scholarly journals Introgression in the genus Campylobacter: generation and spread of mosaic alleles

Microbiology ◽  
2011 ◽  
Vol 157 (4) ◽  
pp. 1066-1074 ◽  
Author(s):  
Samuel K. Sheppard ◽  
Noel D. McCarthy ◽  
Keith A. Jolley ◽  
Martin C. J. Maiden
Keyword(s):  
Gene Transfer ◽  
Clustering Algorithm ◽  
Housekeeping Gene ◽  
Species Group ◽  
Campylobacter Coli ◽  
Model Based Clustering ◽  
Assignment Probability ◽  
Nucleotide Divergence ◽  
Clade 1 ◽  
Taxonomic Groups

Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes – currently classified as microbiological species – evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species, Campylobacter jejuni and Campylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithm structure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using the structure linkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto a clonalframe genealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % of C. coli clade 1 alleles having acquired C. jejuni sequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread within C. coli clade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition of C. coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals A Hybrid Deep Clustering Approach for Robust Cell Type Profiling Using Single-cell RNA-seq Data

2019 ◽  
Author(s):  
Suhas Srinivasan ◽  
Nathan T. Johnson ◽  
Dmitry Korkin
Keyword(s):  
Deep Learning ◽  
Single Cell ◽  
Clustering Algorithm ◽  
Hybrid Approach ◽  
Feature Learning ◽  
Specific Cell ◽  
Clustering Methods ◽  
Model Based Clustering ◽  
Clustering And Classification ◽  
Living Organisms

AbstractSingle-cell RNA sequencing (scRNA-seq) is a recent technology that enables fine-grained discovery of cellular subtypes and specific cell states. It routinely uses machine learning methods, such as feature learning, clustering, and classification, to assist in uncovering novel information from scRNA-seq data. However, current methods are not well suited to deal with the substantial amounts of noise that is created by the experiments or the variation that occurs due to differences in the cells of the same type. Here, we develop a new hybrid approach, Deep Unsupervised Single-cell Clustering (DUSC), that integrates feature generation based on a deep learning architecture with a model-based clustering algorithm, to find a compact and informative representation of the single-cell transcriptomic data generating robust clusters. We also include a technique to estimate an efficient number of latent features in the deep learning model. Our method outperforms both classical and state-of-the-art feature learning and clustering methods, approaching the accuracy of supervised learning. The method is freely available to the community and will hopefully facilitate our understanding of the cellular atlas of living organisms as well as provide the means to improve patient diagnostics and treatment.

scholarly journals Changes in rearing conditions rapidly modify gut microbiota structure in Tenebrio molitor larvae

2018 ◽  
Author(s):  
Marine Cambon ◽  
Jean-Claude Ogier ◽  
Anne Lanois ◽  
Jean-Baptiste Ferdy ◽  
Sophie Gaudriault
Keyword(s):  
Gut Microbiota ◽  
Housekeeping Gene ◽  
Tenebrio Molitor ◽  
Absolute Quantification ◽  
Rrna Gene ◽  
Composition And Structure ◽  
Rearing Conditions ◽  
Mutualistic Relationship ◽  
Taxonomic Groups ◽  
Multicellular Organisms

AbstractThe gut microbiota of multicellular organisms has been shown to play a key role in their host biology. In mammals, it has an invariant component, responsible for establishing a mutualistic relationship with the host. It also contains a dynamic fraction which facilitates adaptation in response to changes in the environment. These features have been well described in mammals, but little is known about microbiota stability or plasticity in insects. We assessed changes in microbiota composition and structure in a reared insect after a change in rearing conditions. We reared Tenebrio molitor (Coleoptera, Tenebrioninae) larvae for five days in soil samples from two river banks and analyzed their gut microbial communities by a metabarcoding technique, using the V3-V4 region of the 16S rRNA gene and the housekeeping gene gyrB. We found that soil-reared insects had a significantly more diverse microbiota than the control insects and that insects reared in soil from different sites had significantly different microbiota. We confirmed this trend by absolute quantification of the two mains fluctuating taxonomic groups: the Enterobacteriaceae family and the Pseudomonas genus, dominant in the soil-reared insects and in the control insects, respectively. Our results suggest the existence of a resident microbiota in T. molitor gut, but indicate that rearing changes can induce rapid and profound changes in the relative abundance of some of the members of this resident microbiota.

