Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures? determined by comparative sequence analysis was assembled to allow optimization of parameters not based on experiments and to test the accuracy of the algorithm. On average, the predicted lowest free energy structure contains 73 % of known base-pairs when domains of fewer than 700 nt are folded; this compares with 64 % accuracy for previous versions of the algorithm and parameters. For a given sequence, a set of 750 generated structures contains one structure that, on average, has 86 % of known base-pairs. Experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.     

Spatial distribution characteristics of stomata at the areole level in Michelia cavaleriei var. platypetala (Magnoliaceae)

Background and AimsIn hierarchically reticulate venation patterns, smaller orders of veins form areoles in which stomata are located. This study aimed to quantify the spatial relationship among stomata at the areole level.MethodsFor each of 12 leaves of M. cavaleriei var. platypetala, we assumed that stomatal characteristics were symmetrical on either side of the midrib, and divided the leaf surface on one side of the midrib into six layers equidistantly spaced along the apical–basal axis. We then further divided each layer into three positions equidistantly spaced from midrib to leaf margin, resulting in a total of 18 sampling locations. In addition, for 60 leaves, we sampled three positions from midrib to margin within only the widest layer of the leaf. Stomatal density and mean nearest neighbour distance (MNND) were calculated for each section. A replicated spatial point pattern approach quantified stomatal spatial relationships at different distances (0–300 μm).Key ResultsA tendency towards regular arrangement (inhibition as opposed to attraction or clustering) was observed between stomatal centres at distances <100 μm. Leaf layer (leaf length dimension) had no significant effect on local stomatal density, MNND or the spatial distribution characteristics of stomatal centres. In addition, we did not find greater inhibition at the centre of areoles, and in positions farther from the midrib.ConclusionsSpatial inhibition might be caused by the one-cell-spacing rule, resulting in more regular arrangement of stomata, and it was found to exist at distances up to ~100 μm. This work implies that leaf hydraulic architecture, consisting of both vascular and mesophyll properties, is sufficient to prevent important spatial variability in water supply at the areole level.     

Genetic targeting of Card19 is linked to disrupted NINJ1 expression,impaired cell lysis,and increased susceptibility to Yersinia infection

Cell death plays a critical role in inflammatory responses. During pyroptosis, inflammatory caspases cleave Gasdermin D (GSDMD) to release an N-terminal fragment that generates plasma membrane pores that mediate cell lysis and IL-1 cytokine release. Terminal cell lysis and IL-1β release following caspase activation can be uncoupled in certain cell types or in response to particular stimuli, a state termed hyperactivation. However, the factors and mechanisms that regulate terminal cell lysis downstream of GSDMD cleavage remain poorly understood. In the course of studies to define regulation of pyroptosis during Yersinia infection, we identified a line of Card19-deficient mice (Card19^lxcn) whose macrophages were protected from cell lysis and showed reduced apoptosis and pyroptosis, yet had wild-type levels of caspase activation, IL-1 secretion, and GSDMD cleavage. Unexpectedly, CARD19, a mitochondrial CARD-containing protein, was not directly responsible for this, as an independently-generated CRISPR/Cas9 Card19 knockout mouse line (Card19^Null) showed no defect in macrophage cell lysis. Notably, Card19 is located on chromosome 13, immediately adjacent to Ninj1, which was recently found to regulate cell lysis downstream of GSDMD activation. RNA-seq and western blotting revealed that Card19^lxcn BMDMs have significantly reduced NINJ1 expression, and reconstitution of Ninj1 in Card19^lxcn immortalized BMDMs restored their ability to undergo cell lysis in response to caspase-dependent cell death stimuli. Card19^lxcn mice exhibited increased susceptibility to Yersinia infection, whereas independently-generated Card19^Null mice did not, demonstrating that cell lysis itself plays a key role in protection against bacterial infection, and that the increased infection susceptibility of Card19^lxcn mice is attributable to loss of NINJ1. Our findings identify genetic targeting of Card19 being responsible for off-target effects on the adjacent gene Ninj1, disrupting the ability of macrophages to undergo plasma membrane rupture downstream of gasdermin cleavage and impacting host survival and bacterial control during Yersinia infection.     

