scholarly journals Pervasive prophage recombination occurs during evolution of spore-forming Bacilli

2020 ◽  
Author(s):  
Anna Dragoš ◽  
Priyadarshini B. ◽  
Zahraa Hasan ◽  
Mikael Lenz-Strube ◽  
Paul J Kempen ◽  
...  
Keyword(s):  
Integration Site ◽  
Empirical Studies ◽  
Spontaneous Release ◽  
Selection Regime ◽  
Phage Evolution ◽  
Evolutionary Changes ◽  
Distinct Cluster ◽  
Low Copy Number ◽  
Phage Dna ◽  
Population Recombination

AbstractPhages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

scholarly journals Ongoing genetic evolution of H9N2 avian influenza viruses in Iranian industrial poultry farms

2020 ◽  
Author(s):  
Mohsen Bashashati ◽  
Zohreh Mojahedi ◽  
Ali Ameghi Roudsari ◽  
Morteza Taghizadeh ◽  
Aidin Molouki ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Vaccine Strain ◽  
Broiler Chickens ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Economic Losses ◽  
Receptor Binding Site ◽  
Evolutionary Changes ◽  
Distinct Cluster ◽  
Wide Scale

AbstractDespite the use of wide-scale vaccination programmes against the H9N2 virus, enzootic outbreaks of H9N2 avian influenza (AI) have often occurred and caused serious nationwide economic losses, particularly in broiler chickens. In this study, the haemagglutinin (HA) and neuraminidase (NA) genes of nine recent H9N2s and a common vaccine strain were fully sequenced and compared with other representative Iranian viruses. Phylogenetic analysis revealed that all Iranian viruses were grouped into the G1 sub-lineage with different clusters in which recent isolates (2014–2017) formed a distinct cluster compared to the vaccine group (1998–2004). All Iranian H9N2s exhibited low pathogenicity AI connecting peptide feature with an R/KSSR motif. Amino acid 226, located in the 220 loop of the receptor binding site, was leucine among the recent Iranian viruses, a characteristic of human influenza viruses. With an overall gradual increase in the genetic diversity of H9N2s, Bayesian skyline plots of Iranian HA and NA genes depicted a fluctuation and a relative stable situation, respectively. It is recommended to apply constant surveillance to assess any increase in viral human adaptation and evolutionary changes in circulating field H9N2s. Moreover, antigenic characterisation of the prevailing H9N2 viruses seems to be necessary for evaluating the possible antigenic drift from the vaccine strain.

scholarly journals Identifying drivers of parallel evolution: A regression model approach

2017 ◽  
Author(s):  
Susan F. Bailey ◽  
Qianyun Guo ◽  
Thomas Bataillon
Keyword(s):  
Evolutionary Biology ◽  
Empirical Studies ◽  
Parallel Evolution ◽  
Published Data ◽  
Genetic Changes ◽  
Selective Pressures ◽  
Evolutionary Changes ◽  
Gene Level ◽  
Peer Community ◽  
Mutation And Selection

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution, however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level. Using this framework we analyze published data from forty experimentally evolved Saccharomyces cerevisiae populations. We can partition the effects of a number of genomic variables into those affecting patterns of parallel evolution via effects on the rate of arising mutations, and those affecting the retention versus loss of the arising mutations (i.e. selection). Our results suggest that gene-to-gene heterogeneity in both mutation and selection, associated with gene length, recombination rate, and number of protein domains drive parallel evolution at both synonymous and nonsynonymous sites. While there are still a number of parallel changes that are not well described, we show that allowing for heterogeneous rates of mutation and selection can provide improved predictions of the prevalence and degree of parallel evolution.Data archival locationDryad, doi to be included later

scholarly journals Φm46.1, the Main Streptococcus pyogenes Element Carrying mef(A) and tet(O) Genes

2009 ◽  
Vol 54 (1) ◽  
pp. 221-229 ◽  
Author(s):  
Andrea Brenciani ◽  
Alessandro Bacciaglia ◽  
Carla Vignaroli ◽  
Armanda Pugnaloni ◽  
Pietro E. Varaldo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Streptococcus Pyogenes ◽  
Integration Site ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
23S Rrna ◽  
Amino Acid Sequence Similarity ◽  
Modular Organization ◽  
Electron Microscopic ◽  
Phage Dna

