Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

Metabolic activation of unsaturated derivatives of valproic acid. Identification of novel glutathione adducts formed through coenzyme A-dependent and -independent processes

The ability of 2-n-propyl-4-pentenoic acid (Δ⁴-VPA) and 2-n-propyl-2(E)-pentenoic acid ([E]-Δ²-VPA), two unsaturated metabolites of valproic acid (VPA), to form reactive intermediates, deplete hepatic glutathione (GSH) and cause accumulation of liver triglycerides was investigated in the rat. With the aid of ionspray liquid chromatography-tandem mass spectrometry (LC-MS/MS), three GSH adducts were detected in the bile of Δ⁴-VPA-treated animals and were identified as 4-hydroxy-5-glutathion-S-yl-VPA-γ-lactone, 5-glutathion-S-yl-(E)-Δ³-VPA and 3-oxo-5-glutathion-S-yl-VPA. A fourth conjugate was identified tentatively as 4-glutathion-S-yl-5-hydroxy-VPA. Quantitative analysis of the corresponding N-acetylcysteine (NAC) conjugates in urine indicated that metabolism of Δ⁴-VPA via the GSH-dependent pathways accounted for approximately 20% of an acute dose (100 mg kg⁻¹ i.p.). In contrast, when rats were given an equivalent dose of (E)-Δ²-VPA, only one GSH adduct (5-glutathion-S-yl-(E)-Δ³-VPA) was detected at low concentrations in bile. In vitro experiments with rat liver mitochondria demonstrated that Δ⁴-VPA undergoes coenzyme A- and ATP-dependent metabolic activation in this organelle via the β-oxidation pathway to intermediates which bind covalently to proteins. When liver homogenates and hepatic mitochondria from rats injected with Δ⁴-VPA, (E)-Δ²-VPA or VPA were analyzed for GSH content, it was found that only Δ⁴-VPA depleted GSH pools significantly. Treatment of rats with Δ⁴-VPA and (to a lesser extent) VPA led to an accumulation of liver triglycerides, whereas (E)-Δ²-VPA had no measurable effect. It is concluded that Δ⁴-VPA undergoes metabolic activation by both microsomal cytochrome P-450-dependent and mitochondrial coenzyme A-dependent processes, and that the resulting electrophilic intermediates, which are trapped in part by GSH, may mediate the hepatotoxic effects of this compound. In contrast, (E)-Δ²-VPA is not transformed to any appreciable extent to reactive metabolites, which thus accounts for the apparent lack of hepatotoxicity of this positional isomer in the rat.     

Polymorphism in the HASPB Repeat Region of East African Leishmania donovani Strains

Background/Objectives

Visceral leishmaniasis (VL) caused by Leishmania donovani is a major health problem in Ethiopia. Parasites in disparate regions are transmitted by different vectors, and cluster in distinctive genotypes. Recently isolated strains from VL and HIV-VL co-infected patients in north and south Ethiopia were characterized as part of a longitudinal study on VL transmission.

Methodology/Principal Findings

Sixty-three L. donovani strains were examined by polymerase chain reaction (PCR) targeting three regions: internal transcribed spacer 1 (ITS1), cysteine protease B (cpb), and HASPB (k26). ITS1- and cpb - PCR identified these strains as L. donovani. Interestingly, the k26 - PCR amplicon size varied depending on the patient''s geographic origin. Most strains from northwestern Ethiopia (36/40) produced a 290 bp product with a minority (4/40) giving a 410 bp amplicon. All of the latter strains were isolated from patients with HIV-VL co-infections, while the former group contained both VL and HIV-VL co-infected patients. Almost all the strains (20/23) from southwestern Ethiopia produced a 450 bp amplicon with smaller products (290 or 360 bp) only observed for three strains. Sudanese strains produced amplicons identical (290 bp) to those found in northwestern Ethiopia; while Kenyan strains gave larger PCR products (500 and 650 bp). High-resolution melt (HRM) analysis distinguished the different PCR products. Sequence analysis showed that the k26 repeat region in L. donovani is comprised of polymorphic 13 and 14 amino acid motifs. The 13 amino acid peptide motifs, prevalent in L. donovani, are rare in L. infantum. The number and order of the repeats in L. donovani varies between geographic regions.

