Through interspecific interactions, inducible defences have major impacts on ecological dynamics, particularly predator-prey stability and phase lag. Researchers have developed multiple distinct approaches, each reflecting assumptions appropriate for particular ecological communities. Read More

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December 2018

Metabolic Rhythms: a framework for coordinating cellular function.

Authors:
Helen C Causton

Eur J Neurosci 2018 Dec 13. Epub 2018 Dec 13.

Dept. of Pathology and Cell Biology, Columbia University Medical Center, New York, NY10032, USA.

Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Read More

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December 2018

Genetic, plastic and environmental contributions to the impact of a range-expanding predator on aquatic ecosystems.

J Anim Ecol 2018 Dec 13. Epub 2018 Dec 13.

CNRS, Université Toulouse III Paul Sabatier, Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, F-09200, Moulis, France.

1.Global change is altering biodiversity locally and globally and subsequently affecting the dynamics of communities and ecosystems. Biodiversity can be impacted both at the interspecific (i. Read More

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December 2018

Radial Glia in Echinoderms.

Dev Neurobiol 2018 Dec 12. Epub 2018 Dec 12.

University of North Florida, Jacksonville, FL.

Radial glial cells are crucial in vertebrate neural development and regeneration. It has been recently proposed that this neurogenic cell type might be older than the chordate lineage itself and might have been present in the last common deuterostome ancestor. Here, we summarize the results of recent studies on radial glia in echinoderms, a highly regenerative phylum of marine invertebrates with shared ancestry to chordates. Read More

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December 2018

Special issue on species interactions, ecological networks and community dynamics: untangling the entangled bank using molecular techniques.

Mol Ecol 2018 Dec 12. Epub 2018 Dec 12.

Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.

In the last paragraph of the Origin of Species, Darwin (1859) marvels at the diversity of life forms, the complexity of links between them, and the forces creating this "tangled bank". In this text, we may see the origins of community ecology - today defined as 'the study of the interactions that determine the distribution and abundance of organisms' (Krebs, 2009). To capture and quantify the key elements of this concept of community structure, we may conveniently describe communities as ecological networks (Hagen et al. Read More

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December 2018

Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting.

Insect Mol Biol 2018 Dec 12. Epub 2018 Dec 12.

Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand.

Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso-activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and PTTH, and the spatially restricted protein Torso-like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. Read More

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December 2018

Plant Polyploidy and Evolution.

Authors:
Gai Huang

J Integr Plant Biol 2018 Dec 11. Epub 2018 Dec 11.

Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.

Polyploidy refers to two or more complete sets of chromosomes that are combined within a nucleus, and includes both autopolyploidy and allopolyploidy (Otto 2007). Polyploidy is a recurring theme in the evolutionary history of plants and it has been considered an important mechanism for speciation and also for adaptability to changing environments (Shimizu-Inatsugi et al. 2017). Read More

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December 2018

Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae.

Yeast 2018 Dec 11. Epub 2018 Dec 11.

Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.

One of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. Read More

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December 2018

Skeletons of the Eye: An Evolutionary and Developmental Perspective.

Anat Rec (Hoboken) 2018 Dec 8. Epub 2018 Dec 8.

Mount Saint Vincent University, Halifax, Nova Scotia, Canada.

The ocular skeleton, composed of the scleral cartilage and scleral ossicles, is present in many vertebrates. The morphology of the scleral cartilage and ossicles varies within different extant reptiles (including birds) and also varies dramatically from the morphology in extant teleosts. This incredible range of diverse morphologies is the result of millions of years of evolution. Read More

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December 2018
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Local Genomic Features Predict the Distinct and Overlapping Binding Patterns of the bHLH-Zip Family Oncoproteins MITF and MYC-MAX.

Pigment Cell Melanoma Res 2018 Dec 7. Epub 2018 Dec 7.

Department of Physics, University of Illinois at Urbana-Champaign, IL.

MITF and MYC are well-known oncoproteins and members of the basic helix-loop-helix leucine zipper (bHLH-Zip) family of transcription factors (TFs) recognizing hexamer E-box motifs. MITF and MYC not only share the core binding motif, but are also the two most highly expressed bHLH-Zip transcription factors in melanocytes, raising the possibility that they may compete for the same binding sites in select oncogenic targets. Mechanisms determining the distinct and potentially overlapping binding modes of these critical oncoproteins remain uncharacterized. Read More

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December 2018

Ice-binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer.

FEBS J 2018 Dec 10. Epub 2018 Dec 10.

Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.

Various microbes, including fungi and bacteria, that live in cold environments produce ice-binding proteins (IBPs) that protect them from freezing. Ascomycota and Basidiomycota are two major phyla of fungi, and Antarctomyces psychrotrophicus is currently designated as the sole ascomycete that produces IBP (AnpIBP). However, its complete amino acid sequence, ice-binding property, and evolutionary history have not yet been clarified. Read More

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December 2018

Gustatory Responsiveness to food-associated acids in the spider monkey (Ateles geoffroyi).

