Population Polymorphism of Nuclear Mitochondrial DNA Insertions Reveals Widespread Diploidy Associated with Loss of Heterozygosity in Debaryomyces hansenii

ABSTRACT Debaryomyces hansenii, a yeast that participates in the elaboration of foodstuff, displays important genetic diversity. Our recent phylogenetic classification of this species led to the subdivision of the species into three distinct clades. D. hansenii harbors the highest number of nuclear mitochondrial DNA (NUMT) insertions known so far for hemiascomycetous yeasts. Here we assessed the intraspecific variability of the NUMTs in this species by testing their presence/absence first in 28 strains, with 21 loci previously detected in the completely sequenced strain CBS 767T, and second in a larger panel of 77 strains, with 8 most informative loci. We were able for the first time to structure populations in D. hansenii, although we observed little NUMT insertion variability within the clades. We determined the chronology of the NUMT insertions, which turned out to correlate with the previously defined taxonomy and provided additional evidence that colonization of nuclear genomes by mitochondrial DNA is a dynamic process in yeast. In combination with flow cytometry experiments, the NUMT analysis revealed the existence of both haploid and diploid strains, the latter being heterozygous and resulting from at least four crosses among strains from the various clades. As in the diploid pathogen Candida albicans, to which D. hansenii is phylogenetically related, we observed a differential loss of heterozygosity in the diploid strains, which can explain some of the large genetic diversity found in D. hansenii over the years.

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Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy

Microbiology Resource Announcements ◽

10.1128/mra.01037-18 ◽

2018 ◽

Vol 7 (11) ◽

Cited By ~ 5

Author(s):

Adelaide Milani ◽

Gianpiero Zamperin ◽

Alice Fusaro ◽

Annalisa Salviato ◽

Luca Bano ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Full Genome Sequence ◽

Full Genome ◽

High Genetic Diversity ◽

Content Type ◽

First Time

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.

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An Improved Method for Assessing Simple Sequence Repeat (SSR) Variation in Echinochloa crus-galli (L.) P. Beauv (Barnyardgrass)

Diversity ◽

10.3390/d14010003 ◽

2021 ◽

Vol 14 (1) ◽

pp. 3

Author(s):

Carlo Maria Cusaro ◽

Carolina Grazioli ◽

Francesco Zambuto ◽

Enrica Capelli ◽

Maura Brusoni

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Control Strategies ◽

Intraspecific Variability ◽

Rice Fields ◽

Lombardy Region ◽

Genetic Groups ◽

Amplification Protocol ◽

First Time ◽

Simple Sequence

Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass) is one of the most noxious weeds infesting Italian rice fields. It is characterized by high genetic intraspecific variability and has developed resistance to several classes of herbicides. The aim of our study was to assess, for the first time in Italy, the genetic diversity in E. crus-galli from differently managed rice fields in the Lombardy region (Northern Italy) using eight specific SSR markers. To this purpose, an amplification protocol was optimized, testing different DNA concentrations, PCR mixtures, and temperatures. A total of 48 alleles were identified in 144 samples. SSR fingerprint analysis using R 3.6.3 software (poppr, polysat, and StAMPP) allowed us to handle SSRs as codominant and polyploid data. The results suggested that genetic richness and diversity were high. The analysis of molecular variance (AMOVA) indicated that genetic variation exists mainly between agronomic managements (47.23%) and among populations (37.01%). Hierarchical clustering and PCoA were in concordance with the identification of four distinct genetic groups. Our results confirm that SSR markers represent a valuable and affordable tool for the assessment of E. crus-galli genetic diversity and would grant useful information to plan more targeted, effective, and sustainable control strategies against barnyardgrass. The improved methodology applied here allowed us to assess the genetic variability of an allo-hexaploid species without information loss and biased results.

