scholarly journals The speciation and hybridization history of the genusSalmonella

2019 ◽  
Author(s):  
Alexis Criscuolo ◽  
Sylvie Issenhuth-Jeanjean ◽  
Xavier Didelot ◽  
Kaisa Thorell ◽  
James Hale ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Binary Fission ◽  
Bacterial Lineage ◽  
Food Borne ◽  
European Nucleotide Archive ◽  
Reference Collection ◽  
Illumina Sequence ◽  
History Of ◽  
Food Borne Infections

AbstractBacteria and archaea make up most of natural diversity but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genusSalmonella, an ecologically diverse bacterial lineage, within whichS. entericasubsp.entericais responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified eleven distinct phylogroups, three of which were previously undescribed. Strains assigned toS. entericasubsp.salamaeare polyphyletic, with two distinct lineages that we designate Salamae A and Salamae B. Strains of subspecieshoutenaeare subdivided into two groups, Houtenae A and B and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages but detected more subtle signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence may not apply inSalmonella.Data summaryIllumina sequence data were submitted to the European Nucleotide Archive under project number PRJEB2099 and are available from INSDC (NCBI/ENA/DDBJ) under accession numbers ERS011101 to ERS011146. The MLST sequence and profile data generated in this study have been publicly available on theSalmonellaMLST web site between 2010 and the migration of theSalmonellaMLST website to EnteroBase (https://enterobase.warwick.ac.uk/), and subsequently from there.

scholarly journals Distribution of serotypes of Listeria monocytogenes in chicken meats in Turkey

2020 ◽  
Vol 70 (4) ◽  
pp. 1859
Author(s):  
S. SAHIN ◽  
R. KALIN ◽  
MN MOGULKOC
Keyword(s):  
Public Health ◽  
Listeria Monocytogenes ◽  
Large Scale ◽  
Meat Products ◽  
Health Problems ◽  
Chicken Meat ◽  
Serotype Distribution ◽  
Food Borne ◽  
Serotype 1 ◽  
Food Borne Infections

Listeria monocytogenes is one of the important causes of food-borne infections. This study was conducted to determine the presence of L. monocytogenes and its serotype distribution in a total of 400 packaged chicken meat products (drumstick, breast, wing, and whole chicken) from different national companies. L. monocytogenes contamination was detected in 26.5% (106 in 400) of all samples when the products considered, drumsticks, breasts, wings, and whole chickens showed 47%, 15%, 35, and 9% positivity respectively. Four important serotypes of L. monocytogenes in human listeriosis (1/2a, 1/2b, 1/2c and 4b) were identified, and serotype 1/2a (94.3%) was determined as predominant in packaged chicken meats. The present study revealed that L. monocytogenes 1/2a serotype is prevalent in chicken meats and this may cause public health problems in Turkey. Further studies in poultry meats should be conducted on a large scale such as regional or national big markets to determine the presence of the pathogen and its dominant serotypes.

scholarly journals Tracing the origin and co-phylogeny of the caliciviruses

2006 ◽  
Vol 87 (5) ◽  
pp. 1229-1235 ◽  
Author(s):  
Graham J. Etherington ◽  
Susan M. Ring ◽  
Michael A. Charleston ◽  
Jo Dicks ◽  
Vic J. Rayward-Smith ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Human Health ◽  
Sequence Data ◽  
Host Switching ◽  
Viral Gastroenteritis ◽  
Analysis Tools ◽  
Food Borne ◽  
Wide Range ◽  
History Of

Caliciviruses infect a wide range of mammalian hosts and include the genus Norovirus, the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus–host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.

scholarly journals annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

2019 ◽  
Author(s):  
Michael Gruenstaeudl
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Sequence Data ◽  
Complete Sequence ◽  
Biological Research ◽  
Sequence Alignments ◽  
European Nucleotide Archive ◽  
Concurrent Development ◽  
Easy Integration ◽  
Central Pillar

ABSTRACTMotivationThe submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with a concurrent development of tools to automate the preparatory work preceding such submissions.ResultsI introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record, and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.

scholarly journals Temporal lags and overlap in the diversification of weevils and flowering plants

2009 ◽  
Vol 106 (17) ◽  
pp. 7083-7088 ◽  
Author(s):  
Duane D. McKenna ◽  
Andrea S. Sequeira ◽  
Adriana E. Marvaldi ◽  
Brian D. Farrell
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Divergence Times ◽  
Resource Tracking ◽  
Crown Group ◽  
Dna Sequence Data ◽  
Angiosperm Diversification ◽  
History Of ◽  
Fossil Data ◽  
Diversification Event

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on ≈8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning ≈166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca.112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.

scholarly journals A genetic history of migration, diversification, and admixture in Asia

2022 ◽  
pp. 1-32
Author(s):  
Melinda A. Yang
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Evolutionary Genetics ◽  
Genetic Distances ◽  
Chromosome 21 ◽  
Late 20Th Century ◽  
Genetic History ◽  
Asian Populations ◽  
Human Dispersal ◽  
History Of

L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.

Materials for the history of the gospel-Baptist movement in Ukraine

1996 ◽  
pp. 4-15
Author(s):  
S. Golovaschenko ◽  
Petro Kosuha
Keyword(s):  
Large Scale ◽  
Religious Studies ◽  
Theological Seminary ◽  
National Academy Of Sciences ◽  
Evangelical Christians ◽  
Evangelical Christian ◽  
First Results ◽  
History Of ◽  
Fruitful Cooperation ◽  
Academy Of Sciences

The report is based on the first results of the study "The History of the Evangelical Christians-Baptists in Ukraine", carried out in 1994-1996 by the joint efforts of the Department of Religious Studies at the Institute of Philosophy of the National Academy of Sciences of Ukraine and the Odessa Theological Seminary of Evangelical Christian Baptists. A large-scale description and research of archival sources on the history of evangelical movements in our country gave the first experience of fruitful cooperation between secular and church researchers.

Integration of Ecological and Engineering Aspects in Planning Large Scale Tidal Power Development in the Bay of Fundy, Canada

1984 ◽  
Vol 16 (1-2) ◽  
pp. 281-295 ◽  
Author(s):  
Donald C Gordon
Keyword(s):  
Large Scale ◽  
Feasibility Studies ◽  
Bay Of Fundy ◽  
Final Decision ◽  
Power Development ◽  
Tidal Power ◽  
History Of ◽  
Scientists And Engineers ◽  
The Many ◽  
University Scientists

Large-scale tidal power development in the Bay of Fundy has been given serious consideration for over 60 years. There has been a long history of productive interaction between environmental scientists and engineers durinn the many feasibility studies undertaken. Up until recently, tidal power proposals were dropped on economic grounds. However, large-scale development in the upper reaches of the Bay of Fundy now appears to be economically viable and a pre-commitment design program is highly likely in the near future. A large number of basic scientific research studies have been and are being conducted by government and university scientists. Likely environmental impacts have been examined by scientists and engineers together in a preliminary fashion on several occasions. A full environmental assessment will be conducted before a final decision is made and the results will definately influence the outcome.

scholarly journals Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

2021 ◽  
Vol 12 (2) ◽  
pp. 1-22
Author(s):  
Jianguo Chen ◽  
Kenli Li ◽  
Keqin Li ◽  
Philip S. Yu ◽  
Zeng Zeng
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Location Prediction ◽  
City Management ◽  
Dynamic Planning ◽  
Graph Sequence ◽  
Graph Modeling ◽  
The Government ◽  
Location Clustering ◽  
Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

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