Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements.

'When they do that kind of bad things to me, I feel that they encourage me to be strong and be who I am': How transfeminine people in Samoa, Tonga and the Cook Islands experience discrimination, acceptance and a sense of place.

Data on transfeminine participants from a 2016 Pacific Multi-Country Mapping and Behavioural Study evidence high levels of verbal, physical and sexual abuse, as well as discrimination. In interviews from the same study, accounts of hardship were frequently countered with assertions of happiness and talk of acceptance. This paper analyses these accounts and, in particular, the ways in which interviewees viewed and managed their place in society. Data provide insights into the factors that support transfeminine occupation of a positive place in some contemporary Pacific settings, highlighting negotiation between modern and traditional, and local and global, cultures and values.

Nisin M: a Bioengineered Nisin A Variant That Retains Full Induction Capacity but Has Significantly Reduced Antimicrobial Activity.

Nisin A is a potent antimicrobial with potential as an alternative to traditional antibiotics, and a number of genetically modified variants have been created that target clinically relevant pathogens. In addition to antimicrobial activity, nisin autoregulates its own production via a signal transduction pathway, a property that has been exploited in a protein expression system termed the nisin-controlled gene expression (NICE) system. Although NICE has become one of the most popular protein expression systems, one drawback is that the inducer peptide, nisin A, also has inhibitory activity. It has already been demonstrated that the N-terminal region of nisin A contributes to antimicrobial activity and signal transduction properties; therefore, we conducted bioengineering of nisin at positions Pro9 and Gly10 within ring B to produce a bank of variants that could potentially be used as alternative induction peptides. One variant, designated nisin M, has threonines at positions 9 and 10 and retains induction capacity comparable to that of wild-type nisin A, while most of the antimicrobial activity is abolished. Further analysis confirmed that nisin M produces a mix of peptides as a result of different degrees of dehydration of the two threonines. We show that nisin M exhibits potential as a more suitable alternative to nisin A for the expression of proteins that may be difficult to express or for production of proteins in strains that are sensitive to wild-type nisin. Moreover, it may address the increasing demand by industry for optimization of peptide fermentations to increase yields or production rates.IMPORTANCE This study describes the generation of a nisin variant with superior characteristics for use in the NICE protein expression system. The variant, termed nisin M, retains an induction capacity comparable to that of wild-type nisin A but exhibits significantly reduced antimicrobial activity and can therefore be used at concentrations that are normally toxic to the expression host.

Increased 30-day readmission rate after craniotomy for tumor resection at safety net hospitals in small metropolitan areas.

PURPOSE: Unplanned readmission of post-operative brain tumor patients is often attributed to hospital and patient characteristics and is associated with higher mortality and cost. Previous studies demonstrate multiple patient outcome disparities in safety net hospitals (SNHs) when compared to non-SNHs. This study uses the Nationwide Readmissions Database (NRD) to determine if initial brain tumor resection at SNHs is associated with increased 30-day non-elective readmission rates. METHODS: Patients with benign or malignant primary or metastatic brain tumor undergoing craniotomy for surgical resection were retrospectively identified in the NRD from 2010 to 2014. SNHs were defined as hospitals with Medicaid and uninsured patient burden in the top quartile. Descriptive and multivariate analyses employing survey-adjusted logistic regression evaluated patient and hospital level factors influencing 30-day readmissions. RESULTS: During the study period, 83,367 patients met inclusion criteria. 44.7% of patients had a benign tumor, and 55.3% had a malignant tumor. Secondary CNS neoplasm (5.99%), post-operative infection (5.96%), and septicemia (4.26%) caused most readmissions within 30 days. Patients had increased unplanned readmission rates if they underwent craniotomy for tumor resection at a SNH in a small metropolitan area (OR 1.11, 95% CI 1.02-1.21, p = 0.01), but not at a SNH in a large metropolitan area (OR 0.99, 95% CI 0.93-1.05, p = 0.73). CONCLUSION: This finding may reflect differences in access to care and disparities in neurosurgical resources between small and large metropolitan areas. Inequities in expertise and capacity are relevant as surgical volume was also related to readmission rates. Further studies may be warranted to address such disparities.

Effects of ambient particulate matter on vascular tissue: a review.

Fine and ultra-fine particulate matter (PM) are major constituents of urban air pollution and recognized risk factors for cardiovascular diseases. This review examined the effects of PM exposure on vascular tissue. Specific mechanisms by which PM affects the vasculature include inflammation, oxidative stress, actions on vascular tone and vasomotor responses, as well as atherosclerotic plaque formation. Further, there appears to be a greater PM exposure effect on susceptible individuals with pre-existing cardiovascular conditions.

