Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis.

Replication-transcription collisions shape genomes, influence evolution, and promote genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is especially disruptive to replication and promotes genomic instability. Here, we find that head-on collisions promote R-loop formation in Bacillus subtilis. We show that pervasive R-loop formation at head-on collision regions completely blocks replication, elevates mutagenesis, and inhibits gene expression. Accordingly, the activity of the R-loop processing enzyme RNase HIII at collision regions is crucial for stress survival in B. subtilis, as many stress response genes are head-on to replication. Remarkably, without RNase HIII, the ability of the intracellular pathogen Listeria monocytogenes to infect and replicate in hosts is weakened significantly, most likely because many virulence genes are head-on to replication. We conclude that the detrimental effects of head-on collisions stem primarily from excessive R-loop formation and that the resolution of these structures is critical for bacterial stress survival and pathogenesis.

First discovered, long out of sight, finally visible: ribosomal DNA.

With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.

Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides.

Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans, Rhodobacter sphaeroides, and Zymomonas mobilis show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis, N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides. We screen a synthetic promoter library to identify isopropyl ß-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in N. aromaticivorans and ~5-fold induction in R. sphaeroides). Combining Tn7 integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for N. aromaticivorans and R. sphaeroides (up to ~10-fold knockdown in N. aromaticivorans and R. sphaeroides) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria.IMPORTANCEIt is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the N. aromaticivorans or R. sphaeroides genome and control of gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to aid in optimizing yield of biofuels and bioproducts.

Strategies for recruiting adolescents in rural areas in firearm injury research.

BACKGROUND: Participant recruitment is a central aspect of human sciences research. Barriers to participant recruitment can be categorised into participant, recruiter and institutional factors. Firearm injury research poses unique barriers to recruitment. This is especially true for rural adolescents, who are at high risk for firearm-related injury and death, and whose voice is often absent in firearms research. In particular, recruitment strategies targeting adolescents should align with developmental changes occurring during this life stage. Identifying strategies to address recruitment barriers tailored to firearm-related research can help future researchers engage rural adolescents in injury prevention efforts. PURPOSE: The purpose of the current methodology paper is to outline barriers and provide strategies for recruiting rural adolescents in firearms research informed by the Youth Experiences in Rural Washington: Research on Firearm Safety project, a mixed-methods, community-based participatory research study of 13-18 year-olds residing in rural Washington. STRATEGIES: Recruitment barriers and related strategies were organised by participant-related and recruiter-related/institutional-related factors. While carrying out the study, key considerations or strategies which addressed multiple participant and recruiter/institutional factors, emerged with potential to enhance firearm-related research with rural adolescents more broadly. Key considerations included logistics (ie, scheduling flexibility, adequate and aligned incentives), use of a community-based participatory research approach and accounting for developmental stage. CONCLUSION: Reducing the burden of firearm injury and death for rural adolescents and developing effective interventions requires understanding and navigating recruitment barriers. Strategies used in the current project can guide future qualitative or mixed methods data collection informing firearm injury prevention.

Association between nurses' personal, professional and work characteristics, and engagement in hospital-based clinical research.

PURPOSE: The purpose of this study was to assess the associations between demographic, professional and other personal nurse characteristics, social support factors and comfort in conducting research with nurses' level of active participation in clinical research. DESIGN: A prospective, cross-sectional, correlational design was used. METHODS: Clinical nurses working in a multihospital healthcare system were recruited by email to complete an anonymous survey that used multiple valid and reliable scales to assess demographic and professional work characteristics, curiosity, grit, locus of control, perceived social support (for research activities), comfort in conducting research, and level of being research-active. Univariate and multivariable analyses were completed. RESULTS: Of 310 participants, 274 (88.4%) were female and mean (SD) age was 42.9 (13.1) years. After condensing 11 levels of research activity to four categories, 179 (57.7%) were not research-active, and 91 (29.4%), 26 (8.3%) and 14 (4.5%) were engaged at low, moderate, and high levels, respectively. Of 78 factors, 69 (88.5%) were associated with being research-active in univariate analyses. In multivariable analysis that adjusted for age, personal experience as a patient, years as a nurse and hours in direct patient care, professionalism characteristics, higher curiosity, internal locus of control, grit perseverance, support of a nurse scientist and nurse friends, and comfort in conducting research remained associated with higher levels of being research-active (all p < 0.01). CONCLUSION: Research-active nurses were more likely to be engaged professionally in hospital-based activities beyond their work roles and displayed higher levels of positive psychological characteristics and mentorship that supported research capacity. CLINICAL RELEVANCE: Research-active nurses were more likely to have internal factors and external resources that promoted higher levels of being research-active. A strong professional governance model may enhance clinical nurses research activities.

