A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs.

Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5' ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5' ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.

Nature of ß-1,3-Glucan-Exposing Features on Candida albicans Cell Wall and Their Modulation.

Candida albicans exists as a commensal of mucosal surfaces and the gastrointestinal tract without causing pathology. However, this fungus is also a common cause of mucosal and systemic infections when antifungal immune defenses become compromised. The activation of antifungal host defenses depends on the recognition of fungal pathogen-associated molecular patterns (PAMPs), such as ß-1,3-glucan. In C. albicans, most ß-1,3-glucan is present in the inner cell wall, concealed by the outer mannan layer, but some ß-1,3-glucan becomes exposed at the cell surface. In response to host signals, such as lactate, C. albicans induces the Xog1 exoglucanase, which shaves exposed ß-1,3-glucan from the cell surface, thereby reducing phagocytic recognition. We show here that ß-1,3-glucan is exposed at bud scars and punctate foci on the lateral wall of yeast cells, that this exposed ß-1,3-glucan is targeted during phagocytic attack, and that lactate-induced masking reduces ß-1,3-glucan exposure at bud scars and at punctate foci. ß-1,3-Glucan masking depends upon protein kinase A (PKA) signaling. We reveal that inactivating PKA, or its conserved downstream effectors, Sin3 and Mig1/Mig2, affects the amounts of the Xog1 and Eng1 glucanases in the C. albicans secretome and modulates ß-1,3-glucan exposure. Furthermore, perturbing PKA, Sin3, or Mig1/Mig2 attenuates the virulence of lactate-exposed C. albicans cells in Galleria. Taken together, the data are consistent with the idea that ß-1,3-glucan masking contributes to Candida pathogenicity. IMPORTANCE Microbes that coexist with humans have evolved ways of avoiding or evading our immunological defenses. These include the masking by these microbes of their "pathogen-associated molecular patterns" (PAMPs), which are recognized as "foreign" and used to activate protective immunity. The commensal fungus Candida albicans masks the proinflammatory PAMP ß-1,3-glucan, which is an essential component of its cell wall. Most of this ß-1,3-glucan is hidden beneath an outer layer of the cell wall on these microbes, but some can become exposed at the fungal cell surface. Using high-resolution confocal microscopy, we examine the nature of the exposed ß-1,3-glucan at C. albicans bud scars and at punctate foci on the lateral cell wall, and we show that these features are targeted by innate immune cells. We also reveal that downstream effectors of protein kinase A (Mig1/Mig2, Sin3) regulate the secretion of major glucanases, modulate the levels of ß-1,3-glucan exposure, and influence the virulence of C. albicans in an invertebrate model of systemic infection. Our data support the view that ß-1,3-glucan masking contributes to immune evasion and the virulence of a major fungal pathogen of humans.

Rechallenge after anti-tuberculosis drug-induced liver injury in a high HIV prevalence cohort.

Background: There are limited data on the outcomes of rechallenge with anti-tuberculosis therapy (ATT) following anti-tuberculosis drug-induced liver injury (AT-DILI) in a high HIV prevalence setting. Objectives: To describe the outcomes of rechallenge with first-line ATT. Method: Hospitalised participants with AT-DILI who were enrolled into a randomised controlled trial of N-acetylcysteine in Cape Town, South Africa, were followed up until completion of ATT rechallenge. We described rechallenge outcomes, and identified associations with recurrence of liver injury on rechallenge (positive rechallenge). Results: Seventy-nine participants were rechallenged of whom 41 (52%) were female. Mean age was 37 years (standard deviation [s.d.] ±10). Sixty-eight (86%) were HIV-positive, of whom 34 (50%) were on antiretroviral therapy (ART) at time of AT-DILI presentation. Five participants had serious adverse reactions to an aminoglycoside included in the alternate ATT regimen given after first-line ATT interruption: acute kidney injury in three and hearing loss in two. The median time from first-line ATT interruption to start of first-line ATT rechallenge was 13 days (interquartile range [IQR]: 8-18 days). Antiretroviral therapy was interrupted for a median of 32 days (IQR: 17-58) among HIV-positive participants on ART before AT-DILI. Fourteen participants had positive rechallenge (18%). Positive rechallenge was associated with pyrazinamide rechallenge (P = 0.005), female sex (P = 0.039) and first episode of tuberculosis (TB) (P = 0.032). Conclusion: Rechallenge was successful in most of our cohort. Pyrazinamide rechallenge should be carefully considered.

