Ethiopian Samples Research Articles

Abstract 2501: High mutation burden and ultraviolet light signature in conjunctival squamous cell carcinoma

Abstract Purpose: Conjunctival squamous cell carcinoma (conjSCC) is endemic in sub-Saharan Africa and is a major cause of ocular morbidity and mortality. This study aims to evaluate Tumor Mutation Burden (TMB), genomic signature, and histologic characteristics of conjunctival squamous cell carcinoma (conjSCC) in two cohorts of patients; one from the USA and one from Ethiopia. Methods: Whole exome sequencing data, PD-L1 expression, histologic features, and human papillomavirus (HPV) status were analyzed in conj SCC tumors of 25 patients treated at an Ethiopian (ETH) cancer center and 29 patients treated at a US cancer center. Genomic alterations in conjSCC were compared with SCCs from other anatomic sites using data from The Cancer Genome Atlas (TCGA). Results: TMB was found to be relatively high in conjunctival SCC (3.01/Mb, log10), was comparable to TMB values associated with cutaneous SCC, and was higher than most other SCC types available in the TCGA database. ETH samples had higher tumor mutational burden compared to the US cohort (3.34 vs 2.73). Solar elastosis was seen in a higher percentage of tumors from Ethiopia compared with the US cohort (78% vs. 10%). HPV status was similar between the cohorts (ETH: 21%, MDA: 28%). PD-L1 positivity defined as > 1% of tumor cells was seen in 33 of 53 tumors (62%). Mutations associated with ultraviolet light (UV) signature were the most frequently encountered signatures in both cohorts (SBS7b: 74% and SBS7a: 72%). UV signatures were more prevalent in the ETH cohort compared with the US cohort. Conclusions: Conjunctival SCC is associated with a high TMB providing the opportunity for immune checkpoint inhibitor therapy for patients with locally advanced and/or metastatic conjunctival SCC. Clinical trials are needed to assess the efficacy of immune checkpoint inhibitors in patients with conjunctival SCC, particularly in sub-Saharan Africa where this cancer is more frequently seen, and is associated with significant morbidity and mortality. Citation Format: Bita Esmaeli, Frederico O. Gleber-Netto, Oded Sagiv, Curtis R. Pickering, Neil Gross, Jing Ning, Melisachew M. Yeshi, Jonas Mitku, Michael T. Tetzlaff, Priyadharsini Nagarajan. High mutation burden and ultraviolet light signature in conjunctival squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2501.

The Potential of NIR Spectroscopy and Chemometrics to Discriminate Roast Degrees and Predict Volatiles in Coffee.

This study aimed to establish a rapid and practical method for monitoring and predicting volatile compounds during coffee roasting using near-infrared (NIR) spectroscopy coupled with chemometrics. Washed Arabica coffee beans from Ethiopia and Congo were roasted to industry-validated light, medium, and dark degrees. Concurrent analysis of the samples was performed using gas chromatography-mass spectrometry (GC-MS) and NIR spectroscopy, generating datasets for partial least squares (PLS) regression analysis. The results showed that NIR spectroscopy successfully differentiated the differently roasted samples, similar to the discrimination achieved by GC-MS. This finding highlights the potential of NIR spectroscopy as a rapid tool for monitoring and standardizing the degree of coffee roasting in the industry. A PLS regression model was developed using Ethiopian samples to explore the feasibility of NIR spectroscopy to indirectly measure the volatiles that are important in classifying the roast degree. For PLSR, the data underwent autoscaling as a preprocessing step, and the optimal number of latent variables (LVs) was determined through cross-validation, utilizing the root mean squared error (RMSE). The model was further validated using Congo samples and successfully predicted (with R2 values > 0.75 and low error) over 20 volatile compounds, including furans, ketones, phenols, and pyridines. Overall, this study demonstrates the potential of NIR spectroscopy as a practical and rapid method to complement current techniques for monitoring and predicting volatile compounds during the coffee roasting process.

Population genomic analyses reveal population structure and major hubs of invasive Anopheles stephensi in the Horn of Africa.

Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome-wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation-by-distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype-environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.