Conclusions/Significance

HASPB repeat region (k26) shows considerable polymorphism among L. donovani strains from different regions in East Africa. This should be taken into account when designing diagnostic assays and vaccines based on this antigen.     

Malaria Infection Has Spatial,Temporal, and Spatiotemporal Heterogeneity in Unstable Malaria Transmission Areas in Northwest Ethiopia

Background

Malaria elimination requires successful nationwide control efforts. Detecting the spatiotemporal distribution and mapping high-risk areas are useful to effectively target pockets of malaria endemic regions for interventions.

Objective

The aim of the study was to identify patterns of malaria distribution by space and time in unstable malaria transmission areas in northwest Ethiopia.

Methods

Data were retrieved from the monthly reports stored in the district malaria offices for the period between 2003 and 2012. Eighteen districts in the highland and fringe malaria areas were included and geo-coded for the purpose of this study. The spatial data were created in ArcGIS10 for each district. The Poisson model was used by applying Kulldorff methods using the SaTScan™ software to analyze the purely temporal, spatial and space-time clusters of malaria at a district levels.

Results

The study revealed that malaria case distribution has spatial, temporal, and spatiotemporal heterogeneity in unstable transmission areas. Most likely spatial malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR =197764.1, p<0.001). Significant spatiotemporal malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR=197764.1, p<0.001) between 2003/1/1 and 2012/12/31. A temporal scan statistics identified two high risk periods from 2009/1/1 to 2010/12/31 (LLR=72490.5, p<0.001) and from 2003/1/1 to 2005/12/31 (LLR=26988.7, p<0.001).

Conclusion

In unstable malaria transmission areas, detecting and considering the spatiotemporal heterogeneity would be useful to strengthen malaria control efforts and ultimately achieve elimination.     

Predominance of Methanolobus spp. and Methanoculleus spp. in the Archaeal Communities of Saline Gas Field Formation Fluids

The microbial communities in sulfate-rich, saline formation fluids of a natural gas reservoir in Lower Saxony, Germany were investigated to enhance the knowledge about microbial communities in potential carbon dioxide sequestration sites. This investigation of the initial state of the deep subsurface microbiota is necessary to predict their influence on the long-term stability and storage capacity of such sites. While the bacterial 16S rDNA gene library was comprised of sequences affiliating with the Firmicutes, the Alphaproteobacteria, the Gammaproteobacteria and the Thermotogales, the archaeal 16S rDNA libraries were simply dominated by two phylotypes related to the genera Methanolobus and Methanoculleus. The monitoring of the archaeal communities in different formation fluid samples by T-RFLP and Real-Time-PCR indicated that these two methanogenic genera dominated at all, whereas the proportion of the two groups varied. Thus, methylotrophic and autotrophic methanogenesis seems to be of importance in the reservoir fluids, dependent on the provided reduction equivalents and substrates and it also may influence the fate of CO₂ in the subsurface.     

Increasing Trends of Diabetes Mellitus and Body Weight: A Ten Year Observation at Gondar University Teaching Referral Hospital,Northwest Ethiopia

Background

Diabetes mellitus is becoming one of the major causes of premature adult mortality in developing countries. However, there is a very little documentation of the morbidity trend in such countries.

Objective

To assess the ten-year trend of diabetes mellitus at Gondar University Teaching Referral Hospital, northwest Ethiopia.

Methods

A hospital-based retrospective record review was done at the main referral hospital in northwest Ethiopia. Data were obtained from medical records of all registered diabetic patients in the Diabetic Follow up Clinic between 2000 and 2009. An Extended Mantel-Haenzel chi-square test for the linear trend was used to examine the trend over time.

Result

Out of the total 354,524 patients who visited the Outpatient Department of the hospital during the study period, 1553 (4.4/1000) were diabetes patients, of which 50.1% was type 1 and 49.9% type 2 diabetes mellitus. The average increase in the proportion of both Type 1 and Type 2 diabetes mellitus cases between 2000 and 2009 was 125%. The mean (±SD) age for Type 1 diabetes mellitus was 29.1 (±12), and 53.5 (±12) for Type 2 diabetes. Overall 42.5% of the diabetes mellitus patients were female and 31.7% were rural residents. The mean body mass index for both type of diabetes mellitus increased from 15.9 to 18.3 kg for type 1 and from 23.8 to 24.6 for type 2 between 2000 and 2009, respectively.