Exploration of the Nurse Shark (Ginglymostoma cirratum) Plasma Immunoproteome Using High-Resolution LC-MS/MS.

Many animals of scientific importance lack species-specific reagents (e.g., monoclonal antibodies) for in-depth studies of immune proteins. Mass spectrometry (MS)-based proteomics has emerged as a useful method for monitoring changes in protein abundance and modifications in non-model species. It can be used to quantify hundreds of candidate immune molecules simultaneously without the generation of new reagents. Here, we used MS-based proteomics to identify and quantify candidate immune proteins in the plasma of the nurse shark (Ginglymostoma cirratum), a cartilaginous fish and representative of the most basal extant vertebrate lineage with an immunoglobulin-based immune system. Mass spectrometry-based LC-MS/MS was performed on the blood plasma of nurse sharks immunized with human serum albumin (n=4) or sham immunized (n=1), and sampled at days 0 (baseline control), 1, 2, 3, 5, 7, 14, 21, 28, 25, 42 and 49. An antigen-specific antibody response was experimentally confirmed post-immunization. To provide a high-quality reference to identify proteins, we assembled and annotated a multi-tissue de novo transcriptome integrating long- and short-read sequence data. This comprised 62,682 contigs containing open reading frames (ORFs) with a length >80 amino acids. Using this transcriptome, we reliably identified 626 plasma proteins which were broadly categorized into coagulation, immune, and metabolic functional groups. To assess the feasibility of performing LC-MS/MS proteomics in nurse shark in the absence of species-specific protein annotations, we compared the results to an alternative strategy, mapping peptides to proteins predicted in the genome assembly of a related species, the whale shark (Rhincodon typus). This approach reliably identified 297 proteins, indicating that useful data on the plasma proteome may be obtained in many instances despite the absence of a species-specific reference protein database. Among the plasma proteins defined against the nurse shark transcriptome, fifteen showed consistent changes in abundance across the immunized shark individuals, indicating a role in the immune response. These included alpha-2-macroglobulin (A2M) and a novel protein yet to be characterized in diverse vertebrate lineages. Overall, this study enhances genetic and protein-level resources for nurse shark research and vastly improves our understanding of the elasmobranch plasma proteome, including its remodelling following immune stimulation.

Biomarkers of caspofungin resistance in Candida albicans isolates: A proteomic approach.

Candida albicans is a clinically important polymorphic fungal pathogen that causes life-threatening invasive infections in immunocompromised patients. Antifungal therapy failure is a substantial clinical problem, due to the emergence of an increasing number of drug-resistant isolates. Caspofungin is a common antifungal drug, often used as first-line therapy that inhibits cell wall ß-(1,3)-glucan synthesis. In this work, the cell surface of different echinocandin-resistant C. albicans clinical isolates was compared with sensitive isolates and their responses to echinocandin treatment analyzed. Proteomic analysis detected changes in the repertoire of proteins involved in cell wall organization and maintenance, in drug-resistant strains compared to susceptible isolates and after incubation with caspofungin. Moreover, an interaction network was created from the differential expression results. Our findings suggest drug resistance may involve not only a different cell wall architecture, but also a different response to drugs.

Changing HCW attitudes: a case study of normalizing HIV service delivery in emergency departments.