Guidelines for the investigation of chronic diarrhoea in adults: British Society of Gastroenterology, 3rd edition.

Chronic diarrhoea is a common problem, hence clear guidance on investigations is required. This is an updated guideline from 2003 for the investigations of chronic diarrhoea commissioned by the Clinical Services and Standards Committee of the British Society of Gastroenterology (BSG). This document has undergone significant revision in content through input by 13 members of the Guideline Development Group (GDG) representing various institutions. The GRADE system was used to appraise the quality of evidence and grading of recommendations.

Understanding the meaning of youth sexual and reproductive well-being in Fiji.

Well-being is a term commonly used in discussions of sexuality, reproduction and sexual health, yet the meaning of the term is elusive and often disregarded. As an example, the 'well-being' component of sexual and reproductive health and well-being is often not explicitly addressed in research, policy and programme development. The goal of this paper is to explore the meanings of sexual and reproductive well-being among young people in Fiji and their implications. Fourteen focus group discussions with young people aged 15 to 19 years and 40 key informant interviews were held in four Fijian settings. We found both different and shared meanings of sexual and reproductive well-being and suggest areas in which it can be strengthened in Fiji.

Knowledge, beliefs, and decisions of pregnant Australian women concerning donation and storage of umbilical cord blood: a population-based survey.

BACKGROUND: Many women giving birth in Australian hospitals can choose to donate their child's umbilical cord blood to a public cord blood bank or pay to store it privately. We conducted a survey to determine the proportion and characteristics of pregnant women who are aware of umbilical cord blood (UCB) banking and who have considered and decided about this option. The survey also sought to ascertain information sources, knowledge, and beliefs about UCB banking, and the effect of basic information about UCB on decisions. METHODS: Researchers and hospital maternity staff distributed a survey with basic information about UCB banking to 1,873 women of at least 24 weeks' gestation who were attending antenatal classes and hospital clinics in 14 public and private maternity hospitals in New South Wales. RESULTS: Most respondents (70.7%) were aware of UCB banking. Their main information sources were leaflets from hospital clinics, print media, antenatal classes, TV, radio, friends, and relatives. Knowledge about UCB banking was patchy, and respondents overestimated the likelihood their child would need or benefit from UCB. Women who were undecided about UCB banking were younger, less educated, or from ethnic or rural backgrounds. After providing basic information about UCB banking, the proportion of respondents who indicated they had decided whether or not to donate or store UCB more than doubled from 30.0 to 67.7 percent. CONCLUSIONS: Basic information for parents about UCB banking can affect planned decisions about UCB banking. Information should be accurate and balanced, should counter misconceptions, and should target specific groups.

Screening canine sources for novel antimicrobials reveals the circular broad-spectrum bacteriocin, caledonicin, produced by Staphylococcus caledonicus.

Introduction: Antimicrobial-resistant pathogens present an ongoing threat to human and animal health, with deaths linked to antimicrobial resistance (AMR) predicted to increase annually. While the misuse and overuse of antibiotics in humans undoubtedly contribute to this escalation, antibiotic use in the veterinary field, including companion animals, also plays a contributing role. Pet owners' desire to improve the quality of life of their pets is likely to support antibiotic use in this field. Consequently, there is a need for antibiotic alternatives to treat bacterial infections. This study set out to screen for antimicrobial peptides known as bacteriocins from bacterial isolates of aerobic/microaerophilic environments of canine sources and determine their potential as antibiotic alternatives against clinically relevant pathogens. Methods: Following a laboratory-based protocol, 22 bacterial isolates were subjected to whole-genome sequencing (WGS), and a total of 14 putative novel bacteriocins were identified from both class I and II bacteriocin classes. One particular bacteriocin, herein named caledonicin, was identified via in silico analysis from a Staphylococcus caledonicus strain and partially purified for further in vitro evaluation. Results: Caledonicin is a 64-amino acid (IAANLGVSSGTAYS MANALNNISNVATA LTIIGTFTGVGTIGSGIA ATILAILKKKGVAAAAAF) novel circular bacteriocin most closely related to enterocin_NKR-5-3B based on core peptide alignment (39.1%), with a molecular weight of 6077.1 Da. Caledonicin exhibits a broad-spectrum of activity against a range of pathogenic bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus pseudintermedius (MRSP), and Listeria monocytogenes; and the gut-related bacterium associated with Crohn's disease, Mediterraneibacter gnavus ATCC 29149 (previously Ruminococcus gnavus ATCC 29149). Discussion: This represents the first bacteriocin screening study involving bacteria from canine sources and confirms this is a rich environment for bacteriocin-producing strains. This study also identifies and characterises the first novel bacteriocin from the staphylococcal species, Staphylococcus caledonicus.

