scholarly journals Pseudogenization, genome streamlining and specific gene repertoire landmark the genomes ofCarnobacterium maltaromaticumisolated from diseased sharks

2019 ◽  
Author(s):  
Laura Martinez Steele ◽  
Christopher G Lowe ◽  
Mark S Okihiro ◽  
Jesse G. Dillon ◽  
Renaud Berlemont
Keyword(s):  
Specific Gene ◽  
Shark Species ◽  
Gene Repertoire ◽  
Genomic Signatures ◽  
Thresher Shark ◽  
Independent Life ◽  
Conserved Gene ◽  
Genomic Regions ◽  
High Degree

AbstractCarnobacterium maltaromaticumis a well-known pathogen of bony fish. More recently,C. maltaromaticumhave been isolated from the brain and inner ear of disorientated and stranded common thresher (Alopias vulpinus) and salmon shark (Lamna ditropis). While thresher shark strandings are recent, salmon sharks have been stranding for decades, suggesting a long-term association betweenC. maltaromaticumand sharks. Interestingly, some strains ofC. maltaromaticumare used by the food industry for their probiotic and antimicrobial activity. Here, we sequenced the genome of 9C. maltaromaticumstrains (SK-isolates) from diseased common thresher and salmon sharks and compared them to otherC. maltaromaticumstrains in order to identify the genomic signatures that differentiate the disease-associated from the innocuousC. maltaromaticumisolates. SK strains formed a monophyletic clade, with a conserved gene repertoire, and shared a high degree of pseudogenization even though isolates were from different shark species, locations, and across years. In addition, these strains displayed few virulence associated genes and unique genomic regions, some resulting from horizontal gene transfer. The association of diseased sharks and SK strains suggests their role as potential pathogens. Although the high degree of pseudogenization suggests a transition to a host-adapted lifestyle, a set of conserved functional genes highlights the need of essential functions required for a host-independent life style. Globally, this work identifies specific genomic signatures ofC. maltaromaticumstrains isolated from infected sharks, provides the framework to elucidate the role of SK strains in the development of the disease in sharks, and further investigate the dissemination of SK strains in populations of wild fish.

scholarly journals Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

2018 ◽  
Author(s):  
Mathieu Seppey ◽  
Panagiotis Ioannidis ◽  
Brent C. Emerson ◽  
Camille Pitteloud ◽  
Marc Robinson-Rechavi ◽  
...  
Keyword(s):  
Gene Family ◽  
Strong Support ◽  
Chemical Defenses ◽  
Detoxification Enzymes ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Plant Interactions ◽  
Dietary Shift ◽  
Genomic Signatures ◽  
Plant Feeding

AbstractBackgroundThe diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed the largest beetle suborder, Polyphaga, mostly includes plant-eaters among its ~315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.ResultsTo address this, we explored the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representing the two most species-rich beetle suborders. We contrasted the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We found gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant-feeding, we identified families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There was especially strong support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.ConclusionsOur explicit modeling of the evolution of gene repertoires across 18 species identifies adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant-feeding in general, in driving beetle diversification.

scholarly journals Bidirectional selection for body weight on standing genetic variation in a chicken model

2018 ◽  
Author(s):  
Mette Lillie ◽  
Christa F. Honaker ◽  
Paul B. Siegel ◽  
Örjan Carlborg
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Model Organisms ◽  
Founder Population ◽  
Genomic Signatures ◽  
History Of ◽  
Signatures Of Selection ◽  
Genomic Regions ◽  
Bidirectional Selection

AbstractExperimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. Using pooled genome resequencing of paired generations of these lines, we reveal the within and between-line genomic signatures of selection. At 55 generations of divergent selection, 14.2% of the genome showed extreme differentiation between the selected lines were contained within 395 genomic regions. The lines often displayed a duality of the sweep signatures: an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consist of short, distinct haploblocks of variable between-line divergence. Formed during what probably was a complex history of bottlenecks, inbreeding, and introgressions, these mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

Hate Crime and Place: The Spatial and Temporal Concentration of Bias-Motivated Crime in Washington, D.C.