Conceptualization of Firearm-Related Terms Among Rural Adolescents: Definitions Matter.

Rural adolescents are at risk for firearm-related injury and death. In response, professional organizations have called for communication between adolescents, parents, and providers about firearms. A shared understanding of firearms between providers and families can facilitate effectiveness of health interventions. However, few studies engage adolescents in identifying their perception of common firearm terminology. The current study aimed to understand how adolescents in rural communities defined firearm-related terms including firearm, carrying, and handling, and differences in terms based on prior firearm training. Data were from a mixed methods community-based participatory study of 93 adolescents from rural Washington state. Thematic qualitative coding identified themes for firearm (gun, weapon, projectile, and tool), carrying (on you/your person, transportation, and holding), and handling (actively using, safe use, and holding) and differences between those with prior firearms training. Findings provide insight into perceptions of firearm-related terms for adolescents, an often-neglected voice, and inform rural policy and prevention efforts.

Perioperative changes in neurocognitive and Alzheimer's disease-related cerebrospinal fluid biomarkers in older patients randomised to isoflurane or propofol for anaesthetic maintenance.

BACKGROUND: Animal studies have shown that isoflurane and propofol have differential effects on Alzheimer's disease (AD) pathology and memory, although it is unclear whether this occurs in humans. METHODS: This was a nested randomised controlled trial within a prospective cohort study; patients age ≥60 yr undergoing noncardiac/non-neurological surgery were randomised to isoflurane or propofol for anaesthetic maintenance. Cerebrospinal fluid (CSF) was collected via lumbar puncture before, 24 h, and 6 weeks after surgery. Cognitive testing was performed before and 6 weeks after surgery. Nonparametric methods and linear regression were used to evaluate CSF biomarkers and cognitive function, respectively. RESULTS: There were 107 subjects (54 randomised to isoflurane and 53 to propofol) who completed the 6-week follow-up and were included in the analysis. There was no significant effect of anaesthetic treatment group, time, or group-by-time interaction for CSF amyloid-beta (Aß), tau, or phospho-tau181p levels, or on the tau/Aß or p-tau181p/Aß ratios (all P>0.05 after Bonferroni correction). In multivariable-adjusted intention-to-treat analyses, there were no significant differences between the isoflurane and propofol groups in 6-week postoperative change in overall cognition (mean difference [95% confidence interval]: 0.01 [-0.12 to 0.13]; P=0.89) or individual cognitive domains (P>0.05 for each). Results remained consistent across as-treated and per-protocol analyses. CONCLUSIONS: Intraoperative anaesthetic maintenance with isoflurane vs propofol had no significant effect on postoperative cognition or CSF Alzheimer's disease-related biomarkers within 6 weeks after noncardiac, non-neurological surgery in older adults. CLINICAL TRIAL REGISTRATION: NCT01993836.

Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates.

Extant genomes are largely shaped by global transposition, copy-number fluctuation, and rearrangement of DNA sequences rather than by substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution and undermine common models of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short sequences. The scale and extent of this 'non-substitution' variation has recently come into focus through the advent of new genomic technologies; however, it is still not widely considered in genotype-phenotype association studies. In this review we identify common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns.