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Nuclear and mitochondrial markers reveal the existence of several geographically concordant lineages within a Sahelian gecko species, Ptyodactylus ragazzii

Amphibia-Reptilia ◽

10.1163/15685381-00002873 ◽

2013 ◽

Vol 34 (1) ◽

pp. 85-93 ◽

Cited By ~ 5

Author(s):

Elsa Froufe ◽

Duarte V. Gonçalves ◽

José Carlos Brito ◽

David James Harris

Keyword(s):

Genetic Diversity ◽

Intraspecific Variability ◽

Distinct Species ◽

12S Rrna ◽

Nuclear Markers ◽

Mitochondrial Markers ◽

Species Complexes ◽

Mitochondrial 12S Rrna ◽

Mtdna Lineages ◽

First Time

The genetic diversity within Ptyodactylus ragazzii was analysed for the first time across the Western part of its range. We have used two mitochondrial (12s rRNA and 16s rRNA) and one nuclear (Cmos) marker to compare results directly with other related Ptyodactylus species, P. oudrii and P. hasselquistii. Results show high levels of intraspecific variability, with at least three divergent mtDNA lineages that have different haplotypes for Cmos and that are geographically concordant. P. ragazzii from Mauritania is probably a distinct species and possibly other lineages too, such as those from the Aïr Mountains in Niger, although more nuclear markers are needed to confirm this. All analysed Ptyodactylus species appear to be cryptic species complexes containing multiple deeply divergent forms, highlighting the need for a careful reassessment of the taxonomy of the whole genus.

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Epistemic warrant for categorizational activities and the development of controlled vocabularies

Journal of Documentation ◽

10.1108/jd-10-2016-0129 ◽

2017 ◽

Vol 73 (4) ◽

pp. 700-715 ◽

Cited By ~ 2

Author(s):

Daniel Martínez-Ávila ◽

John M. Budd

Keyword(s):

Information Science ◽

Controlled Vocabulary ◽

Knowledge Organization ◽

Library And Information Science ◽

Controlled Vocabularies ◽

Content Type ◽

Epistemic Warrant ◽

Ontological Approach ◽

First Time

Purpose The purpose of this paper is to update and review the concept of warrant in Library and Information Science (LIS) and to introduce the concept of epistemic warrant from philosophy. Epistemic warrant can be used to assess the content of a work; and therefore, it can be a complement to existing warrants, such as literary warrant, in the development of controlled vocabularies. In this proposal, the authors aim to activate a theoretical discussion on warrant in order to revise and improve the validity of the concept of warrant from the user and classifier context to the classificationist context. Design/methodology/approach The authors have conducted an extensive literary review and close reading of the concept of warrant in LIS and knowledge organization in order to detect the different stances and gaps in which the concept of epistemic warrant might apply. The authors adopted an epistemological approach, in the vein of some of the previous commenters on warrant, such as Hope Olson and Birger Hjørland, and built upon the theoretical framework of different authors working with the concept of warrant outside knowledge organization, such as Alvin Plantinga and Alvin Goldman. Findings There are some authors and critics in the literature that have voiced for a more epistemological approach to warrant (in opposition to a predominantly ontological approach). In this sense, epistemic warrant would be an epistemological warrant and also a step forward toward pragmatism in a prominently empiricist context such as the justification of the inclusion of terms in a controlled vocabulary. Epistemic warrant can be used to complement literary warrant in the development of controlled vocabularies as well as in the classification of works. Originality/value This paper presents an exhaustive update and revision of the concept of warrant, analyzing, systematizing, and reviewing the different warrants discussed in the LIS literary warrant in a critical way. The concept of epistemic warrant for categorizational activities is introduced to the LIS field for the first time. This paper, and the proposal of epistemic warrant, has the potential to contribute to the theoretical and practical discussions on the development of controlled vocabularies and assessment of the content of works.

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Use of Natural Transformation To Establish an Easy Knockout Method in Riemerella anatipestifer

Applied and Environmental Microbiology ◽

10.1128/aem.00127-17 ◽

2017 ◽

Vol 83 (9) ◽

Cited By ~ 11

Author(s):