Conclusion

The number of diabetes mellitus cases seen at Gondar Referral Hospital is rising steadily. A comprehensive diabetes prevention, treatment, and care program is needed to improve the quality of life of the increasing diabetes mellitus cases in Ethiopia.     

High Prevalence of Cryptococcal Antigenemia among HIV-infected Patients Receiving Antiretroviral Therapy in Ethiopia

Background

Cryptococcal disease is estimated to be responsible for significant mortality in Sub-Saharan Africa; however, only scarce epidemiology data exists. We sought to evaluate the prevalence of and risk factors for cryptococcal antigenemia in Ethiopia.

Methods

Consecutive adult HIV-infected patients from two public HIV clinics in Addis Ababa, Ethiopia were enrolled into the study. A CD4 count ≤200 cells/μl was required for study participation. Patients receiving anti-retroviral therapy (ART) were not excluded. A cryptococcal antigen test was performed for all patients along with an interview, physical exam, and medical chart abstraction. Logistic regression analysis was used to assess risk factors for cryptococcal antigenemia.

Results

369 HIV-infected patients were enrolled; mean CD4 123 cells/μl and 74% receiving ART. The overall prevalence of cryptococcal antigenemia was 8.4%; 11% in patients with a CD4 count <100 cells/μl, 8.9% with CD4 100 to 150 cells/μl and 5.7% with CD4150-200 cell/μl. 84% of patients with cryptococcal antigenemia were receiving ART. In multivariable analysis, increasing age, self reported fever, CD4 count <100 cells/μl, and site of screening were associated with an increased risk of cryptococcal antigenemia. No individual or combination of clinical symptoms had optimal sensitivity or specificity for cryptococcal antigenemia.

Conclusion

Cryptococcal antigenemia is high in Ethiopia and rapid scale up of screening programs is needed. Screening should be implemented for HIV-infected patients with low CD4 counts regardless of symptoms or receipt of ART. Further study into the effect of location and environment on cryptococcal disease is warranted.     

Reliability and Validity of an Interviewer-Administered Adaptation of the Youth Self-Report for Mental Health Screening of Vulnerable Young People in Ethiopia

Objective

Evaluate the reliability and validity of the Youth Self-Report (YSR) as a screening tool for mental health problems among young people vulnerable to HIV in Ethiopia.

Design

A cross-sectional assessment of young people currently receiving social services.

Methods

Young people age 15–18 participated in a study where a translated and adapted version of the YSR was administered by trained nurses, followed by an assessment by Ethiopian psychiatrists. Internal reliability of YSR syndrome scales were assessed using Chronbach''s alpha. Test-retest reliability was assessed through repeating the YSR one month later. To assess validity, analysis of the sensitivity and specificity of the YSR compared to the psychiatrist assessment was conducted.

Results

Across the eight syndrome scales, the YSR best measured the diagnosis of anxiety/depression and social problems among young women, and attention problems among young men. Among individual YSR syndrome scales, internal reliability ranged from unacceptable (Chronback’s alpha = 0.11, rule-breaking behavior among young women) to good (α≥0.71, anxiety/depression among young women). Anxiety/depression scores of ≥8.5 among young women also had good sensitivity (0.833) and specificity (0.754) to predict a true diagnosis. The YSR syndrome scales for social problems among young women and attention problems among young men also had fair consistency and validity measurements. Most YSR scores had significant positive correlations between baseline and post-one month administration. Measures of reliability and validity for most other YSR syndrome scales were fair to poor.

Conclusions

The adapted, personally administered, Amharic version of the YSR has sufficient reliability and validity in identifying young vulnerable women with anxiety/depression and/or social problems, and young men with attention problems; which were the most common mental health disorders observed by psychiatrists among the migrant populations in this study. Further assessment of the applicability of the YSR among vulnerable young people for less common disorders in Ethiopia is needed.     

High‐density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome‐specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome‐wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker‐assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat.