scholarly journals Recombination Shapes the Structure of an EnvironmentalVibrio choleraePopulation

2010 ◽  
Vol 77 (2) ◽  
pp. 537-544 ◽  
Author(s):  
Daniel P. Keymer ◽  
Alexandria B. Boehm
Keyword(s):  
Bacterial Species ◽  
Housekeeping Genes ◽  
Small Sample ◽  
Detection Methods ◽  
Significant Linkage Disequilibrium ◽  
Central California ◽  
Intraspecies Diversity ◽  
The Individual ◽  
Significant Linkage ◽  
Sequence Types

ABSTRACTVibrio choleraeconsists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shownV. choleraeto be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmentalV. choleraeisolates and 13 other putativeVibrioisolates from coastal waters and sediments in central California, as well as four clinicalV. choleraeisolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of ourV. choleraeisolates. Despite frequent recombination, significant linkage disequilibrium was still detected among theV. choleraesequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate inV. choleraeof 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination amongV. choleraemay hinder the identification of ecotypes in this bacterioplankton population.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals A multilocus sequence typing scheme of Pseudomonas putida for clinical and environmental isolates

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kohei Ogura ◽  
Kayo Shimada ◽  
Tohru Miyoshi-Akiyama
Keyword(s):  
Pseudomonas Putida ◽  
Multilocus Sequence Typing ◽  
Haplotype Network ◽  
Significant Linkage Disequilibrium ◽  
Environmental Isolates ◽  
Single Nucleotide ◽  
Mlst Scheme ◽  
Network Tree ◽  
Significant Linkage ◽  
Sequence Types

Abstract Pseudomonas putida is a bacterium commonly found in soils, water and plants. Although P. putida group strains are considered to have low virulence, several nosocomial isolates with carbapenem- or multidrug-resistance have recently been reported. In the present study, we developed a multilocus sequence typing (MLST) scheme for P. putida. MLST loci and primers were selected and designed using the genomic information of 86 clinical isolates sequenced in this study as well as the sequences of 20 isolates previously reported. The genomes were categorised into 68 sequence types (STs). Significant linkage disequilibrium was detected for the 68 STs, indicating that the P. putida isolates are clonal. The MLST tree was similar to the haplotype network tree based on single nucleotide morphisms, demonstrating that our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites.

scholarly journals MLSTar: automatic multilocus sequence typing of bacterial genomes in R

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5098 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Multilocus Sequence Typing ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Bacterial Genomes ◽  
Standard Tool ◽  
Comparable Performance ◽  
R Packages ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals Combining Inter-Subject Modeling with a Subject-Based Data Transformation to Improve Affect Recognition from EEG Signals

Sensors ◽  
2019 ◽  
Vol 19 (13) ◽  
pp. 2999 ◽  
Author(s):  
Miguel Arevalillo-Herráez ◽  
Maximo Cobos ◽  
Sandra Roger ◽  
Miguel García-Pineda
Keyword(s):  
Detection System ◽  
Data Transformation ◽  
Small Sample ◽  
Detection Methods ◽  
Eeg Signals ◽  
Individual Traits ◽  
Emotional Aspects ◽  
Public Repositories ◽  
Small Sample Problem ◽  
The Individual

Existing correlations between features extracted from Electroencephalography (EEG) signals and emotional aspects have motivated the development of a diversity of EEG-based affect detection methods. Both intra-subject and inter-subject approaches have been used in this context. Intra-subject approaches generally suffer from the small sample problem, and require the collection of exhaustive data for each new user before the detection system is usable. On the contrary, inter-subject models do not account for the personality and physiological influence of how the individual is feeling and expressing emotions. In this paper, we analyze both modeling approaches, using three public repositories. The results show that the subject’s influence on the EEG signals is substantially higher than that of the emotion and hence it is necessary to account for the subject’s influence on the EEG signals. To do this, we propose a data transformation that seamlessly integrates individual traits into an inter-subject approach, improving classification results.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.org/iferres/MLSTar.

scholarly journals Multi Locus Sequence Typing and spa Typing of Staphylococcus Aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia

2021 ◽  
Vol 9 (4) ◽  
pp. 725
Author(s):  
Luka Cvetnić ◽  
Marko Samardžija ◽  
Sanja Duvnjak ◽  
Boris Habrun ◽  
Marija Cvetnić ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Housekeeping Genes ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Multi Locus Sequence Typing ◽  
Spa Typing ◽  
Heterogenous Group ◽  
Sequence Types ◽  
Spa Types ◽  
Frequent Allele