MaFeng Liu ◽

Li Zhang ◽

Li Huang ◽

Francis Biville ◽

DeKang Zhu ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Transformation ◽

Genetic Manipulation ◽

Gene Knockout ◽

Targeted Mutagenesis ◽

Chromosomal Dna ◽

Content Type ◽

Riemerella Anatipestifer ◽

The Family ◽

First Time

ABSTRACT Riemerella anatipestifer is a member of the family Flavobacteriaceae and a major causative agent of duck serositis. Little is known about its genetics and pathogenesis. Several bacteria are competent for natural transformation; however, whether R. anatipestifer is also competent for natural transformation has not been investigated. Here, we showed that R. anatipestifer strain ATCC 11845 can uptake the chromosomal DNA of R. anatipestifer strain RA-CH-1 in all growth phases. Subsequently, a natural transformation-based knockout method was established for R. anatipestifer ATCC 11845. Targeted mutagenesis gave transformation frequencies of ∼10−5 transformants. Competition assay experiments showed that R. anatipestifer ATCC 11845 preferentially took up its own DNA rather than heterogeneous DNA, such as Escherichia coli DNA. Transformation was less efficient with the shuttle plasmid pLMF03 (transformation frequencies of ∼10−9 transformants). However, the efficiency of transformation was increased approximately 100-fold using pLMF03 derivatives containing R. anatipestifer DNA fragments (transformation frequencies of ∼10−7 transformants). Finally, we found that the R. anatipestifer RA-CH-1 strain was also naturally transformable, suggesting that natural competence is widely applicable for this species. The findings described here provide important tools for the genetic manipulation of R. anatipestifer. IMPORTANCE Riemerella anatipestifer is an important duck pathogen that belongs to the family Flavobacteriaceae. At least 21 different serotypes have been identified. Genetic diversity has been demonstrated among these serotypes. The genetic and pathogenic mechanisms of R. anatipestifer remain largely unknown because no genetic tools are available for this bacterium. At present, natural transformation has been found in some bacteria but not in R. anatipestifer. For the first time, we showed that natural transformation occurred in R. anatipestifer ATCC 11845 and R. anatipestifer RA-CH-1. Then, we established an easy gene knockout method in R. anatipestifer based on natural transformation. This information is important for further studies of the genetic diversity and pathogenesis in R. anatipestifer.

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Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

Journal of Bacteriology ◽

10.1128/jb.00347-16 ◽

2016 ◽

Vol 198 (20) ◽

pp. 2829-2840 ◽

Cited By ~ 11

Author(s):

Alejandra Culebro ◽

Joana Revez ◽

Ben Pascoe ◽

Yasmin Friedmann ◽

Matthew D. Hitchings ◽

...

Keyword(s):

Genetic Diversity ◽

Population Dynamics ◽

Chemical Composition ◽

Phenotypic Diversity ◽

Host Adaptation ◽

Campylobacter Coli ◽

Genomic Information ◽

Content Type ◽

Species Specific ◽

First Time

ABSTRACTDespite the importance of lipooligosaccharides (LOSs) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS inCampylobacter coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelatedC. coliisolates sampled from several different host species. Furthermore, we pairedC. coligenomic information and LOS chemical composition for the first time to investigate possible associations between LOS locus class sequence diversity and biochemical heterogeneity. After identifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structural heterogeneity. Mass spectrometry analysis of the LOSs of nine isolates, representing four different LOS classes, identified two features distinguishingC. coliLOS from that ofCampylobacter jejuni. 2-Amino-2-deoxy-d-glucose (GlcN)–GlcN disaccharides were present in the lipid A backbone, in contrast to the β-1′-6-linked 3-diamino-2,3-dideoxy-d-glucopyranose (GlcN3N)–GlcN backbone observed inC. jejuni. Moreover, despite the fact that many of the genes putatively involved in 3-acylamino-3,6-dideoxy-d-glucose (Quip3NAcyl) were apparently absent from the genomes of various isolates, this rare sugar was found in the outer core of allC. coliisolates. Therefore, regardless of the high genetic diversity of the LOS biosynthesis locus inC. coli, we identified species-specific phenotypic features ofC. coliLOS that might explain differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.IMPORTANCEDespite the importance ofC. colito human health and its controversial role as a causative agent of Guillain-Barré syndrome, little is known about the genetic and phenotypic diversity ofC. coliLOSs. Therefore, we pairedC. coligenomic information and LOS chemical composition for the first time to address this paucity of information. We identified two species-specific phenotypic features ofC. coliLOS, which might contribute to elucidating the reasons behind the differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.

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Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans

mBio ◽

10.1128/mbio.00129-11 ◽

2011 ◽

Vol 2 (4) ◽

Cited By ~ 136

Author(s):

A. Forche ◽

D. Abbey ◽

T. Pisithkul ◽

M. A. Weinzierl ◽

T. Ringstrom ◽

...

