Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor

Aryl hydrocarbon receptor (AhR) is a transcription factor that regulates gene expression upon ligand activation, enabling microbiota-dependent induction, training, and function of the host immune system. A spectrum of metabolites, encompassing indole and tryptophan derivatives, have been recognized as activators. This work introduces an integrated, mass spectrometry-centric workflow that employs a bioassay-guided, fractionation-based methodology for the identification of AhR activators derived from human bacterial isolates. By leveraging the workflow efficiency, the complexities inherent in metabolomics profiling are significantly reduced, paving the way for an in-depth and focused mass spectrometry analysis of bioactive fractions isolated from bacterial culture supernatants. Validation of AhR activator candidates used multiple criteria─MS/MS of the synthetic reference compound, bioassay of AhR activity, and elution time confirmation using a C-13 isotopic reference─and was demonstrated for N-formylkynurenine (NFK). The workflow reported provides a roadmap update for improved efficiency of identifying bioactive metabolites using mass spectrometry-based metabolomics. Mass spectrometry datasets are accessible at the National Metabolomics Data Repository (PR001479, Project DOI: 10.21228/M8JM7Q).

Adherence to Infant Feeding Guidelines in the First Foods New Zealand Study

Infant feeding guidelines provide evidence-based recommendations to support optimal infant health, growth, and development, and exploring adherence to guidelines is a useful way of assessing diet quality. The aim of this study was to determine adherence to the recently updated Ministry of Health "Healthy Eating Guidelines for New Zealand Babies and Toddlers (0-2 years old)". Data were obtained from First Foods New Zealand, a multicentre observational study of 625 infants aged 7.0-10.0 months. Caregivers completed two 24-h diet recalls and a demographic and feeding questionnaire. Nearly all caregivers (97.9%) initiated breastfeeding, 37.8% exclusively breastfed to around six months of age, and 66.2% were currently breastfeeding (mean age 8.4 months). Most caregivers met recommendations for solid food introduction, including appropriate age (75.4%), iron-rich foods (88.3%), puréed textures (80.3%), and spoon-feeding (74.1%). Infants consumed vegetables (63.2%) and fruit (53.9%) more frequently than grain foods (49.5%), milk and milk products (38.6%), and meat and protein-rich foods (31.8%). Most caregivers avoided inappropriate beverages (93.9%) and adding salt (76.5%) and sugar (90.6%). Our findings indicated that while most infants met the recommendations for the introduction of appropriate solid foods, the prevalence of exclusive breastfeeding could be improved, indicating that New Zealand families may need more support.

The Relations between Systems of Oppression and Oral Care Access in the United States

We applied a structural intersectionality approach to cross-sectionally examine the relationships between macro-level systems of oppression, their intersections, and access to oral care in the United States. Whether and the extent to which the provision of government-funded dental services attenuates the emerging patterns of associations was also assessed in the study. To accomplish these objectives, individual-level information from over 300,000 respondents of the 2010 US Behavioral Risk Factor Surveillance System was linked with state-level data for 2000 and 2010 on structural racism, structural sexism, and income inequality, as provided by Homan et al. Using multilevel models, we investigated the relationships between systems of oppression and restricted access to oral health services among respondents at the intersections of race, gender, and poverty. The degree to which extended provision of government-funded dental services weakens the observed associations was determined in models stratified by state-level coverage of oral care. Our analyses bring to the fore intersectional groups (e.g., non-Hispanic Black women and men below the poverty line) with the highest odds of not seeing a dentist in the previous year. We also show that residing in states where high levels of structural sexism and income inequality intersect was associated with 1.3 greater odds (95% confidence interval, 1.1-1.5) of not accessing dental services in the 12 mo preceding the survey. Stratified analyses demonstrated that a more extensive provision of government-funded dental services attenuates associations between structural oppressions and restricted access to oral health care. On the basis of these and other findings, we urge researchers and health care planners to increase access to dental services in more effective and inclusive ways. Most important, we show that counteracting structural drivers of inequities in dental services access entails providing dental care for all.

Skin microbiome attributes associate with biophysical skin ageing

Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we explored how skin microbial species, strains and gene content interact with the biophysical traits of the skin during ageing. With a dataset well-controlled for confounding factors, we found that skin biophysical traits, especially the collagen diffusion coefficient, are associated with the composition and the functional potential of the skin microbiome, including the abundance of bacterial strains found in nosocomial infections and the abundance of antibiotic resistance genes. Our findings reveal important associations between skin biophysical features and ageing-related changes in the skin microbiome and generate testable hypotheses for the mechanisms of such associations.

High-throughput bioprinting of the nasal epithelium using patient-derived nasal epithelial cells

Progenitor human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models through biofabrication. However, this approach has limitations in terms of achieving the intricate three-dimensional (3D) structure of the natural nasal epithelium. 3D bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies for reconstruction of the nasal epithelium. In this study, for the first time, we demonstrate the reconstruction of the nasal epithelium with the use of primary hNECs deposited on Transwell inserts via droplet-based bioprinting (DBB), which enabled high-throughput fabrication of the nasal epithelium in Transwell inserts of 24-well plates. DBB of progenitor hNECs ranging from one-tenth to one-half of the cell seeding density employed during the conventional cell seeding approach enabled a high degree of differentiation with the presence of cilia and tight-junctions over a 4 weeks air-liquid interface culture. Single cell RNA sequencing of these cultures identified five major epithelial cells populations, including basal, suprabasal, goblet, club, and ciliated cells. These cultures recapitulated the pseudostratified columnar epithelial architecture present in the native nasal epithelium and were permissive to respiratory virus infection. These results denote the potential of 3D bioprinting for high-throughput fabrication of nasal epithelial tissue models not only for infection studies but also for other purposes, such as disease modeling, immunological studies, and drug screening.

Equity, Diversity, and Inclusion Best Practices for Oral Health Researchers

KNOWLEDGE TRANSFER STATEMENT

By following best practices related to equity, diversity, and inclusion, oral health researchers may be able to advance the study of health equity, grow a diverse research workforce, and better respond to pressing public health problems.