Background: The bacterial species S. aureus is the most common causative agent of mastitis in cows in most countries with a dairy industry. The prevalence of infection caused by S. aureus ranges from 2% to more than 50%, and it causes 10–12% of all cases of clinical mastitis. Aim: The objective was to analyze 237 strains of S. aureus isolated from the milk of cows with subclinical mastitis regarding the spa, mecA, mecC and pvl genes and to perform spa and multi-locus sequence typing (MLST). Methods: Sequencing amplified gene sequences was conducted at Macrogen Europe. Ridom StaphType and BioNumerics software was used to analyze obtained sequences of spa and seven housekeeping genes. Results: The spa fragment was present in 204 (86.1%) of strains, while mecA and mecC gene were detected in 10 strains, and the pvl gene was not detected. Spa typing successfully analyzed 153 tested isolates (64.3%), confirming 53 spa types, four of which were new types. The most frequent spa type was t2678 (14%). MLST typed 198 (83.5%) tested strains and defined 32 different allele profiles, of which three were new. The most frequent allele profile was ST133 (20.7%). Six groups (G) and 15 singletons were defined. Conclusion: Taking the number of confirmed spa types and sequence types (STs) into account, it can be concluded that the strains of S. aureus isolated from the milk of cows with subclinical mastitis form a heterogenous group. To check the possible zoonotic potential of isolates it would be necessary to test the persons and other livestock on the farms.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 541-552 ◽  
Author(s):  
S W Schaeffer ◽  
E L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Alcohol Dehydrogenase ◽  
Distance Effect ◽  
Theoretical Distribution ◽  
Drosophila Pseudoobscura ◽  
Significant Linkage Disequilibrium ◽  
Effective Population ◽  
Nucleotide Distance ◽  
Significant Linkage ◽  
Recombination Parameter

Abstract The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.

scholarly journals Within-Site Variability of Liana Wood Anatomical Traits: A Case Study in Laussat, French Guiana

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 523 ◽  
Author(s):  
Félicien Meunier ◽  
Sruthi M. Krishna Moorthy ◽  
Hannes P. T. De Deurwaerder ◽  
Robin Kreus ◽  
Jan Van den Bulcke ◽  
...  
Keyword(s):  
Specific Gravity ◽  
French Guiana ◽  
Growth Form ◽  
Vessel Diameter ◽  
Small Sample ◽  
Diameter Distribution ◽  
Hydraulic Architecture ◽  
Woody Vines ◽  
Wood Trait ◽  
The Individual

Research Highlights: We investigated the variability of vessel diameter distributions within the liana growth form among liana individuals originating from a single site in Laussat, French Guiana. Background and Objectives: Lianas (woody vines) are key components of tropical forests. Lianas are believed to be strong competitors for water, thanks to their presumed efficient vascular systems. However, unlike tropical trees, lianas are overlooked in field data collection. As a result, lianas are often referred to as a homogeneous growth form while little is known about the hydraulic architecture variation among liana individuals. Materials and Methods: We measured several wood hydraulic and structural traits (e.g., basic specific gravity, vessel area, and vessel diameter distribution) of 22 liana individuals in a single sandy site in Laussat, French Guiana. We compared the liana variability of these wood traits and the correlations among them with an existing liana pantropical dataset and two published datasets of trees originating from different, but species-rich, tropical sites. Results: Liana vessel diameter distribution and density were heterogeneous among individuals: there were two orders of magnitude difference between the smallest (4 µm) and the largest (494 µm) vessel diameters, a 50-fold difference existed between extreme vessel densities ranging from 1.8 to 89.3 vessels mm−2, the mean vessel diameter varied between 26 µm and 271 µm, and the individual theoretical stem hydraulic conductivity estimates ranged between 28 and 1041 kg m−1 s−1 MPa−1. Basic specific gravity varied between 0.26 and 0.61. Consequently, liana wood trait variability, even within a small sample, was comparable in magnitude with tree surveys from other tropical sites and the pantropical liana dataset. Conclusions: This study illustrates that even controlling for site and soil type, liana traits are heterogeneous and cannot be considered as a homogeneous growth form. Our results show that the liana hydraulic architecture heterogeneity across and within sites warrants further investigation in order to categorize lianas into functional groups in the same way as trees

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