Gemological and Mineralogical Characteristics of Emerald from Ethiopia

Ethiopia has been gaining attention in recent years as an emerging source of high-quality emerald. Ethiopian emerald samples with different colors ranging from dark green to light green were selected to study the gemological properties, chemical composition, and spectral characteristics. The Ethiopian emeralds were examined using conventional gemological instruments, including X-ray fluorescence spectrometry, LA-ICP-MS, UV/Vis/NIR, infrared spectrometry, and Raman spectrometry, providing a wealth of data and research information related to Ethiopian emeralds. The EDXRF results show that the chemical composition of Ethiopian emeralds is distinctly regional compared to emeralds of Colombian origin, being low in Cr, low in V, and high in Fe. LA-ICP-MS results demonstrate consistent results for Cr (734.34 to 1644.3 ppmw), V (89.61 to 106.61 ppmw), and Fe (4468.04 to 5022.3 ppmw) based on the chemical composition analysis by EDXRF. In addition, the LA-ICP-MS assay revealed that the combination of alkali metals (Li, Na, K, Rb, and Cs) and some trace elements (Sc, V, Cr, and Fe) could distinguish the Ethiopian emeralds from those from other regions. The Ethiopian emerald had absorption of Fe2+, Cr3+, V3+, and Fe3+, and the typical absorption intensity of Fe2+ (around 850 nm) was higher than that of Fe3+ (around 371 nm) in the UV/Vis/NIR spectra. The infrared spectrum of samples indicated that the absorption of type II H2O was higher than type I H2O in the emeralds from Ethiopia, which is consistent with the high content of alkali metals detected by LA-ICP-MS that would lead to an increase in the content of type II H2O. The Raman spectra showed absorption at 410 cm−1, 569 cm−1, 687 cm−1, 995 cm−1, and 1067 cm−1, with an emerald species recognition pattern. The gas–liquid two-phase inclusions of the emerald in this area were mainly CO2 and H2O, and the samples contained typical dark inclusions of magnesium-rich biotite sheets that revealed the tectonic-magmatic-related geological environment in this region.

Excessive replacement changes drive evolution of global sheep prion protein (PRNP) sequences.

Sheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.

Solid-phase optimisation for simultaneous determination of thirteen pharmaceuticals in Ethiopian water samples with HPLC-DAD detection: an initial assessment.

Pharmaceutical consumption is increasing worldwide as it is essential to treat and prevent health issues but they end up in the environment. However, in many African countries like Ethiopia, the status of these compounds in various environmental samples is not very well known. In this study, a simple method for the extraction and determination of thirteen pharmaceutical compounds of different therapeutic classes in water samples using solid-phase extraction and HPLC-DAD was developed. Different parameters affecting extraction were optimised and obtained as hydrophilic-lipophilic balance (HLB) extraction cartridge, water sample pH of 5, elution solvent of 2% formic acid in water with methanol (20:80%, v/v), a sample volume of 150mL and addition of 0.5% w/v EDTA in the sample. The limits of detection and quantification of the optimised method were in the range of 0.1-0.8µg/L and 0.2-2.6µg/L, respectively. The relative recovery in the spiked environmental water sample was in the range of 70-117% except for amoxicillin and acetylsalicylic acid in influent wastewater. The precision for all ranged from 0.3 to 11%. The proposed method was successfully tested for the detection and quantification of different environmental water samples collected from Addis Ababa, Ethiopia. Trimethoprim, caffeine and albendazole concentrations of 7.8 (1.1), 3.2 (0.4) and 2.1 (0.1) µg/L were quantified in hospital wastewater, respectively. The concentration of norfloxacin was found to be below the limit of quantification in the same water. Trimethoprim and ciprofloxacin were also found in the sewage treatment plant influent sample at a concentration of 0.5 (0.02) and 0.3 (0.01) µg/L, respectively.