2021 ◽  
pp. 088626052098781
Author(s):  
Marin R. Wenger ◽  
Brendan Lantz
Keyword(s):  
Hate Crime ◽  
Hate Crimes ◽  
Temporal Perspective ◽  
Spatial Stability ◽  
Units Of Analysis ◽  
Crime Types ◽  
High Degree ◽  
Block Groups ◽  
Street Segments

Prior research suggests that many crime types are spatially concentrated and stable over time. Hate crime, however, is a unique crime type that is etiologically distinct from others. As such, examination of hate crime from a spatial and temporal perspective offers an opportunity to understand hate crime and the spatial concentration of crime more generally. The current study examines the spatial stability of hate crimes reported to the police in Washington, D.C., from 2012 through 2018 using street segments, intersections, and block groups as units of analysis. Findings reveal that hate crime is spatially concentrated, with less than 4% of street segments and intersections experiencing hate crime over the study period. Results reveal a high degree of spatial stability, both year-to-year and over the long term even when restricting the analysis to units that experienced at least one hate crime.

scholarly journals Influence of the Share of Renewable Energy Sources on the Level of Energy Security in EECCA Countries

Energies ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 903 ◽  
Author(s):  
Ivan Trifonov ◽  
Dmitry Trukhan ◽  
Yury Koshlich ◽  
Valeriy Prasolov ◽  
Beata Ślusarczyk
Keyword(s):  
Renewable Energy ◽  
Energy Security ◽  
Structural Characteristics ◽  
Renewable Energy Sources ◽  
Energy Resource ◽  
Energy Sources ◽  
Structural Content ◽  
High Degree

In this study we aimed to determine the extent to which changes in the share of renewable energy sources, their structural complex, and the level of energy security in Eastern Europe, Caucasus and Central Asia (EECCA) countries in the medium- and long-term are interconnected. The study was performed through modeling and determination of the structural characteristics of energy security in the countries. The methodology of the approach to modeling was based on solving the problem of nonlinear optimization by selecting a certain scenario. For the study, the data of EECCA countries were used. The ability of EECCA countries to benefit from long-term indirect and induced advantages of the transformation period depends on the extent to which their domestic supply chains facilitate the deployment of energy transformation and induced economic activity. This study provides an opportunity to assess the degree of influence of renewable energy sources on the level of energy security of countries in the context of energy resource diversification. The high degree of influence of renewable energy sources on energy security in the EECCA countries has been proven in the implementation of the developed scenarios for its increase. Energy security is growing. At the same time, its level depends not only on an increase in the share of renewable sources but also on the structure of energy resources complex of countries, and the development of various renewable energy sources. Therefore, today the EECCA countries are forced not only to increase the share of renewable energy sources but also to attach strategic importance to the structural content of their energy complex.

Development of a Performance-Related Framework for Asphalt Mixture Design for the Illinois Tollway

2021 ◽  
pp. 036119812110148
Author(s):  
Behnam Jahangiri ◽  
Punyaslok Rath ◽  
Hamed Majidifard ◽  
William G. Buttlar
Keyword(s):  
Asphalt Mixture ◽  
Field Performance ◽  
Compact Tension ◽  
T Test ◽  
Novel Approach ◽  
Final Adjustment ◽  
Development And Validation ◽  
High Degree ◽  
Selection Of

Various agencies have begun to research and introduce performance-related specifications (PRS) for the design of modern asphalt paving mixtures. The focus of most recent studies has been directed toward simplified cracking test development and evaluation. In some cases, development and validation of PRS has been performed, building on these new tests, often by comparison of test values to accelerated pavement test studies and/or to limited field data. This study describes the findings of a comprehensive research project conducted at Illinois Tollway, leading to a PRS for the design of mainline and shoulder asphalt mixtures. A novel approach was developed, involving the systematic establishment of specification requirements based on: 1) selection of baseline values based on minimally acceptable field performance thresholds; 2) elevation of thresholds to account for differences between short-term lab aging and expected long-term field aging; 3) further elevation of thresholds to account for variability in lab testing, plus variability in the testing of field cores; and 4) final adjustment and rounding of thresholds based on a consensus process. After a thorough evaluation of different candidate cracking tests in the course of the project, the Disk-shaped Compact Tension—DC(T)—test was chosen to be retained in the Illinois Tollway PRS and to be presented in this study for the design of crack-resistant mixtures. The DC(T) test was selected because of its high degree of correlation with field results and its excellent repeatability. Tailored Hamburg rut depth and stripping inflection point thresholds were also established for mainline and shoulder mixes.