The development of a representative multidimensional transient duty cycle for in-service switcher locomotives

2021 ◽  
pp. 095440972110418
Author(s):  
Mohamed A Hegazi ◽  
Andreas Hoffrichter ◽  
Jeffrey L Andrews ◽  
Gordon Lovegrove
Keyword(s):  
Duty Cycle ◽  
Electric Propulsion ◽  
Clustering Algorithm ◽  
Power Level ◽  
Time Data ◽  
Major Drawback ◽  
Model Based Clustering ◽  
Engine Efficiency ◽  
Duty Cycles ◽  
Acceleration And Deceleration

Switcher locomotives operate in railway yards where they shunt railcars and assemble trains. Shunting railcars requires frequent aggressive acceleration and deceleration events in order for the locomotive to push or pull railcars onto specific tracks. As a result, switcher locomotives rarely sustain tractive power for any significant period of time. Given that all switchers in North America rely on diesel-electric propulsion; the result is rapid and frequent transitions in engine power leading to a very low engine efficiency and high levels of emissions. Any attempt to quantify or remedy these issues will face a lack of a representative profile or test cycle. A locomotive duty cycle is a breakdown of time spent at each power level of the locomotive’s engine. A major drawback of current duty cycles is that they only account for steady power. Such cycles are not representative of real switcher locomotive operation. This paper presents a real-world transient duty cycle for switcher locomotives that accounts for the rapid power transitions and is argued to be more statistically representative of actual operations. The methodology adopted relies on real-time data collection, microtrip based trip segmentation, and a finite mixture model-based clustering algorithm. Measurements were collected on a EMD 16-645 GP9 locomotive. The duty cycle developed herein is representative of switching operations in Southern Railway of British Columbia’s New Westminster Yard as an example of the methodology which can be repeated in other cases as well.

scholarly journals Distribution of fungi and their toxic metabolites in melon and sesame seeds marketed in two major producing states in Nigeria

2020 ◽  
Vol 36 (4) ◽  
pp. 361-369
Author(s):  
Adetoun O. Esan ◽  
Stephen O. Fapohunda ◽  
Chibundu N. Ezekiel ◽  
Michael Sulyok ◽  
Rudolf Krska
Keyword(s):  
Monomethyl Ether ◽  
Species Group ◽  
Fusarium Fujikuroi ◽  
Human Consumption ◽  
The European Union ◽  
Alternariol Monomethyl Ether ◽  
Total Aflatoxin ◽  
Sesame Seeds ◽  
Mycotoxin Contamination ◽  
Taxonomic Groups

Abstract In this study, melon (n = 60) and sesame (n = 60) seeds purchased from markets within Benue and Nasarawa states, respectively, in Nigeria, during two seasons (dry and wet), were analysed for fungal and mycotoxin contamination in order to determine the safety of these foods for human consumption. Molecular analysis revealed the following seven fungal taxonomic groups in the foods: Aspergillus section Candidi, Aspergillus section Flavi, Aspergillus section Nigri, Cladosporium, Fusarium fujikuroi species group, Penicillium, and Pleosporales/Didymellaceae. A total of 78 microbial metabolites, including several mycotoxins, occurred in the foods. The most frequent mycotoxins in melon and sesame were aflatoxin B1 (occurrence: 76%) and alternariol monomethyl ether (occurrence: 59%), respectively. However, higher mean total aflatoxin levels occurred in sesame (17 μg kg−1) than in melon (11 μg kg−1). About 28 and 5% of melon and sesame, respectively, exceeded the 4 μg kg−1 total aflatoxin limit for oilseeds intended for direct human consumption in the European Union. Additionally, fumonisin B1 and moniliformin occurred only in sesame, whilst ochratoxins A and B occurred only in melon; ochratoxin B being reported for the first time in this food. Our data indicated seasonal variations in the fungal and mycotoxin contamination levels in both foods.

scholarly journals 205 Runs of homozygosity and analysis of inbreeding depression

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 39-40
Author(s):  
Pattarapol Sumreddee ◽  
Sajjad Toghiani ◽  
Andrew J Roberts ◽  
El H Hay ◽  
Samuel E Aggrey ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Clustering Algorithm ◽  
Search Algorithm ◽  
Pedigree Information ◽  
Minimum Length ◽  
Runs Of Homozygosity ◽  
Model Based Clustering ◽  
Genome Wide ◽  
Hereford Cattle ◽  
Density Marker