BACKGROUND: Delays in the implementation of evidence-based practices are significant and ubiquitous, compromising health outcomes. Resistance to change is a key factor in hindering adoption and integration of new evidence-based interventions. This study seeks to understand the impact of exposure to HIV testing within a research context on provider attitudes towards HIV counselling and testing (HCT) in emergency departments (ED). METHODS: This is a pre-and-post study design measuring the effect of a new ED-based HCT intervention, conducted by lay counsellors, on provider attitudes in Eastern Cape, South Africa. A validated, anonymized, 7-item survey was self-completed by routine care providers (physicians, nurses, and case managers). Questions were scored on a 5-point Likert scale with 5 consistently reflecting a positive attitude. Mean scores were calculated for each question and compared using a two-sample t-test to assess change in sample means for attitudes among providers surveyed before and after the intervention. RESULTS: A total of 132 surveys were completed across three EDs. Majority of respondents were female (70.5%), 20-29 years old (37.9%), of African race (81.1%), nurses (39.4%), and practicing medicine for 0-4 years (37.9%). Pre-intervention, providers displayed a positive attitude towards 'the benefit of offering ED-based HCT to patients' (4.33), 'the ED offering HCT' (3.53), 'all ED patients receiving HCT' (3.42), 'concern about patient reaction to HCT' (3.26), and 'comfort with disclosing HCT results' (3.21); and a mildly negative attitude towards 'only high-risk ED patients receiving HCT' (2.68), and 'the burden of offering HCT in a clinical environment' (2.80). Post-intervention, provider attitudes improved significantly towards 'all ED patients receiving HCT' (3.86, p < 0.05), 'only high-risk ED patients receiving HCT' (2.30, p < 0.05), 'the burden of offering HCT in a clinical environment' (3.21, p < 0.05), and 'comfort with disclosing HCT results' (3.81, p < 0.05). CONCLUSIONS: Controlled exposure to new practices with a structured implementation period can shift attitudes beginning a process of practice normalization. In our study, we observed improvements in provider attitudes regarding the benefits of HCT and the burden of offering HCT to all patients in the ED. Research activities may have a role in mitigating resistance to change and supporting intervention adoption.

Cumulative incidence of SARS-CoV-2 and associated risk factors among healthcare workers: a cross-sectional study in the Eastern Cape, South Africa.

OBJECTIVES: This study assesses the cumulative incidence of SARS-CoV-2 infection among healthcare workers (HCWs) during South Africa's first wave and examines the associated demographic, health-related and occupational risk factors for infection. METHODS: Multistage cluster sampling was used in a cross-sectional study to recruit 1309 HCWs from two academic hospitals in the Eastern Cape, South Africa over 6 weeks in November and December 2020. Prior test results for SARS-CoV-2 PCR and participants' characteristics were recorded while a blood sample was drawn for detection of IgG antibodies against SARS-CoV-2 nucleocapsid protein. The primary outcome measure was the SARS-CoV-2 cumulative incidence rate, defined as the combined total of positive results for either PCR or IgG antibodies, divided by the total sample. The secondary outcome was significant risk factors associated with infection. RESULTS: Of the total participants included in the analysis (n=1295), the majority were women (81.5%), of black race (78.7%) and nurses (44.8%). A total of 390 (30.1%) HCWs had a positive SARS-CoV-2 PCR result and SARS-CoV-2 antibodies were detected in 488 (37.7%), yielding a cumulative incidence of 47.2% (n=611). In the adjusted logistic regression model, being overweight (adjusted OR (aOR)=2.15, 95% CI 1.44 to 3.20), obese (aOR=1.37, 95% CI 1.02 to 1.85) and living with HIV (aOR=1.78, 95% CI 1.38 to 2.08) were independently associated with SARS-CoV-2 infection. There was no significant difference in infection rates between high, medium and low COVID-19 exposure working environments. CONCLUSIONS: The high SARS-CoV-2 cumulative incidence in the cohort was surprising this early in the epidemic and probably related to exposure both in and outside the hospitals. To mitigate the impact of SARS-CoV-2 among HCWs, infection prevention and control strategies should target community transmission in addition to screening for HIV and metabolic conditions.

The geography of emergency department-based HIV testing in South Africa: Can patients link to care?

BACKGROUND: Emergency Departments (EDs) can serve as clinical sites for identification of new HIV infections and their entry into care. We examined if HIV-positive patients who present to EDs in South Africa are able to successfully link to care. METHODS: We conducted a one-year longitudinal prospective cohort study in four hospitals across the Eastern Cape, South Africa, with participants followed between July 2016 and July 2018. All adult, non-critical patients presenting to the ED were systematically approached, asked about their HIV status, and, if unknown, offered a point-of-care (POC) HIV test. All HIV-positive patients were further consented to participate in a follow-up study to assess subsequent linkage to care and distance from "home" to ED. Linkage to care was defined as self-reported linkage (telephonic) or evidence of repeated CD4/viral load testing in the National Health Laboratory System (NHLS) at either the 6- or 12-months post index ED visit. FINDINGS: A total of 983 HIV-positive patients consented to participate in the study. In the 12 months following their ED visit, 34·1% of patients demonstrated linkage to care (335/983), 23·8% did not link to care (234/983), and 42·1% (414/983) were lost to follow-up. Though not statistically significant, a high percentage of young men (27/50, 54%) and those presenting with a trauma-related complaints (100/205, 48.8%) did not link to care. A considerable proportion of patients (105/454, 23·2%,) resided 50 or more kilometers from their index ED sites, though there was not a significant difference in linkage to care rate between those who lived closer or further from the ED. INTERPRETATION: We have shown that strategies to improve linkage to care from the ED should consider the high rates of poor linkage among young men and those presenting to the ED with trauma. Furthermore, innovative linkage to care solutions will need to account for the unique geographical consideration of this population, given that many ED patients will need to continue care at a site distant from the diagnosis site. FUNDING: This research was supported by the South African Medical Research Council, the Division of Intramural Research, the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the Johns Hopkins Center for Global Health.