China’s evolving humanitarian diplomacy: Evidence from China’s disaster-related aid to Nepal

2021 ◽  
pp. 205789112110192
Author(s):  
Peng Lin
Keyword(s):  
Humanitarian Assistance ◽  
Underdeveloped Countries ◽  
The Past ◽  
Belt And Road ◽  
High Degree ◽  
The Belt And Road ◽  
Post Disaster ◽  
Effective Channel ◽  
India And China

Engaging in disaster relief and, more recently, post-disaster reconstruction in developing countries with critical geoeconomic and geopolitical interests has become an increasingly regular and institutionalized component of China’s evolving humanitarian diplomacy over the past decade. Drawn upon novel evidence from China’s growing disaster-related humanitarian assistance to Nepal and unprecedented engagement in Nepal’s long-term post-earthquake rebuild since 2015, this article explores the dynamics behind China’s transforming humanitarian diplomacy. The findings of this article suggest that: 1) geopolitical and geoeconomic interests, represented by the Belt-and-Road Initiative, serve as a critical driver for the development of China’s bilateral partnership with other countries in the disaster sector; 2) long-term cooperation with underdeveloped countries like Nepal provides China, both government and non-state actors (NSAs), with an effective channel to engage with the international humanitarian community and to internalize humanitarian norms; 3) although humanitarian missions remain contingent and instrumental in China’s international relations, they are laying the foundations for a specialized humanitarian policy area with more relevant normative assets, more professional actors, and more sophisticated institutions; 4) NSAs, represented by private foundations and civil NGOs, have played active roles in the state-dominant cooperation in disaster management. This article also suggests that intensified geopolitical confrontations, such as military clashes between India and China along their disputed borders over the past year, would lead to a high degree of politicization of humanitarian missions and partnerships counter-conducive to humanitarian goals.

scholarly journals Microscale Heterogeneous Distribution and Speciation of Phosphorus in Soils Amended with Mineral Fertilizer and Cattle Manure Compost

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 121
Author(s):  
Noriko Yamaguchi ◽  
Toshiaki Ohkura ◽  
Atsuko Hikono ◽  
Yohey Hashimoto ◽  
Aomi Suda ◽  
...  
Keyword(s):  
Hot Spots ◽  
Mineral Fertilizer ◽  
Chemical Extraction ◽  
Heterogeneous Distribution ◽  
Edge Structure ◽  
Soil P ◽  
Macro Scale ◽  
Cattle Manure Compost ◽  
High Degree

Global concerns for the sustainability of agriculture have emphasized the need to reduce the use of mineral fertilizer. Although phosphorus (P) is accumulated in farmland soils due to the long-term application of fertilizer, most soil P is not readily available to plants. The chemical speciation of P in soils, which comprise heterogeneous microenvironments, cannot be evaluated with a high degree of specificity using only macroscopic analyses. In this study, we investigated the distribution and speciation of P accumulated in soils by using both macro- and microscopic techniques including chemical extraction, solution and solid-state 31P NMR, bulk- and micro- P K-edge X-ray absorption near edge structure (XANES), and electron probe microanalysis (EPMA). Soil samples were collected from a field in which cabbage was cultivated under three amendment treatments: i) mineral fertilizer (NPK), ii) mineral fertilizer and compost (NPK + compost), and iii) mineral fertilizer plus compost but without nitrogen fertilizer (PK + compost). Macro-scale analyses suggested that accumulated P was predominantly inorganic P and associated with Al-bearing minerals. The repeated application of compost to the soils increased the proportion of P associated with Ca which accounted for 17% in the NPK + compost plot and 40% in the PK + compost plot. At the microscale, hot spots of P were heterogeneously distributed, and P was associated with Fe and Ca in hot spots of the NPK + compost (pH 6) and PK + compost (pH 7) treated samples, respectively. Our results indicate that application of compost contributed to creating diverse microenvironments hosting P in these soils.

