scholarly journals Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

2019 ◽  
Vol 222 (3) ◽  
pp. 1584-1598 ◽  
Author(s):  
Emmanuelle Morin ◽  
Shingo Miyauchi ◽  
Hélène San Clemente ◽  
Eric C. H. Chen ◽  
Adrian Pelin ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Rhizophagus Irregularis ◽  
Gigaspora Rosea ◽  
Genetic Features

scholarly journals Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

2020 ◽  
Author(s):  
Camilla Fagorzi ◽  
Alexandru Ilie ◽  
Francesca Decorosi ◽  
Lisa Cangioli ◽  
Carlo Viti ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Comparative Genomics ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Associated Bacteria ◽  
Phenotypic Differences ◽  
Genetic Features ◽  
Alkaline Conditions ◽  
High Throughput Phenotyping ◽  
Acidic Conditions

ABSTRACTRhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF emerged several times within the genus Ensifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

scholarly journals DNA-foraging bacteria in the seafloor

2019 ◽  
Author(s):  
Kenneth Wasmund ◽  
Claus Pelikan ◽  
Margarete Watzka ◽  
Andreas Richter ◽  
Amy Noel ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Stable Isotope ◽  
Carbon Source ◽  
Marine Sediments ◽  
Ecosystem Function ◽  
Stable Isotope Probing ◽  
Extracellular Dna ◽  
Genetic Features ◽  
Close Relatives ◽  
Globally Distributed

AbstractExtracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of key DNA-foraging microorganisms in marine sediments are completely unknown. Here we combined microcosm experiments, stable isotope probing and genome-centric metagenomics to study microbial catabolism of DNA and its sub-components in anoxic marine sediments.13C-DNA added to sediment microcosms was degraded within ten days and mineralised to13CO2. Stable isotope probing showed that diverseCandidatusIzemoplasma,Lutibacter, Shewanella, FusibacteraceaeandNitrincolaceaeincorporated DNA-derived13C-carbon. Genomes representative of the13C-labelled taxa were recovered and all encoded enzymatic repertoires for catabolism of DNA. Comparative genomics indicated that DNA can be digested by diverse members of the orderCandidatusIzemoplasmatales (formerTenericutes), which appear to be specialised DNA-degraders that encode multiple extracellular nucleases.Fusibacteraceaelacked genes for extracellular nucleases but utilised various individual purine- and pyrimidine-based molecules, suggesting they ‘cheated’ on liberated sub-components of DNA. Close relatives of the DNA-degrading taxa are globally distributed in marine sediments, suggesting that these poorly understood taxa contribute widely to the key ecosystem function of degrading and recycling DNA in the seabed.

scholarly journals Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species

2020 ◽  
Vol 21 (14) ◽  
pp. 4922
Author(s):  
Artur Pinski ◽  
Joanna Zur ◽  
Robert Hasterok ◽  
Katarzyna Hupert-Kocurek
Keyword(s):  
Comparative Genomics ◽  
Stenotrophomonas Maltophilia ◽  
Growth Promotion ◽  
Genetic Differences ◽  
Cold Shock Protein ◽  
Promising Alternative ◽  
Genetic Features ◽  
Characteristic Features ◽  
Stenotrophomonas Rhizophila ◽  
Chitin Binding Protein

Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.

scholarly journals Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping

2020 ◽  
Vol 12 (12) ◽  
pp. 2521-2534
Author(s):  
Camilla Fagorzi ◽  
Alexandru Ilie ◽  
Francesca Decorosi ◽  
Lisa Cangioli ◽  
Carlo Viti ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Comparative Genomics ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Phenotypic Differences ◽  
Genetic Features ◽  
Alkaline Conditions ◽  
High Throughput Phenotyping ◽  
Acidic Conditions

Abstract Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

Abstract #1061: Cribriform-Morular Variant Thyroid Cancer(C-MV TC): Clinical, Histopathological and Genetic Features

2015 ◽  
Vol 21 ◽  
pp. 222
Author(s):  
Mohammed Ahmed ◽  
Abdulrahman Alkabbani ◽  
Tarek Amin ◽  
Hindi Alhindi
Keyword(s):  
Thyroid Cancer ◽  
Genetic Features ◽  
Cribriform Morular Variant

Ethical Issues Relevant to the Assessment of Suicide Risk in Nonclinical Research Settings

Crisis ◽  
2012 ◽  
Vol 33 (1) ◽  
pp. 54-59 ◽  
Author(s):  
Carolyn M. Wilson ◽  
Bruce K. Christensen
Keyword(s):  
Undergraduate Students ◽  
Suicide Risk ◽  
Ethical Issues ◽  
Current Paper ◽  
Self Report ◽  
Ethical Guidelines ◽  
Schizotypal Personality ◽  
Increased Risk ◽  
Genetic Features ◽  
Conducting Research

Background: Our laboratory recently confronted this issue while conducting research with undergraduate students at the University of Waterloo (UW). Although our main objective was to examine cognitive and genetic features of individuals with schizotypal personality disorder (SPD), the study protocol also entailed the completion of various self-report measures to identify participants deemed at increased risk for suicide. Aims and Methods: This paper seeks to review and discuss the relevant ethical guidelines and legislation that bear upon a psychologist’s obligation to further assess and intervene when research participants reveal that they are at increased risk for suicide. Results and Conclusions: In the current paper we argue that psychologists are ethically impelled to assess and appropriately intervene in cases of suicide risk, even when such risk is revealed within a research context. We also discuss how any such obligation may potentially be modulated by the research participant’s expectations of the role of a psychologist, within such a context. Although the focus of the current paper is on the ethical obligations of psychologists, specifically those practicing within Canada, the relevance of this paper extends to all regulated health professionals conducting research in nonclinical settings.

WNT Medulloblastoma: More than just β-Catenin Mutations – Rare Genetic Features in the Focus

2019 ◽  
Author(s):  
T Goschzik ◽  
E Dörner ◽  
A zur Mühlen ◽  
T Pietsch
Keyword(s):  
Genetic Features
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