High-Throughput Bioprinting of the Nasal Epithelium using Patient-derived Nasal Epithelial Cells

Human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models. However, the manual approach is slow, low-throughput and has limitations in terms of achieving the intricate 3D structure of the natural nasal epithelium in a uniform manner. 3D Bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies for reconstruction of the nasal epithelium. In this study, for the first time, we demonstrate the reconstruction of the nasal epithelium with the use of primary hNECs deposited on Transwell inserts via droplet-based bioprinting (DBB), which enabled high-throughput fabrication of the nasal epithelium in Transwell inserts of 24-well plates. DBB of nasal progenitor cells ranging from one-tenth to one-half of the cell seeding density employed during the conventional cell seeding approach enabled a high degree of differentiation with the presence of cilia and tight-junctions over a 4-week air-liquid interface culture. Single cell RNA sequencing of these cultures identified five major epithelial cells populations, including basal, suprabasal, goblet, club, and ciliated cells. These cultures recapitulated the pseudostratified columnar epithelial architecture present in the native nasal epithelium and were permissive to respiratory virus infection. These results denote the potential of 3D bioprinting for high-throughput fabrication of nasal epithelial tissue models not only for infection studies but also for other purposes such as disease modeling, immunological studies, and drug screening.

Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, debilitating disorder manifesting as severe fatigue and post-exertional malaise. The etiology of ME/CFS remains elusive. Here, we present a deep metagenomic analysis of stool combined with plasma metabolomics and clinical phenotyping of two ME/CFS cohorts with short-term (<4 years, n = 75) or long-term disease (>10 years, n = 79) compared with healthy controls (n = 79). First, we describe microbial and metabolomic dysbiosis in ME/CFS patients. Short-term patients showed significant microbial dysbiosis, while long-term patients had largely resolved microbial dysbiosis but had metabolic and clinical aberrations. Second, we identified phenotypic, microbial, and metabolic biomarkers specific to patient cohorts. These revealed potential functional mechanisms underlying disease onset and duration, including reduced microbial butyrate biosynthesis and a reduction in plasma butyrate, bile acids, and benzoate. In addition to the insights derived, our data represent an important resource to facilitate mechanistic hypotheses of host-microbiome interactions in ME/CFS.

Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility

Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. IMPORTANCE Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults

Older adults represent a vulnerable population with elevated risk for numerous morbidities. To explore the association of the microbiome with aging and age-related susceptibilities including frailty and infectious disease risk, we conducted a longitudinal study of the skin, oral, and gut microbiota in 47 community- or skilled nursing facility-dwelling older adults vs. younger adults. We found that microbiome changes were not associated with chronological age so much as frailty: we identified prominent changes in microbiome features associated with susceptibility to pathogen colonization and disease risk, including diversity, stability, heterogeneity, and biogeographic determinism, which were moreover associated with a loss of Cutibacterium (C.) acnes in the skin microbiome. Strikingly, the skin microbiota were also the primary reservoir for antimicrobial resistance, clinically important pathobionts, and nosocomial strains, suggesting a potential role particularly for the skin microbiome in disease risk and dissemination of multidrug resistant pathogens.

Embryonic exposure to benzo[a]pyrene causes age-dependent behavioral alterations and long-term metabolic dysfunction in zebrafish

Polycyclic aromatic hydrocarbons (PAH) are products of incomplete combustion which are ubiquitous pollutants and constituents of harmful mixtures such as tobacco smoke, petroleum and creosote. Animal studies have shown that these compounds exert developmental toxicity in multiple organ systems, including the nervous system. The relative persistence of or recovery from these effects across the lifespan remain poorly characterized. These studies tested for persistence of neurobehavioral effects in AB* zebrafish exposed 5-120 h post-fertilization to a typical PAH, benzo[a]pyrene (BAP). Study 1 evaluated the neurobehavioral effects of a wide concentration range of BAP (0.02-10 μM) exposures from 5 to 120 hpf during larval (6 days) and adult (6 months) stages of development, while study 2 evaluated neurobehavioral effects of BAP (0.3-3 μM) from 5 to 120 hpf across four stages of development: larval (6 days), adolescence (2.5 months), adulthood (8 months) and late adulthood (14 months). Embryonic BAP exposure caused minimal effects on larval motility, but did cause neurobehavioral changes at later points in life. Embryonic BAP exposure led to nonmonotonic effects on adolescent activity (0.3 μM hyperactive, Study 2), which attenuated with age, as well as startle responses (0.2 μM enhanced, Study 1) at 6 months of age. Similar startle changes were also detected in Study 2 (1.0 μM), though it was observed that the phenotype shifted from reduced pretap activity to enhanced posttap activity from 8 to 14 months of age. Changes in the avoidance (0.02-10 μM, Study 1) and approach (reduced, 0.3 μM, Study 2) of aversive/social cues were also detected, with the latter attenuating from 8 to 14 months of age. Fish from study 2 were maintained into aging (18 months) and evaluated for overall and tissue-specific oxygen consumption to determine whether metabolic processes in the brain and other target organs show altered function in late life based on embryonic PAH toxicity. BAP reduced whole animal oxygen consumption, and overall reductions in total basal, mitochondrial basal, and mitochondrial maximum respiration in target organs, including the brain, liver and heart. The present data show that embryonic BAP exposure can lead to neurobehavioral impairment across the life-span, but that these long-term risks differentially emerge or attenuate as development progresses.

Oral Health Equity Must Address Oppression: On the BSSOH Consensus Statement

The Consensus Statement on Future Directions for the Behavioral and Social Sciences in Oral Health (Consensus Statement) is a transformational contribution to oral health research synthesizing a wide array of conceptual, methodological, and disciplinary concerns and offering strategies to improve scientific inquiry. The Consensus Statement explicates global oral health equity as a foundational concern of our field. Given this context, a key concern is missing from the statement: oppression!