Acceptance of COVID-19 Vaccine among the Healthcare Workers in the Eastern Cape, South Africa: A Cross Sectional Study.

BACKGROUND: This study assesses the perceptions and acceptance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccination. It also examines its influencing factors among the healthcare workers (HCWs) in the Eastern Cape, South Africa. METHODS: In this cross-sectional study performed in November and December 2020, a total of 1308 HCWs from two large academic hospitals participated in the Eastern Cape Healthcare Workers Acquisition of SARS-CoV-2 (ECHAS) study. Validated measures of vaccine hesitancy were explored using a questionnaire. Logistic regression was used to identify the determinants of vaccine hesitancy. RESULTS: The majority were nurses (45.2%), and at risk for unfavourable Covid-19 outcome, due to obesity (62.9%) and having direct contact with individuals confirmed to have Covid-19 (77.1%). The overall acceptance of SARS-CoV-2 vaccine was 90.1%, which differed significantly by level of education. Individuals with lower educational attainment (primary and secondary education) and those with prior vaccine refusal were less likely to accept the SARS-CoV-2 vaccine. However, positive perceptions about the SARS-CoV-2 vaccine were independently associated with vaccine acceptance. CONCLUSIONS: The high level of acceptance of SARS-CoV-2 vaccine is reassuring; however, HCWs with a lower level of education and those with prior vaccine refusal should be targeted for further engagements to address their concerns and fears.

Anthemosoma garnhami in an HIV-Infected Man from Zimbabwe Living in South Africa.

An HIV-positive man from Zimbabwe living in South Africa sought treatment for multiple clinical signs, including fever, weight loss, anemia, and splenomegaly. We identified in his blood an African rodent piroplasm, Anthemosoma garnhami, related to Babesia species. This finding extends the known geographic and host range of A. garnhami.

Eastern Cape Healthcare Workers Acquisition of SARS-CoV-2 (ECHAS): Cross-Sectional (Nested Cohort) Study Protocol.

Healthcare workers (HCWs) are at increased risk of infection by the virulent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Though data exist on the positivity rate of the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) test as well as COVID-19-related deaths amongst HCWs in South Africa, the overall infection rate remains underestimated by these indicators. It is also unclear whether the humoral immune response after SARS-CoV-2 infection offers durable protection against reinfection. This study will assess the SARS-CoV-2 seroprevalence amongst HCWs in the Eastern Cape (EC) and examine the longitudinal changes (rate of decay) in the antibody levels after infection in this cohort. Using a multi-stage cluster sampling of healthcare workers in selected health facilities in the EC, a cross-sectional study of 2250 participants will be recruited. In order to assess the community infection rate, 750 antenatal women in the same settings will be recruited. Relevant demographic and clinical characteristics will be obtained by a self-administered questionnaire. A chemiluminescent microparticle immunoassay (CMIA) will be used for the qualitative detection of IgG antibodies against SARS-CoV-2 nucleocapsid protein. A nested cohort study will be conducted by performing eight-weekly antibody assays (X2) from 201 participants who tested positive for both SARS-CoV-2 RT-PCR and serology. Logistic regression models will be fitted to identify the independent risk factors for SARS-CoV-2 infection. The cumulative SARS-CoV-2 infection rate and infection fatality rate among the frontline HCWs will be estimated. In addition, the study will highlight the overall effectiveness of infection prevention and control measures (IPC) per exposure sites/wards at the selected health facilities. Findings will inform the South African Department of Health's policies on how to protect HCWs better as the country prepares for the second wave of the SARS-CoV pandemic.

