Erratum: The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding RNA 2016, 2, 9.

Please note that in the published editorial [1], affiliations 1, and 8 contained errors.[...]

A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.

Microbial metabolites are an emerging class of mediators influencing CD4+ T-cell function. To advance the understanding of direct causal microbial factors contributing to Crohn's disease, we screened 139 predicted Crohn's disease-associated microbial metabolites for their bioactivity on human CD4+ T-cell functions induced by disease-associated T helper 17 (Th17) polarizing conditions. We observed 15 metabolites with CD4+ T-cell bioactivity, 3 previously reported, and 12 unprecedented. A deeper investigation of the microbe-derived metabolite, ascorbate, revealed its selective inhibition on activated human CD4+ effector T cells, including IL-17A-, IL-4-, and IFNγ-producing cells. Mechanistic assessment suggested the apoptosis of activated human CD4+ T cells associated with selective inhibition of energy metabolism. These findings suggest a substantial rate of relevant T-cell bioactivity among Crohn's disease-associated microbial metabolites, and evidence for novel modes of bioactivity, including targeting of T-cell energy metabolism

Helicobacter pylori versus the Host: Remodeling of the Bacterial Outer Membrane Is Required for Survival in the Gastric Mucosa

Modification of bacterial surface structures, such as the lipid A portion of lipopolysaccharide (LPS), is used by many pathogenic bacteria to help evade the host innate immune response. Helicobacter pylori, a gram-negative bacterium capable of chronic colonization of the human stomach, modifies its lipid A by removal of phosphate groups from the 1- and 4′-positions of the lipid A backbone. In this study, we identify the enzyme responsible for dephosphorylation of the lipid A 4′-phosphate group in H. pylori, Jhp1487 (LpxF). To ascertain the role these modifications play in the pathogenesis of H. pylori, we created mutants in lpxE (1-phosphatase), lpxF (4′-phosphatase) and a double lpxE/F mutant. Analysis of lipid A isolated from lpxE and lpxF mutants revealed lipid A species with a 1 or 4′-phosphate group, respectively while the double lpxE/F mutant revealed a bis-phosphorylated lipid A. Mutants lacking lpxE, lpxF, or lpxE/F show a 16, 360 and 1020 fold increase in sensitivity to the cationic antimicrobial peptide polymyxin B, respectively. Moreover, a similar loss of resistance is seen against a variety of CAMPs found in the human body including LL37, β-defensin 2, and P-113. Using a fluorescent derivative of polymyxin we demonstrate that, unlike wild type bacteria, polymyxin readily associates with the lpxE/F mutant. Presumably, the increase in the negative charge of H. pylori LPS allows for binding of the peptide to the bacterial surface. Interestingly, the action of LpxE and LpxF was shown to decrease recognition of Helicobacter LPS by the innate immune receptor, Toll-like Receptor 4. Furthermore, lpxE/F mutants were unable to colonize the gastric mucosa of C57BL/6J and C57BL/6J tlr4 -/- mice when compared to wild type H. pylori. Our results demonstrate that dephosphorylation of the lipid A domain of H. pylori LPS by LpxE and LpxF is key to its ability to colonize a mammalian host

Human oral viruses are personal, persistent and gender-consistent.

Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem

Visual Stability and the Motion Aftereffect: A Psychophysical Study Revealing Spatial Updating

Eye movements create an ever-changing image of the world on the retina. In particular, frequent saccades call for a compensatory mechanism to transform the changing visual information into a stable percept. To this end, the brain presumably uses internal copies of motor commands. Electrophysiological recordings of visual neurons in the primate lateral intraparietal cortex, the frontal eye fields, and the superior colliculus suggest that the receptive fields (RFs) of special neurons shift towards their post-saccadic positions before the onset of a saccade. However, the perceptual consequences of these shifts remain controversial. We wanted to test in humans whether a remapping of motion adaptation occurs in visual perception

