scholarly journals Evidence of Extensive Homologous Recombination in the Core Genome ofRickettsia

2009 ◽  
Vol 2009 ◽  
pp. 1-5 ◽  
Author(s):  
Jinyu Wu ◽  
Tonghai Yu ◽  
Qiyu Bao ◽  
Fangqing Zhao
Keyword(s):  
Homologous Recombination ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Phylogenetic Network ◽  
Genomic Analysis ◽  
Intracellular Bacteria ◽  
The Core ◽  
Evolutionary Genomic ◽  
The Impact

The important role of homologous recombination has been extensively demonstrated to be fundamental for genetic variation in bacterial genomes. In contrast to extracellular or facultative intracellular bacteria, obligate intracellular bacteria are considered to be less prone to recombination, especially for their core genomes. InRickettsia, only antigen-related genes were identified to have experienced homologous recombination. In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome ofRickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently duringRickettsiaevolution. 28% ofRickettsiacore genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into the substantial role of recombination in the evolution of the intracellular pathogenic bacteriaRickettsia.

The impact of applying good governance standards in reducing corruption and achieving sustainable development in Yemen

2021 ◽  
Vol 26 ◽  
pp. 769-791
Keyword(s):  
Sustainable Development ◽  
Development Process ◽  
Good Governance ◽  
Arab Countries ◽  
Significant Decline ◽  
The Core ◽  
Efficiency And Effectiveness ◽  
Political Economic ◽  
The Impact

This paper aims to highlight the role of applying good governance standards in reducing corruption and achieving sustainable development in Yemen, since good governance represents the core of the development process of countries and societies. Good governance is based on the principle of transparency, accountability, efficiency and effectiveness in order to raise the capacity and efficiency of the state and make it more capable and effective to achieve sustainable development. Corruption in all its forms is one of the biggest obstacles to sustainable development in Yemen, and a major reason for wasting state resources and limiting foreign investment, and thus the expansion of poverty, the poor, and other effects related to the failure to achieve sustainable development. Yemen is one of the most Arab countries facing major challenges in the field of implementing good governance and combating corruption in order to achieve sustainable development and achieve its goals at all political, economic, social and environment. This paper concluded that Yemen suffers from a lack of implementation and enforcement of good governance standards, as well as a rampant corruption, which has led to an expansion of poverty and a significant decline in development rates. Key words: Good Governance, Corruption, Sustainable development.

scholarly journals Audio Mining: The Role of Vocal Tone in Persuasion

2021 ◽  
Author(s):  
Xin (Shane) Wang ◽  
Shijie Lu ◽  
X I Li ◽  
Mansur Khamitov ◽  
Neil Bendle
Keyword(s):  
Empirical Study ◽  
Large Scale ◽  
Controlled Experiments ◽  
The Core ◽  
Content Model ◽  
Stereotype Content ◽  
Key Indicators ◽  
The Impact ◽  
Insight Into

Abstract Persuasion success is often related to hard-to-measure characteristics, such as the way the persuader speaks. To examine how vocal tones impact persuasion in an online appeal, this research measures persuaders’ vocal tones in Kickstarter video pitches using novel audio mining technology. Connecting vocal tone dimensions with real-world funding outcomes offers insight into the impact of vocal tones on receivers’ actions. The core hypothesis of this paper is that a successful persuasion attempt is associated with vocal tones denoting (1) focus, (2) low stress, and (3) stable emotions. These three vocal tone dimensions—which are in line with the stereotype content model—matter because they allow receivers to make inferences about a persuader’s competence. The hypotheses are tested with a large-scale empirical study using Kickstarter data, which is then replicated in a different category. In addition, two controlled experiments provide evidence that perceptions of competence mediate the impact of the three vocal tones on persuasion attempt success. The results identify key indicators of persuasion attempt success and suggest a greater role for audio mining in academic consumer research.

scholarly journals Multiple origins of obligate nematode and insect symbionts by a clade of bacteria closely related to plant pathogens

2020 ◽  
Vol 117 (50) ◽  
pp. 31979-31986
Author(s):  
Vincent G. Martinson ◽  
Ryan M. R. Gawryluk ◽  
Brent E. Gowen ◽  
Caitlin I. Curtis ◽  
John Jaenike ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Pathogenic Bacteria ◽  
Plant Pathogens ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Intracellular Bacteria ◽  
Multiple Origins ◽  
Severe Reduction ◽  
Insect Symbionts ◽  
Erosion Characteristic