NASA GEOS Composition Forecast Modeling System GEOS-CF v1.0: Stratospheric Composition

The NASA Goddard Earth Observing System (GEOS) Composition Forecast (GEOS-CF) provides recent estimates and 5-day forecasts of atmospheric composition to the public in near-real time. To do this, the GEOS Earth system model is coupled with the GEOS-Chem tropospheric-stratospheric unified chemistry extension (UCX) to represent composition from the surface to the top of the GEOS atmosphere (0.01 hPa). The GEOS-CF system is described, including updates made to the GEOS-Chem UCX mechanism within GEOS-CF for improved representation of stratospheric chemistry. Comparisons are made against balloon, lidar, and satellite observations for stratospheric composition, including measurements of ozone (O₃) and important nitrogen and chlorine species related to stratospheric O₃ recovery. The GEOS-CF nudges the stratospheric O₃ toward the GEOS Forward Processing (GEOS FP) assimilated O₃ product; as a result the stratospheric O₃ in the GEOS-CF historical estimate agrees well with observations. During abnormal dynamical and chemical environments such as the 2020 polar vortexes, the GEOS-CF O₃ forecasts are more realistic than GEOS FP O₃ forecasts because of the inclusion of the complex GEOS-Chem UCX stratospheric chemistry. Overall, the spatial patterns of the GEOS-CF simulated concentrations of stratospheric composition agree well with satellite observations. However, there are notable biases-such as low NO _x and HNO₃ in the polar regions and generally low HCl throughout the stratosphere-and future improvements to the chemistry mechanism and emissions are discussed. GEOS-CF is a new tool for the research community and instrument teams observing trace gases in the stratosphere and troposphere, providing near-real-time three-dimensional gridded information on atmospheric composition.

Sodium in the New Zealand diet: proposed voluntary food reformulation targets will not meet the WHO goal of a 30% reduction in total sodium intake

PURPOSE

To simulate the potential impact of the HeartSAFE 2020 programme, a food reformulation initiative by the New Zealand (NZ) Heart Foundation, on sodium intake in the NZ adult population.

METHODS

A representative sample of NZ adults aged 15 years and older completed a 24-h diet recall survey, with 25% of participants completing a second diet recall, in the 2008/09 New Zealand Adult Nutrition Survey (n = 4721). These data were used to estimate sodium intakes of participants. The effect of altering the sodium content of 840 foods in 17 categories and 35 sub-categories included in the NZ HeartSAFE 2020 programme was simulated. The simulated sodium intake reductions in each food sub-category for the entire sample were calculated. Using sampling weights, simulated reductions in population sodium intake and by sociodemographic subgroups were also analysed.

RESULTS

Sodium intake from foods included in the HeartSAFE 2020 programme was 1307 mg/day (95% CI 1279, 1336) at baseline. After applying the HeartSAFE 2020 targets, potential sodium intake was 1048 mg/day (95% CI 1024, 1027). The absolute sodium reduction was 260 mg/day (95% CI 252, 268), corresponding to 20% sodium reduction for the foods included in the NZ HeartSAFE programme.

CONCLUSION

Current sodium targets featured in the NZ HeartSAFE programme will not meet the 30% sodium intake reduction set out by the WHO Global Action Plan. A more comprehensive strategy consistent with the WHO SHAKE Technical Package is needed to advance the goal of sodium intake reduction.

A Sample of Female Adolescent Self-Identified Vegetarians in New Zealand Consume Less Protein and Saturated Fat, but More Fiber than Their Omnivorous Peers

This study aimed to describe the intake and food sources of macronutrients in vegetarian and non-vegetarian adolescent females. Cross-sectional data was collected between February and September 2019. Adolescent females, aged 15 to 18 years old, were recruited throughout New Zealand. Intakes were assessed via two 24-h diet recalls, adjusted to represent usual intake using the multiple source method. Of the 254 participants, 38 self-identified as vegetarian. Vegetarians had similar carbohydrate and fat intakes compared to non-vegetarians; however, their protein intakes were 2.1% kJ lower (95% confidence interval (CI) −3.0 to −1.1%). Vegetarians also consumed 1.1% kJ less saturated fat (95% CI –2.1 to −0.1%), 1.3% kJ (95% CI 0.7 to 1.9) more polyunsaturated fat, and 5 g/day (95% CI 1.8 to 8.0) more fiber than non-vegetarians. When consumed, bread-based dishes and discretionary foods were the highest sources of energy, fat, and carbohydrate in both vegetarians and non-vegetarians. This suggests that some adolescents, including vegetarians, were obtaining high amounts of fat and carbohydrate from food groups associated with poorer dietary quality. We recommend further research to assess how the changing food environment is influencing vegetarian eating patterns and their associations with health outcomes in the wider population.

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota

BACKGROUND

Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.

RESULTS

Of total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1-44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2-95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance.

CONCLUSIONS

Use of a streamlined set of conditions selected for cultivation of skin, oral, and gut microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.

Palliative care simulation for internal medicine trainees: development and pilot study

OBJECTIVES

Shape of training has recognised that 'Managing End-of-Life and Applying Palliative Care Skills' is a key competency for internal medicine trainees. It provides the opportunity and challenge to improve palliative care training for generalist physicians. Simulation has been recognised internationally as a holistic teaching and assessment method. This study aimed to produce a palliative medicine simulation training package for internal medicine trainees for delivery by palliative medicine trainees providing the former opportunity to practice assessment and management of patients with life-limiting illness and the latter teaching and management opportunities.

METHODS

A regional group of palliative medicine trainees were trained in simulation and debrief. Nominal and focus group techniques designed a simulation training package. Learning outcomes were mapped to the internal medicine curriculum descriptors.

RESULTS

Palliative simulation for internal medicine trainees (PALL-SIM-IMT) is a training package meeting internal medicine trainees' curriculum requirements. Regional pilots have demonstrated feasibility for delivery by palliative medicine trainees and improvement in recipients' confidence in all curriculum descriptors.

CONCLUSIONS

PALL-SIM-IMT can aid competency achievement for the provision of generalist palliative care by internal medicine trainees. It allows reciprocal development of palliative medicine trainees' leadership and teaching skills. National adoption and evaluation is ongoing.

Multicenter Evaluation of 434 Hospital Deaths From COVID-19: How Can We Improve End-of-Life Care During a Pandemic?

