scholarly journals Virulence Traits and Population Genomics of the Black Yeast Aureobasidium melanogenum

2021 ◽  
Vol 7 (8) ◽  
pp. 665
Author(s):  
Anja Černoša ◽  
Xiaohuan Sun ◽  
Cene Gostinčar ◽  
Chao Fang ◽  
Nina Gunde-Cimerman ◽  
...  
Keyword(s):  
Hemolytic Activity ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Siderophore Production ◽  
Black Yeast ◽  
Phenotypic Data ◽  
Virulence Potential ◽  
Opportunistic Human Pathogen ◽  
Phylogenetic Lineages ◽  
Aureobasidium Melanogenum

The black yeast-like fungus Aureobasidium melanogenum is an opportunistic human pathogen frequently found indoors. Its traits, potentially linked to pathogenesis, have never been systematically studied. Here, we examine 49 A. melanogenum strains for growth at 37 °C, siderophore production, hemolytic activity, and assimilation of hydrocarbons and human neurotransmitters and report within-species variability. All but one strain grew at 37 °C. All strains produced siderophores and showed some hemolytic activity. The largest differences between strains were observed in the assimilation of hydrocarbons and human neurotransmitters. We show for the first time that fungi from the order Dothideales can assimilate aromatic hydrocarbons. To explain the background, we sequenced the genomes of all 49 strains and identified genes putatively involved in siderophore production and hemolysis. Genomic analysis revealed a fairly structured population of A. melanogenum, raising the possibility that some phylogenetic lineages have higher virulence potential than others. Population genomics indicated that the species is strictly clonal, although more than half of the genomes were diploid. The existence of relatively heterozygous diploids in an otherwise clonal species is described for only the second time in fungi. The genomic and phenotypic data from this study should help to resolve the non-trivial taxonomy of the genus Aureobasidium and reduce the medical hazards of exploiting the biotechnological potential of other, non-pathogenic species of this genus.

scholarly journals Hemolytic Activity and Siderophore Production in Different Aeromonas Species Isolated from Fish

1999 ◽  
Vol 65 (12) ◽  
pp. 5612-5614 ◽  
Author(s):  
Jesús A. Santos ◽  
César J. González ◽  
Andrés Otero ◽  
María-Luisa García-López
Keyword(s):  
Plasmid Dna ◽  
Hemolytic Activity ◽  
Siderophore Production ◽  
Aeromonas Species ◽  
Aeromonas Caviae ◽  
Apparent Relationship

ABSTRACT The hemolytic activity and siderophore production of several strains of motile aeromonads were determined. The hemolytic activity ofAeromonas caviae and Aeromonas eucrenophila was enhanced after trypsinization of the samples. The enhancement of hemolysis was observed in strains that carried an aerolysin-like gene, detected by a PCR procedure. Siderophore production was demonstrated in all but one strain of Aeromonas jandaei. No apparent relationship was observed between the presence of plasmid DNA and hemolysis or siderophore production.

scholarly journals Auxological and endocrine phenotype in a population-based cohort of patients with PROP1 gene defects

2005 ◽  
Vol 153 (3) ◽  
pp. 389-396 ◽  
Author(s):  
Jan Lebl ◽  
Jan Vosáhlo ◽  
Roland W Pfaeffle ◽  
Heike Stobbe ◽  
Jana Černá ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Population Based ◽  
Hormone Deficiency ◽  
Heterozygous Mutation ◽  
Pituitary Hormone ◽  
Phenotypic Analysis ◽  
Phenotypic Data ◽  
Sibling Pairs ◽  
Pituitary Development ◽  
Gene Defects