ED point-of-care ultrasonography is associated with earlier drainage of pericardial effusion: A retrospective cohort study.

OBJECTIVES: To determine the association between emergency department point-of-care cardiac ultrasonography (POCUS) utilization and time to pericardial effusion drainage during an 8-year period when the emergency ultrasound program was established at our institution. METHODS: We performed a single-center retrospective cohort study in patients undergoing pericardiocentesis or other procedure for evacuation of pericardial effusion. Data was collected using both direct queries to the electronic health record database and two-examiner chart review. The primary outcome was time to intervention for pericardial effusion drainage. Multivariable Cox regression, with and without inverse probability weighting for likelihood to receive POCUS, was used to determine the association between POCUS and time to intervention. Secondary outcomes included 28-day mortality. RESULTS: 257 patient encounters were included with 137 receiving POCUS and 120 who did not. The proportion of patients receiving POCUS increased from 18.5% to 69.5% during the early to late periods of the study. POCUS was associated with an earlier median time to intervention of 21.6 h (95% CI 17.2, 24.2) compared to 34.6 h (27.0, 50.5) in the No POCUS group. After adjustment for patient demographics, anticoagulation, time of presentation and hemodynamic instability, POCUS was associated with earlier intervention (HR 2.08 [95% CI 1.56, 2.77]). POCUS use was not associated with a difference in 28-day mortality, which was evaluated as a secondary outcome. However, diagnosis of pericardial effusion by the ED physician using any means (POCUS or other imaging) was associated with decreased 28-day mortality (9.7% vs. 26.0%, -16.3% for POCUS [95% CI -29.1, -3.5]). CONCLUSION: POCUS was associated with an earlier time to intervention for pericardial effusions after adjustment for multiple confounding factors. Failure to diagnose pericardial effusion in the ED using any diagnostic testing including POCUS, was associated with increased 28-day mortality.

Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.

Short tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana, genotyping 2046 STR loci each, using highly parallel STR sequencing with molecular inversion probes. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR across these strains. STR expansions (large copy number increases) are found in most strains, several of which have evident functional effects. These include three of six intronic STR expansions we found to be associated with intron retention. Coding STRs were depleted of variation relative to noncoding STRs, and we detected a total of 56 coding STRs (11%) showing low variation consistent with the action of purifying selection. In contrast, some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detected 133 novel STR-phenotype associations under stringent criteria, most of which could not be detected with SNPs alone, and validated some with follow-up experiments. Our results support the conclusion that STRs constitute a large, unascertained reservoir of functionally relevant genomic variation.

Perioperative neurocognitive and functional neuroimaging trajectories in older APOE4 carriers compared with non-carriers: secondary analysis of a prospective cohort study.

BACKGROUND: Cognitive dysfunction after surgery is a major issue in older adults. Here, we determined the effect of APOE4 on perioperative neurocognitive function in older patients. METHODS: We enrolled 140 English-speaking patients ≥60 yr old scheduled for noncardiac surgery under general anaesthesia in an observational cohort study, of whom 52 underwent neuroimaging. We measured cognition; Aß, tau, p-tau levels in CSF; and resting-state intrinsic functional connectivity in six Alzheimer's disease-risk regions before and 6 weeks after surgery. RESULTS: There were no significant APOE4-related differences in cognition or CSF biomarkers, except APOE4 carriers had lower CSF Aß levels than non-carriers (preoperative median CSF Aß [median absolute deviation], APOE4 305 pg ml-1 [65] vs 378 pg ml-1 [38], respectively; P=0.001). Controlling for age, APOE4 carriers had significantly greater preoperative functional connectivity than non-carriers between several brain regions implicated in Alzheimer's disease, including between the left posterior cingulate cortex and left angular gyrus (ß [95% confidence interval, CI], 0.218 [0.137-0.230]; PFWE=0.016). APOE4 carriers, but not non-carriers, experienced significant connectivity decreases from before to 6 weeks after surgery between several brain regions including between the left posterior cingulate cortex and left angular gyrus (ß [95% CI], -0.196 [-0.256 to -0.136]; PFWE=0.001). Most preoperative and postoperative functional connectivity differences did not change after controlling for preoperative CSF Aß levels. CONCLUSIONS: Postoperative change trajectories for cognition and CSF Aß, tau or p-tau levels did not differ between community dwelling older APOE4 carriers and non-carriers. APOE4 carriers showed greater preoperative functional connectivity and greater postoperative decreases in functional connectivity in key Alzheimer's disease-risk regions, which occur via Aß-independent mechanisms.