CONTEXT

The pandemic has substantially increased the workload of hospital palliative care providers, requiring them to be responsive and innovative despite limited information on the specific end of life care needs of patients with COVID-19. Multi-site data detailing clinical characteristics of patient deaths from large populations, managed by specialist and generalist palliative care providers are lacking.

OBJECTIVES

To conduct a large multicenter study examining characteristics of COVID-19 hospital deaths and implications for care.

METHODS

A multi-center retrospective evaluation examined 434 COVID-19 deaths in 5 hospital trusts over the period March 23, 2020 to May 10, 2020.

RESULTS

Eighty three percent of patients were over 70%-32% were admitted from care homes. Diagnostic timing indicated over 90% of those who died contracted the virus in the community. Dying was recognized in over 90% of patients, with the possibility of dying being identified less than 48 hours from admission for a third. In over a quarter, death occurred less than 24 hours later. Patients who were recognized to be dying more than 72 hours prior to death are most likely to have access to medication for symptom control.

CONCLUSION

This large multicenter study comprehensively describes COVID-19 deaths throughout the hospital setting. Clinicians are alert to and diagnose dying appropriately in most patients. Outcomes could be improved by advance care planning to establish preferences, including whether hospital admission is desirable, and alongside this, support the prompt use of anticipatory subcutaneous medications and syringe drivers if needed. Finally, rapid discharges and direct hospice admissions could better utilize hospice beds and improve care.

547. A Retrospective Cohort Study of Treatment Patterns and Clinical Outcomes in Patients with COVID-19

Background

The SARS-CoV-2 pandemic has caused over 400,000 deaths worldwide thus far, and poses therapeutic challenges for millions of patients. There is currently no treatment for SARS-CoV-2 infection approved by the United States Food and Drug Administration. Multiple agents have been used off-label to treat SARS-CoV-2 infection based on small observational cohorts and in vitro data. Here we present the experience of a large academic medical center in treating SARS-CoV-2 infection.

Methods

We performed a retrospective cohort study of patients admitted for greater than 24 hours with a nasopharyngeal, oropharyngeal, and/or bronchoalveolar lavage sample positive for SARS-CoV-2 by polymerase chain reaction (PCR). Demographic data, comorbidities, clinical data, and treatment data were collected from the electronic medical record. Off-label therapies were used at the discretion of the treating providers guided by regularly updated treatment guidelines assembled by infectious diseases physicians and antimicrobial stewardship pharmacists. The primary outcome assessed was in-hospital mortality. Secondary outcomes included admission to the intensive care unit (ICU), endotracheal intubation, initiation of vasopressors, and drug-related adverse events.

Results

Data collection was completed for 448 patients admitted between March 18, 2020 and May 8, 2020. All-cause in-hospital mortality was 13.4% (60/448) during this time. Mortality rates increased with age, up to 45% for patients over 80 years old. Male sex, hypertension, chronic pulmonary disease, end-stage renal disease, chronic liver disease were also risk factors for increased mortality. QTc interval prolongation occurred significantly more frequently in patients who received hydroxychloroquine (HCQ) with or without azithromycin(AZM) than those who did not (HCQ 6%, HCQ+AZM 7.8% vs all other patients, 0%, p< .0001). Review of treatment trends showed close adherence to the treatment recommendations at that time (Figure 1).

Patient Characteristics

Admission Laboratory Data by Disease Severity

QTc Prolongation

Conclusion

SARS-CoV-2 infection is associated with significant inpatient mortality, and use of off-label treatments was associated with significant drug-related adverse events. Treatment regimens changed rapidly, and providers adhered closely to institutional guidelines as they evolved.

Treatment Trends by Week

QTC pre/post Treatment by Hydroxychloroquine Use vs. No Hydroxychloroquine Use

Disclosures

Samir Gupta, MD, Gilead Sciences (Consultant, Scientific Research Study Investigator, Advisor or Review Panel member)ViiV (Consultant, Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member, Research Grant or Support)

Peanut protein acts as a TH2 adjuvant by inducing RALDH2 in human antigen-presenting cells

BACKGROUND

Peanut is a potent inducer of proallergenic T_H2 responses in susceptible individuals. Antigen-presenting cells (APCs) including dendritic cells and monocytes instruct naive T cells to differentiate into various effector cells, determining immune responses such as allergy and tolerance.

OBJECTIVE

We sought to detect peanut protein (PN)-induced changes in gene expression in human myeloid dendritic cells (mDCs) and monocytes, identify signaling receptors that mediate these changes, and assess how PN-induced genes in mDCs impact their ability to promote T-cell differentiation.

METHODS

mDCs, monocytes, and naive CD4⁺ T cells were isolated from blood bank donors and peanut-allergic patients. APCs were incubated with PN and other stimulants, and gene expression was measured using microarray and RT quantitative PCR. To assess T-cell differentiation, mDCs were cocultured with naive T_H cells.

RESULTS

PN induced a unique gene expression profile in mDCs, including the gene that encodes retinaldehyde dehydrogenase 2 (RALDH2), a rate-limiting enzyme in the retinoic acid (RA)-producing pathway. Stimulation of mDCs with PN also induced a 7-fold increase in the enzymatic activity of RALDH2. Blocking antibodies against Toll-like receptor (TLR)1/TLR2, as well as small interfering RNA targeting TLR1/TLR2, reduced the expression of RALDH2 in PN-stimulated APCs by 70%. Naive T_H cells cocultured with PN-stimulated mDCs showed an RA-dependent 4-fold increase in production of IL-5 and expression of integrin α₄β₇.

CONCLUSIONS

PN induces RALDH2 in human APCs by signaling through the TLR1/TLR2 heterodimer. This leads to production of RA, which acts on T_H cells to induce IL-5 and gut-homing integrin. RALDH2 induction by PN in APCs and RA-promoted T_H2 differentiation could be an important factor determining allergic responses to peanut.

Inequalities in awareness and availability of bereavement services in North-East England

OBJECTIVES

National guidance recommends equality in access to bereavement services; despite this, awareness and availability appears inconsistent. The aim of this study was to explore availability and accessibility of bereavement services across the North-East of England and to highlight issues potentially applicable across the UK, at a time of unprecedented need due to the impact of COVID-19.

