scholarly journals Correlates of Nonrandom Patterns of Serotype Switching in Pneumococcus

2019 ◽  
Vol 221 (10) ◽  
pp. 1669-1676
Author(s):  
Shreyas S Joshi ◽  
Mohammad A Al-Mamun ◽  
Daniel M Weinberger
Keyword(s):  
Genetic Diversity ◽  
Regression Model ◽  
Genetic Background ◽  
Glucuronic Acid ◽  
Genetic Lineage ◽  
Sequencing Project ◽  
Genetic Lineages ◽  
Polysaccharide Capsule ◽  
The Relationship

Abstract Background Pneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to occur on the same genetic background as a results of serotype switching, but the drivers of these patterns are not well understood. Methods We used the PubMLST and Global Pneumococcal Sequencing Project databases to quantify the number of genetic lineages on which different serotype pairs occur together. We also quantified the genetic diversity of each serotype. Regression model were used to evaluate the relationship between shared polysaccharide components and the frequency of serotype co-occurrence and diversity. Results A number of serotype pairs occurred together on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid, any-N-acetylated sugar, or ribitol). Diversity also varied markedly by serotype and was associated with the presence of specific sugars in the capsule. Conclusions Certain pairs of serotypes are more likely to co-occur on the same genetic background. These patterns were correlated with shared polysaccharide components. This might reflect adaptation of strains to produce capsules with specific characteristics.

scholarly journals Correlates of non-random patterns of capsule switching in pneumococcus

2019 ◽  
Author(s):  
Shreyas S. Joshi ◽  
M. A. Al-Mamun ◽  
Daniel M. Weinberger
Keyword(s):  
Genetic Diversity ◽  
Genetic Background ◽  
Regression Models ◽  
Glucuronic Acid ◽  
Genetic Lineage ◽  
Structural Components ◽  
Genetic Lineages ◽  
Polysaccharide Capsule ◽  
Random Patterns ◽  
The Relationship

ABSTRACTBackgroundPneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood.MethodsWe used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity.ResultsA number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule.ConclusionsCertain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics.

scholarly journals Patterns of Genetic Diversity in Highly Invasive Species: Cogongrass (Imperata cylindrica) Expansion in the Invaded Range of the Southern United States (US)

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 423 ◽  
Author(s):  
Rima D. Lucardi ◽  
Lisa E. Wallace ◽  
Gary N. Ervin
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Invasive Species ◽  
Imperata Cylindrica ◽  
Southern United States ◽  
Genetic Lineage ◽  
Us States ◽  
Genetic Lineages ◽  
Genetic Diversity And Structure ◽  
Pinus Spp

The spatial expansions of invasive organisms in the novel range are generally expected to follow an isolation-by-distance relationship (IBD) if the invasion is biologically driven; however, many invasions are facilitated anthropogenically. This research focused on the extant expansion patterns of cogongrass (Imperata cylindrica). Cogongrass is a widespread invasive species throughout the southern United States (US). Patterns of infestation vary among US states. Cogongrass is pyrogenic, and its invasion threatens softwood (Pinus spp.) plantations, a substantial economic market for this US region. Over 600 individuals were sampled from seven invaded US states, using amplified fragment length polymorphisms (AFLPs) to assess genetic diversity and population structure. We suspected that differences in historical management efforts among US states influenced differences in genetic diversity and structure. We detected two genetic lineages at the highest level of analysis. One genetic lineage was locally restricted, whereas the other was found throughout the study region. Admixed individuals were found in all US states and consistently co-occurred with the dominant lineage, suggesting that secondary contact and hybridization may have facilitated expansion. The widespread prevalence of only one of the two detected genetic lineages suggests a primary genetic lineage responsible for on-going population expansion in the US.

Using The Fully Modified M Method In Estimating The Effect Of Cultivated Area On Barley Production In Iraq For The Period 1970-2018

2020 ◽  
Vol 2020 (66) ◽  
pp. 101-110
Author(s):  
. Azhar Kadhim Jbarah ◽  
Prof Dr. Ahmed Shaker Mohammed
Keyword(s):  
Regression Model ◽  
Moving Average ◽  
Estimation Method ◽  
Estimation Methods ◽  
Autoregressive Moving Average ◽  
Moving Average Models ◽  
Error Terms ◽  
Relationship Of ◽  
The Relationship ◽  
Barley Crop

The research is concerned with estimating the effect of the cultivated area of barley crop on the production of that crop by estimating the regression model representing the relationship of these two variables. The results of the tests indicated that the time series of the response variable values is stationary and the series of values of the explanatory variable were nonstationary and that they were integrated of order one ( I(1) ), these tests also indicate that the random error terms are auto correlated and can be modeled according to the mixed autoregressive-moving average models ARMA(p,q), for these results we cannot use the classical estimation method to estimate our regression model, therefore, a fully modified M method was adopted, which is a robust estimation methods, The estimated results indicate a positive significant relation between the production of barley crop and cultivated area.