An intervention to improve teacher well-being support and training to support students in UK high schools (the WISE study): A cluster randomised controlled trial

BackgroundTeachers are at heightened risk of poor mental health and well-being, which is likely to impact on the support they provide to students, and student outcomes. We conducted a cluster randomised controlled trial, to test whether an intervention to improve mental health support and training for high school teachers led to improved mental health and well-being for teachers and students, compared to usual practice. We also conducted a cost evaluation of the intervention.Methods and findingsThe intervention comprised (i) Mental Health First Aid training for teachers to support students; (ii) a mental health awareness session; and (iii) a confidential staff peer support service. In total 25 mainstream, non-fee-paying secondary schools stratified by geographical area and free school meal entitlement were randomly allocated to intervention (n = 12) or control group (n = 13) after collection of baseline measures. We analysed data using mixed-effects repeated measures models in the intention-to-treat population, adjusted for stratification variables, sex, and years of experience. The primary outcome was teacher well-being (Warwick-Edinburgh Mental Well-being Scale). Secondary outcomes were teacher depression, absence, and presenteeism, and student well-being, mental health difficulties, attendance, and attainment. Follow-up was at months 12 (T1) and 24 (T2). We collected process data to test the logic model underpinning the intervention, to aid interpretation of the findings. A total of 1,722 teachers were included in the primary analysis. Teacher well-being did not differ between groups at T2 (intervention mean well-being score 47.5, control group mean well-being score 48.4, adjusted mean difference −0.90, 95% CI –2.07 to 0.27, p = 0.130). The only effect on secondary outcomes was higher teacher-reported absence among the intervention group at T2 (intervention group median number of days absent 0, control group median number of days absent 0, ratio of geometric means 1.04, 95% CI 1.00 to 1.09, p = 0.042). Process measures indicated little change in perceived mental health support, quality of relationships, and work-related stress. The average cost of the intervention was £9,103 per school. The study’s main limitations were a lack of blinding of research participants and the self-report nature of the outcome measures.ConclusionsIn this study, we observed no improvements to teacher or student mental health following the intervention, possibly due to a lack of impact on key drivers of poor mental health within the school environment. Future research should focus on structural and cultural changes to the school environment, which may be more effective at improving teacher and student mental health and well-being.Trial registrationwww.isrctn.com ISRCTN95909211.

Using a cluster randomized study, Judi Kidger and colleagues study an intervention to improve teacher wellbeing support and training to support students in UK high schools (the WISE study).     

Extracellular DNA from Serpulina hyodysenteriae consists of 6.5 kbp random fragments of chromosomal DNA

Preparations of chromosomal DNA from a number of Serpulina hyodysenteriae strains have shown, using agarose gel electrophoresis, the presence of an additional band with a mobility similar to that of a 6.5 kbp linear DNA fragment. Analysis showed that this is not a plasmid but rather a form of extracellular DNA like that observed for Gram-negative bacteria. However, unlike the extracellular DNA from Gram-negative bacteria, which showed a similar band profile to that of the DNA from whole cells, that from S. hyodysenteriae consisted primarily of fragments of a fixed 6.5 kbp.     

Perinatal outcomes of midwife-led care,stratified by medical risk: a retrospective cohort study from British Columbia (2008–2018)

Background:Anecdotal evidence suggests that the profile of midwifery clients in British Columbia has changed over the past 20 years and that midwives are increasingly caring for clients with moderate to high medical risk. We sought to compare perinatal outcomes with a registered midwife as the most responsible provider (MRP) versus outcomes among clients with physicians as their MRP across medical risk strata.Methods:This retrospective cohort study (2008–2018) used data from the BC Perinatal Data Registry. We included all births that had a family physician, obstetrician or midwife listed as the MRP (n = 425 056) and stratified the analysis by pregnancy risk status (low, moderate or high) according to an adapted perinatal risk scoring system. We estimated differences in outcomes between MRP groups by calculating adjusted absolute and relative risks.Results:The adjusted absolute and relative risks of adverse neonatal outcomes were consistently lower among those who chose midwifery care across medical risk strata, compared with clients who had a physician as MRP. Midwifery clients experienced higher rates of spontaneous vaginal births, vaginal births after cesarean delivery and breastfeeding initiation, and lower rates of cesarean deliveries and instrumental births, with no increase in adverse neonatal outcomes. We observed an increased risk of oxytocin induction among high-risk birthers with a midwife versus an obstetrician as MRP.Interpretation:Our findings suggest that compared with other providers in BC, midwives provide safe primary care for clients with varied levels of medical risk. Future research might examine how different practice and remuneration models affect clinical outcomes, client and provider experiences, and costs to the health care system.