Keyword(s):

Oxidative Stress ◽

Genetic Diversity ◽

Candida Albicans ◽

Loss Of Heterozygosity ◽

Mitotic Recombination ◽

Stress Conditions ◽

Dependent Manner ◽

Content Type ◽

Different Types ◽

Stress Dependent

ABSTRACTGenetic diversity is often generated during adaptation to stress, and in eukaryotes some of this diversity is thought to arise via recombination and reassortment of alleles during meiosis.Candida albicans, the most prevalent pathogen of humans, has no known meiotic cycle, and yet it is a heterozygous diploid that undergoes mitotic recombination during somatic growth. It has been shown that clinical isolates as well as strains passaged once through a mammalian host undergo increased levels of recombination. Here, we tested the hypothesis that stress conditions increase rates of mitotic recombination inC. albicans, which is measured as loss of heterozygosity (LOH) at specific loci. We show that LOH rates are elevated duringin vitroexposure to oxidative stress, heat stress, and antifungal drugs. In addition, an increase in stress severity correlated well with increased LOH rates. LOH events can arise through local recombination, through homozygosis of longer tracts of chromosome arms, or by whole-chromosome homozygosis. Chromosome arm homozygosis was most prevalent in cultures grown under conventional lab conditions. Importantly, exposure to different stress conditions affected the levels of different types of LOH events, with oxidative stress causing increased recombination, while fluconazole and high temperature caused increases in events involving whole chromosomes. Thus,C. albicansgenerates increased amounts and different types of genetic diversity in response to a range of stress conditions, a process that we term “stress-induced LOH” that arises either by elevating rates of recombination and/or by increasing rates of chromosome missegregation.IMPORTANCEStress-induced mutagenesis fuels the evolution of bacterial pathogens and is mainly driven by genetic changes via mitotic recombination. Little is known about this process in other organisms.Candida albicans, an opportunistic fungal pathogen, causes infections that require adaptation to different host environmental niches. We measured the rates of LOH and the types of LOH events that appeared in the absence and in the presence of physiologically relevant stresses and found that stress causes a significant increase in the rates of LOH and that this increase is proportional to the degree of stress. Furthermore, the types of LOH events that arose differed in a stress-dependent manner, indicating that eukaryotic cells generate increased genetic diversity in response to a range of stress conditions. We propose that this “stress-induced LOH” facilitates the rapid adaptation ofC. albicans, which does not undergo meiosis, to changing environments within the host.

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Identification of VAR2CSA Domain-Specific Inhibitory Antibodies of the Plasmodium falciparum Erythrocyte Membrane Protein 1 Using a Novel Flow Cytometry Assay

Clinical and Vaccine Immunology ◽

10.1128/cvi.00638-12 ◽

2013 ◽

Vol 20 (3) ◽

pp. 433-442 ◽

Cited By ~ 14

Author(s):

Harold Obiakor ◽

Marion Avril ◽

Nicholas J. MacDonald ◽

Prakash Srinivasan ◽

Karine Reiter ◽

...

Keyword(s):

Flow Cytometry ◽

Plasmodium Falciparum ◽

Membrane Protein ◽

Chondroitin Sulfate ◽

Erythrocyte Membrane ◽

Recombinant Proteins ◽

Binding Assay ◽

Content Type ◽

Erythrocyte Membrane Protein ◽

First Time

ABSTRACTVAR2CSA, a member of thePlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1) family, is a leading candidate for use in vaccines to protect first-time mothers from placental malaria (PM). VAR2CSA, which is comprised of a series of six Duffy binding-like (DBL) domains, binds chondroitin sulfate A (CSA) on placental syncytiotrophoblast. Several recombinant DBL domains have been shown to bind CSA. In order to identify and develop recombinant proteins suitable for clinical development, DBL2X and DBL3X, as well as their respective third subdomain (S3) from the FCR3 parasite clone, were expressed inEscherichia coli, refolded, and purified. All but DBL3X-S3 recombinant proteins bound to CSA expressed on Chinese hamster ovary (CHO)-K1 cells but not to CHO-pgsA745 cells, which are CSA negative as determined by flow cytometry. All but DBL3X-S3 bound to CSA on chondroitin sulfate proteoglycan (CSPG) as determined by surface plasmon resonance (SPR) analysis. Purified IgG from rats and rabbits immunized with these four recombinant proteins bound homologous and some heterologous parasite-infected erythrocytes (IE). Using a novel flow cytometry inhibition-of-binding assay (flow-IBA), antibodies against DBL3X-S3 inhibited 35% and 45% of IE binding to CSA on CHO-K1 cells compared to results for soluble CSA (sCSA) and purified multigravida (MG) IgG, respectively, from areas in Tanzania to which malaria is endemic. Antibodies generated against the other domains provided little or no inhibition of IE binding to CSA on CHO-K1 cells as determined by the flow cytometry inhibition-of-binding assay. These results demonstrate for the first time the ability to identify antibodies to VAR2CSA DBL domains and subdomains capable of inhibiting VAR2CSA parasite-IE binding to CSA by flow cytometry. The flow cytometry inhibition-of-binding assay was robust and provided an accurate, reproducible, and reliable means to identify blocking of IE binding to CSA and promises to be significant in the development of a vaccine to protect pregnant women.

