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https://www.readbyqxmd.com/read/28231526/enhanced-identification-of-%C3%AE-lactamases-and-its-classes-using-sequence-physicochemical-and-evolutionary-information-with-sequence-feature-characterization-of-the-classes
#1
Abhigyan Nath, S Karthikeyan
β-lactamases provides one of the most successful means of evading the therapeutic effects of β lactam class of antibiotics by many gram positive and gram negative bacteria. On the basis of sequence identity, β-lactamases have been identified into four distinct classes- A, B, C and D. The classes A, C and D are the serine β-lactamases and class B is the metallo-lactamse. In the present study, we developed a two stage cascade classification system. The first-stage performs the classification of β-lactamases from non-β-lactamases and the second-stage performs the further classification of β-lactamases into four different β-lactamase classes...
February 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28231471/pathogenic-potential-and-virulence-genotypes-of-intestinal-and-faecal-isolates-of-porcine-post-weaning-enteropathogenic-escherichia-coli
#2
Anna Malik, Béla Nagy, Renáta Kugler, Ama Szmolka
Enteropathogenic Escherichia coli (EPEC) are frequent causes of diarrhoea in infants and in young mammals by inducing attaching effacing (AE) lesions of the intestinal epithelium. EPEC bacteria have also been implicated in cases of porcine post-weaning diarrhoea but their pathogenicity for conventional weaned pigs remains less elucidated. This present study investigates differences in pathogenic potential and virulence genotypes of intestinal and faecal isolates of EPEC from newly-weaned pigs. For this we inoculated ligated ileal loops of four weeks old weaned pigs to assess EPEC adherence to enterocytes by histology and immunohistology...
February 9, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28230247/digest-less-than-the-sum-of-its-parts-negative-epistasis-in-bacterial-swarming
#3
Sonia Singhal, Katrina van Raay
Understanding how mutations change phenotypes is vital to evolutionary biology. However, predicting evolutionary outcomes is complicated by the fact that a mutation's effect may depend on the individual's genetic background. Epistasis occurs when interactions among different genes or mutations result in phenotypes that differ from the sum of their parts. Uncovering epistasis usually involves genetic engineering of point mutations and then comparing the phenotypic effect of each mutation individually against its effect in combination with others (e...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28230246/functional-and-evolutionary-consequences-of-cranial-fenestration-in-birds
#4
Sander W S Gussekloo, Michael A Berthaume, Daniel R Pulaski, Irene Westbroek, Jan H Waarsing, Robin Heinen, Ian R Grosse, Elizabeth R Dumont
Ostrich-like birds (Palaeognathae) show very little taxonomic diversity while their sister taxon (Neognathae) contains roughly 10000 species. The main anatomical differences between the two taxa are in the crania. Palaeognaths lack an element in the bill called the lateral bar that is present in both ancestral theropods and modern neognaths, have thin zones in the bones of the bill, and robust bony elements on the ventral surface of their crania. Here we use a combination of modelling and developmental experiments to investigate the processes that might have led to these differences...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28230239/common-evolutionary-trends-underlie-the-four-bar-linkage-systems-of-sunfish-and-mantis-shrimp
#5
Yinan Hu, Nathan Nelson-Maney, Philip S L Anderson
Comparative biomechanics offers an opportunity to explore the evolution of disparate biological systems that share common underlying mechanics. Four-bar linkage modelling has been applied to various biological systems such as fish jaws and crustacean appendages to explore the relationship between biomechanics and evolutionary diversification. Mechanical sensitivity states that the functional output of a mechanical system will show differential sensitivity to changes in specific morphological components. We document similar patterns of mechanical sensitivity in two disparate four-bar systems from different phyla: the opercular four-bar system in centrarchid fishes and the raptorial appendage of stomatopods...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28230235/seeing-overweight-adults-as-babies-physical-cues-and-implications-for-stigmatization
#6
Anton J M Dijker, Rutger DeLuster, Nicolas Peeters, Nanne K de Vries
Human babies not only are reliable triggers of tender feelings and protective tendencies, they also happen to be exceptionally fat compared to the newborns of most other species. These two facts are used to formulate a hypothesis predicting that overweight males, due to their great physical resemblance to babies, not only are perceived as cute, but also are associated with negatively evaluated traits (e.g., immaturity, lack of willpower) that are saliently inconsistent with traits required for adults. In this study, a great many physical features of adult males varying widely in weight were measured and correlated with subjective judgements...