Cervical spinal cord compression from subdural hematoma caused by traumatic nerve root avulsion: illustrative case.

BACKGROUND: Posttraumatic intradural hematomas of the cervical spine are rare findings that may yield significant neurological deficits if they compress the spinal cord. These compressive hematomas require prompt surgical evacuation. In certain instances, intradural hematomas may form from avulsion of cervical nerve roots. OBSERVATIONS: The authors present the case of a 29-year-old male who presented with right upper-extremity weakness in the setting of polytrauma after a motor vehicle accident. He had no cervical fractures but subsequently developed right lower-extremity weakness. Magnetic resonance imaging (MRI) demonstrated a compressive hematoma of the cervical spine that was initially read as an epidural hematoma. However, intraoperatively, it was found to be a subdural hematoma, eccentric to the right, stemming from an avulsion of the right C6 nerve root. LESSONS: Posttraumatic cervical subdural hematomas require rapid surgical evacuation if neurological deficits are present. The source of the hematoma may be an avulsed nerve root, and the associated deficits may be unilateral if the hematoma is eccentric to one side. Surgeons should be prepared for the possibility of an intradural hematoma even in instances in which MRI appears consistent with an epidural hematoma.

Impact of the Thompson method on breastfeeding exclusivity and duration: Multi-method design.

BACKGROUND: How hospital clinicians facilitate breastfeeding in the first 48-72 h is critical to breastfeeding exclusivity and duration. Mothers who discharge hospital directly breastfeeding are more likely to continue exclusively breastfeeding at 3-months. OBJECTIVE: To assess the impact of facility-wide implementation of a physiological breastfeeding method (the Thompson method) on direct breastfeeding at hospital discharge and exclusive breastfeeding at 3-months of age. DESIGN: Multi-method design using interrupted time series analysis and surveys. SETTING(S): An Australian tertiary maternity hospital. PARTICIPANTS: 13,667 mother-baby pairs (interrupted time series analysis) and 495 postnatal mothers (surveys). METHODS: The Thompson method includes cradle position and hold, alignment of mouth-to-nipple, baby-led connection and seal, maternal fine-tuning for symmetry, and leisurely duration. We used a large pre-post implementation dataset and conducted interrupted time series analysis using a 24-month baseline period (January 2016 - December 2017); and a 15-month post-implementation period (April 2018 - June 2019). We recruited a sub-sample of women to complete surveys at hospital discharge and 3-months postpartum. Surveys were primarily used to measure impact of Thompson method on exclusive breastfeeding at 3-months, compared with a baseline survey conducted in same setting. RESULTS: Following implementation of the Thompson method, the declining trend in direct breastfeeding at hospital discharge was significantly averted by 0.39% each month relative to baseline (95% CI: 0.03% to 0.76%; p = 0.037). While the 3-month exclusive breastfeeding rate in the Thompson group was 3 percentage points higher than the baseline group; this result did not reach statistical significance. However, a subgroup analysis of women who discharged hospital exclusively breastfeeding revealed the relative odds of exclusive breastfeeding at 3-months in the Thompson group was 0.25 (95% CI: 0.17 to 0.38; p < 0.001), significantly better than the baseline group (Z = 3.23, p < 0.01) where the relative odds was only 0.07 (95% CI: 0.03 to 0.19; p < 0.001). CONCLUSIONS: Implementation of the Thompson method for well mother-baby pairs improved direct breastfeeding trends at hospital discharge. For women who discharged hospital exclusively breastfeeding, exposure to the Thompson method reduced the risk of exclusive breastfeeding discontinuation by 3-months. The positive impact of the method was potentially confounded by partial implementation and a parallel rise in birth interventions which undermine breastfeeding. We recommend strategies to strengthen clinician buy-in to the method, and future research using a cluster randomised trial design. TWEETABLE ABSTRACT: Facility-wide implementation of the Thompson method improves direct breastfeeding at hospital discharge and predicts breastfeeding exclusivity at 3-months.

Progress towards triple elimination of mother-to-child transmission of HIV, hepatitis B and syphilis in Pacific Island Countries and Territories: a systematic review.

