scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

scholarly journals Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States

2015 ◽  
Vol 81 (11) ◽  
pp. 3671-3678 ◽  
Author(s):  
Sarah A. Ison ◽  
Sabine Delannoy ◽  
Marie Bugarel ◽  
Kendra K. Nightingale ◽  
Hattie E. Webb ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Genetic Diversity ◽  
The United States ◽  
Pathogenic Potential ◽  
Content Type ◽  
Genomic Plasticity ◽  
E Coli ◽  
Short Palindromic Repeat ◽  
Bovine Feces

ABSTRACTEscherichia coliO26 has been identified as the most common non-O157 Shiga toxin-producingE. coli(STEC) serogroup to cause human illnesses in the United States and has been implicated in outbreaks around the world.E. colihas high genomic plasticity, which facilitates the loss or acquisition of virulence genes. Attaching and effacingE. coli(AEEC) O26 strains have frequently been isolated from bovine feces, and there is a need to better characterize the relatedness of these strains to defined molecular pathotypes and to describe the extent of their genetic diversity. High-throughput real-time PCR was used to screen 178E. coliO26 isolates from a single U.S. cattle feedlot, collected from May to July 2011, for the presence or absence of 25 O26 serogroup-specific and virulence-associated markers. The selected markers were capable of distinguishing these strains into molecularly defined groups (yielding 18 unique marker combinations). Analysis of the clustered regularly interspaced short palindromic repeat 1 (CRISPR1) and CRISPR2a loci further discriminated isolates into 24 CRISPR types. The combination of molecular markers and CRISPR typing provided 20.8% diversity. The recent CRISPR PCR target SP_O26-E, which was previously identified only instx2-positive O26:H11 human clinical strains, was identified in 96.4% (161/167 [95% confidence interval, 99.2 to 93.6%]) of thestx-negative AEEC O26:H11 bovine fecal strains. This supports that thesestx-negative strains may have previously contained a prophage carryingstxor could acquire this prophage, thus possibly giving them the potential to become pathogenic to humans. These results show that investigation of specific genetic markers may further elucidate our understanding of the genetic diversity of AEEC O26 strains in bovine feces.

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽  
2006 ◽  
Vol 1 (4) ◽  
pp. 392-398
Author(s):  
Kazima Bulayeva ◽  
John McGrath
Keyword(s):  
Genetic Diversity ◽  
Family History ◽  
Age Of Onset ◽  
Population Genetic Study ◽  
Season Of Birth ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Prevalence ◽  
History Of ◽  
Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

Cold War consumption and the marketing of childhood in the Soviet Union and the United States, 1950-1960

2016 ◽  
Vol 8 (1) ◽  
pp. 83-98 ◽  
Author(s):  
Margaret Peacock
Keyword(s):  
Cold War ◽  
Soviet Union ◽  
The United States ◽  
Content Type ◽  
The Soviet Union ◽  
The Status ◽  
The Usa ◽  
History Of ◽  
Global Discourse ◽  
The Cold War

Purpose – This paper aims to explore the relationship between childhood, consumption and the Cold War in 1950s America and the Soviet Union. The author argues that Soviet and American leaders, businessmen, and politicians worked hard to convince parents that buying things for their children offered the easiest way to raise good American and Soviet kids and to do their part in waging the economic battles of the Cold War. The author explores how consumption became a Cold War battleground in the late 1950s and suggests that the history of childhood and Cold War consumption alters the way we understand the conflict itself. Design/Methodology/Approach – Archival research in the USA and the Russian Federation along with close readings of Soviet and American advertisements offer sources for understanding the global discourse of consumption in the 1950s and 1960s. Findings – Leaders, advertisers, and propagandists in the Soviet Union and the USA used the same images in the same ways to sell the ethos of consumption to their populations. They did this to sell the Cold War, to bolster the status quo, and to make profits. Originality/Value – This paper offers a previously unexplored, transnational perspective on the role that consumption and the image of the child played in shaping the Cold War both domestically and abroad.