Primates 2000 Apr;41(2):213-221

Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.

The gustatory responsiveness of four adult spider monkeys to five food-associated acids was assessed in two-bottle preference tests of brief duration (3 min). The animals were given the choice between a 30 mM sucrose solution and defined concentrations of citric acid, ascorbic acid, malic acid, acetic acid, or tannic acid dissolved in a 30 mM sucrose solution. With this procedure,Ateles geoffroyi was found to significantly discriminate concentrations as low as 5 mM ascorbic acid, citric acid, and acetic acid, 10 mM malic acid, and 0. Read More

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Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest.

Methods Mol Biol 2019 ;1903:45-59

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.

Drug repurposing has garnered much interest as an effective method for drug development among biopharmaceutical companies. The availability of information on complete sequences of genomes and their associated biological data, genotype-phenotype-disease relationships, and properties of small molecules offers opportunities to explore the repurpose-able potential of existing pharmacopoeia. This method gains further importance, especially, in the context of development of drugs against infectious diseases, some of which pose serious complications due to emergence of drug-resistant pathogens. Read More

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January 2019

Inferring Gene Regulatory Networks from Multiple Datasets.

Methods Mol Biol 2019 ;1883:251-282

Department of Statistics and Systems Biology Centre, University of Warwick, Coventry, UK.

Gaussian process dynamical systems (GPDS) represent Bayesian nonparametric approaches to inference of nonlinear dynamical systems, and provide a principled framework for the learning of biological networks from multiple perturbed time series measurements of gene or protein expression. Such approaches are able to capture the full richness of complex ODE models, and can be scaled for inference in moderately large systems containing hundreds of genes. Related hierarchical approaches allow for inference from multiple datasets in which the underlying generative networks are assumed to have been rewired, either by context-dependent changes in network structure, evolutionary processes, or synthetic manipulation. Read More

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January 2019

Advanced applications of nanotechnology in veterinary medicine.

Environ Sci Pollut Res Int 2018 Dec 13. Epub 2018 Dec 13.

Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Giza, Egypt.

The invention of new techniques to manipulate materials at their nanoscale had an evolutionary effect on various medical sciences. At the time, there are thousands of nanomaterials which can be divided according to their shape, origin, or their application. The nanotechnology provided new solutions for old problems. Read More

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December 2018
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Freshwater neotropical oligochaetes as native test species for the toxicity evaluation of cadmium, mercury and their mixtures.

Ecotoxicology 2018 Dec 13. Epub 2018 Dec 13.

Department of Ecology and Evolutionary Biology, Federal University of São Carlos, Rodovia Washington Luís, km 235, São Carlos, SP, 13565-905, Brazil.

The toxicity of metals, whether isolated or in mixtures, involves changes in biochemical processes as well as in cell membranes, which may lead to deleterious short- and long-term effects on the affected organisms. Among metals, cadmium and mercury stand out due to their abundance in nature, frequent use for industrial activities and biological accumulation, with high levels of residence in trophic chains. Benthic communities are particularly prone to metal pollution since metals usually accumulate in sediments. Read More

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December 2018

Eucalypt leaf litter impairs growth and development of amphibian larvae, inhibits their antipredator responses and alters their physiology.

Conserv Physiol 2018 10;6(1):coy066. Epub 2018 Dec 10.

Ecology, Evolution and Development Group, Doñana Biological Station (CSIC), C/ Americo Vespucio 26, Sevilla, Spain.

Consequences of human actions like global warming, spread of exotic species or resource consumption are pushing species to extinction. Even species considered to be at low extinction risk often show signs of local declines. Here, we evaluate the impact of eucalypt plantations, the best-known exotic tree species worldwide and its interaction with temperature and predators on amphibian development, growth, antipredator responses and physiology. Read More

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December 2018

Urban tinkering.

Sustain Sci 2018 6;13(6):1549-1564. Epub 2018 Aug 6.

19University of the Witwatersrand, Johannesburg, South Africa.

Cities are currently experiencing serious, multifaceted impacts from global environmental change, especially climate change, and the degree to which they will need to cope with and adapt to such challenges will continue to increase. A complex systems approach inspired by evolutionary theory can inform strategies for policies and interventions to deal with growing urban vulnerabilities. Such an approach would guide the design of new (and redesign of existing) urban structures, while promoting innovative integration of grey, green and blue infrastructure in service of environmental and health objectives. Read More

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Framing natural assets for advancing sustainability research: translating different perspectives into actions.

Sustain Sci 2018 17;13(6):1519-1531. Epub 2018 Jul 17.

10Basque Centre for Climate Change, University of the Basque Country (UPV-EHU), Sede Building 1, 1st Floor, Scientific Campus, Leioa, 48940 Bilbao, Spain.