A descriptive study of factors that facilitate nurses' participation in shared governance and attendance at unit meetings.

AIM: To identify factors that facilitate participation in shared governance and attendance at unit meetings. BACKGROUND: Shared governance and unit meetings are crucial for education and communication. Current literature explores barriers to participation and attendance; however, removal of barriers may be insufficient to bring about behaviour change in nurses. METHOD: Secondary analysis of data from 511 clinical nurses, who worked at one of nine facilities within one large health care system in the Midwest United States, was used to address our aim. RESULTS: Shared governance participants and unit meeting attendees were most satisfied with nursing as a career and more likely to be optimistic that nurses could change things, than non-participants and non-attendees, and this difference was statistically significant (p < .05). The organizational variable most associated with participation and attendance dealt with paid time-off to attend meetings. Personal reasons for participation and attendance were the opportunity to express opinions and to hear opinions of others. CONCLUSION: Organizations should encourage nurses to express their opinions and ensure that nurses are paid for the time spent participating in meetings. IMPLICATIONS FOR NURSING MANAGEMENT: While some variables cannot be controlled by organizations, nursing leadership can provide opportunities for nurses to become more active and participate in decision-making.

The Parkinson's Disease Genome-Wide Association Study Locus Browser.

BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disease with an often complex component identifiable by genome-wide association studies. The most recent large-scale PD genome-wide association studies have identified more than 90 independent risk variants for PD risk and progression across more than 80 genomic regions. One major challenge in current genomics is the identification of the causal gene(s) and variant(s) at each genome-wide association study locus. The objective of the current study was to create a tool that would display data for relevant PD risk loci and provide guidance with the prioritization of causal genes and potential mechanisms at each locus. METHODS: We included all significant genome-wide signals from multiple recent PD genome-wide association studies including themost recent PD risk genome-wide association study, age-at-onset genome-wide association study, progression genome-wide association study, and Asian population PD risk genome-wide association study. We gathered data for all genes 1 Mb up and downstream of each variant to allow users to assess which gene(s) are most associated with the variant of interest based on a set of self-ranked criteria. Multiple databases were queried for each gene to collect additional causal data. RESULTS: We created a PD genome-wide association study browser tool (https://pdgenetics.shinyapps.io/GWASBrowser/) to assist the PD research community with the prioritization of genes for follow-up functional studies to identify potential therapeutic targets. CONCLUSIONS: Our PD genome-wide association study browser tool provides users with a useful method of identifying potential causal genes at all known PD risk loci from large-scale PD genome-wide association studies. We plan to update this tool with new relevant data as sample sizes increase and new PD risk loci are discovered. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Letter to the editor regarding "TGM6 variants in Parkinson's disease: clinical findings and functional evidence".

No abstract present.

Genetic Risk Profiling in Parkinson's Disease and Utilizing Genetics to Gain Insight into Disease-Related Biological Pathways.

Parkinson's disease (PD) is a complex disorder underpinned by both environmental and genetic factors. The latter only began to be understood around two decades ago, but since then great inroads have rapidly been made into deconvoluting the genetic component of PD. In particular, recent large-scale projects such as genome-wide association (GWA) studies have provided insight into the genetic risk factors associated with genetically ''complex'' PD (PD that cannot readily be attributed to single deleterious mutations). Here, we discuss the plethora of genetic information provided by PD GWA studies and how this may be utilized to generate polygenic risk scores (PRS), which may be used in the prediction of risk and trajectory of PD. We also comment on how pathway-specific genetic profiling can be used to gain insight into PD-related biological pathways, and how this may be further utilized to nominate causal PD genes and potentially druggable therapeutic targets. Finally, we outline the current limits of our understanding of PD genetics and the potential contribution of variation currently uncaptured in genetic studies, focusing here on uncatalogued structural variants.