A Randomized Controlled Trial of Intravenous N-Acetylcysteine in the Management of Anti-tuberculosis Drug-Induced Liver Injury.

BACKGROUND: Liver injury is a common complication of anti-tuberculosis therapy. N-acetylcysteine (NAC) used in patients with paracetamol toxicity with limited evidence of benefit in liver injury due to other causes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial to assess the efficacy of intravenous NAC in hospitalized adult patients with anti-tuberculosis drug-induced liver injury (AT-DILI). The primary endpoint was time for serum alanine aminotransferase (ALT) to fall below 100 U/L. Secondary endpoints included length of hospital stay, in-hospital mortality, and adverse events. RESULTS: Fifty-three participants were randomized to NAC and 49 to placebo. Mean age was 38 (SD±10) years, 58 (57%) were female, 89 (87%) were HIV positive. Median (IQR) serum ALT and bilirubin at presentation were 462 (266-790) U/L and 56 (25-100) µmol/L, respectively. Median time to ALT <100 U/L was 7.5 (6-11) days in the NAC arm and 8 (5-13) days in the placebo arm. Median time to hospital discharge was shorter in the NAC arm (9 [6-15] days) than in the placebo arm (18 [10-25] days) (HR, 1.73; 95% CI, 1.13-2.65). Mortality was 14% overall and did not differ by study arm. The study infusion was stopped early due to an adverse reaction in 5 participants receiving NAC (nausea and vomiting [3], anaphylaxis [1], pain at drip site [1]). CONCLUSIONS: NAC did not shorten time to ALT <100 U/L in participants with AT-DILI, but significantly reduced length of hospital stay. NAC should be considered in management of AT-DILI. CLINICAL TRIALS REGISTRATION: South African National Clinical Trials Registry (SANCTR: DOH-27-0414-4719).

Plasma Proteome Responses in Salmonid Fish Following Immunization.

Vaccination plays a critical role in the protection of humans and other animals from infectious diseases. However, the same vaccine often confers different protection levels among individuals due to variation in genetics and/or immunological histories. While this represents a well-recognized issue in humans, it has received little attention in fish. Here we address this knowledge gap in a proteomic study of rainbow trout (Oncorhynchus mykiss, Walbaum), using non-lethal repeated blood sampling to establish the plasma protein response of individual fish following immunization. Six trout were immunized with adjuvanted hen egg-white lysozyme (HEL) and peripheral blood sampled at ten time points from day 0 to day 84 post-injection. We confirm that an antigen-specific antibody response to HEL was raised, showing differences in timing and magnitude among individuals. Using label-free liquid chromatography-mass spectrometry, we quantified the abundance of 278 plasma proteins across the timecourse. As part of the analysis, we show that this approach can distinguish many (but not all) duplicated plasma proteins encoded by paralogous genes retained from the salmonid-specific whole genome duplication event. Global variation in the plasma proteome was predominantly explained by individual differences among fish. However, sampling day explained a major component of variation in abundance for a statistically defined subset of 41 proteins, representing 15% of those detected. These proteins clustered into five groups showing distinct temporal responses to HEL immunization at the population level, and include classical immune (e.g. complement system members) and acute phase molecules (e.g. apolipoproteins, haptoglobins), several enzymes and other proteins supporting the immune response, in addition to evolutionarily conserved molecules that are as yet uncharacterized. Overall, this study improves our understanding of the fish plasma proteome, provides valuable marker proteins for different phases of the immune response, and has implications for vaccine development and the design of immune challenge experiments.

Addition of Broad Bean Hull to Wheat Flour for the Development of High-Fiber Bread: Effects on Physical and Nutritional Properties.