Binding of lead and copper(II) cations to hemicelluloses of rye bran

1986 ◽  
Vol 51 (10) ◽  
pp. 2250-2258 ◽  
Author(s):  
Rudolf Kohn ◽  
Zdena Hromádková ◽  
Anna Ebringerová
Keyword(s):  
Uronic Acid ◽  
Equilibrium Solution ◽  
Glucuronic Acid ◽  
The Other ◽  
Carboxyl Groups ◽  
Stoichiometric Ratio ◽  
Molar Ratios ◽  
Free Ions ◽  
Uronic Acid Content ◽  
The Relationship

Several fractions of acid hemicelluloses isolated from rye bran were characterized by molar ratios of saccharides (D-Xyl, L-Ara, D-Glc, D-Gal) and 4-O-methyl-D-glucuronic acid and protein content. Binding of Pb2+ and Cu2+ ions to these acid polysaccharides was considered according to function (M)b = f([M2+]f), expressing the relationship between the amount of metal (M)b bound to 1 g of the substance and the concentration of free ions [M2+]f in the equilibrium solution and according to the association degree β of these cations with carboxyl groups of uronic acid at a stoichiometric ratio of both components in the system under investigation. Acid hemicelluloses contained only a very small portion of uronic acid ((COOH) 0.05-0.18 mmol g-1); the model polysaccharide, 4-O-methyl-D-glucurono-D-xylan of beech, was substantially richer in uronic acid content ((COOH) 0.73 mmol g-1). Consequently, the amount of lead and copper bound to acid hemicelluloses is very small ((M)b 0.017-0.025 mmol g-1) at [M2+]f = 0.10 mmol l-1. On the other hand, much greater amount of cations ((M)f 0.09-0.10 mmol g-1) was bound to the glucuronoxylan. The association degree β was like with the majority of samples (β = 0.31-0.38). The amount of lead and copper(II) bound to acid hemicelluloses from rye bran is several times lower than that bound to dietary fiber isolated from vegetables (cabbage, carrot), rich in pectic substances.

scholarly journals Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 302
Author(s):  
Malik Sallam ◽  
Azmi Mahafzah
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rapid Evolution ◽  
Molecular Signature ◽  
Special Focus ◽  
Genetic Lineage ◽  
Synonymous Mutation ◽  
Spike Gene ◽  
Genetic Lineages ◽  
The Uk

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be further investigated.

scholarly journals Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation

2000 ◽  
Vol 23 (3) ◽  
pp. 541-544 ◽  
Author(s):  
José Alexandre Felizola Diniz-Filho ◽  
Mariana Pires de Campos Telles
Keyword(s):  
Genetic Diversity ◽  
Spatial Pattern ◽  
Stochastic Models ◽  
Population Differentiation ◽  
Real Data ◽  
Population Heterogeneity ◽  
Data Set ◽  
Mantel’S Test ◽  
The Relationship ◽  
Diversity Estimates

In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively) is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.

The relationship between disability and suicide: prospective evidence from the Ten to Men cohort

2018 ◽  
Vol 41 (4) ◽  
pp. 707-713 ◽  
Author(s):  
Allison Milner ◽  
Anne-Marie Bollier ◽  
Eric Emerson ◽  
Anne Kavanagh
Keyword(s):  
Mental Health ◽  
Logistic Regression ◽  
Regression Model ◽  
Logistic Regression Model ◽  
People With Disabilities ◽  
Cross Sectional ◽  
Longitudinal Cohort ◽  
The Past ◽  
The Relationship

Abstract Background People with disabilities often face a range of social and economic adversities. Evidence suggests that these disadvantages result in poorer mental health. Some research also indicates that people with disabilities are more likely experience thoughts about suicide than people without disability, although most of this research is based on small cross-sectional samples. Methods We explored the relationship between self-reported disability (measured at baseline) and likelihood of reporting thoughts of suicide (measured at follow up) using a large longitudinal cohort of Australian males. A logistic regression model was conducted with thoughts of suicide within the past 12 months (yes or no) as the outcome and disability as the exposure. The models adjusted for relevant confounders, including mental health using the SF-12 MCS, and excluded males who reported thoughts of suicide at baseline. Results After adjustment, there was a 1.48 (95% CI: 0.98–2.23, P = 0.063) increase in the odds of thoughts of suicide among men who also reported a disability. The size of association was similar to that of being unemployed. Conclusions Males reporting disability may also suffer from thoughts of suicide. We speculate that discrimination may be one explanation for the observed association. More research on this topic is needed.

scholarly journals Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2

Acta Naturae ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 77-89
Author(s):  
Aleksandra A. Nikonova ◽  
Eugene B. Faizuloev ◽  
Anastasia V. Gracheva ◽  
Igor Yu. Isakov ◽  
Vitaly V. Zverev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Large Scale ◽  
Biological Properties ◽  
Viral Genomes ◽  
Biological Features ◽  
Health Measures ◽  
Common Genetic Variants ◽  
Coronavirus Infection ◽  
The Relationship

The new coronavirus infection (COVID-19) represents a challenge for global health. Since the outbreak began, the number of confirmed cases has exceeded 117 million, with more than 2.6 million deaths worldwide. With public health measures aimed at containing the spread of the disease, several countries have faced a crisis in the availability of intensive care units. Currently, a large-scale effort is underway to identify the nucleotide sequences of the SARS-CoV-2 coronavirus that is an etiological agent of COVID-19. Global sequencing of thousands of viral genomes has revealed many common genetic variants, which enables the monitoring of the evolution of SARS-CoV-2 and the tracking of its spread over time. Understanding the current evolution of SARS-CoV-2 is necessary not only for a retrospective analysis of the new coronavirus infection spread, but also for the development of approaches to the therapy and prophylaxis of COVID-19. In this review, we have focused on the general characteristics of SARS-CoV-2 and COVID-19. Also, we have analyzed available publications on the genetic diversity of the virus and the relationship between the diversity and the biological properties of SARS-CoV-2, such as virulence and contagiousness.

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