Obligate symbioses involving intracellular bacteria have transformed eukaryotic life, from providing aerobic respiration and photosynthesis to enabling colonization of previously inaccessible niches, such as feeding on xylem and phloem, and surviving in deep-sea hydrothermal vents. A major challenge in the study of obligate symbioses is to understand how they arise. Because the best studied obligate symbioses are ancient, it is especially challenging to identify early or intermediate stages. Here we report the discovery of a nascent obligate symbiosis in Howardula aoronymphium, a well-studied nematode parasite of Drosophila flies. We have found that H. aoronymphium and its sister species harbor a maternally inherited intracellular bacterial symbiont. We never find the symbiont in nematode-free flies, and virtually all nematodes in the field and the laboratory are infected. Treating nematodes with antibiotics causes a severe reduction in fly infection success. The association is recent, as more distantly related insect-parasitic tylenchid nematodes do not host these endosymbionts. We also report that the Howardula nematode symbiont is a member of a widespread monophyletic group of invertebrate host-associated microbes that has independently given rise to at least four obligate symbioses, one in nematodes and three in insects, and that is sister to Pectobacterium, a lineage of plant pathogenic bacteria. Comparative genomic analysis of this group, which we name Candidatus Symbiopectobacterium, shows signatures of genome erosion characteristic of early stages of symbiosis, with the Howardula symbiont’s genome containing over a thousand predicted pseudogenes, comprising a third of its genome.

PML isoform expression and DNA break location relative to PML nuclear bodies impacts the efficiency of homologous recombination

2020 ◽  
Vol 98 (3) ◽  
pp. 314-326 ◽  
Author(s):  
Kathleen M. Attwood ◽  
Jayme Salsman ◽  
Dudley Chung ◽  
Sabateeshan Mathavarajah ◽  
Carter Van Iderstine ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Gene Editing ◽  
Genotoxic Stress ◽  
Nuclear Bodies ◽  
Homology Directed Repair ◽  
Pml Nuclear Bodies ◽  
Promyelocytic Leukemia Nuclear Bodies ◽  
Chromosomal Break ◽  
The Impact

Promyelocytic leukemia nuclear bodies (PML NBs) are nuclear subdomains that respond to genotoxic stress by increasing in number via changes in chromatin structure. However, the role of the PML protein and PML NBs in specific mechanisms of DNA repair has not been fully characterized. Here, we have directly examined the role of PML in homologous recombination (HR) using I-SceI extrachromosomal and chromosome-based homology-directed repair (HDR) assays, and in HDR by CRISPR/Cas9-mediated gene editing. We determined that PML loss can inhibit HR in an extrachromosomal HDR assay but had less of an effect on CRISPR/Cas9-mediated chromosomal HDR. Overexpression of PML also inhibited both CRISPR HDR and I-SceI-induced HDR using a chromosomal reporter, and in an isoform-specific manner. However, the impact of PML overexpression on the chromosomal HDR reporter was dependent on the intranuclear chromosomal positioning of the reporter. Specifically, HDR at the TAP1 gene locus, which is associated with PML NBs, was reduced compared with a locus not associated with a PML NB; yet, HDR could be reduced at the non-PML NB-associated locus by PML overexpression. Thus, both loss and overexpression of PML isoforms can inhibit HDR, and proximity of a chromosomal break to a PML NB can impact HDR efficiency.

scholarly journals Role of infection in wound healing

2020 ◽  
Vol 19 (4) ◽  
pp. 598-602
Author(s):  
Malik Asif Hussain ◽  
Flavia Huygens
Keyword(s):  
Wound Healing ◽  
Pathogenic Bacteria ◽  
Chronic Wounds ◽  
Medical Science ◽  
Vascular Diseases ◽  
Research Papers ◽  
Patients With Diabetes ◽  
Research Findings ◽  
The Impact

Chronic wounds, particularly infected wounds are clinically very important due to their significant impact on health budgets as well as patients` health worldwide. Patients with diabetes mellitus, vascular diseases especially peripheral vascular disease and pressure ulcers are major categories of patients presenting with chronic wounds. It is known that there are multiple factors determining chronic wound prognosis. The presence of multiple types of pathogenic bacteria, with specific virulence and adherent (biofilm) properties, contribute a significant role to the development of chronic wounds. This review article is based on the research project entitled” An investigation of the impact of bacterial diversity, pathogenic determinants and biofilms on chronic wounds”. The research findings have been published in form of research papers as well as conference posters. The aim of this article is to highlight various important aspects of bacterial impact on wound healing. Bangladesh Journal of Medical Science Vol.19(4) 2020 p.598-602

scholarly journals What counts for quality in interdisciplinary accounting research in the next decade