No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

2021 ◽  
Vol 46 (4) ◽  
pp. 951-961
Author(s):  
Jasper John A. Obico ◽  
Hemres Alburo ◽  
Julie F. Barcelona ◽  
Marie Hale ◽  
Lisa Paguntalan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Tropical Forests ◽  
Forest Cover ◽  
Genetic Connectivity ◽  
Philippine Island ◽  
Low Genetic Diversity ◽  
History Of ◽  
Gap Data ◽  
The Impact

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

Income and healthcare financing system in the United States: an asymmetric analysis

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Mehdi Barati ◽  
Hadiseh Fariditavana
Keyword(s):  
The United States ◽  
Set Covering ◽  
Healthcare Financing ◽  
Financing System ◽  
Data Set ◽  
Content Type ◽  
Funding Sources ◽  
Distributed Lag ◽  
The Impact ◽  
The Relationship

PurposeThe purpose of this study is to first assess how the US healthcare financing system is influenced by income variation. Then, it examines whether or not the impact of income variation is asymmetric.Design/methodology/approachFor the analyses of this paper, the autoregressive distributed lag (ARDL) model is implemented to a data set covering the period from 1960 to 2018.FindingsThe results provide evidence that major funding sources of aggregate healthcare expenditure (HCE) respond differently to changes in income. The results also imply that the effect of income is not always symmetric.Originality/valueMany studies have attempted to identify the relationship between income and HCE. A common feature of past studies is that they have only focused on aggregate HCE, while one might be interested in knowing how major funders of aggregate HCE would be affected by changes in income. Another common feature of past studies is that they have assumed that the relationship between income and HCE is symmetric.

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
The West ◽  
European Settlement ◽  
Low Genetic Diversity ◽  
Eastern Australia ◽  
Wide Range ◽  
History Of ◽  
Open Forests ◽  
Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

scholarly journals Serotype and Genotype (Multilocus Sequence Type) ofStreptococcus suisIsolates from the United States Serve as Predictors of Pathotype

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
April A. Estrada ◽  
Marcelo Gottschalk ◽  
Stephanie Rossow ◽  
Aaron Rendahl ◽  
Connie Gebhart ◽  
...  
Keyword(s):  
United States ◽  
Odds Ratio ◽  
Clinical Information ◽  
The United States ◽  
Growing Pigs ◽  
Sequence Type ◽  
Primary Methods ◽  
Content Type ◽  
History Of ◽  
Sequence Types

ABSTRACTStreptococcus suisis a significant cause of mortality in piglets and growing pigs worldwide. The species contains pathogenic and commensal strains, with pathogenic strains causing meningitis, arthritis, endocarditis, polyserositis, and septicemia. Serotyping and multilocus sequence typing (MLST) are primary methods to differentiate strains, but the information is limited for strains found in the United States. The objective of this study was to characterize the diversity of 208S. suisisolates collected between 2014 and 2017 across North America (mainly the United States) by serotyping and MLST and to investigate associations between subtype and pathotype classifications (pathogenic, possibly opportunistic, and commensal), based on clinical information and site of isolation. Twenty serotypes were identified, and the predominant serotypes were 1/2 and 7. Fifty-eight sequence types (STs) were identified, and the predominant ST was ST28. Associations among serotypes, STs, and pathotypes were investigated using odds ratio and clustering analyses. Evaluation of serotype and ST with pathotype identified a majority of isolates of serotypes 1, 1/2, 2, 7, 14, and 23 and ST1, ST13, ST25, ST28, ST29, ST94, ST108, ST117, ST225, ST373, ST961, and ST977 as associated with the pathogenic pathotype. Serotypes 21 and 31, ST750, and ST821 were associated with the commensal pathotype, which is composed of isolates from farms with no known history ofS. suis-associated disease. Our study demonstrates the use of serotyping and MLST to differentiate pathogenic from commensal isolates and establish links between pathotype and subtype, thus increasing the knowledge aboutS. suisstrains circulating in the United States.