Population structure of Phytophthora infestans (Mont.) de Bary in Ethiopia

Late blight disease caused by an Oomycete Phytophthora infestans is a major constraint to potato production and is causing significant yield losses in Ethiopia. This study was conducted to characterize the genetic diversity of the pathogen population in the major potato growing regions Awi, East Hararghe, South Gondar, West Arsi, West Gojjam and West Shewa in Ethiopia. In total 138 P. infestans isolates were collected using FTA cards in 2017, genotyped using 12-plex SSR markers and characterized for the mitochondrial haplotype. The genotypic patterns were compared to those of reference isolates from the EU2_A1 and US-1 clonal lineages. The population structure analysis using discriminant analysis of principal components (DAPC) and STRUCTURE indicated that most of the Ethiopian isolates were similar to the EU2_A1, while a second cluster of isolates was formed that was clearly different from EU2_A1 as well as the US-1 reference isolates. This new genotype was characterized by private alleles in the SSR D13 locus. We named this new genotype as ET-1 lineage. All isolates had the same mitochondrial haplotype (Ia). EU2_A1 was dominant clonal lineage in all locations except West Arsi which was dominated with ET-1 lineage. The old US-1 lineage was not discovered among the Ethiopian samples which suggest that it has been displaced. The West Arsi, West Gojjam and West Shewa populations were found to contain the highest genetic diversity, with the greatest number of multi locus genotypes (MLGs) and a higher diversity index compared to the other locations. The findings of this study establish a baseline of the pathogen population diversity in Ethiopia. Continuous tracking of P. infestans population in both potato and tomato is recommended to monitor the changes and migration patterns.

Disentangling Ethiopian Honey Bee (Apis mellifera) Populations Based on Standard Morphometric and Genetic Analyses.

Simple SummaryWe conducted this population study of Ethiopian honey bees, using morphometric and genetic methods, to decipher their controversial classification. These honey bees are highly diverse and showed differentiation based on size and genetic information according to prevailing agro-ecological conditions, demonstrating morphological and molecular signatures of local adaptation. The results of both morphometric and genetic analyses suggest that Ethiopian honey bees differ from populations in the neighboring geographic regions and are characterized by extensive gene flow within the country, enhanced by honey bee colony trade. Consequently, future research that includes studying traits of vitality, behavior and colony performance of honey bees in remaining pocket areas of highland agro-ecological zones could contribute to the development of appropriate conservation management.The diversity and local differentiation of honey bees are subjects of broad general interest. In particular, the classification of Ethiopian honey bees has been a subject of debate for decades. Here, we conducted an integrated analysis based on classical morphometrics and a putative nuclear marker (denoted r7-frag) for elevational adaptation to classify and characterize these honey bees. Therefore, 660 worker bees were collected out of 66 colonies from highland, midland and lowland agro-ecological zones (AEZs) and were analyzed in reference to populations from neighboring countries. Multivariate morphometric analyses show that our Ethiopian samples are separate from Apis mellifera scutellata, A. m. jemenitica, A. m. litorea and A. m. monticola, but are closely related to A. m. simensis reference. Linear discriminant analysis showed differentiation according to AEZs in the form of highland, midland and lowland ecotypes. Moreover, size was positively correlated with elevation. Similarly, our Ethiopian samples were differentiated from A. m. monticola and A. m. scutellata based on r7-frag. There was a low tendency towards genetic differentiation between the Ethiopian samples, likely impacted by increased gene flow. However, the differentiation slightly increased with increasing elevational differences, demonstrated by the highland bees that showed higher differentiation from the lowland bees (FST = 0.024) compared to the midland bees (FST = 0.015). An allelic length polymorphism was detected (denoted as d) within r7-frag, showing a patterned distribution strongly associated with AEZ (X2 = 11.84, p < 0.01) and found predominantly in highland and midland bees of some pocket areas. In conclusion, the Ethiopian honey bees represented in this study are characterized by high gene flow that suppresses differentiation.

Abstract SS1-07: Gene expression profiles of Ghanaian and Ethiopian triple-negative breast tumors