Objective: Multiple pituitary hormone deficiency (MPHD) may result from defects of transcription factors that govern early pituitary development. We aimed to establish the prevalence of HESX1, PROP1, and POU1F1 gene defects in a population-based cohort of patients with MPHD and to analyse the phenotype of affected individuals. Design and methods: Genomic analysis was carried out on 74 children and adults with MPHD from the Czech Republic (including four sibling pairs). Phenotypic data were collected from medical records and referring physicians. Results: One patient carried a heterozygous mutation of POU1F1 (71C > T), and 18 patients (including three sibling pairs) had a PROP1 mutation (genotypes 150delA/301delGA/9/, 301delGA/301-delGA/8/, or 301delGA/349T > A/1/). A detailed longitudinal phenotypic analysis was performed for patients with PROP1 mutations (n = 17). The mean ( ±s.d.) birth length SDS of these patients (0.12 ± 0.76) was lower than expected based on their mean ( ±s.d.) birth weight SDS (0.63 ± 1.27; P = 0.01). Parental heights were normal. The patients’ mean ( ±s.d.) height SDS declined to −1.5 ± 0.9, −3.6 ± 1.3 and −4.1 ± 1.2 at 1.5, 3 and 5 years of age, respectively. GH therapy, initiated at 6.8 ± 3.2 years of age (mean dose: 0.022 mg/kg per day), led to substantial growth acceleration in all patients. Mean adult height (n = 7) was normal when adjusted for mid-parental height. ACTH deficiency developed in two out of seven young adult patients. Conclusions: PROP1 defects are a prevalent cause of MPHD. We suggest that testing for PROP1 mutations in patients with MPHD might become standard practice in order to predict risk of additional pituitary hormone deficiencies.

Large-Scale Analysis of Genetic and Clinical Patient Data

2018 ◽  
Vol 1 (1) ◽  
pp. 263-274 ◽  
Author(s):  
Marylyn D. Ritchie
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Data Science ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Data Sets ◽  
Biomedical Data ◽  
Data Types ◽  
Phenotypic Data ◽  
Clinical Patient

Biomedical data science has experienced an explosion of new data over the past decade. Abundant genetic and genomic data are increasingly available in large, diverse data sets due to the maturation of modern molecular technologies. Along with these molecular data, dense, rich phenotypic data are also available on comprehensive clinical data sets from health care provider organizations, clinical trials, population health registries, and epidemiologic studies. The methods and approaches for interrogating these large genetic/genomic and clinical data sets continue to evolve rapidly, as our understanding of the questions and challenges continue to emerge. In this review, the state-of-the-art methodologies for genetic/genomic analysis along with complex phenomics will be discussed. This field is changing and adapting to the novel data types made available, as well as technological advances in computation and machine learning. Thus, I will also discuss the future challenges in this exciting and innovative space. The promises of precision medicine rely heavily on the ability to marry complex genetic/genomic data with clinical phenotypes in meaningful ways.

scholarly journals Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

2020 ◽  
Vol 8 (12) ◽  
pp. 2043
Author(s):  
Shawn M. Higdon ◽  
Bihua C. Huang ◽  
Alan B. Bennett ◽  
Bart C. Weimer
Keyword(s):  
Machine Learning ◽  
Nitrogen Fixation ◽  
Genome Wide Association Study ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Oxidation Reduction ◽  
Genome Wide ◽  
Biological Nitrogen ◽  
Carbohydrate Catabolism ◽  
Comparative Population

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

scholarly journals Hypervirulent Klebsiella pneumoniae Sequence Type 420 with a Chromosomally Inserted Virulence Plasmid

2021 ◽  
Vol 22 (17) ◽  
pp. 9196
Author(s):  
Elias Eger ◽  
Stefan E. Heiden ◽  
Karsten Becker ◽  
Andrea Rau ◽  
Katharina Geisenhainer ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bioinformatics Analysis ◽  
Genomic Analysis ◽  
Sequence Type ◽  
Siderophore Production ◽  
Virulence Plasmid ◽  
Site Infection ◽  
Multiple Site ◽  
Human Patient ◽  
Clinical Appearance

