Biology subjects

Daniel, R.

Publications and source records attributed to Daniel, R..

41 records · Page 3Linked to original sources

bioRxiv2019

Alanine Metabolism in Bacillus subtilis

Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers in genetic manipulation, the genes involved in alanine metabolism have not been characterised fully. Here we show that B. subtilis expresses an alanine uptake permease, YtnA (DatA), that has a major role in the assimilation of D-alanine from the environment. Since this isomer of the amino acid is not normally abundant it likely source is form the cells own cell wall probably through the action of carboxypeptidases and/or the spontaneous release of D-alanine from the teichoic acids. Also in this work we clarify the synthetic pathways acting in the biosynthesis of alanine. Genetically we show that, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, in B. subtilis the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, is present that can support slow growth of an alanine auxotroph however our data suggests that this enzyme probably synthesises D-alanine. In summary this work has provided an explanation of the observation that growth of B. subtilis is linked with an efficient recycling system for D-alanine that is released from the cell as the cell envelope is processed to permit cell enlargement. The results also suggest that the relative abundance of D- and L-alanine that might be linked with cytosolic pool of D and L-glutamate, and so enabling tight coupling protein and cell envelope synthesis with the metabolic status of the cell.

microbiology↗

bioRxiv2018

Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences

Main text Main text Methods Statistical data analysis Data availability Author Contributions Competing interests References Assessing the functional capability and redundancy of a microbial community is a major challenge in environmental microbiology. To address this challenge, we developed Tax4Fun2, a R-based tool for the rapid prediction of functional profiles and functional redundancy of prokaryotic communities from 16S rRNA gene sequences. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles can be substantially enhanced.\n\nMicroorganisms play a key role in ecosystem functioning1. High-throughput sequencing of 16S rRNA genes is a powerful and widely used approach to study the composi ...

bioinformatics↗

bioRxiv2018

The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes

Bacterial growth and cell division requires precise spatiotemporal regulation of the synthesis and remodelling of the peptidoglycan layer that surrounds the cytoplasmic membrane. GpsB is a cytosolic protein that affects cell wall synthesis by binding to the cytoplasmic mini-domains of peptidoglycan synthases to ensure their correct subcellular localisation. Here we have discovered critical structural features for the interaction of GpsB with peptidoglycan synthases from three different bacteria and demonstrated their importance for cell wall growth and viability. We have used these structural motifs to predict and confirm novel partners of GpsB in Bacillus subtilis, illuminating the role of this key regulator of peptidoglycan synthesis. GpsB thus functions as an adaptor, to mediate the interaction between membrane proteins, scaffolding proteins, signalling proteins and enzymes to generate larger protein complexes at specific sites in a bacterial cell cycle-dependent manner. Given the importance of GpsB in pathogenic bacteria, this study has not only revealed mechanistic details of how cell wall synthesis is co-ordinated with the bacterial cell cycle but could also represent a starting point for the design of much needed new antibiotics.

microbiology↗

bioRxiv2018

The impact of a governmental cash transfer programme on tuberculosis cure rate in Brazil: A quasi-experimental approach

BackgroundSocial vulnerability is strongly associated with tuberculosis (TB) indicators like cure rate. By addressing key social determinants, social protection policies such as Brazils Bolsa Familia Programme (BFP), a governmental conditional cash transfer, may play a role in TB control. Evidence is consolidating around a positive effect of social protection on TB outcomes, however methodological limitations prevent strong conclusions. This paper uses a quasi-experimental approach to more rigorously evaluate the effect of BFP on TB cure rate.\n\nMethods & FindingsThe data source was Brazils TB notification system (SINAN), linked to the national registry of those in poverty (CadUnico) and the BFP payroll. Propensity scores (PSs) were estimated from a complete-case logistic regression using covariates from this linked dataset, informed by a directed acyclic graph. Control patients were matched to exposed patients on the PS and the average effect of treatment on the treated (ATT) was estimated as the difference in TB cure rate between matched groups (n = 2167). The ATT was estimated as 10{middle dot}58 (95% CIs: 4{middle dot}39, 16{middle dot}77). This suggests that 10{middle dot}58% of the TB patients receiving BFP who were cured would not have been cured had they not received BFP. The direction of this effect was robust to sensitivity analyses performed and the PS matching broadly improved balance, although missing data limited the sample size.\n\nConclusionsThis work is the first quasi-experimental evaluation of social protection in wide-scale practice on TB outcomes. It demonstrates a positive effect of conditional cash transfers on TB cure rate consistent with existing work, suggesting changes to policy and future research on increasing access to social protection for TB patients who remain uncovered by the programme.

epidemiology↗

bioRxiv2016

No evidence for a bovine mastitis Escherichia coli pathotype

BackgroundEscherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli.\n\nResultsWe sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel.\n\nConclusionsThis is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract. Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC.

genomics↗