Abstract Background: Triple-negative breast cancer (TNBC) remains the most aggressive molecular subtype of breast cancer, with worse survival outcomes compared to other breast cancer subtypes. TNBC prevalence is highest among women of African descent worldwide, and through our previous work we have established a connection between West African ancestry (WAa) and higher rates of TNBC. Specifically, we have shown that prevalence rates of TNBC among West African and African American women are similar and higher than that of East African and White American women. We have also shown that quantified African ancestry is higher among TNBC cases compared to non-TNBC cases. To determine the influence African ancestry on the TNBC tumor environment, we sought to determine any differences in gene expression profiles of Ghanaian (West African) compared to Ethiopian (East African) women. Methods: RNA was extracted and sequenced from a pilot cohort of archival FFPE tumor tissue among Ghanaian (n = 19) and Ethiopian (n = 20) women. RNAseq reads were aligned, and quality of alignments were assessed, where de-duplicated samples with counts above 10M reads were included in the final analysis. Genetic ancestry was quantified by obtaining SNVs called from the RNAseq alignments, using GATK best practices. Differentially expressed genes lists were determined comparing Ghanaian vs. Ethiopian TNBC tumors, and also by identifying genes that were associated with increasing African ancestry. These gene lists, and log-fold change between comparison groups, were used as input for Ingenuity Pathway Analysis (IPA), to identify canonical pathways and de novo networks that are specific to Ghanaian or Ethiopian TNBC tumors. Results: Using 1KG populations as our reference to quantify genetic ancestry, we show that Ghanaian samples have &amp;gt;94% AFR ancestry, specifically matching population groups representative of WAa. The Ethiopian samples showed between 37-48% AFR ancestry, primarily represented by East African groups. Interestingly, there seems to be a significant proportion of EUR ancestry among the Ethiopians samples (30-49%), primarily represented by Italian ancestry. We have conducted the differential gene expression analysis in two ways. First, we have compared gene expression profiles between Ghanaian and Ethiopian tumors. In our preliminary analysis, we identified &amp;gt;600 genes (p &amp;lt; 0.01) that were differentially expressed between Ghanaian and Ethiopian TNBC tumors. Second, we used AFR ancestry as a continuous variable, where we conducted a linear regression analysis to identify genes associated with AFR ancestry. We identified &amp;gt;900 genes associated with AFR ancestry (p &amp;lt; 0.01), and this gene signature distinguished Ghanaian from Ethiopian tumors in an unsupervised hierarchical clustering. In comparing the differentially expressed gene lists from these two approaches, approximately 200 genes were shared, indicating the distinct value of both analyses. Using these gene lists as input for IPA analysis, we have begun to identify canonical pathways that have been altered by our differentially expressed genes, alongside de novo networks that differ between our Ghanaian and Ethiopian tumors. In our overlapping gene list, we see predicted differences in functions such as quantity of T lymphocytes, where genes downregulated in Ethiopian tumors may indicated reduced presence of these immune cells. Using CIBERSORT and xCell deconvolution methods, validation of these findings are ongoing. Conclusions and Ongoing work: This work highlights how ancestry-specific gene regulation can delineate differences in the tumor microenvironment among a cohort of African tumors. We are currently evaluating distribution of TNBC subtypes and estimation of immune cell populations in these tumors, to determine ancestry-specific differences in tumor heterogeneity and immune response. Citation Format: Rachel Martini, Endale Gebregzabher, Princesca Dorsaint, Timothy Chu, Kanika Arora, Lee Gibbs, Zarko Manojlovic, Nicolas Robine, Andrea Sboner, Olivier Elemento, John Carpten, Lisa Newman, Melissa Davis. Gene expression profiles of Ghanaian and Ethiopian triple-negative breast tumors [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SS1-07.

Abstract PO-187: Identification of ancestry-specific gene expression profiles of African triple- negative breast tumors

