Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility

<p>Abstract</p> <p>Background</p> <p>African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus <it>Trypanosoma </it>is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR) validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with <it>Trypanosoma congolense </it>across a 34-day infection time course.</p> <p>Results</p> <p>Trypanotolerant N'Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post-infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in response to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO) analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle.</p> <p>Conclusion</p> <p>This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N'Dama cattle respond more rapidly and with a greater magnitude to infection compared to the trypanosusceptible Boran cattle. Specifically, a subset of the genes analyzed by real time qRT-PCR, which display significant breed differences, could collectively contribute to the trypanotolerance trait in N'Dama.</p

Vaginal probiotic adherence and acceptability in Rwandan women with high sexual risk participating in a pilot randomised controlled trial: a mixed-methods approach

OBJECTIVES: To evaluate adherence and acceptability of intermittent vaginal probiotic or antibiotic use to prevent bacterial vaginosis (BV) recurrence. DESIGN: Repeated adherence and acceptability assessments using mixed methods within a pilot randomised controlled trial. SETTING: Research clinic in Kigali, Rwanda. PARTICIPANTS: Rwandan women with high sexual risk. INTERVENTIONS: Women diagnosed with BV and/or trichomoniasis were randomised to four groups (n=17 each) after completing metronidazole treatment: behavioural counselling only, or behavioural counselling plus 2-month intermittent use of oral metronidazole, Ecologic Femi+ (EF+) vaginal capsule or Gynophilus LP (GynLP) vaginal tablet. OUTCOME MEASURES: Adherence and acceptability were assessed by structured face-to-face interviews, semi-structured focus group discussions and in-depth interviews, daily diaries and counting of used/unused study products in randomised women (n=68). Vaginal infection knowledge was assessed by structured face-to-face interviews in randomised women and women attending recruitment sessions (n=131). RESULTS: Most women (93%) were sex workers, 99.2% were unfamiliar with BV and none had ever used probiotics. All probiotic users (n=32) reported that insertion became easier over time. Triangulated adherence data showed that 17/17 EF+ users and 13/16 GynLP users used ≥80% of required doses (Fisher's exact p=0.103). Younger age (p=0.076), asking many questions at enrolment (p=0.116), having menses (p=0.104) and reporting urogenital symptoms (p=0.103) were non-significantly associated with lower perfect adherence. Women believed that the probiotics reduced BV recurrence, but reported that partners were sometimes unsupportive of study participation. Self-reported vaginal washing practices decreased during follow-up, but sexual risk behaviours did not. Most women (12/15) with an uncircumcised steady partner discussed penile hygiene with him, but many women found this difficult, especially with male clients. CONCLUSIONS: High-risk women require education about vaginal infections. Vaginal probiotic acceptability and adherence were high in this cohort. Our results can be used to inform future product development and to fine-tune counselling messages in prevention programmes. TRIAL REGISTRATION NUMBER: NCT02459665

Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background

<p>Abstract</p> <p>Background</p> <p>Differences in gene expression may be caused by nearby DNA polymorphisms (<it>cis </it>regulation) or by interactions of gene control regions with polymorphic transcription factors (<it>trans </it>regulation). <it>Trans </it>acting loci are much harder to detect than <it>cis </it>acting loci and their effects are much more sensitive to genetic background.</p> <p>Results</p> <p>To quantify <it>cis </it>and <it>trans </it>regulation we correlated haplotype data with gene expression in two inbred mouse strains and two derived congenic lines. Upstream haplotype differences between the parental strains suggested that 30-43% of differentially expressed genes were differentially expressed because of <it>cis </it>haplotype differences. These <it>cis </it>regulated genes displayed consistent and relatively tissue-independent differential expression. We independently estimated from the congenic mice that 71-85% of genes were <it>trans </it>regulated. <it>Cis </it>regulated genes were associated with low p values (p < 0.005) for differential expression, whereas <it>trans </it>regulated genes were associated with values 0.005 < p < 0.05. The genes differentially expressed between congenics and controls were not a subset of those that were differentially expressed between the founder lines, showing that these were dependent on genetic background. For example, the cholesterol synthesis pathway was strongly differentially expressed in the congenic mice by indirect <it>trans </it>regulation but this was not observable in the parental mice.</p> <p>Conclusions</p> <p>The evidence that most gene regulation is <it>trans </it>and strongly influenced by genetic background, suggests that pathways that are modified by an allelic variant, may only exhibit differential expression in the specific genetic backgrounds in which they were identified. This has significant implications for the interpretation of any QTL mapping study.</p

