Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

APC Activation Restores Functional CD4+CD25+ Regulatory T Cells in NOD Mice that Can Prevent Diabetes Development

BACKGROUND: Defects in APC and regulatory cells are associated with diabetes development in NOD mice. We have shown previously that NOD APC are not effective at stimulating CD4(+)CD25(+) regulatory cell function in vitro. We hypothesize that failure of NOD APC to properly activate CD4(+)CD25(+) regulatory cells in vivo could compromise their ability to control pathogenic cells, and activation of NOD APC could restore this defect, thereby preventing disease. METHODOLOGY/PRINCIPAL FINDINGS: To test these hypotheses, we used the well-documented ability of complete Freund's adjuvant (CFA), an APC activator, to prevent disease in NOD mice. Phenotype and function of CD4(+)CD25(+) regulatory cells from untreated and CFA-treated NOD mice were determined by FACS, and in vitro and in vivo assays. APC from these mice were also evaluated for their ability to activate regulatory cells in vitro. We have found that sick NOD CD4(+)CD25(+) cells expressed Foxp3 at the same percentages, but decreased levels per cell, compared to young NOD or non-NOD controls. Treatment with CFA increased Foxp3 expression in NOD cells, and also increased the percentages of CD4(+)CD25(+)Foxp3(+) cells infiltrating the pancreas compared to untreated NOD mice. Moreover, CD4(+)CD25(+) cells from pancreatic LN of CFA-treated, but not untreated, NOD mice transferred protection from diabetes. Finally, APC isolated from CFA-treated mice increased Foxp3 and granzyme B expression as well as regulatory function by NOD CD4(+)CD25(+) cells in vitro compared to APC from untreated NOD mice. CONCLUSIONS/SIGNIFICANCE: These data suggest that regulatory T cell function and ability to control pathogenic cells can be enhanced in NOD mice by activating NOD APC

Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.

Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent-child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder. We searched for variants in 31 genes linked to GPI-anchor biogenesis and detected rare biallelic variants in PGAP3, PIGN, PIGT (n=2), PIGO and PIGL, providing a likely diagnosis for six families. In five families, the variants were in a compound heterozygous configuration while in a consanguineous Afghani kindred, a homozygous c.709G>C; p.(E237Q) variant in PIGT was identified within 10-12 Mb of autozygosity. Validation and segregation analysis was performed using Sanger sequencing. Across the six families, five siblings were available for testing and in all cases variants co-segregated consistent with them being causative. In four families, abnormal alkaline phosphatase results were observed in the direction expected. FACS analysis of knockout HEK293 cells that had been transfected with wild-type or mutant cDNA constructs demonstrated that the variants in PIGN, PIGT and PIGO all led to reduced activity. Splicing assays, performed using leucocyte RNA, showed that a c.336-2A>G variant in PIGL resulted in exon skipping and p.D113fs*2. Our results strengthen recently reported disease associations, suggest that defective GPI-anchor biogenesis may explain ~0.15% of individuals with developmental disorders and highlight the benefits of data sharing

Gut microbiota and diabetes: from pathogenesis to therapeutic perspective

More than several hundreds of millions of people will be diabetic and obese over the next decades in front of which the actual therapeutic approaches aim at treating the consequences rather than causes of the impaired metabolism. This strategy is not efficient and new paradigms should be found. The wide analysis of the genome cannot predict or explain more than 10–20% of the disease, whereas changes in feeding and social behavior have certainly a major impact. However, the molecular mechanisms linking environmental factors and genetic susceptibility were so far not envisioned until the recent discovery of a hidden source of genomic diversity, i.e., the metagenome. More than 3 million genes from several hundreds of species constitute our intestinal microbiome. First key experiments have demonstrated that this biome can by itself transfer metabolic disease. The mechanisms are unknown but could be involved in the modulation of energy harvesting capacity by the host as well as the low-grade inflammation and the corresponding immune response on adipose tissue plasticity, hepatic steatosis, insulin resistance and even the secondary cardiovascular events. Secreted bacterial factors reach the circulating blood, and even full bacteria from intestinal microbiota can reach tissues where inflammation is triggered. The last 5 years have demonstrated that intestinal microbiota, at its molecular level, is a causal factor early in the development of the diseases. Nonetheless, much more need to be uncovered in order to identify first, new predictive biomarkers so that preventive strategies based on pre- and probiotics, and second, new therapeutic strategies against the cause rather than the consequence of hyperglycemia and body weight gain

Leistungsauswirkungen von Simulationstraining für Medizinstudierende - eine systematische Übersichtsarbeit