A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus.

The hominid SINE-VNTR-Alu (SVA) retrotransposons represent a repertoire of genomic variation which could have significant effects on genome function. A human-specific SVA in the promoter region of the gene leucine-rich repeats and immunoglobulin-like domains 2 (LRIG2), which we termed SVA_LRIG2, is a common retrotransposon insertion polymorphism (RIP), defined as an element which is polymorphic for its presence or absence in the genome. We hypothesised that this RIP might be associated with differential levels of expression of LRIG2. The RIP genotype of SVA_LRIG2 was determined in a subset of frontal cortex DNA samples from the North American Brain Expression Consortium (NABEC) cohort and was imputed for a larger set of that cohort. Utilising available frontal cortex total RNA-seq and CpG methylation data for this cohort, we observed that increased allele dosage of SVA_LRIG2 was non-significantly associated with a decrease in transcription from the region and significantly associated with increased methylation of the CpG probe nearest to SVA_LRIG2, i.e., SVA_LRIG2 is a significant methylation quantitative trait loci (mQTL) at the LRIG2 locus. These data are consistent with SVA_LRIG2 being a transcriptional regulator, which in part may involve epigenetic modulation.

An interdisciplinary review of the thanatomicrobiome in human decomposition.

Death does not occur instantaneously and organs do not decompose at the same rate or in the same way. Nulligravid human uteri and prostate glands are the last internal organs to deteriorate during decomposition; however, the reason for this very important observation is still enigmatic. Recent studies have elucidated that the composition and abundance of microbes in the human thanatomicrobiome (microbiome of death) varies by organ and changes as a function of time and temperature. The ileocecal area has the largest absolute postmortem burden that spreads to the liver and spleen and continues to the heart and brain depending on the cause of death. To truly understand the mechanisms of microbial assembly during decomposition, a thorough examination of different strategies utilized by the trillions of microbes that colonize decaying tissues is needed from a multi-organ and multidisciplinary approach. In this review, we highlight interdisciplinary research and provide an overview of human decomposition investigations of thanatomicrobiomic changes in internal organs.

SwrD (YlzI) Promotes Swarming in Bacillus subtilis by Increasing Power to Flagellar Motors.

The bacterium Bacillus subtilis is capable of two kinds of flagellum-mediated motility: swimming, which occurs in liquid, and swarming, which occurs on a surface. Swarming is distinct from swimming in that it requires secretion of a surfactant, an increase in flagellar density, and perhaps additional factors. Here we report a new gene, swrD, located within the 32 gene fla-che operon dedicated to flagellar biosynthesis and chemotaxis, which when mutated abolished swarming motility. SwrD was not required for surfactant production, flagellar gene expression, or an increase in flagellar number. Instead, SwrD was required to increase flagellar power. Mutation of swrD reduced swimming speed and torque of tethered flagella, and all swrD-related phenotypes were restored when the stator subunits MotA and MotB were overexpressed either by spontaneous suppressor mutations or by artificial induction. We conclude that swarming motility requires flagellar power in excess of that which is needed to swim.IMPORTANCE Bacteria swim in liquid and swarm over surfaces by rotating flagella, but the difference between swimming and swarming is poorly understood. Here we report that SwrD of Bacillus subtilis is necessary for swarming because it increases flagellar torque and cells mutated for swrD swim with reduced speed. How flagellar motors generate power is primarily studied in Escherichia coli, and SwrD likely increases power in other organisms, like the Firmicutes, Clostridia, Spirochaetes, and the Deltaproteobacteria.