Abstract Pedigree information was traditionally used to assess inbreeding. Availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) is emerging as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify chromosomal contribution to genome-wide inbreeding. Unfortunately, identifying ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify a ROH segment has major effects on the estimation of inbreeding, yet it is arbitrarily set. Understanding the rise, purging, and the effects of deleterious mutations requires the ability to discriminate between ancient and recent inbreeding. However, thresholds to discriminate between short and long ROH segments are largely unknown. To address these questions, an inbred Hereford cattle population of 785 animals genotyped for 30,220 SNPs was used. A search algorithm to approximate mutation loads was used to determine the minimum length of ROH segments. It consisted of finding genome segments with significant differences in trait means between animals with high and low autozygosity intervals at certain threshold values. The minimum length was around 1 Mb for weaning and yearling weights and ADG, and 2.5 Mb for birth weight. Using a model-based clustering algorithm, a mixture of three Gaussian distributions was clearly separable, resulting in three classes of short (< 6.16 Mb), medium (6.16–12.57 Mb), and long (>12.27 Mb) ROH segments, representing ancient, intermediate, and recent inbreeding. Contribution of ancient, intermediate and recent to genome-wide inbreeding was 37.4%, 40.1% and 22.5%, respectively. Inbreeding depression analyses showed a greater damaging effect of recent inbreeding, likely due to purging of old highly deleterious haplotypes.

scholarly journals Genetic Diversity and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1193
Author(s):  
Clementine Namazzi ◽  
Julius Pyton Sserumaga ◽  
Swidiq Mugerwa ◽  
Martina Kyalo ◽  
Collins Mutai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Crop Production ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Model Based Clustering ◽  
High Gene ◽  
Nj Tree ◽  
Improvement Programs ◽  
The Tropics

Brachiaria (syn. Urochloa) grass is an important tropical forage of African origin that supports millions of livestock and wildlife in the tropics. Overgrazing, conversion of grasslands for crop production and non-agricultural uses, and the introduction of improved forages have threatened the natural diversity of Brachiaria grass in Uganda. This study established a national collection of Brachiaria ecotypes in Uganda and analyzed them for genetic diversity and population structure using 24 simple sequence repeats (SSR) markers. These markers had a high discriminating ability with an average polymorphism information content (PIC) of 0.89 and detected 584 alleles in 99 ecotypes. Analysis of molecular variance revealed a high within populations variance (98%) indicating a high gene exchange or low genetic differentiation (PhiPT = 00.016) among the ecotype populations. The Bayesian model based clustering algorithm showed three allelic pools in Ugandan ecotypes. The principal component analysis (PCA) of ecotypes, and Neighbor-joining (NJ) tree of ecotypes and six commercial cultivars showed three main groups with variable membership coefficients. About 95% of ecotype pairs had Rogers’ genetic distance above 0.75, suggesting most of them were distantly related. This study confirms the high value of these ecotypes in Brachiaria grass conservation and improvement programs in Uganda and elsewhere.

scholarly journals Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov.

2006 ◽  
Vol 56 (3) ◽  
pp. 577-581 ◽  
Author(s):  
Pavel Švec ◽  
Marc Vancanneyt ◽  
Ivo Sedláček ◽  
Sabri M. Naser ◽  
Cindy Snauwaert ◽  
...  
Keyword(s):  
Housekeeping Gene ◽  
Species Group ◽  
Cell Protein ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Novel Taxa ◽  
Respective Type ◽  
Type Strains

Three enterococci constituted two aberrant branches after numerical analysis of (GTG)5-PCR fingerprints: analogous patterns were found for two water isolates, strains W213 and W442T, and a separate position was found for an isolate from the gut of a termite, strain LMG 8895T. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. Further sequencing analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase α-subunit) and whole-cell-protein analysis confirmed a distinct position for the two water isolates and the termite strain, respectively. DNA–DNA hybridization experiments and distinct phenotypic features between the strains studied and representatives of the E. faecalis species group confirmed novel species status, respectively, for the two water isolates, strains W213 and W442T, and for strain LMG 8895T. The names Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov. are proposed for the novel taxa, with W442T (=CCM 7319T=LMG 23085T) and LMG 8895T (=CCM 7300T) as the respective type strains.

scholarly journals Molecular Phylogeny of the Salmonellae: Relationships among Salmonella Species and Subspecies Determined from Four Housekeeping Genes and Evidence of Lateral Gene Transfer Events

2008 ◽  
Vol 190 (21) ◽  
pp. 7060-7067 ◽  
Author(s):  
J. R. McQuiston ◽  
S. Herrera-Leon ◽  
B. C. Wertheim ◽  
J. Doyle ◽  
P. I. Fields ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Salmonella Enterica ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Diverse Group ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Common Serotypes

ABSTRACT The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

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