METHODS

Phase 1: an eight item, web-based survey was produced. A survey link was cascaded to all GP practices (General Practitioners) in the region. Phase 2: an email was sent to all services identified in phase 1, requesting details such as referral criteria and waiting times.

RESULTS

All 392 GP practices in the region were invited to participate. The response rate was 22% (85/392). Twenty-one per cent (18/85) of respondents reported that they do not refer patients, comments included 'not aware of any services locally'. A total of 36 services were contacted with 72% responding with further information. Most bereavement specific support was reliant on charity-funded services including hospices, this sometimes required a pre-existing link with the hospice. Waiting times were up to 4 months.

CONCLUSIONS

Although multiple different, usually charity-funded services were identified, awareness and accessibility were variable. This survey was conducted prior to the COVID-19 pandemic, where complex situations surrounding death is likely to impact on the usual grieving process and increase the need for bereavement support. Meanwhile, charities providing this support are under severe financial strain. There is an urgent need to bridge the gap between need and access to bereavement services.

Correction: Selective colonization ability of human fecal microbes in different mouse gut environments

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Hearing Aid Uptake in Children with Unilateral Microtia and Canal Atresia: A Comparison between a Tertiary Center and Peripheral Centers

OBJECTIVES

To review the trialing and uptake of hearing aids in children with unilateral microtia or canal atresia, known collectively as congenital unilateral conductive hearing loss (CUCHL), observed in a tertiary hospital and local peripheral services.

MATERIALS AND METHODS

A retrospective review of medical records for patients with CUCHL was conducted using data from a shared audiology database at a tertiary children's hospital.

RESULTS

We identified 45 patients with CUCHL and excluded seven of them due to missing data. Of the 38 patients, 16 (16/38, 42%) did not have any subjective hearing complaints. Furthermore, 32% (12/38) of patients attended audiology at a tertiary centre and 83% (10/12) from this group trialled a hearing aid. In comparison, 46% (12/46) whose audiology care was delivered peripherally trialled aiding. Of the patients from the tertiary center, 58% (7/12) are still using a hearing aid compared to 27% (7/26) of patients from peripheral centers.

CONCLUSION

Our analysis shows that patients with CUCHL are more likely to try hearing aids and continue using them if their audiology care is in a tertiary center. Allowing for a small sample size, this may indicate a health inequality. Agreeing on minimum standards for the management of patients with CUCHL or managing them in a designated center could increase consistency.

A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful-focusing on CRISPRi as a potential application-as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species.IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin

Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.

Expansion of the CD4+ effector T-cell repertoire characterizes peanut-allergic patients with heightened clinical sensitivity

BACKGROUND

Individuals with peanut allergy range in clinical sensitivity: some can consume grams of peanut before experiencing any symptoms, whereas others suffer systemic reactions to 10 mg or less. Current diagnostic testing only partially predicts this clinical heterogeneity.

OBJECTIVE

We sought to identify characteristics of the peanut-specific CD4+ T-cell response in peanut-allergic patients that correlate with high clinical sensitivity.

METHODS

We studied the T-cell receptor β-chain (TCRβ) usage and phenotypes of peanut-activated, CD154+ CD4+ memory T cells using fluorescence-activated cell sorting, TCRβ sequencing, and RNA-Seq, in reactive and hyporeactive patients who were stratified by clinical sensitivity.

RESULTS

TCRβ analysis of the CD154+ and CD154- fractions revealed more than 6000 complementarity determining region 3 sequences and motifs that were significantly enriched in the activated cells and 17% of the sequences were shared between peanut-allergic individuals, suggesting strong convergent selection of peanut-specific clones. These clones were more numerous among the reactive patients, and this expansion was identified within effector, but not regulatory T-cell populations. The transcriptional profile of CD154+ T cells in the reactive group skewed toward a polarized TH2 effector phenotype, and expression of TH2 cytokines strongly correlated with peanut-specific IgE levels. There were, however, also non-TH2-related differences in phenotype. Furthermore, the ratio of peanut-specific clones in the effector versus regulatory T-cell compartment, which distinguished the clinical groups, was independent of specific IgE concentration.

CONCLUSIONS

Expansion of the peanut-specific effector T-cell repertoire is correlated with clinical sensitivity, and this observation may be useful to inform our assessment of disease phenotype and to monitor disease longitudinally.

Serotonin regulates dynamics of cerebellar granule cell activity by modulating tonic inhibition

Understanding how afferent information is integrated by cortical structures requires identifying the factors shaping excitation and inhibition within their input layers. The input layer of the cerebellar cortex integrates diverse sensorimotor information to enable learned associations that refine the dynamics of movement. Specifically, mossy fiber afferents relay sensorimotor input into the cerebellum to excite granule cells, whose activity is regulated by inhibitory Golgi cells. To test how this integration can be modulated, we have used an acute brain slice preparation from young adult rats and found that encoding of mossy fiber input in the cerebellar granule cell layer can be regulated by serotonin (5-hydroxytryptamine, 5-HT) via a specific action on Golgi cells. We find that 5-HT depolarizes Golgi cells, likely by activating 5-HT2A receptors, but does not directly act on either granule cells or mossy fibers. As a result of Golgi cell depolarization, 5-HT significantly increases tonic inhibition onto both granule cells and Golgi cells. 5-HT-mediated Golgi cell depolarization is not sufficient, however, to alter the probability or timing of mossy fiber-evoked feed-forward inhibition onto granule cells. Together, increased granule cell tonic inhibition paired with normal feed-forward inhibition acts to reduce granule cell spike probability without altering spike timing. Hence, these data provide a circuit mechanism by which 5-HT can reduce granule cell activity without altering temporal representations of mossy fiber input. Such changes in network integration could enable flexible, state-specific suppression of cerebellar sensorimotor input that should not be learned or enable reversal learning for unwanted associations. NEW & NOTEWORTHY Serotonin (5-hydroxytryptamine, 5-HT) regulates synaptic integration at the input stage of cerebellar processing by increasing tonic inhibition of granule cells. This circuit mechanism reduces the probability of granule cell spiking without altering spike timing, thus suppressing cerebellar input without altering its temporal representation in the granule cell layer.