ABSTRACT Φm46.1, the recognized representative of the most common variant of mobile, prophage-associated genetic elements carrying resistance genes mef(A) (which confers efflux-mediated erythromycin resistance) and tet(O) (which confers tetracycline resistance) in Streptococcus pyogenes, was fully characterized. Sequencing of the Φm46.1 genome (55,172 bp) demonstrated a modular organization typical of tailed bacteriophages. Electron microscopic analysis of mitomycin-induced Φm46.1 revealed phage particles with the distinctive icosahedral head and tail morphology of the Siphoviridae family. The chromosome integration site was within a 23S rRNA uracil methyltransferase gene. BLASTP analysis revealed that the proteins of Φm46.1 had high levels of amino acid sequence similarity to the amino acid sequences of proteins from other prophages, especially Φ10394.4 of S. pyogenes and λSa04 of S. agalactiae. Phage DNA was present in the host cell both as a prophage and as free circular DNA. The lysogeny module appears to have been split due to the insertion of a segment containing tet(O) (from integrated conjugative element 2096-RD.2) and mef(A) (from a Tn1207.1-like transposon) into the unintegrated phage DNA. The phage attachment sequence lies in the region between tet(O) and mef(A) in the unintegrated form. Thus, whereas in this form tet(O) is ∼5.5 kb upstream of mef(A), in the integrated form, tet(O), which lies close to the right end of the prophage, is ∼46.3 kb downstream of mef(A), which lies close to the left end of the prophage.

scholarly journals Clownfishes evolution below and above the species level

2018 ◽  
Vol 285 (1873) ◽  
pp. 20171796 ◽  
Author(s):  
Jonathan Rolland ◽  
Daniele Silvestro ◽  
Glenn Litsios ◽  
Laurélène Faye ◽  
Nicolas Salamin
Keyword(s):  
Morphological Evolution ◽  
Empirical Studies ◽  
Evolutionary Process ◽  
Species Level ◽  
Receptor Protein ◽  
Effective Population ◽  
Selective Pressures ◽  
Rates Of Evolution ◽  
Evolutionary Changes ◽  
The Difference

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1 , a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.

scholarly journals Local differentiation in the defensive morphology of an invasive zooplankton species is not genetically based

2017 ◽  
Author(s):  
Giuseppe E. Fiorino ◽  
Andrew G. McAdam
Keyword(s):  
Local Adaptation ◽  
Empirical Studies ◽  
Common Garden ◽  
Bythotrephes Longimanus ◽  
Fish Predator ◽  
Spine Length ◽  
Lake Ecosystems ◽  
Phenotypic Differences ◽  
Evolutionary Changes ◽  
Distal Spine

AbstractEvolutionary changes in functional traits represent one possible reason why exotic species spread to become invasive, but empirical studies of the mechanisms driving phenotypic differentiation between populations of invasive species are rare. This study tested whether differences in distal spine length among populations of the invasive cladoceran, Bythotrephes longimanus, could be explained by local adaptation or phenotypic plasticity. We collected Bythotrephes from six lakes and found that distal spine lengths and natural selection on distal spine length differed among populations, but were unrelated to the gape-limitation of the dominant fish predator in the lake from which they were collected. A common garden experiment revealed significant genetic and maternal variation for distal spine length, but phenotypic differences among populations were not genetically based. Phenotypic differences among lakes in this ecologically important trait are, therefore, the result of plasticity and not local adaptation, despite spatially variable selection on this heritable trait. The ability of Bythotrephes to plastically adjust distal spine length may explain the success of this species at invading lake ecosystems with diverse biotic environments.

Replication of Bacteriophage 186 DNA

1972 ◽  
Vol 30 ◽  
pp. 194-195
Author(s):  
Dhruba K. Chattoraj ◽  
Ross B. Inman
Keyword(s):  
Electron Microscopy ◽  
Dna Replication ◽  
Frame Of Reference ◽  
Dna Molecules ◽  
E Coli ◽  
Phage Dna ◽  
Partial Denaturation

Electron microscopy of replicating intermediates has been quite useful in understanding the mechanism of DNA replication in DNA molecules of bacteriophage, mitochondria and plasmids. The use of partial denaturation mapping has made the tool more powerful by providing a frame of reference by which the position of the replicating forks in bacteriophage DNA can be determined on the circular replicating molecules. This provided an easy means to find the origin and direction of replication in λ and P2 phage DNA molecules. DNA of temperate E. coli phage 186 was found to have an unique denaturation map and encouraged us to look into its mode of replication.

An empirical review of gambling expansion and gambling-related harm

2018 ◽  
Vol 64 (5-6) ◽  
pp. 295-306 ◽  
Author(s):  
Debi A. LaPlante ◽  
Heather M. Gray ◽  
Pat M. Williams ◽  
Sarah E. Nelson
Keyword(s):  
Literature Review ◽  
Peer Review ◽  
Empirical Data ◽  
Empirical Studies ◽  
Expansion Method ◽  
Responsible Gambling ◽  
Review Literature ◽  
Evidence Based ◽  
Empirical Comparison ◽  
Related Harm

Abstract. Aims: To discuss and review the latest research related to gambling expansion. Method: We completed a literature review and empirical comparison of peer reviewed findings related to gambling expansion and subsequent gambling-related changes among the population. Results: Although gambling expansion is associated with changes in gambling and gambling-related problems, empirical studies suggest that these effects are mixed and the available literature is limited. For example, the peer review literature suggests that most post-expansion gambling outcomes (i. e., 22 of 34 possible expansion outcomes; 64.7 %) indicate no observable change or a decrease in gambling outcomes, and a minority (i. e., 12 of 34 possible expansion outcomes; 35.3 %) indicate an increase in gambling outcomes. Conclusions: Empirical data related to gambling expansion suggests that its effects are more complex than frequently considered; however, evidence-based intervention might help prepare jurisdictions to deal with potential consequences. Jurisdictions can develop and evaluate responsible gambling programs to try to mitigate the impacts of expanded gambling.