In British Columbia, registered midwives are autonomous, primary health care providers, regulated and integrated into the publicly funded health care system. Midwives typically work in small-team continuity-of-care models, providing medical care during pregnancy, birth and up to 3 months postpartum in the community and in hospitals. Midwives hold hospital privileges and consult with physician colleagues as medically indicated.Since the regulation of midwifery in BC in 1998, the number of pregnant people who are attended by midwives during birth has steadily increased, from 4.8% in 2004/05¹ to 15.6% in 2019/20.² In 2018/19, 1 in 4 childbearing people in BC (25.4%) had a midwife involved in their care at some point during their pregnancy, birth or postpartum period.²Several studies have examined the safety of midwifery care in BC after regulation. Janssen and colleagues analyzed the outcomes of low-risk clients from 2000 to 2004, providing important evidence for the safety of midwife-attended planned home births in the early years after regulation.³ Other researchers have described good perinatal outcomes for subsets of midwifery clients in BC, including those residing in rural areas⁴ and those planning vaginal births after cesarean (VBAC) at home.⁵ However, these studies focused on subsamples of childbearing people or did not use recent data.The benefits of midwife-led care for clients with more complex needs are beginning to emerge in BC. Using BC perinatal data, McRae and colleagues^6,7 demonstrated that those affected by low socioeconomic position, substance use and mental illness had lower odds of small-for-gestational-age babies, pretermbirth and low-birth-weight babies when they were cared for by midwives antenatally rather than by physicians.This analysis is part of a larger mixed-methods study that aimed to better understand the changing profile of midwifery clients in BC and the implications this has for education, research and practice. The goal of the current analysis is to present complete and recent data from all births in BC that had a midwife, family physician or obstetrician listed as the most responsible provider (MRP). Specifically, we sought to document neonatal and maternal outcomes of childbearing people who had a mid-wife as their MRP compared with those who had a physician as the MRP, with similar medical risk profiles.     

Microsomal triglyceride transfer protein -493T variant reduces IDL plus LDL apoB production and the plasma concentration of large LDL particles

The microsomal triglyceride transfer protein (MTP) is essential for the synthesis and secretion of apolipoprotein B (apoB)-containing lipoproteins. We investigated the role the MTP -493G/T gene polymorphism in determining the apoB-100 secretion pattern and LDL heterogeneity in healthy human subjects. Groups of carriers of the T and the G variants (n = 6 each) were recruited from a cohort of healthy 50-yr-old men. Kinetic studies were performed by endogenous [(2)H(3)]leucine labeling of apoB and subsequent quantification of the stable isotope incorporation. apoB production rates, metabolic conversions, and eliminations were calculated by multicompartmental modeling (SAAM-II). LDL subfraction distribution was analyzed in the entire cohort (n = 377). Carriers of the MTP -493T allele had lower plasma LDL apoB and lower concentration of large LDL particles [LDL-I: 136 +/- 57 (TT) vs. 175 +/- 55 (GG) mg/l, P < 0.01]. Kinetic modeling suggested that MTP -493T homozygotes had a 60% lower direct production rate of intermediate-density lipoprotein (IDL) plus LDL compared with homozygotes for the G allele (P < 0.05). No differences were seen in production rates of large and small VLDL, nor were there any differences in metabolic conversion or elimination rates of apoB between the genotype groups. This study shows that a polymorphism in the MTP gene affects the spectrum of endogenous apoB-containing lipoprotein particles produced in humans. Reduced direct production of LDL plus IDL appears to be related to lower plasma concentrations of large LDL particles.