SunGold Kiwifruit Supplementation of Individuals with Prediabetes Alters Gut Microbiota and Improves Vitamin C Status, Anthropometric and Clinical Markers

Kiwifruit are a nutrient dense food and an excellent source of vitamin C. Supplementation of the diet with kiwifruit enhances plasma vitamin C status and epidemiological studies have shown an association between vitamin C status and reduced insulin resistance and improved blood glucose control. In vitro experiments suggest that eating kiwifruit might induce changes to microbiota composition and function; however, human studies to confirm these findings are lacking. The aim of this study was to investigate the effect of consuming two SunGold kiwifruit per day over 12 weeks on vitamin C status, clinical and anthropometric measures and faecal microbiota composition in people with prediabetes. This pilot intervention trial compared baseline measurements with those following the intervention. Participants completed a physical activity questionnaire and a three-day estimated food diary at baseline and on completion of the trial. Venous blood samples were collected at each study visit (baseline, 6, 12 weeks) for determination of glycaemic indices, plasma vitamin C concentrations, hormones, lipid profiles and high-sensitivity C-reactive protein. Participants provided a faecal sample at each study visit. DNA was extracted from the faecal samples and a region of the 16S ribosomal RNA gene was amplified and sequenced to determine faecal microbiota composition. When week 12 measures were compared to baseline, results showed a significant increase in plasma vitamin C (14 µmol/L, p < 0.001). There was a significant reduction in both diastolic (4 mmHg, p = 0.029) and systolic (6 mmHg, p = 0.003) blood pressure and a significant reduction in waist circumference (3.1 cm, p = 0.001) and waist-to-hip ratio (0.01, p = 0.032). Results also showed a decrease in HbA1c (1 mmol/mol, p = 0.005) and an increase in fasting glucose (0.1 mmol/L, p = 0.046), however, these changes were small and were not clinically significant. Analysis of faecal microbiota composition showed an increase in the relative abundance of as yet uncultivated and therefore uncharacterised members of the bacterial family Coriobacteriaceae. Novel bacteriological investigations of Coriobacteriaceae are required to explain their functional relationship to kiwifruit polysaccharides and polyphenols.

Incidental diagnosis of tuberous sclerosis complex by exome sequencing in three families with subclinical findings

Tuberous sclerosis complex (TSC) is an autosomal-dominant neurocutaneous disorder characterized by lesions and benign tumors in multiple organ systems including the brain, skin, heart, eyes, kidneys, and lungs. The phenotype is highly variable, although penetrance is reportedly complete. We report the molecular diagnosis of TSC in individuals exhibiting extreme intra-familial variability, including the incidental diagnosis of asymptomatic family members. Exome sequencing was performed in three families, with probands referred for epilepsy, autism, and absent speech (Family 1); epileptic spasms (Family 2); and connective tissue disorders (Family 3.) Pathogenic variants in TSC1 or TSC2 were identified in nine individuals, including relatives with limited or no medical concerns at the time of testing. Of the nine individuals reported here, six had post-diagnosis examinations and three met clinical diagnostic criteria for TSC. One did not meet clinical criteria for a possible or definite diagnosis of TSC, and two had only a possible clinical diagnosis following post-diagnosis workup. These individuals as well as their mothers demonstrated limited features that would not raise concern for TSC in the absence of molecular results. In addition, three individuals exhibited epilepsy with normal brain MRIs, and two without seizures or intellectual disability had MRI findings fulfilling major criteria for TSC highlighting the difficulty providers face when relying on clinical criteria to guide genetic testing. Given the importance of a timely TSC diagnosis for clinical management, such cases demonstrate a potential benefit for clinical criteria to include seizures and an unbiased molecular approach to genetic testing.

Scombrotoxic Fish Poisoning Secondary to Tuna Ingestion

Scombrotoxic poisoning results from the improper handling and refrigeration of fish containing naturally occurring histidine. Scombroid fish species such as tuna, mackerel and swordfish contain histidine, which is converted to histamine when inadequately chilled. European legislation states that scombroid fish species should be tested for the presence of histamine and mean values should be <100mg/kg1. The authors report an outbreak of scombrotoxic fish poisoning in 12 individuals following ingestion of tuna. Symptoms occurred rapidly and included flushing, headache, palpitations and diarrhoea. Fortunately, symptoms were short lived and self-limiting except in one individual, who required anti-histamine medication. Adequate refrigeration practices are crucial in preventing scombrotoxic food poisoning.

Inadequate Vitamin C Status in Prediabetes and Type 2 Diabetes Mellitus: Associations with Glycaemic Control, Obesity, and Smoking

Vitamin C (ascorbate) is an essential micronutrient in humans, being required for a number of important biological functions via acting as an enzymatic cofactor and reducing agent. There is some evidence to suggest that people with type 2 diabetes mellitus (T2DM) have lower plasma vitamin C concentrations compared to those with normal glucose tolerance (NGT). The aim of this study was to investigate plasma vitamin C concentrations across the glycaemic spectrum and to explore correlations with indices of metabolic health. This is a cross-sectional observational pilot study in adults across the glycaemic spectrum from NGT to T2DM. Demographic and anthropometric data along with information on physical activity were collected and participants were asked to complete a four-day weighed food diary. Venous blood samples were collected and glycaemic indices, plasma vitamin C concentrations, hormone tests, lipid profiles, and high-sensitivity C-reactive protein (hs-CRP) were analysed. A total of 89 participants completed the study, including individuals with NGT (n = 35), prediabetes (n = 25), and T2DM managed by diet alone or on a regimen of Metformin only (n = 29). Plasma vitamin C concentrations were significantly lower in individuals with T2DM compared to those with NGT (41.2 µmol/L versus 57.4 µmol/L, p < 0.05) and a higher proportion of vitamin C deficiency (i.e. <11.0 µmol/L) was observed in both the prediabetes and T2DM groups. The results showed fasting glucose (p = 0.001), BMI (p = 0.001), smoking history (p = 0.003), and dietary vitamin C intake (p = 0.032) to be significant independent predictors of plasma vitamin C concentrations. In conclusion, these results suggest that adults with a history of smoking, prediabetes or T2DM, and/or obesity, have greater vitamin C requirements. Future research is required to investigate whether eating more vitamin C rich foods and/or taking vitamin C supplements may reduce the risk of progression to, and/or complications associated with, T2DM.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Proper functioning of an organism requires cells and tissues to behave in uniform, well-organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here, we carried out a multi-faceted and single-cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi-gene microRNA (miRNA) families. We found that embryos lacking particular miRNA-dependent signaling pathways develop a vascular trait similar to wild-type, but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.