The diverse geographic, demographic, and societal factors in the Pacific Island Countries and Territories (PICTs) have contributed to unique epidemiological patterns of HIV, syphilis, and hepatitis B. Transmission can be during pregnancy, at the time of birth or via breastfeeding for HIV, and can have long-term adverse outcomes. Given the similarities in prevention of mother-to-child transmission of these infections, coordinated interventions for triple elimination are used. This systematic review has evaluated the peer-reviewed literature, grey literature, and global databases to assess the availability of data to report against elimination targets in the WHO Regional Framework for the Triple Elimination of Mother-to-Child Transmission of HIV, Hepatitis B and Syphilis in Asia and the Pacific 2018-2030. The secondary objective is to report on progress towards these targets. The findings show that none of the PICTs are on track to achieve triple elimination by 2030. Amongst the limited publicly available indicator data, there is suboptimal coverage for most indicators. It is important that there is an increase in availability of and access to antenatal care, testing, and treatment for pregnant women. Increased efforts are needed to collect data on key indicators and integrate reporting into existing systems to avoid extra burden. Funding: Leila Bell was supported by an Australian Government Research Training Program (RTP) Scholarship, Australia. Funding sources had no role in paper design, data collection, data analysis, interpretation, or writing of the paper.

Pharmacogenomic knowledge and awareness among diverse patients treated with angiotensin converting enzyme inhibitors.

We developed novel electronic phenotyping algorithms for the BioMe biobank data, which accurately identified angiotensin converting enzyme inhibitor (ACEi)-induced angioedema cases and controls. A survey was mailed to all 1075 patients and 91 were returned. Over a third reported that prescribing physicians had not discussed with them the concepts of interindividual drug response variability or adverse event risk, and 73% of patients were previously unaware of pharmacogenomics; however, most patients were interested in having pharmacogenomic testing. Moreover, 67% of patients indicated that pharmacogenomic testing would positively influence their medication compliance. In addition to identifying an innovative approach to define biobank cohorts for pharmacogenomic studies, these results indicate that patients are interested in pharmacogenomic testing, which could translate to improved adherence.

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA.

Half the ribosomes translating the mRNA for phage T4 gene 60 topoisomerase subunit bypass a 50 nucleotide coding gap between codons 46 and 47. The pairing of codon 46 with its cognate peptidyl-tRNA anticodon dissociates, and following mRNA slippage, peptidyl-tRNA re-pairs to mRNA at a matched triplet 5' adjacent to codon 47, where translation resumes. Here, in studies with gene 60 cassettes, it is shown that the peptidyl-tRNA anticodon does not scan the intervening sequence for potential complementarity. However, certain coding gap mutants allow peptidyl-tRNA to scan sequences in the bypassed segment. A model is proposed in which the coding gap mRNA enters the ribosomal A-site and forms a structure that precludes peptidyl-tRNA scanning of its sequence. Dissipation of this RNA structure, together with the contribution of 16S rRNA anti-Shine-Dalgarno sequence pairing with GAG, facilitates peptidyl-tRNA re-pairing to mRNA.

Umbilical cord blood banking: beyond the public-private divide.

Umbilical cord blood is a source of haematopoietic progenitor cells, which are used to treat a range of malignant, genetic, metabolic and immune disorders. Until recently, cord blood was either collected through donations to publicly funded cord blood banks for use in allogeneic transplantation, or stored in commercial cord blood banks for use in autologous transplantation. The line between public and private cord blood banking is being blurred by the emergence of "hybrid" models that combine aspects of both the public and private systems. The authors describe these hybrid models and argue that their emergence is explained by both market forces and public sector policy They propose that the future of the sector will depend heavily on several key developments that will differentially affect public, private and hybrid banking models.

Religious perspectives on umbilical cord blood banking.

Umbilical cord blood is a valuable source of haematopoietic stem cells. There is little information about whether religious affiliations have any bearing on attitudes to and decisions about its collection, donation and storage. The authors provided information about umbilical cord blood banking to expert commentators from six major world religions (Catholicism, Anglicanism, Islam, Judaism, Hinduism and Buddhism) and asked them to address a specific set of questions in a commentary. The commentaries suggest there is considerable support for umbilical cord blood banking in these religions. Four commentaries provide moral grounds for favouring public donation over private storage. None attach any particular religious significance to the umbilical cord or to the blood within it, nor place restrictions on the ethnicity or religion of donors and recipients. Views on ownership of umbilical cord blood vary. The authors offer a series of general points for those who seek a better understanding of religious perspectives on umbilical cord blood banking.