Background: Klebsiella pneumoniae causes severe diseases including sepsis, pneumonia and wound infections and is differentiated into hypervirulent (hvKp) and classic (cKp) pathotypes. hvKp isolates are characterized clinically by invasive and multiple site infection and phenotypically in particular through hypermucoviscosity and increased siderophore production, enabled by the presence of the respective virulence genes, which are partly carried on plasmids. Methods: Here, we analyzed two K. pneumoniae isolates of a human patient that caused severe multiple site infection. By applying both genomic and phenotypic experiments and combining basic science with clinical approaches, we aimed at characterizing the clinical background as well as the two isolates in-depth. This also included bioinformatics analysis of a chromosomal virulence plasmid integration event. Results: Our genomic analysis revealed that the two isolates were clonal and belonged to sequence type 420, which is not only the first description of this K. pneumoniae subtype in Germany but also suggests belonging to the hvKp pathotype. The latter was supported by the clinical appearance and our phenotypic findings revealing increased siderophore production and hypermucoviscosity similar to an archetypical, hypervirulent K. pneumoniae strain. In addition, our in-depth bioinformatics analysis suggested the insertion of a hypervirulence plasmid in the bacterial chromosome, mediated by a new IS5 family sub-group IS903 insertion sequence designated ISKpn74. Conclusion: Our study contributes not only to the understanding of hvKp and the association between hypervirulence and clinical outcomes but reveals the chromosomal integration of a virulence plasmid, which might lead to tremendous public health implications.

scholarly journals Integrative Genomic Analysis and Functional Studies Reveal GP5, GRN, MPO and MCAM as Causal Protein Biomarkers for Platelet Traits

2019 ◽  
Author(s):  
Dong Heon Lee ◽  
Chen Yao ◽  
Arunoday Bhan ◽  
Thorsten Schlaeger ◽  
Joshua Keefe ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Plasma Proteins ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Gene Knockdown ◽  
Sequencing Analysis ◽  
Protein Biomarkers ◽  
Association Analyses ◽  
Platelet Production ◽  
Platelet Counts

ABSTRACTRationaleMean platelet volume (MPV) and platelet count (PLT) are platelet measures that have been linked to cardiovascular disease (CVD) and mortality risk. Identifying protein biomarkers for these measures may yield insights into CVD mechanisms.ObjectiveWe aimed to identify causal protein biomarkers for MPV and PLT among 71 CVD-related plasma proteins measured in Framingham Heart Study (FHS) participants.Methods and ResultsWe conducted integrative analyses of genetic variants associated with PLT and MPV with protein quantitative trait locus (pQTL) variants associated with plasma proteins followed by Mendelian randomization (MR) to infer causal relations of proteins for PLT/MPV, and tested protein-PLT/MPV association in FHS participants. Utilizing induced pluripotent stem cell (iPSC)-derived megakaryocyte (MK) clones that produce functional platelets, we conducted RNA-sequencing and analyzed transcriptome-wide differences between low- and high-platelet producing clones. We then performed small interfering RNA (siRNA) gene knockdown experiments targeting genes encoding proteins with putatively causal platelet effects in MK clones to examine effects on platelet production. Protein-trait association analyses were conducted for MPV (n = 4,348) and PLT (n = 4,272). Eleven proteins were associated with MPV and 31 with PLT. MR identified four putatively causal proteins for MPV and four for PLT. Glycoprotein V (GP5), granulin (GRN), and melanoma cell adhesion molecule (MCAM) were associated with PLT in both protein-trait and MR analyses. Myeloperoxidase (MPO) showed significant association with MPV in both analyses. MK RNA-sequencing analysis results were directionally concordant with observed and MR-inferred associations for GP5, GRN, and MCAM. In siRNA gene knockdown experiments, silencing GP5, GRN, and MPO decreased platelet counts.ConclusionsBy integrating population genomics data, epidemiological data, and iPSC-derived MK experiments, we identified four proteins that are causally linked to platelet counts. These proteins and genes may be further explored for their utility in increasing platelet production in bioreactors for transfusion medicine purposes as well as their roles in the pathogenesis of CVD via a platelet/blood coagulation-based mechanism.

scholarly journals Virulence Potential of Penicillium Chrysogenum Isolated from Subclinical Bovine Mastitis

2021 ◽  
pp. 2131-2142
Author(s):  
Fadwa Abdul Razaq Jameel ◽  
Shaimaa Nabhan Yassein
Keyword(s):  
Virulence Factors ◽  
Hemolytic Activity ◽  
Penicillium Chrysogenum ◽  
Bovine Mastitis ◽  
Its Region ◽  
Blood Agar ◽  
Isolation And Identification ◽  
Virulence Potential ◽  
Urease Production ◽  
Polymerase Chain