Abstract Women with shared West African ancestry suffer from disproportionately higher breast cancer (BC) mortality and are more frequently diagnosed with the most aggressive form of BC, triple negative BC (TNBC). We and others have shown a higher prevalence of TNBC in West African (Ghanaian) and AA women, compared to lower levels of TNBC in East African (Ethiopian) and White/European American (EA) women, and that higher levels of quantified West African ancestry are found among women with TNBC compared to non-TNBC breast tumors. To further understand the role of West African ancestry in the TNBC tumor microenvironment, we conducted RNA sequencing on a pilot cohort of archival FFPE tumor tissue obtained from Ghanaian (n = 19) and Ethiopian (n = 20) women with TNBC disease to study differences in gene expression profiles. SNV calls were obtained from the RNAseq data, and 1K Genome subpopulations were used as references to quantify ancestry of each patient. We observed that our Ghanaian samples have over 94% African ancestry (corresponding to West African populations), where our Ethiopian samples showed between 37-48% African ancestry (corresponding to East African populations). Quantified ancestry among our Ethiopian samples also revealed a significant proportion of European ancestry (30-49%), corresponding to Italian ancestry. Differentially expressed genes (DEGs) were identified by comparing self- reported ethnicity and correlations with genetic ancestry. We have identified over 600 DEGs between Ghanaian vs Ethiopian TNBC samples (p &amp;lt; 0.01). We found over 900 genes that were associated with quantified African ancestry (p &amp;lt; 0.01), using African ancestry as a continuous variable with linear regression methods. Unsupervised hierarchical clustering of this gene set was able to separate Ghanaian and Ethiopian samples. We compared the output of both approaches, and found that only ~200 genes were shared, showing the distinct value of both approaches. We have begun to investigate the role of our differential gene lists in canonical pathways and gene networks using Ingenuity Pathway analysis methods. Using our overlapping differential gene list from both approaches, we observed differences such as quantity of T lymphocytes, where downregulation of genes may indicate differing levels this immune cell population in the TNBC tumor environment. In our ongoing analysis, we are using deconvolution methods, such as CIBERSORT and xCell, to validate and further characterize the presence of various immune cell populations in our TNBC tumors. This study shows that quantified genetic ancestry can be used to identify ancestry-specific gene regulation in African TNBC tumors. Specifically, with our ongoing analysis of the immune cell representation in our samples, we can define differences in tumor heterogeneity and immune response in an ancestry- specific manor. Citation Format: Rachel Martini, Endale Gebregzabher, Princesca Dorsaint, Timothy Chu, Kanika Arora, Lee Gibbs, Zarko Manojlovic, Nicolas Rovine, Andrea Sboner, Olivier Elemento, John Carpten, Lisa Newman, Melissa Davis. Identification of ancestry-specific gene expression profiles of African triple- negative breast tumors [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-187.

Lack of intraspecific variations of the mitochondrial cytochrome b gene in the greater mouse-tailed bat Rhinopoma microphyllum (Chiroptera: Rhinopomatidae) in Iran.

Rhinopoma microphyllum is one of the species of bats that lives in arid and semi-arid areas of Iran. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni based on their morphological characteristics has been questioned on the basis of small differences between the populations. Later, other researchers assigned Iranian populations of this species to one or two subspecies based on their morphological and molecular characteristics. The present study provides a phylogeographical analysis of this species using 687bp of the mitochondrial cytochrome b in 81 bats in Iran, Jordan, Levant and Ethiopia. Based on mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. microphyllum (π = 0.0025), which shows a close relationship between the haplotypes. The analysis of genetic distance (0.15-1.93%), phylogenetic trees, and statistical parsimony network showed that all Iranian samples were grouped in the same clade, while Levant, Jordan and Ethiopian samples belonged to a different clade. Molecular dating suggested the Iranian R. microphyllum lineage split from the R. microphyllum of the Levant and Jordan clade during the Pliocene 3.18 (2.11-4.32Ma). Taking these results into consideration, we can conclude that all Iranian specimens belong to the same subspecies as R. m. harrisoni since molecular results indicate that Iranian samples are differ from Levant subspecies (R. m. microphyllum).

Insights into Ethiopian honey bee diversity based on wing geomorphometric and mitochondrial DNA analyses

Traditional beekeeping has been playing important socio-economic roles in Ethiopia for millennia. The country is situated in northeast Africa, where ranges of major evolutionary lineages of Apis mellifera adjoin. However, studies on the classification and distribution of subspecies and lineages of honey bees in the country are partly inconsistent, either proposing multiple subspecies and lineages or a unique A. m. simensis. This study was conducted with the aim of elucidating Ethiopian honey bees in reference to African subspecies and major global lineages using wing geometric morphometrics and COI-COII mitochondrial DNA analyses. For this purpose, 660 worker bees were collected from 66 colonies representing highland, midland, and lowland zones in different locations. Both methods indicated that the samples from this study form a distinct cluster together with A. m. simensis reference. In addition, forewing venation patterns showed that most of the Ethiopian samples are separate from all reference subspecies, except A. m. simensis. Analysis of COI-COII sequences revealed five DraI haplotypes (Y2, Y1, A1, and O5’), of which one was new denoted as Y3. Moreover, centroid size strongly associated with elevation. In conclusion, the results supported that Ethiopian honey bees are distinct both at lineage and subspecies levels; however, there is an indication of lineage O in the north.