Resection of an Intradural Extramedullary Capillary Hemangioma in the Lumbar Spine.

BACKGROUND AND IMPORTANCE: Capillary hemangiomas are space-occupying lesions that rarely affect the central nervous system. When they present within the spinal canal, they can cause insidious symptoms and threaten neurological function. In this study, we present a case of an intradural extramedullary capillary hemangioma of the lumbar spine, discuss our management strategy, and review the current literature. For the first time for this diagnosis, we also provide an operative video. CLINICAL PRESENTATION: The patient is a previously healthy 40-year-old man who presented with complaints of progressive low back and leg pain, numbness, and intermittent subjective urinary incontinence. MRI revealed a discrete, homogenously enhancing intradural extramedullary lesion at L4. This lesion was resected by performing an L4 laminoplasty, which entails en bloc removal of the L4 lamina and then securing it back into place once the intradural resection and dural closure are completed. Histological analysis revealed a diagnosis of capillary hemangioma. The patient had full resolution of his symptoms postoperatively. DISCUSSION: Definitive management of spinal capillary hemangiomas involves gross total resection and can be accomplished with laminoplasty. Because these benign tumors can be adherent to adjacent structures, intraoperative neuromonitoring is helpful adjunct to preserve neurological function for a good outcome. CONCLUSION: Capillary hemangiomas rarely affect the spine but should be considered on the list of differential diagnoses of intradural lesions.

Tobacco Use Is Associated With Increased 90-Day Readmission Among Patients Undergoing Surgery for Degenerative Spine Disease.

STUDY DESIGN: Retrospective database study. OBJECTIVE: Tobacco use is associated with complications after surgical procedures, including poor wound healing, surgical site infections, and cardiovascular events. We used the Nationwide Readmissions Database (NRD) to determine if tobacco use is associated with increased 30- and 90-day readmission among patients undergoing surgery for degenerative spine disorders. METHODS: Patients who underwent elective spine surgery were identified in the NRD from 2010 to 2014. The study population included patients with degenerative spine disorders treated with discectomy, fusion, or decompression. Descriptive and multivariate logistic regression analyses were performed to identify patient and hospital factors associated with 30- and 90-day readmission, with significance set at P value <.001. RESULTS: Within 30 days, 4.8% of patients were readmitted at a median time of 9 days. The most common reasons for 30-day readmission were postoperative infection (12.5%), septicemia (3.5%), and postoperative pain (3.0%). Within 90 days, 7.3% were readmitted at a median time of 18 days. The most common reasons for 90-day readmission were postoperative infection (9.6%), septicemia (3.5%), and pneumonia (2.3%). After adjustment for patient and hospital characteristics, tobacco use was independently associated with readmission at 90 days (odds ratio 1.05, 95% confidence interval 1.03-1.07, P < .0001) but not 30 days (odds ratio 1.02, 95% confidence interval 1.00-1.05, P = .045). CONCLUSIONS: Tobacco use is associated with readmission within 90 days after cervical and thoracolumbar spine surgery for degenerative disease. Tobacco use is a known risk factor for adverse health events and therefore should be considered when selecting patients for spine surgery.

BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis.

Introduction: In colitis, macrophage functionality is altered compared to normal homeostatic conditions. Loss of IL-10 signaling results in an inappropriate chronic inflammatory response to bacterial stimulation. It remains unknown if inhibition of bromodomain and extra-terminal domain (BET) proteins alters usage of DNA regulatory elements responsible for driving inflammatory gene expression. We determined if the BET inhibitor, (+)-JQ1, could suppress inflammatory activation of macrophages in Il10-/- mice. Methods: We performed ATAC-seq and RNA-seq on Il10-/- bone marrow-derived macrophages (BMDMs) cultured in the presence and absence of lipopolysaccharide (LPS) with and without treatment with (+)-JQ1 and evaluated changes in chromatin accessibility and gene expression. Germ-free Il10-/- mice were treated with (+)-JQ1, colonized with fecal slurries and underwent histological and molecular evaluation 14-days post colonization. Results: Treatment with (+)-JQ1 suppressed LPS-induced changes in chromatin at distal regulatory elements associated with inflammatory genes, particularly in regions that contain motifs for AP-1 and IRF transcription factors. This resulted in attenuation of inflammatory gene expression. Treatment with (+)-JQ1 in vivo resulted in a mild reduction in colitis severity as compared with vehicle-treated mice. Conclusion: We identified the mechanism of action associated with a new class of compounds that may mitigate aberrant macrophage responses to bacteria in colitis.