Objective: Simulation based medical education (SBME) is fast becoming embedded into undergraduate medical curricula with many publications now describing its various modes and student self-reported impacts. This systematic review synthesizes the available literature for evidence of performance effects of SBME as an adjunct within traditional teaching programmes. Methods: A narrative systematic review was conducted according to PRISMA guidelines using Ovid MEDLINE, EMBASE, and PubMed databases for studies, published in English, reporting on general medical and surgical undergraduate SBME between 2010 to 2020. Two reviewers independently assessed potential studies for inclusion. Methods and topics of simulation with their assessments were evaluated. Descriptive statistics were used to describe pooled student cohorts. Results: 3074 articles were initially identified using the search criteria with 92 full-text articles then screened for eligibility. Nineteen articles, including nine randomised trials, concerning 2459 students (median 79/study), were selected for review. Cardiac scenarios were commonest (n=6) with three studies including surgical topics. Nine studies used mannequin simulators (median time/session 17.5minutes) versus standardised patients in seven (median time/session=82 minutes). Educational impact was measured by written (n=10), checklist (n=5) and OSCEs (n=3) assessment either alone or in combination (n=1, OSCE/written assessment). All articles reported a positive effect of SBME on knowledge including improved retention in three.Conclusion: SBME, as an adjunct to existing curricula, improves knowledge-based performance of medical students at least in the short-term. Future studies should broaden its topics, assess longer term impacts and cost-effectiveness while also considering whether and what areas of traditional undergraduate learning it can replace.Zielsetzung: Die simulationsbasierte medizinische Ausbildung (SBME, Simulation Based Medical Education) wird zunehmend zu einem festen Bestandteil des vorklinischen Curriculums. Es gibt inzwischen viele Veröffentlichungen, in denen die verschiedenen Formen der simulationsbasierten medizinischen Ausbildung und die von den Studierenden selbst beschriebenen Auswirkungen beschrieben werden. In dieser systematischen Übersichtsarbeit wird die verfügbare Literatur hinsichtlich nachweislicher Leistungsauswirkungen der SBME zusammengefasst, die als Ergänzung zu traditionellen Lehrprogrammen eingesetzt wird. Methodik: Es wurde eine narrative systematische Übersichtsarbeit gemäß den PRISMA-Leitlinien durchgeführt, bei der die Datenbanken Ovid MEDLINE, EMBASE und PubMed nach englischsprachigen Studien durchsucht wurden, die zwischen 2010 und 2020 über allgemeinmedizinische und chirurgische SBME-Maßnahmen in der Vorklinik berichtet haben. Zwei Reviewer werteten unabhängig voneinander potenzielle Studien für die Aufnahme in die Übersichtsarbeit aus. Es wurden Methoden und Themen der Simulation mit ihren Bewertungen untersucht. Zur Beschreibung gepoolter Studierendenkohorten wurde deskriptive Statistik verwendet. Ergebnisse: Anhand der Suchkriterien wurden zunächst 3074 Artikel ermittelt, von denen 92 Volltextartikel auf ihre Eignung geprüft wurden. Neunzehn Artikel, darunter neun randomisierte Studien, an denen 2459 Studierende teilnahmen (Median 79 pro Studie), wurden zur Auswertung ausgewählt. Am häufigsten waren kardiologische Szenarien (n=6). Drei Studien umfassten chirurgische Themen. In neun Studien wurden Simulationspuppen verwendet (mittlerer Zeitaufwand pro Sitzung: 17,5 Minuten), während in sieben Studien standardisierte Patienten eingesetzt wurden (mittlerer Zeitaufwand pro Sitzung: 82 Minuten). Die ausbildungsrelevanten Auswirkungen wurden durch schriftliche Bewertungen (n=10), Checklisten (n=5) und OSCE-Bewertungen (n=3) einzeln oder in Kombination (n=1, OSCE-Bewertung/schriftliche Bewertung) gemessen. Alle Artikel berichteten über eine positive Auswirkung der SBME auf die Wissensentwicklung. In drei Artikeln wurde darüber hinaus über eine verbesserte Beibehaltung von Wissen berichtet.Schlussfolgerung: SBME als Ergänzung zu bestehenden Curricula verbessert zumindest kurzfristig die wissensbasierte Leistung von Medizinstudierenden. Künftige Studien sollten die diesbezüglichen Untersuchungsthemen ausweiten, die längerfristigen Auswirkungen und die Kosteneffizienz bewerten und zudem auch prüfen, welche Bereiche der vorklinischen Ausbildung die SBME gegebenenfalls ersetzen kann