The seed coat (hull) of broad bean (Vicia faba) (BBH) is a significant secondary product of processing with a promising nutritional profile. Bean hull has a high fiber content (49%), yet it remains underexploited as an ingredient by the food industry. This study investigated the potential of this secondary product to partially replace wheat flour for the development of high-fiber breads. Bread formulations with a range of supplementation levels (0%, 11%, 21% and 31%) were developed and tested for their nutritional and physical properties. The proximate composition of breads revealed that at 31% replacement, the fiber content was 19.19 g/100 g bread, which was significantly higher (p < 0.05) than control breads (3.62 g/100 g bread). The physical (specific volume, density and color) and textural properties of breads were affected by the addition of bean hull. Specific volume and hardness of breads were significantly reduced at ≥21% replacement compared to the control, which may reduce acceptability of the product by some consumer groups. Enzyme-linked immunosorbent assay (ELISA) showed that the gluten content of breads was significantly reduced with bean hull addition (62% depletion for 31% replacement). At 11%, 21% and 31% replacement, one portion (80 g of bread) contains 6.8 g, 11.6 g and 15.3 g of dietary fiber, respectively, which contributes 23%, 38% and 51% of the recommended daily fiber intake (30 g/day). In conclusion, bean hull can be a valuable source of dietary fiber in bread formulations. The study showed BBH could be used to replace up to 21% of the wheat flour without significantly impacting on bread texture and volume.

Patient acceptance of HIV testing services in rural emergency departments in South Africa.

BACKGROUND: South Africa faces the highest burden of HIV infection globally. The National Strategic Plan on HIV recommends provider-initiated HIV counselling and testing (HCT) in all healthcare facilities. However, HIV continues to overwhelm the healthcare system. Emergency department (ED)-based HCT could address unmet testing needs. OBJECTIVES: This study examines the reasons for accepting or declining HCT in South African EDs to inform the development of HCT implementation strategies. METHOD: We conducted a prospective observational study in two rural EDs, from June to September 2017. Patients presenting to the ED were systematically approached and offered a point-of-care test in accordance with national guidelines. Patients demographics, presenting compaint, medical history and reasons for accepting/declining testing, were recorded. A pooled analysis is presented. RESULTS: Across sites, 2074 adult, non-critical patients in the ED were approached; 1880 were enrolled in the study. Of those enrolled, 19.7% had a previously known positive diagnosis, and 80.3% were unaware of their HIV status. Of those unaware, 90% patients accepted and 10% declined testing. The primary reasons for declining testing were 'does not want to know status' (37.6%), 'in too much pain' (34%) and 'does not believe they are at risk' (19.9%). CONCLUSIONS: Despite national guidelines, a high proportion of individuals remain undiagnosed, of which a majority are young men. Our study demonstrated high patient acceptance of ED-based HCT. There is a need for investment and innovation regarding effective pain management and confidential service delivery to address patient barriers. Findings support a routine, non-targeted HCT strategy in EDs.

ß-Glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus.

A clone encoding carboxymethyl cellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert carried a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus eutactus ART55/1. Genome surveys indicated a limited distribution of GH9 domains among dominant human colonic anaerobes. Genomes of C. eutactus-related strains harboured two GH9-encoding and four GH5-encoding genes, but the strains did not appear to degrade cellulose. Instead, they grew well on ß-glucans and one of the strains also grew on galactomannan, galactan, glucomannan and starch. Coprococcus comes and Coprococcus catus strains did not harbour GH9 genes and were not able to grow on ß-glucans. Gene expression and proteomic analysis of C. eutactus ART55/1 grown on cellobiose, ß-glucan and lichenan revealed similar changes in expression in comparison to glucose. On ß-glucan and lichenan only, one of the four GH5 genes was strongly upregulated. Growth on glucomannan led to a transcriptional response of many genes, in particular a strong upregulation of glycoside hydrolases involved in mannan degradation. Thus, ß-glucans are a major growth substrate for species related to C. eutactus, with glucomannan and galactans alternative substrates for some strains.

Calretinin is a novel candidate marker for adverse ovarian effects of early life exposure to mixtures of endocrine disruptors in the rat.

Disruption of sensitive stages of ovary development during fetal and perinatal life can have severe and life-long consequences for a woman's reproductive life. Exposure to endocrine disrupting chemicals may affect ovarian development, leading to subsequent reproductive disorders. Here, we investigated the effect of early life exposure to defined mixtures of human-relevant endocrine disrupting chemicals on the rat ovary. We aimed to identify molecular events involved in pathogenesis of ovarian dysgenesis syndrome that have potential for future adverse outcome pathway development. We therefore focused on the ovarian proteome. Rats were exposed to a mixture of phthalates, pesticides, UV-filters, bisphenol A, butyl-paraben, and paracetamol during gestation and lactation. The chemicals were tested together or in subgroups of chemicals with anti-androgenic or estrogenic potentials at doses 450-times human exposure. Paracetamol was tested separately, at a dose of 360 mg/kg. Using shotgun proteomics on ovaries from pup day 17 offspring, we observed exposure effects on the proteomes. Nine proteins were affected in more than one exposure group and of these, we conclude that calretinin is a potential key event biomarker of early endocrine disruption in the ovary.