Sustainability is a key challenge for humanity in the context of complex and unprecedented global changes. Future Earth, an international research initiative aiming to advance global sustainability science, has recently launched knowledge-action networks (KANs) as mechanisms for delivering its research strategy. The research initiative is currently developing a KAN on "natural assets" to facilitate and enable action-oriented research and synthesis towards natural assets sustainability. Read More

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A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants.

Front Plant Sci 2018 28;9:1734. Epub 2018 Nov 28.

Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.

The impact of deleterious variation on both plant fitness and crop productivity is not completely understood and is a hot topic of debates. The deleterious mutations in plants have been solely predicted using sequence conservation methods rather than function-based classifiers due to lack of well-annotated mutational datasets in these organisms. Here, we developed a machine learning classifier based on a dataset of deleterious and neutral mutations in by extracting 18 informative features that discriminate deleterious mutations from neutral, including 9 novel features not used in previous studies. Read More

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November 2018
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Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in .

Front Plant Sci 2018 28;9:1590. Epub 2018 Nov 28.

Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.

Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Read More

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November 2018
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The Structural Effects of Modality on the Rise of Symbolic Language: A Rebuttal of Evolutionary Accounts and a Laboratory Demonstration.

Front Psychol 2018 28;9:2300. Epub 2018 Nov 28.

Laboratoire de Sciences Phonétiques, Département de Linguistique, Université de Montréal, Montreal, QC, Canada.

Why does symbolic communication in humans develop primarily in an oral medium, and how do theories of language origin explain this? Non-human primates, despite their ability to learn and use symbolic signs, do not develop symbols as in oral language. This partly owes to the lack of a direct cortico-motoneuron control of vocalizations in these species compared to humans. Yet such modality-related factors that can impinge on the rise of symbolic language are interpreted differently in two types of evolutionary storylines. Read More

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November 2018

The Female Heart: Sex Differences in the Dynamics of ECG in Response to Stress.

Front Physiol 2018 28;9:1616. Epub 2018 Nov 28.

Communications and Signal Processing, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom.

Sex differences in the study of the human physiological response to mental stress are often erroneously ignored. To this end, we set out to show that our understanding of the stress response is fundamentally altered once sex differences are taken into account. This is achieved by comparing the heart rate variability (HRV) signals acquired during mental maths tests from ten females and ten males of similar maths ability; all females were in the follicular phase of their menstrual cycle. Read More

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November 2018

Clinical Efficacy of a Novel Therapeutic Principle, Anakoinosis.

Front Pharmacol 2018 28;9:1357. Epub 2018 Nov 28.

Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany.

Classic tumor therapy, consisting of cytotoxic agents and/or targeted therapy, has not overcome therapeutic limitations like poor risk genetic parameters, genetic heterogeneity at different metastatic sites or the problem of undruggable targets. Here we summarize data and trials principally following a completely different treatment concept tackling systems biologic processes: the principle of communicative reprogramming of tumor tissues, i.e. Read More

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November 2018
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Heritability and genetic architecture of reproduction-related traits in a temperate oak species.

2019 Feb 7;15(1). Epub 2018 Dec 7.

UMR BIOGECO 1202-INRA, University of Bordeaux, 33615, Pessac, France.

Reproduction, one of the main components of plant fitness, is highly variable in response to environmental cues, but little is known about the genetic determinism underlying reproduction-related traits in forest tree species. There is therefore an urgent need to characterize the genetic architecture of those traits if we are to predict the evolutionary trajectories of forest populations facing rapidly changing environment and mitigate their impacts. Using a full-sib family of pedunculate oak (), we investigated the within population variability of seed production and mean seed mass during four consecutive years. Read More

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February 2019

Rethinking Causation in Cancer with Evolutionary Developmental Biology.

Authors:
Katherine E Liu

Biol Theory 2018 27;13(4):228-242. Epub 2018 Jul 27.

Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN USA.

Despite the productivity of basic cancer research, cancer continues to be a health burden to society because this research has not yielded corresponding clinical applications. Many proposed solutions to this dilemma have revolved around implementing organizational and policy changes related to cancer research. Here I argue for a different solution: a new conceptualization of causation in cancer. Read More

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Why We Do Not Evolve Software? Analysis of Evolutionary Algorithms.

Evol Bioinform Online 2018 1;14:1176934318815906. Epub 2018 Dec 1.

Department of Computer Engineering and Computer Science, J.B. Speed School of Engineering, University of Louisville, Louisville, KY, USA.

In this article, we review the state-of-the-art results in evolutionary computation and observe that we do not evolve nontrivial software from scratch and with no human intervention. A number of possible explanations are considered, but we conclude that computational complexity of the problem prevents it from being solved as currently attempted. A detailed analysis of necessary and available computational resources is provided to support our findings. Read More

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December 2018