High adherence to intermittent and continuous use of a contraceptive vaginal ring among women in a randomized controlled trial in Kigali, Rwanda

Background: The introduction of female-initiated drug-delivery methods, including vaginal rings, have proven to be a promising avenue to address sexually transmitted infections and unintended pregnancies, which disproportionally affects women and girls in sub-Saharan Africa. Efficient uptake of existing and new technologies such as vaginal rings requires in depth understanding of product adherence. This remains a major challenge as data on adherence to vaginal rings from African countries is limited. In this study, we explored adherence of contraceptive vaginal ring (NuvaRing®) use in Kigali, Rwanda using a mixed methods approach. Methods: We collected quantitative and qualitative data at multiple time points from women participating in a clinical trial exploring the safety and acceptability of either intermittent or continuous use of the NuvaRing®. Various adherence categories were used including monthly and cumulative adherence measurement. The quantitative data were analysed using R and the qualitative data were analysed using a deductive, content-analytical approach based on categories related to the quantitative adherence measures. All data were compared and triangulated. Results: Data from 120 enrolled participants showed that self-reported adherence was high at every study visit in both study groups. At first study visit 80% of the intermittent ring users and 79.7% of the continuous ring users reported perfect adherence (assessed as “the ring was never out”). Reporting of ring expulsions and removals were highest (28.3%) at the beginning of the trial. Self-reported perfect ring adherence increased during the study and reports of ring expulsions and removals declined as familiarity with this contraceptive method increased. The percentage of women with perfect cumulative adherence was non-significantly higher in the intermittent (61.7%) than in the continuous use group (54.3%). The low rate of discrepant adherence data after triangulation (6%) is in line with the perception of the participants as adherent throughout the study. Conclusions: Self-reported adherence in both study groups was high with removals and expulsions being within the expected product range. Comprehensive adherence data triangulation allowed for a deeper understanding of context-driven behaviour that shaped adherence patterns and challenges. Our data categorisation and triangulation approach has shown potential for implementation in future vaginal ring studies aiming to better understand and measure adherence

Treatment Outcomes in a Decentralized Antiretroviral Therapy Program: A Comparison of Two Levels of Care in North Central Nigeria

Background. Decentralization of antiretroviral therapy (ART) services is a key strategy to achieving universal access to treatment for people living with HIV/AIDS. Our objective was to assess clinical and laboratory outcomes within a decentralized program in Nigeria. Methods. Using a tiered hub-and-spoke model to decentralize services, a tertiary hospital scaled down services to 13 secondary-level hospitals using national and program guidelines. We obtained sociodemographic, clinical, and immunovirologic data on previously antiretroviral drug naïve patients aged ≥15 years that received HAART for at least 6 months and compared treatment outcomes between the prime and satellite sites. Results. Out of 7,747 patients, 3729 (48.1%) were enrolled at the satellites while on HAART, prime site patients achieved better immune reconstitution based on CD4+ cell counts at 12 (P < 0.001) and 24 weeks (P < 0.001) with similar responses at 48 weeks (P = 0.11) and higher rates of viral suppression (<400 c/mL) at 12 (P < 0.001) and 48 weeks (P = 0.03), but similar responses at 24 weeks (P = 0.21). Mortality was 2.3% versus 5.0% (P < 0.001) at prime and satellite sites, while transfer rate was 8.7% versus 5.5% (P = 0.001) at prime and satellites. Conclusion. ART decentralization is feasible in resource-limited settings, but efforts have to be intensified to maintain good quality of care

Variability in body weight and morphology of Uganda’s indigenous goat breeds across agroecological zones