Investigating the Multimodal Nature of Human Communication

2009 ◽  
Vol 23 (2) ◽  
pp. 63-76 ◽  
Author(s):  
Silke Paulmann ◽  
Sarah Jessen ◽  
Sonja A. Kotz
Keyword(s):  
Visual Information ◽  
Empirical Studies ◽  
Physical Property ◽  
Event Related Potentials ◽  
Accurate Information ◽  
Human Communication ◽  
Channel Condition ◽  
Prosodic Cues ◽  
Early Processing ◽  
Related Potentials

The multimodal nature of human communication has been well established. Yet few empirical studies have systematically examined the widely held belief that this form of perception is facilitated in comparison to unimodal or bimodal perception. In the current experiment we first explored the processing of unimodally presented facial expressions. Furthermore, auditory (prosodic and/or lexical-semantic) information was presented together with the visual information to investigate the processing of bimodal (facial and prosodic cues) and multimodal (facial, lexic, and prosodic cues) human communication. Participants engaged in an identity identification task, while event-related potentials (ERPs) were being recorded to examine early processing mechanisms as reflected in the P200 and N300 component. While the former component has repeatedly been linked to physical property stimulus processing, the latter has been linked to more evaluative “meaning-related” processing. A direct relationship between P200 and N300 amplitude and the number of information channels present was found. The multimodal-channel condition elicited the smallest amplitude in the P200 and N300 components, followed by an increased amplitude in each component for the bimodal-channel condition. The largest amplitude was observed for the unimodal condition. These data suggest that multimodal information induces clear facilitation in comparison to unimodal or bimodal information. The advantage of multimodal perception as reflected in the P200 and N300 components may thus reflect one of the mechanisms allowing for fast and accurate information processing in human communication.

Handwriting Analysis and Personality Assessment

2000 ◽  
Vol 5 (1) ◽  
pp. 44-51 ◽  
Author(s):  
Peter Greasley
Keyword(s):  
Personality Traits ◽  
Personality Assessment ◽  
Personnel Selection ◽  
Empirical Studies ◽  
Handwriting Analysis ◽  
Recruitment Process ◽  
Academic Literature ◽  
Personnel Recruitment ◽  
The Subject ◽  
Better Than

It has been estimated that graphology is used by over 80% of European companies as part of their personnel recruitment process. And yet, after over three decades of research into the validity of graphology as a means of assessing personality, we are left with a legacy of equivocal results. For every experiment that has provided evidence to show that graphologists are able to identify personality traits from features of handwriting, there are just as many to show that, under rigorously controlled conditions, graphologists perform no better than chance expectations. In light of this confusion, this paper takes a different approach to the subject by focusing on the rationale and modus operandi of graphology. When we take a closer look at the academic literature, we note that there is no discussion of the actual rules by which graphologists make their assessments of personality from handwriting samples. Examination of these rules reveals a practice founded upon analogy, symbolism, and metaphor in the absence of empirical studies that have established the associations between particular features of handwriting and personality traits proposed by graphologists. These rules guide both popular graphology and that practiced by professional graphologists in personnel selection.

Parenting and Adolescents’ Sexual Development in Western Societies

2011 ◽  
Vol 16 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Hanneke de Graaf ◽  
Ine Vanwesenbeeck ◽  
Liesbeth Woertman ◽  
Wim Meeus
Keyword(s):  
Sexual Behavior ◽  
Parenting Styles ◽  
Sexual Development ◽  
Parental Support ◽  
Empirical Studies ◽  
Sexual Practices ◽  
Psychosexual Development ◽  
First Sexual Intercourse ◽  
Parenting Influences ◽  
Reciprocal Associations

This review examines associations between parenting styles and the psychosexual development of adolescents. Methods and results of empirical studies of associations between parental support, control, and knowledge and the sexual behavior and sexual health of adolescents are described and evaluated. The results show that, in general, higher scores on support, control, and knowledge relate to a delay of first sexual intercourse, safer sexual practices, and higher sexual competence. Despite the vast amount of literature on this subject, the majority of these studies focus on single dimensions of parenting and unidirectional parenting influences. This review generates hypotheses regarding interactions of different parenting styles and reciprocal associations between parents and their children. There is a need for more dynamic, dialectical studies of parenting, and children’s sexual development.

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