Main approaches to treatment of hypoxia in acute respiratory distress syndrome, bacterial and viral pneumonia (part III)

2021 ◽  
pp. 38-55
Author(s):  
A. V. Vlasenko ◽  
E. A. Evdokimov ◽  
E. P. Rodionov
Keyword(s):  
Respiratory Failure ◽  
Distress Syndrome ◽  
Experimental Studies ◽  
Viral Pneumonia ◽  
Medical Technologies ◽  
Clinical Observations ◽  
Wide Range ◽  
Prevention And Treatment ◽  
High Degree

The paper summarizes data on modern approaches to the diagnosis, prevention and treatment of severe acute parenchymal respiratory failure of various origins, including ARDS due to bacterial viral pneumonia. The work is based on the data of modern well-organized studies, analysis of international clinical guidelines with a high degree of evidence, as well as the results of our own long-term experimental studies and clinical observations of the treatment of patients with ARDS of various origins, including viral pneumonia of 2009, 2016, 2020. Scientifically grounded algorithms for prevention, differential diagnosis and personalized therapy of severe acute respiratory failure using innovative medical technologies and a wide range of respiratory and adjuvant treatment methods have been formulated. The authors tried to adapt as much as possible the existing current recommendations for the daily clinical practice of anesthesiologists and resuscitators.

scholarly journals Genetic linkage map of Phaseolus vulgaris and identification of QTLs responsible for resistance to Xanthomonas axonopodis pv. phaseoli

2003 ◽  
Vol 28 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Amaury S. Santos ◽  
Ricardo E. Bressan-Smith ◽  
Messias G. Pereira ◽  
Rosana Rodrigues ◽  
Claudia F. Ferreira
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Linkage Map ◽  
Linkage Groups ◽  
Resistant Genotype ◽  
Xanthomonas Axonopodis ◽  
Low Degree ◽  
Phenotypic Variations ◽  
Genomic Regions ◽  
High Degree

Common bean (Phaseolus vulgaris) cultivars with a high degree of resistance to Xanthomonas axonopodis pv. phaseoli (Xap) are not available in Brazil. Despite many studies, a low degree of resistance to Xap continues to exist due to its complex genetic inheritance, which is not well known. The objectives of this research were to complement a common bean genetic map based on the cross between a susceptible genotype 'HAB-52' and a resistant genotype 'BAC-6', and to map and analyze genomic regions (quantitative trait loci – QTLs) related to Xap resistance. Eleven linkage groups were determined using 143 RAPD markers, covering 1,234.5 cM of the genome. This map was used to detect QTLs associated with Xap resistance on leaves and pods. The averages of disease severity on leaves (represented by the transformed disease index – TDI) and pods (represented by the diameter of lesion on pods – DLP) were added to the data of the linkage map. Five TDI QTLs and only one LDP QTL were detected. The TDI QTLs were placed in the A, B, G and J linkage groups, with phenotypic variations ranging from 12.7 to 71.6%. The DLP QTL explained 12.9% of the phenotypic variation and was mapped in a distinct linkage group. These results indicate that there are different genes involved in the control of resistance on leaves and pods.

scholarly journals Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

2010 ◽  
Vol 84 (24) ◽  
pp. 12555-12563 ◽  
Author(s):  
Hervé Moreau ◽  
Gwenael Piganeau ◽  
Yves Desdevises ◽  
Richard Cooke ◽  
Evelyne Derelle ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Viral Evolution ◽  
Genome Comparison ◽  
Evolutionary Divergence ◽  
Gene Repertoire ◽  
Whole Genomes ◽  
Complete Sequences ◽  
Virus Genomes ◽  
High Degree ◽  
Ostreococcus Lucimarinus

ABSTRACT Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.

Sign in / Sign up

Export Citation Format

Share Document