    The present study aimed to the isolation and identification of Penicillium chrysogenum from subclinical bovine mastitis as well as the evaluation of their potential to produce the main virulence factors by assessing proteinase production, urease production, growth rate at 37 ̊C, and hemolytic activity on Blood agar. One hundred milk samples were assembled from the White Gold village and surrounded outlying farms of Abu-Ghraib, Baghdad province, during the period from November 2018 to March 2019. Each milk sample was tested for California Mastitis (CMT). The results indicated that 85% of the samples gave positive (+ve) results for CMT. Sixty six mycotic isolates were detected, including 31 isolates of Penicillium spp. (46.9%) and 23 isolates of P. chrysogenum (34.8%). All of P. chrysogenum isolates were identified by culturing on Sabouraud Dextrose Agar and Czapek Doxes Agar at 25 ºC for 5-7 days. P. chrysogenum was diagnosed by polymerase chain reaction (PCR) based on the internal transcribed spacer (ITS) region of fungal ribosomal DNA (rDNA). The results of genetic identities showed that this fungus had 94% matching with the reference strain. Also, this study indicated that P. chrysogenum has several virulence factors with the ability of this fungus to degrade both proteins (albumin and casein), hydrolyse urea, and grow ate 37 ̊C, but not to confer hemolytic activity on Blood Agar.

scholarly journals Siderophore production by Gram-negative rods isolated from human polymicrobial infections

2011 ◽  
Vol 48 (2) ◽  
pp. 147-157 ◽  
Author(s):  
Joanna Mokracka ◽  
Ewa Cichoszewska ◽  
Adam Kaznowski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Infections ◽  
Iron Chelator ◽  
Siderophore Production ◽  
The Other ◽  
Mixed Infections ◽  
Gram Negative ◽  
E Coli ◽  
Virulence Potential ◽  
Polymicrobial Infections

Siderophore production by Gram-negative rods isolated from human polymicrobial infectionsA total of 137 strains isolated from 67 mixed bacterial infections were examined for production and interchangeability of siderophores. The isolates comprised 109 strains belonging to 15 species of Enterobacteriaceae and 28 isolates of 6 species of non-fermenting rods. In 36 mixed infections (53.7%), the strains secreted siderophores of the same type. This concerned mostly strains belonging to the Enterobacteriaceae (46.3%), which produced enterobactin. We selected 37 pairs of strains that produced different siderophores. The strains examined were not able to use siderophores produced by the other isolate of the pair, except for 3 strains ofPseudomonas aeruginosathat used chelators excreted by enterobactin-producingE. coli.Our research indicates that in mixed polymicrobial infections the interchangeability of siderophores is possible, although it seems to be rare. More common is the production and secretion of the same chelator by strains participating in one infection, which definitely leads to an increase in the amount of iron chelator at the site of infection and, consequently, may enhance the virulence potential of bacteria, as the amount of siderophore seems to be directly related to the pathogenicity of a strain.

scholarly journals Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Eva Wagner ◽  
Andreas Zaiser ◽  
Rebekka Leitner ◽  
Narciso M. Quijada ◽  
Nadja Pracser ◽  
...  
Keyword(s):  
Food Processing ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Specific Sequence ◽  
Equal Distribution ◽  
Genetic Traits ◽  
Virulence Potential ◽  
Genetic Features ◽  
Source Category

Abstract Background Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years. Results The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase. Conclusions This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments, as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.

scholarly journals Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

2020 ◽  
Vol 21 (11) ◽  
pp. 3952 ◽  
Author(s):  
Alena Sokolkova ◽  
Sergey V. Bulyntsev ◽  
Peter L. Chang ◽  
Noelia Carrasquilla-Garcia ◽  
Anna A. Igolkina ◽  
...  
Keyword(s):  
Association Studies ◽  
Genomic Analysis ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Multiple Traits ◽  
Phenotypic Data ◽  
Genome Wide ◽  
Bioclimatic Variables ◽  
Modern Breeding

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.

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