US academic libraries' staffing and expenditure trends (1996–2016)

2020 ◽  
Vol 41 (4/5) ◽  
pp. 247-268 ◽  
Author(s):  
Starr Hoffman ◽  
Samantha Godbey
Keyword(s):  
Academic Libraries ◽  
The United States ◽  
Data Sets ◽  
Size Category ◽  
Data Set ◽  
Content Type ◽  
Education Statistics ◽  
Trends Over Time ◽  
Doctoral Institutions ◽  
Over Time

PurposeThis paper explores trends over time in library staffing and staffing expenditures among two- and four-year colleges and universities in the United States.Design/methodology/approachResearchers merged and analyzed data from 1996 to 2016 from the National Center for Education Statistics for over 3,500 libraries at postsecondary institutions. This study is primarily descriptive in nature and addresses the research questions: How do staffing trends in academic libraries over this period of time relate to Carnegie classification and institution size? How do trends in library staffing expenditures over this period of time correspond to these same variables?FindingsAcross all institutions, on average, total library staff decreased from 1998 to 2012. Numbers of librarians declined at master’s and doctoral institutions between 1998 and 2016. Numbers of students per librarian increased over time in each Carnegie and size category. Average inflation-adjusted staffing expenditures have remained steady for master's, baccalaureate and associate's institutions. Salaries as a percent of library budget decreased only among doctoral institutions and institutions with 20,000 or more students.Originality/valueThis is a valuable study of trends over time, which has been difficult without downloading and merging separate data sets from multiple government sources. As a result, few studies have taken such an approach to this data. Consequently, institutions and libraries are making decisions about resource allocation based on only a fraction of the available data. Academic libraries can use this study and the resulting data set to benchmark key staffing characteristics.

scholarly journals History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology

2018 ◽  
Vol 200 (7) ◽  
Author(s):  
Yoshizumi Ishino ◽  
Mart Krupovic ◽  
Patrick Forterre
Keyword(s):  
Genome Editing ◽  
Functional Characterization ◽  
Halophilic Archaea ◽  
Repeated Sequence ◽  
Hyperthermophilic Archaea ◽  
Content Type ◽  
Origin And Evolution ◽  
History Of ◽  
Short Palindromic Repeat ◽  
Original Observation

ABSTRACTClustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in theEscherichia coligenome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence inE. colito genome editing in humans.

The phylogenomics of diversification on an island: applying anchored hybrid enrichment to New Zealand Leptospermum scoparium (Myrtaceae)

2019 ◽  
Vol 191 (1) ◽  
pp. 1-17 ◽  
Author(s):  
Matt H Buys ◽  
Richard C Winkworth ◽  
Peter J de Lange ◽  
Peter G Wilson ◽  
Nora Mitchell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Sequence Data ◽  
Large Data ◽  
Data Matrix ◽  
Data Set ◽  
Important Species ◽  
Anchored Hybrid Enrichment ◽  
Data Signal ◽  
Leptospermum Scoparium

Abstract Leptospermum scoparium (Myrtaceae) is a morphologically highly variable species found in mainland Australia, Tasmania and New Zealand. For example, in New Zealand up to six morphologically distinct varieties of this species have been described, although only two (var. scoparium and var. incanum) are now formally recognized. In the present study we provide a first examination of genetic diversity in this culturally and commercially important species with the aim of gaining insights into its origins and evolution. We used anchored hybrid enrichment to acquire sequence data from 485 orthologous low-copy nuclear loci for 27 New Zealand and three Australian accessions of L. scoparium and representatives of several other Leptospermum spp. The final concatenated data matrix contained 421 687 nucleotide positions of which 55 102 were potentially informative. Despite the relative large data set, our analyses suggest that a combination of low and incompatible data signal limits the resolution of relationships among New Zealand populations of L. scoparium. Nevertheless, our analyses are consistent with genetic diversity being geographically structured, with three groups of L. scoparium recovered. We discuss the evolutionary and taxonomic implications of our findings.

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