February 23, 2017: British Journal of Psychology
https://www.readbyqxmd.com/read/28230170/modeling-continuous-admixture-using-admixture-induced-linkage-disequilibrium
#7
Ying Zhou, Hongxiang Qiu, Shuhua Xu
Recent migrations and inter-ethnic mating of long isolated populations have resulted in genetically admixed populations. To understand the complex population admixture process, which is critical to both evolutionary and medical studies, here we used admixture induced linkage disequilibrium (LD) to infer continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general scenario with isolation after a certain duration of continuous gene flow...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230052/unraveling-the-processes-shaping-mammalian-gut-microbiomes-over-evolutionary-time
#8
Mathieu Groussin, Florent Mazel, Jon G Sanders, Chris S Smillie, Sébastien Lavergne, Wilfried Thuiller, Eric J Alm
Whether mammal-microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28229335/knowledge
#9
Jürgen Jost
We investigate the basic principles of structural knowledge. Structural knowledge underlies cognition, and it organizes, selects and assigns meaning to information. It is the result of evolutionary, cultural and developmental processes. Because of its own constraints, it needs to discover and exploit regularities and thereby achieve a complexity reduction.
February 22, 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28229287/role-of-neurochemicals-in-the-interaction-between-the-microbiota-and-the-immune-and-the-nervous-system-of-the-host-organism
#10
Alexander V Oleskin, Boris A Shenderov, Vladimir S Rogovsky
This work is concerned with the role of evolutionary conserved substances, neurotransmitters, and neurohormones, within the complex framework of the microbial consortium-immune system-nervous system axis in the human or animal organism. Although the operation of each of these systems per se is relatively well understood, their combined effects on the host organism still await further research. Drawing on recent research on host-produced and microbial low-molecular-weight neurochemicals such as biogenic amines, amino acids, and short-chain fatty acids (SCFAs), we suggest that these mediators form a part of a universal neurochemical "language...
February 22, 2017: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/28229106/neonatal-corticosterone-administration-in-rodents-as-a-tool-to-investigate-the-maternal-programming-of-emotional-and-immune-domains
#11
Simone Macrì
Neonatal experiences exert persistent influences on individual development. These influences encompass numerous domains including emotion, cognition, reactivity to external stressors and immunity. The comprehensive nature of the neonatal programming of individual phenotype is reverberated in the large amount of experimental data collected by many authors in several scientific fields: biomedicine, evolutionary and molecular biology. These data support the view that variations in precocious environmental conditions may calibrate the individual phenotype at many different levels...
February 2017: Neurobiology of Stress
https://www.readbyqxmd.com/read/28228750/evolutionary-roots-and-diversification-of-the-genus-aeromonas
#12
Ariadna Sanglas, Vicenta Albarral, Maribel Farfán, J G Lorén, M C Fusté
Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28228545/ablation-of-rnai-and-retrotransposons-accompany-acquisition-and-evolution-of-transposases-to-heterochromatin-protein-cenpb
#13
Udita Upadhyay, Suchita Srivastava, Indu Khatri, Jagpreet Singh Nanda, Srikrishna Subramanian, Amit Arora, Jagmohan Singh
Inactivation of retrotransposons is accompanied by the emergence of CENPB (centromere binding protein-B) in Schizosaccharomyces as well as in metazoans. The RNAi-induced Transcriptional Silencing (RITS) Complex, comprising Chp1 (chromodomain protein-1), Tas3 (protein with unknown function) and Ago1 (Argonaute), plays an important role in RNAi-mediated heterochromatinization. We find that while the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in S. cryophilus and S...