The influence of culture on diabetes self-management: perspectives of Gujarati Muslim men who reside in northwest England

AIM

To present the findings of a study which explored the influence of culture on (type 2) diabetes self-management in Gujarati Muslim men who reside in northwest England.

BACKGROUND

This study was informed by an embodied perspective of culture, in which culture is grounded in the body and self. This contrasts with some contemporary health research and policy which adopts an oversimplified perspective, portraying culture as static and deterministic and being responsible for non-adherent self-management behaviours.

METHOD

A case-study approach was used, which combined interview and participant observation methods. Data were collected from Gujarati Muslim men about their lived experiences of diabetes self-management. These accounts, along with further narrative data from 'significant other' participants, were analysed over several cycles.

RESULTS

Two central concepts guide the results: embodied culture and dynamic culture. These concepts reflect the subjective and contextual nature of culture and are illustrated in the themes 'past experiences and socio-economic factors', 'social and gendered roles' and 'personal choice and contextual factors'. The findings highlight that the complexity of life means that culture never exists in isolation, but is one of the many factors that a man negotiates to inform his diabetes self-management.

CONCLUSION

We draw attention to the dissonance between the way culture is presented in some government policy and research, and the way it is understood in an embodied approach. The National Service Framework for Diabetes advocates the provision of individualized culturally appropriate care, and in this paper, we make suggestions as to how an embodied approach can be incorporated within the framework.

RELEVANCE TO CLINICAL PRACTICE

Nurses have an integral role in implementing the National Service Framework for Diabetes. This paper contributes to the debate about how nurses can best deliver this framework to a diverse patient population.

Association of Nut Consumption with Cardiometabolic Risk Factors in the 2008/2009 New Zealand Adult Nutrition Survey

Nut consumption has been associated with improvements in risk factors for chronic disease in populations within North America, Europe and Iran. This relationship has not been investigated in New Zealand (NZ). The associations between nut consumption and cardiometabolic risk factors among New Zealanders were examined. Data from the 24-h diet recalls of 4721 participants from the NZ Adult Nutrition Survey 2008/2009 (2008/2009 NZANS) were used to determine whole and total nut intake. Anthropometric data and blood pressure were collected, as well as blood samples analysed for total cholesterol (total-C) and HDL cholesterol (HDL-C), glycated haemoglobin (HbA1c), C-reactive protein (CRP) and folate. Participants were classified according to their five-year cardiovascular disease (CVD) risk. Both whole and total nut consumers had significantly lower weight, body mass index (BMI), waist circumference and central adiposity than non-nut consumers (all p ≤ 0.044). Whole blood, serum and red blood cell folate concentrations were significantly higher among whole nut consumers compared to non-whole nut consumers (all p ≤ 0.014), with only serum folate higher in total nut consumers compared to non-total nut consumers (p = 0.023). There were no significant differences for blood pressure, total-C, HDL-C and HbA1c; however, significant negative associations between total nut consumption and CVD risk category (p < 0.001) and CRP (p = 0.045) were apparent. Nut consumption was associated with more favourable body composition and a number of risk factors, which could collectively reduce chronic disease.

A novel miR-451a isomiR, associated with amelanotypic phenotype, acts as a tumor suppressor in melanoma by retarding cell migration and invasion

miRNAs are key regulatory small non-coding RNAs involved in critical steps of melanoma tumorigenesis; however, the relationship between sequence specific variations at the 5′ or 3′ termini (isomiR) of a miRNA and cancer phenotype remains unclear. Deep-sequencing and qRT-PCR showed reduced expression of miR-144/451a cluster and most abundant isomiR (miR451a.1) in dysplastic nevi, in-situ and invasive melanomas compared to common nevi and normal skin (n = 101). miRNA in situ hybridization reproducibly confirmed lost miR-451a.1 in melanoma compared to nevus cells or adjacent keratinocytes. Significantly higher expression of miR-451a.1 was associated with amelanotic phenotype in melanomas (n = 47). In contrast, miR-451a was associated with melanotic phenotype, absent pagetoid scatter of intraepidermal melanocytes, superficial spreading histological subtype and tumor inflammation. Sequencing miRNAs from cultured melanocytes with cytoplasmic melanin gradient (light, medium to dark) showed absent miR-451a while revealing other melanin-associated miRNAs, e.g. miR-30b, miR-100 and miR-590 in darkly and let-7a, let-7i and let-7f in lightly to moderately pigmented cultured melanocytes. Ectopic expression of miR-144/451a in melanoma cell lines resulted in markedly higher levels of mature miR-451a.1 than miR451a or miR-144; and significantly retarded cell migration and inhibited invasion in a glucose-sensitive manner. Surprisingly, these effects were not mediated by calcium binding protein 39 (CAB39), a proven miR451a gene target. miR-144/miR-451a cluster is a novel miRNA locus with tumor suppressive activity in melanoma.