Targeting the HIV Epidemic in South Africa: The Need for Testing and Linkage to Care in Emergency Departments.

BACKGROUND: The Eastern Cape province of South Africa has one of the highest burdens of HIV in the world. Emergency Departments (EDs) can serve as optimal clinical sites for the identification of new HIV infections and entry into care. We sought to determine the current burden of HIV disease among ED patients in the Eastern Cape. METHODS: We conducted a prospective cross-sectional observational study in the EDs of three Hospitals in the Eastern Cape province of South Africa from June 2017 to July 2018. All adult, non-critical patients presenting to the ED were systematically approached and offered a Point-Of-Care (POC) HIV test in accordance with South African guidelines. All HIV-positive individuals had their blood tested for the presence of antiretroviral therapy (ART) and the presence of viral suppression (≤ 1000 copies/ml). HIV incidence was estimated using a multi-assay algorithm, validated for a subtype C epidemic. FINDINGS: Of the 2901 patients for whom HIV status was determined (either known HIV-positive or underwent POC HIV testing), 811 (28.0%) were HIV positive, of which 234 (28.9%) were newly diagnosed. HIV prevalence was higher in Mthatha [34% (388/1134) at Mthatha Regional Hospital and 28% (142/512) at Nelson Mandela Academic Hospital], compared to Port Elizabeth [22% (281/1255) at Livingstone Hospital]. HIV incidence was estimated at 4.5/100 person-years (95% CI: 2.4, 6.50) for women and 1.5 (CI 0.5, 2.5) for men. Of all HIV positive individuals tested for ART (585), 54% (316/585) tested positive for the presence of ARTs, and for all HIV positive participants with viral load data (609), 49% (299/609) were found to be virally suppressed. INTERPRETATION: Our study not only observed a high prevalence and incidence of HIV among ED patients but also highlights significant attrition along the HIV care cascade for HIV positive individuals. Furthermore, despite developing an optimal testing environment, we were only able to enrol a small sub-set of the ED population. Given the high HIV prevalence and high attrition in the ED population, HIV services in the ED should also develop strategies that can accommodate large testing volumes and ART initiation.

Proteomic comparison of selective breeding and growth hormone transgenesis in fish: Unique pathways to enhanced growth.

In fish used for food production and scientific research, fast growth can be achieved via selective breeding or induced instantaneously via growth hormone (GH) transgenesis (GHT). The proteomic basis for these distinct routes towards a similar higher phenotype remains uncharacterized, as are associated implications for health parameters. We addressed this knowledge gap using skeletal muscle proteomics in coho salmon (Oncorhynchus kisutch), hypothesising that i) selective breeding and GHT are underpinned by both parallel and unique changes in growth systems, and ii) rapidly-growing fish strains have lowered scope to allocate resources towards immune function. Quantitative profiling of GHT and growth-selected strains was done in comparison to wild-type after injection with PBS (control) or Poly I:C (to mimic infection). We identified remodelling of the muscle proteome in each growth-enhanced strain that was strikingly non-overlapping. GHT was characterized by focal upregulation of systems driving protein synthesis, while the growth-selected fish presented a larger and more diverse set of changes, consistent with complex alterations to many metabolic and cellular pathways. Poly I:C had little detectable effect on the muscle proteome. This study demonstrates that distinct proteome profiles can explain outwardly similar enhanced growth phenotypes, improving our understanding of growth mechanisms in anthropogenic animal strains. SIGNIFICANCE: This work provides the first proteomic insights into mechanisms underpinning different anthropogenic routes to rapid growth in salmon. High-throughput proteomic profiling was used to reveal changes supporting enhanced growth, comparing skeletal muscle of growth hormone transgenic (GHT) and selectively-bred salmon strains with their wild-type counterparts. Contrasting past mRNA-level comparisons of the same fish strains, our data reveals a surprisingly substantial proteomic divergence between the GHT and selectively bred strains. The findings demonstrate that many unique molecular mechanisms underlie growth-enhanced phenotypes in different types of fish strain used for food production and scientific research.