February 22, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28228542/accelerated-simulation-of-evolutionary-trajectories-in-origin-fixation-models
#14
Ashley I Teufel, Claus O Wilke
We present an accelerated algorithm to forward-simulate origin-fixation models. Our algorithm requires, on average, only about two fitness evaluations per fixed mutation, whereas traditional algorithms require, per one fixed mutation, a number of fitness evaluations of the order of the effective population size, Ne Our accelerated algorithm yields the exact same steady state as the original algorithm but produces a different order of fixed mutations. By comparing several relevant evolutionary metrics, such as the distribution of fixed selection coefficients and the probability of reversion, we find that the two algorithms behave equivalently in many respects...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228515/intrafamily-and-intragenomic-conflicts-in-human-warfare
#15
Alberto J C Micheletti, Graeme D Ruxton, Andy Gardner
Recent years have seen an explosion of multidisciplinary interest in ancient human warfare. Theory has emphasized a key role for kin-selected cooperation, modulated by sex-specific demography, in explaining intergroup violence. However, conflicts of interest remain a relatively underexplored factor in the evolutionary-ecological study of warfare, with little consideration given to which parties influence the decision to go to war and how their motivations may differ. We develop a mathematical model to investigate the interplay between sex-specific demography and human warfare, showing that: the ecology of warfare drives the evolution of sex-biased dispersal; sex-biased dispersal modulates intrafamily and intragenomic conflicts in relation to warfare; intragenomic conflict drives parent-of-origin-specific patterns of gene expression-i...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28228513/shape-matters-animal-colour-patterns-as-signals-of-individual-quality
#16
REVIEW
Lorenzo Pérez-Rodríguez, Roger Jovani, Martin Stevens
Colour patterns (e.g. irregular, spotted or barred forms) are widespread in the animal kingdom, yet their potential role as signals of quality has been mostly neglected. However, a review of the published literature reveals that pattern itself (irrespective of its size or colour intensity) is a promising signal of individual quality across species of many different taxa. We propose at least four main pathways whereby patterns may reliably reflect individual quality: (i) as conventional signals of status, (ii) as indices of developmental homeostasis, (iii) by amplifying cues of somatic integrity and (iv) by amplifying individual investment in maintenance activities...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28228512/what-do-territory-owners-defend-against
#17
REVIEW
Martin Hinsch, Jan Komdeur
Theoretical research on evolutionary aspects of territoriality has a long history. Existing studies, however, differ widely in modelling approach and research question. A generalized view on the evolution of territoriality is accordingly still missing. In this review, we show that territorial conflicts can be classified into qualitatively distinct types according to what mode of access to a territory which competitor attempts to gain. We argue that many of the inconsistencies between existing studies can be traced back to the fact that, while using the same terminology, different instances of these types of conflicts have been investigated...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28228511/the-opiliones-tree-of-life-shedding-light-on-harvestmen-relationships-through-transcriptomics
#18
Rosa Fernández, Prashant P Sharma, Ana Lúcia Tourinho, Gonzalo Giribet
Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#19
Alex Marchand-Austin, Raymond S W Tsang, Jennifer L Guthrie, Jennifer H Ma, Gillian Lim, Natasha S Crowcroft, Shelley L Deeks, David J Farrell, Frances B Jamieson
Bordetella pertussis (BP) is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of BP acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labour intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole genome sequencing data generated from 40 clinical BP isolates and analyzed using the SRST2 bioinformatic package...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228475/parallel-evolution-of-mound-building-and-grass-feeding-in-australian-nasute-termites
#20
Daej A Arab, Anna Namyatova, Theodore A Evans, Stephen L Cameron, David K Yeates, Simon Y W Ho, Nathan Lo
Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets...
February 2017: Biology Letters
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