In-depth characterization of microRNA transcriptome in melanoma

The full repertoire of human microRNAs (miRNAs) that could distinguish common (benign) nevi from cutaneous (malignant) melanomas remains to be established. In an effort to gain further insight into the role of miRNAs in melanoma, we applied Illumina next-generation sequencing (NGS) platform to carry out an in-depth analysis of miRNA transcriptome in biopsies of nevi, thick primary (>4.0 mm) and metastatic melanomas with matched normal skin in parallel to melanocytes and melanoma cell lines (both primary and metastatic) (n = 28). From this data representing 698 known miRNAs, we defined a set of top-40 list, which properly classified normal from cancer; also confirming 23 (58%) previously discovered miRNAs while introducing an additional 17 (42%) known and top-15 putative novel candidate miRNAs deregulated during melanoma progression. Surprisingly, the miRNA signature distinguishing specimens of melanoma from nevus was significantly different than that of melanoma cell lines from melanocytes. Among the top list, miR-203, miR-204-5p, miR-205-5p, miR-211-5p, miR-23b-3p, miR-26a-5p and miR-26b-5p were decreased in melanomas vs. nevi. In a validation cohort (n = 101), we verified the NGS results by qRT-PCR and showed that receiver-operating characteristic curves for miR-211-5p expression accurately discriminated invasive melanoma (AUC = 0.933), melanoma in situ (AUC = 0.933) and dysplastic (atypical) nevi (AUC = 0.951) from common nevi. Target prediction analysis of co-transcribed miRNAs showed a cooperative regulation of key elements in the MAPK signaling pathway. Furthermore, we found extensive sequence variations (isomiRs) and other non-coding small RNAs revealing a complex melanoma transcriptome. Deep-sequencing small RNAs directly from clinically defined specimens provides a robust strategy to improve melanoma diagnostics.

The LKB1 tumor suppressor controls spindle orientation and localization of activated AMPK in mitotic epithelial cells

Orientation of mitotic spindles plays an integral role in determining the relative positions of daughter cells in a tissue. LKB1 is a tumor suppressor that controls cell polarity, metabolism, and microtubule stability. Here, we show that germline LKB1 mutation in mice impairs spindle orientation in cells of the upper gastrointestinal tract and causes dramatic mislocalization of the LKB1 substrate AMPK in mitotic cells. RNAi of LKB1 causes spindle misorientation in three-dimensional MDCK cell cysts. Maintaining proper spindle orientation, possibly mediated by effects on the downstream kinase AMPK, could be an important tumor suppressor function of LKB1.

Up-regulated Dicer expression in patients with cutaneous melanoma

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs (18-24 nucleotides) that have recently been shown to regulate gene expression during cancer progression. Dicer, a central enzyme in the multi-component miRNA biogenesis pathway, is involved in cutting precursor miRNAs to functionally mature forms. Emerging evidence shows that Dicer expression is deregulated in some human malignancies and it correlates with tumor progression, yet this role has not yet been investigated in skin cancers.

METHODS AND FINDINGS

Using an anti-human monoclonal antibody against Dicer and immunohistochemistry, we compared the expression of Dicer protein among 404 clinically annotated controls and skin tumors consisting of melanocytic nevi (n = 71), a variety of melanomas (n = 223), carcinomas (n = 73) and sarcomas (n = 12). Results showed a cell-specific up-regulated Dicer in 81% of cutaneous, 80% of acrolentiginous and 96% of metastatic melanoma specimens compared to carcinoma or sarcoma specimens (P<0.0001). The expression of Dicer was significantly higher in melanomas compared to benign melanocytic nevi (P<0.0001). In patients with cutaneous melanomas, Dicer up-regulation was found to be significantly associated with an increased tumor mitotic index (P = 0.04), Breslow's depth of invasion (P = 0.03), nodal metastasis (P = 0.04) and a higher American Joint Committee on Caner (AJCC) clinical stage (P = 0.009). Using western blot analysis, we confirmed the cell-specific up-regulation of Dicer protein in vitro. A pooled-analysis on mRNA profiling in cutaneous tumors showed up-regulation of Dicer at the RNA level in cutaneous melanoma, also showing deregulation of other enzymes that participate in the biogenesis and maturation of canonical miRNAs.

CONCLUSIONS

Increased Dicer expression may be a clinically useful biomarker for patients with cutaneous melanoma. Understanding deregulation of Dicer and its influence on miRNA maturation is needed to predict the susceptibility of melanoma patients to miRNA-based therapy in the future.

An exploration of culture, diabetes, and nursing in the South Asian community: a metasynthesis of qualitative studies

South Asian people are often perceived as a homogenous group whose culture is prescriptive and constraining. A metasynthesis of how culture influences diabetes self-management in the context of a South Asian population was undertaken. Theory explication was used to deconstruct and reconceptualize the findings of the studies. Eleven publications reported themes of health beliefs, individuality, context, and shared experiences. The results indicate that culture does not influence diabetes self-management in a rigid and prescriptive way; instead, individuals negotiate and interpret culture in a shifting and diverse context. An individualized approach to delivering culturally appropriate nursing care should be taken.

Thyroid hormone positively regulates the enterocyte differentiation marker intestinal alkaline phosphatase gene via an atypical response element

Thyroid hormone (T3) is a critical regulator of intestinal epithelial development and homeostasis, but its mechanism of action within the gut is not well understood. We have examined the molecular mechanisms underlying the T3 activation of the enterocyte differentiation marker intestinal alkaline phosphatase (IAP) gene. RT-PCR and Western blotting showed that thyroid hormone receptors TRalpha1 and TRbeta1 were expressed in human colorectal adenocarcinoma Caco-2 cells. Northern blotting detected expression of two IAP transcripts, which were increased approximately 3-fold in response to T3. Transient transfection studies with luciferase reporter plasmids carrying various internal and 5' deletion mutations of the IAP promoter localized a putative thyroid hormone response element (TRE) to a region approximately 620 nucleotides upstream (-620) of the ATG start codon. EMSAs using TRalpha1-retinoid X receptor alpha (RXRalpha) on sequential 5' and 3' single nucleotide deletions defined the TRE between -632 and -612 (5'-TTGAACTCAgccTGAGGTTAC-3'). Compared with the consensus TRE, the IAP-TRE is novel in that it contains an everted repeat of two nonamers (not hexamers) separated by three nucleotides. Neither TRalpha1 nor RXRalpha binds to the IAP-TRE; however, TRbeta1 binds to this TRE with minimal affinity. In the presence of TR and RXRalpha, only the TR-RXRalpha heterodimer binds to the IAP-TRE. Mutagenesis of either nonamer abolishes the biological activity of IAP promoter. We have thus identified a novel response element that appears to mediate the T3-induced activation of the enterocyte differentiation marker, intestinal alkaline phosphatase.