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Entrepreneurial intentions: a bibliometric analysis

Journal of Small Business and Enterprise Development ◽

10.1108/jsbed-07-2019-0221 ◽

2020 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

José L. Ruiz-Alba ◽

Vanesa F. Guzman-Parra ◽

José Roberto Vila Oblitas ◽

Javier Morales Mediano

Keyword(s):

Research Study ◽

Current Knowledge ◽

Entrepreneurial Intentions ◽

Content Type ◽

Main Research ◽

Subject Areas ◽

First Time ◽

Bibliometric Studies ◽

Shed Light

PurposeThe purpose of this research is to identify the main authors, the main influential universities doing research on entrepreneurial intentions (EIs), the main subject areas and the main productive academic journals on this topic. This paper also aims to shed light on the current knowledge and contributions to the field, in particular co-authorships, co-words, research topics and cluster of themes.Design/methodology/approachThe methodology is based on bibliometric techniques using mapping and clustering. The study has been conducted on 377 articles published in journals indexed in the Scopus database for a period of almost 24 years, that is, from 1 January 1993 to 8 July 2016. VOSviewer software was used to conduct the analysis.FindingsFindings highlight the top authors, the ranking of the main journals and universities doing research in the field of EIs. Another relevant contribution is the identification and classification of main research streams and gaps that have been highlighted.Originality/valueThis paper is an attempt to clarify the state of the research study and to analyse the progress of the studies on EIs and to elaborate bibliometric studies that help to give some order to the variety of sources. This is helpful for new researchers approaching EIs for the first time and also for those who are familiar with the field.

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A review of the Toulon-Verona Conference Excellence in Services best papers 2008-2016

The TQM Journal ◽

10.1108/tqm-11-2017-0145 ◽

2018 ◽

Vol 30 (5) ◽

pp. 638-646

Author(s):

Antigoni Papadimitriou

Keyword(s):

Methodological Approach ◽

Geographic Location ◽

Scientific Committee ◽

Lead Author ◽

Future Research ◽

Content Type ◽

Number Of Citations ◽

First Time ◽

Practical Implications

Purpose The purpose of this paper is to review and explore the primary characteristics of the best papers, which have been selected by the Toulon-Verona Conference (TVC) Excellence in Services scientific committee for the period 2008-2016. Design/methodology/approach The study includes a review of the best papers (n = 51) selected by the TVC’s scientific committee from 2008 to 2016 and obtained through the TVC’s archives. The primary highlights of each paper include number of authors, authorship profile (i.e. lead author affiliation, gender, and geographic location), co-authors’ geographic locations, classification of the papers, research topics, varieties of research methods used, number of electronic downloads (as of June 2017), number of citations, and subject keywords. Coding sheet developed to ensure standardization, consistency and to ensure the relevant data were collected for the content analysis. Mixed methods analysis (analyze quantitative data qualitative and and vice versa) was used to provide descriptive statistics. Findings In total, 51 best papers have been selected by the TVC scientific committee and reflected 145 authors. Lead authors were from a total of 50 HEIs worldwide and one consultant (private sector). Six papers were self-authored while the 45 were multi-authored. The majority of the papers written by Italian authors (58.8 percent); followed by France, Greece, and Sweden (5.9 percent each); Australia, Portugal, Spain, and UK (4 percent each); Austria, Norway, Slovenia, and Vietnam (1.9 percent each). In total, 37 papers were classified as a research paper, 10 case studies, and 4 theoretical. Practical implications The analysis for the first time define methodological trends for the TVC’s best papers and suggest possible future research topic and methodological approach for research in the management field. Originality/value The findings are unique for the TVC conference, for the TQM’s special issue, which provide practical implications for researchers and conference organizers and contribute to the literature of analyzing published papers.

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