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process

The regulation of microRNA activity

MicroRNAs are short, single-stranded, non-protein coding RNAs that negatively regulate gene expression. MicroRNAs have been shown to play a critical role in many biological processes and diseases. Therefore, it is critical to gain an understanding of the factors that can regulate microRNA activity. It has been established that, microRNA activity is exerted by a class of RNA-binding proteins called Argonautes. MicroRNAs arise from a transient duplex (the microRNA duplex) from which only one strand (the microRNA strand) is specifically sorted into an Argonaute protein, whereas the other strand (the microRNA* strand) is not. This observation provokes the question; how is the microRNA specifically sorted into an Argonaute protein? To this effect we have found that the differing 5\u27 terminal nucleotides of the microRNA and microRNA* strand are a critical determinant for strand specific sorting of the microRNA into Argonaute. Knowing that microRNAs proceed through a duplex intermediate we set out to identify a microRNA duplex unwindase. Biochemical purification of a microRNA duplex specific unwinding activity from cells yielded P68 RNA Helicase. We showed that P68 RNA Helicase is sufficient to unwind a microRNA duplex, and also that P68 is necessary for microRNA function in cells. Next we asked if silent mutations could create novel, non-canonical microRNA target sites. We identified a silent variant (G4304A) in the BRCA1 mRNA, creates a novel microRNA target site for microRNA-501.

The regulation of microRNA activity

MicroRNAs are short, single-stranded, non-protein coding RNAs that negatively regulate gene expression. MicroRNAs have been shown to play a critical role in many biological processes and diseases. Therefore, it is critical to gain an understanding of the factors that can regulate microRNA activity. It has been established that, microRNA activity is exerted by a class of RNA-binding proteins called Argonautes. MicroRNAs arise from a transient duplex (the microRNA duplex) from which only one strand (the microRNA strand) is specifically sorted into an Argonaute protein, whereas the other strand (the microRNA* strand) is not. This observation provokes the question; how is the microRNA specifically sorted into an Argonaute protein? To this effect we have found that the differing 5\u27 terminal nucleotides of the microRNA and microRNA* strand are a critical determinant for strand specific sorting of the microRNA into Argonaute. Knowing that microRNAs proceed through a duplex intermediate we set out to identify a microRNA duplex unwindase. Biochemical purification of a microRNA duplex specific unwinding activity from cells yielded P68 RNA Helicase. We showed that P68 RNA Helicase is sufficient to unwind a microRNA duplex, and also that P68 is necessary for microRNA function in cells. Next we asked if silent mutations could create novel, non-canonical microRNA target sites. We identified a silent variant (G4304A) in the BRCA1 mRNA, creates a novel microRNA target site for microRNA-501.

An Investigation of the Relationship Between Emergency Medicine Trainee Burnout and Clinical Performance in a High-fidelity Simulation Environment.

Objective: Burnout is prevalent among emergency medicine (EM) physicians, with physicians experiencing burnout more likely to report committing medical errors or delivering suboptimal care. The relationship between physician burnout and identifiable differences in clinical care, however, remains unclear. We examined if EM trainee burnout was associated with differences in clinical performance using high-fidelity simulation as a proxy for patient care. Methods: In this cross-sectional study across six institutions, we measured trainee performance over four simulation scenarios based on recognized EM milestones. For each scenario a faculty rater assessed whether the trainee performed predefined critical actions specific to each case. A summation of performed actions across all cases resulted in a cumulative task (CT) score (range = 0-85). Raters also assigned an impression score on a 10-point scale (0 = poor; 10 = outstanding) assessing the trainee\u27s overall performance after each scenario, with the mean of the scores resulting in an overall impression (OI) score. After the simulation assessment, we measured trainees\u27 burnout via the Maslach Burnout Inventory through a confidential, electronic survey. Trainee depression, quality of life (QOL) and daytime sleepiness were also evaluated. Survey results were compared to simulation scores using analysis of variance and covariance. Results: Fifty-eight of 89 (65.2%) eligible participants completed the survey and simulation assessment. Thirty-one of 58 (53.4%, 95% CI = 40.2% to 66.7%) trainees reported burnout. In trainees with burnout compared to those without, mean CT scores (73.4 vs. 75.2, 95% CI of difference Conclusion: Emergency medicine trainees with burnout received lower cumulative performance scores over four high-fidelity simulation scenarios than trainees without burnout