2019 ◽  
Vol 32 (1) ◽  
pp. 2-25 ◽  
Author(s):  
James Guthrie ◽  
Lee D. Parker ◽  
John Dumay ◽  
Markus J. Milne
Keyword(s):  
Core Values ◽  
Research Quality ◽  
Journal Ranking ◽  
Content Type ◽  
Accounting Research ◽  
The Core ◽  
Citation Metrics ◽  
The Impact

Purpose The purpose of this paper is to reflect upon the focus and changing nature of measuring academic accounting research quality. The paper addresses contemporary changes in academic publishing, metrics for determining research quality and the possible impacts on accounting scholars. These are considered in relation to the core values of interdisciplinary accounting research ‒ that is, the pursuit of novel, rigorous, significant and authentic research motivated by a passion for scholarship, curiosity and solving wicked problems. The impact of changing journal rankings and research citation metrics on the traditional and highly valued role of the accounting academic is further considered. In this setting, the paper also provides a summary of the journal’s activities for 2018, and in the future. Design/methodology/approach Drawing on contemporary data sets, the paper illustrates the increasingly diverse and confusing array of “evidence” brought to bear on the question of the relative quality of accounting research. Commercial products used to rate and rank journals, and judge the academic impact of individual scholars and their papers not only offer insight and visibility, but also have the potential to misinform scholars and their assessors. Findings In the move from simple journal ranking lists to big data and citations, and increasingly to concerns with impact and engagement, the authors identify several challenges facing academics and administrators alike. The individual academic and his or her contribution to scholarship are increasingly marginalised in the name of discipline, faculty and institutional performance. A growing university performance management culture within, for example, the UK and Australasia, has reached a stage in the past decade where publication and citation metrics are driving allocations of travel grants, research grants, promotions and appointments. With an expanded range of available metrics and products to judge their worth, or have it judged for them, scholars need to be increasingly informed of the nuanced or not-so-nuanced uses to which these measurement systems will be put. Narrow, restricted and opaque peer-based sources such as journal ranking lists are now being challenged by more transparent citation-based sources. Practical implications The issues addressed in this commentary offer a critical understanding of contemporary metrics and measurement in determining the quality of interdisciplinary accounting research. Scholars are urged to reflect upon the challenges they face in a rapidly moving context. Individuals are increasingly under pressure to seek out preferred publication outlets, developing and curating a personal citation profile. Yet such extrinsic outcomes may come at the cost of the core values that motivate the interdisciplinary scholar and research. Originality/value This paper provides a forward-looking focus on the critical role of academics in interdisciplinary accounting research.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

scholarly journals OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 ◽  
Author(s):  
Param Priya Singh ◽  
Hervé Isambert
Keyword(s):  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Diseases ◽  
Genomic Analysis ◽  
Biased Sampling ◽  
Whole Genome ◽  
Genome Duplications ◽  
Evolutionary Genomic ◽  
The Impact

Abstract All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

PARLIAMENTARY REWARDS AND THE EVOLUTION OF THE PATENT SYSTEM

2015 ◽  
Vol 74 (3) ◽  
pp. 423-449 ◽  
Author(s):  
Robert Burrell ◽  
Catherine Kelly
Keyword(s):  
Reward System ◽  
Patent Law ◽  
The State ◽  
Patent System ◽  
Public Disclosure ◽  
Minimum Requirement ◽  
The Core ◽  
The Impact ◽  
Special Provision

AbstractThis article examines the impact on the patent system of rewards for innovation across the eighteenth and early nineteenth centuries. During this period, Parliament would regularly grant rewards to inventors, with many of these rewards being set out in legislation. This legislation provided Parliament with the opportunity to promote a model of state support for inventors: a model that made public disclosure of the invention a precondition for assistance. This had important implications for patent law, in particular, in helping to develop the role of the patent specification and the doctrine of sufficiency of disclosure. In this way, the reward system helped establish the framework under which the state would provide support for inventors. Simultaneously, however, the reward system created a space in which inventors would have to do more than meet the minimum requirement of public disclosure. Rewards allowed the state to distinguish between different classes of inventor and to make special provision for particularly worthy individuals. In this way, the reward system recognised the contribution of the “heroic inventor”, whilst leaving the core of the patent system undisturbed.

scholarly journals Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

mSystems ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Roshan Kumar ◽  
Helianthous Verma ◽  
Shazia Haider ◽  
Abhay Bajaj ◽  
Utkarsh Sood ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Core Genome ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Genomic Analysis ◽  
Specific Protein ◽  
Comparative Genomic ◽  
Ecological Groups ◽  
Functional And Phylogenetic Diversity

ABSTRACT This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium. Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

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