A research article was published by PLoS ONE volume 19,2024Indigenous goat breeds in Uganda are classified based on average body size parameters and coat color. However, variations in the body size of animals may be influenced by several factors, including management and the environment. To understand the effect of the agro- ecological zone on the physical characteristics and live weight of Uganda’s indigenous goats, this study evaluated the body size characteristics of the three indigenous goat breeds of Uganda across ten agroecological zones. The cross-sectional survey was conducted in 323 households from the ten zones, where 1020 goats composed of three breeds (Mubende, Kigezi, and Small East African) were sampled and measured for body weight, lin- ear body size, and age. We confirmed that Mubende and Kigezi goats from the original homeland had a higher mean body weight than reported in FAO reports. In addition, Mubende appeared to perform better in pastoral rangelands, with a higher mean body weight (38.1 kg) and body size being significantly higher (P < 0.0001) compared to other zones. The mean body weight for the Kigezi breed in the original homeland (34 kg) was com- parable to those from Western Savannah grasslands and pastoral rangelands and less than that initially reported by FAO (30 kg). Similarly, there was no significant difference in the lin- ear body size characteristics of Kigezi goats in the home zone of highland ranges relative to those found in other agroecological zones (P > 0.05). Although the Small East African goats were originally found in Northwestern Savannah grassland and Northeastern dryland zones, they performed poorly regarding mean body weight and body size characteristics in the for- mer zone. In the Northwestern Savannah grasslands, the mean body weight (23.8 kg) was even less than that reported by FAO, which ranged between 25 and 30 kg. Finally, we con- firmed that Mubende and Kigezi goats are significantly heavier than small East African goats (p � 0.0001). The results of this study can be useful in designing precise management strat- egies to improve indigenous goat productivity in different environments in Uganda

A mini-atlas of gene expression for the domestic goat (Capra hircus)

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: A Pilot Study Incorporating Microscopy and Sequencing

Bacterial vaginosis (BV) is associated with HIV acquisition and adverse pregnancy outcomes. Recurrence after metronidazole treatment is high. HIV-negative, non-pregnant Rwandan BV patients were randomized to four groups (n=17/group) after seven-day oral metronidazole treatment: behavioral counseling only (control), or counseling plus intermittent use of oral metronidazole, Ecologic Femi+ vaginal capsule (containing multiple Lactobacillus and one Bifidobacterium species), or Gynophilus LP vaginal tablet (L. rhamnosus 35) for two months. Vaginal microbiota assessments at all visits included Gram stain Nugent scoring and 16S rRNA gene qPCR and HiSeq sequencing. All interventions were safe. BV (Nugent 7-10) incidence was 10.18 per person-year at risk in the control group, and lower in the metronidazole (1.41/person-year; p=0.004), Ecologic Femi+ (3.58/person-year; p=0.043), and Gynophilus LP groups (5.36/person-year; p=0.220). In mixed effects models adjusted for hormonal contraception/pregnancy, sexual risk-taking, and age, metronidazole and Ecologic Femi+ users, each compared to controls, had higher Lactobacillus and lower BV-anaerobes concentrations and/or relative abundances, and were less likely to have a dysbiotic vaginal microbiota type by sequencing. Inter-individual variability was high and effects disappeared soon after intervention cessation. Lactobacilli-based vaginal probiotics warrant further evaluation because, in contrast to antibiotics, they are not expected to negatively affect microbiota or cause antimicrobial resistance

Mechanisms controlling anaemia in Trypanosoma congolense infected mice.

Trypanosoma congolense are extracellular protozoan parasites of the blood stream of artiodactyls and are one of the main constraints on cattle production in Africa. In cattle, anaemia is the key feature of disease and persists after parasitaemia has declined to low or undetectable levels, but treatment to clear the parasites usually resolves the anaemia. The progress of anaemia after Trypanosoma congolense infection was followed in three mouse strains. Anaemia developed rapidly in all three strains until the peak of the first wave of parasitaemia. This was followed by a second phase, characterized by slower progress to severe anaemia in C57BL/6, by slow recovery in surviving A/J and a rapid recovery in BALB/c. There was no association between parasitaemia and severity of anaemia. Furthermore, functional T lymphocytes are not required for the induction of anaemia, since suppression of T cell activity with Cyclosporin A had neither an effect on the course of infection nor on anaemia. Expression of genes involved in erythropoiesis and iron metabolism was followed in spleen, liver and kidney tissues in the three strains of mice using microarrays. There was no evidence for a response to erythropoietin, consistent with anaemia of chronic disease, which is erythropoietin insensitive. However, the expression of transcription factors and genes involved in erythropoiesis and haemolysis did correlate with the expression of the inflammatory cytokines Il6 and Ifng. The innate immune response appears to be the major contributor to the inflammation associated with anaemia since suppression of T cells with CsA had no observable effect. Several transcription factors regulating haematopoiesis, Tal1, Gata1, Zfpm1 and Klf1 were expressed at consistently lower levels in C57BL/6 mice suggesting that these mice have a lower haematopoietic capacity and therefore less ability to recover from haemolysis induced anaemia after infection