First record of the nematode Libyostrongylus dentatus Hoberg, Lloyd & Omar, 1995 (Trichostrongylidae) in ostriches (Struthio camelus Linnaeus, 1758) (Struthionidae) outside the Americas

BackgroundLibyostrongylus douglassii, Libyostrongylus dentatus and Libyostrongylus magnus are nematodes that infect ostriches. The first species has been identified in ostriches from Africa, Europe, Americas and Oceania. Although the natural range of ostriches is Africa, L. dentatus was first described in birds from the USA and later identified in Brazil, where co-infections with L. douglassii have been commonly reported. Libyostrongylus magnus is known from the original description only. There are a few reports on infections with L. douglassii in ostriches from Africa and all farmed birds examined are from the southern region of the continent. The aim of this report was to verify Libyostrongylus spp. infections in wild ostriches from Ethiopia. Fecal samples from ostriches, Struthio molybdophanes, were collected and submitted to coproculture. Infective larvae were identified to the species level based on general morphology and morphometry. In addition, phylogenetic analysis of the first and second internal transcribed spacer (ITS1 and ITS2) of the nuclear ribosomal DNA was performed.ResultsInfective larvae from Ethiopian ostriches had the morphological characteristics of L. dentatus. Confidence interval estimate for sheath tail length from Ethiopian Libyostrongylus sp. isolates overlapped one for Brazilian L. dentatus. Neighbor-joining and Maximum Likelihood phylogenetic trees based on sequences of the ITS1 and ITS2 regions revealed that the Ethiopian samples belong to the L. dentatus species clade. Monospecific infections with L. dentatus were confirmed in Ethiopian wild ostriches, opposed to the co-infections typically found in the Americas.ConclusionsTo our knowledge, this is the first record of L. dentatus from African ostriches, the region from which this parasite originated.

Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers.

Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin—i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south.

Detection and characterization of Maize chlorotic mottle virus and Sugarcanemosaic virus associated with maize lethal necrosis disease in Ethiopia: an emerging threat to maize production in the region

Maize Lethal Necrosis Disease (MLND) develops from synergistic co-infection by Sugarcane mosaic virus and Maize chlorotic mottle virus. The disease causes symptoms ranging from leaf tissue mottling and malformed ears to premature plant death. Information on the diversity and transmission of those viruses are limited in Ethiopia. No attempts were made to characterize and identify SCMV and MCMV strains of Oromia and Benishangul-Gumuz regions. The aim of this research was to study MLND responsible viruses via serological and molecular techniques. A total of 174 symptomatic maize leaf samples were collected. Using Double Antibody Sandwich-ELISA (DAS-ELISA), 43 samples showed strong reaction for MCMV antibody and only 14 samples were clearly positive for SCMV. Reverse transcriptase polymerase chain reaction (RT-PCR) technique revealed the presence of MCMV and SCMV in most samples. Analysis of the genetic diversity of MCMV and SCMV by sequencing the coat protein of all isolates shows strong homology with previous East African isolates deposited in the GenBank. The phylogenetic analysis indicated that the virus isolates are highly similar with each other. In conclusion, this study unequivocally confirmed the association of MCMV and SCMV with MLND in the investigated areas and for the first time provided information on the genetic variability by sequence analysis of several Ethiopian samples. Since the risk posed by MLND in the investigated area is high, there is an urgent need for developing integrated management options for controlling the disease.

The tight junction gene Claudin-1 is associated with atopic dermatitis among Ethiopians.

The strong association between epidermal barrier gene variants and Atopic Dermatitis (AD) highlights that impaired skin barrier is a key feature in the pathogenesis of AD. Although the filaggrin (FLG) gene is the major AD risk gene in European and Asian populations, disease-associated variants remain elusive in African populations. A previous study has reported that variants in the tight junction gene CLDN1 have been associated with AD susceptibility and disease severity in African-Americans. Our aim was therefore to investigate the association of CLDN1 with AD in the Ethiopian population. To investigate how CLDN1 variants may be involved in increasing the risk of AD in the Ethiopian population, we analysed whole exome sequencing (WES) data for all exons in CLDN1, and in addition, assayed four SNPs (rs17501010, rs9290927, rs9290929 and rs893051) which had previously showed association in African-American AD patients. No damaging variants were detected through WES in 22 Ethiopian samples. Genotyping of disease-associated CLDN1 SNPs in Ethiopian cases and control material showed no overall association. However, significant association was seen for rs893051 in patients who developed AD before the age of 5 years (P < 0.03). Taken together, we demonstrate that tight junction genes and, in particular, CLDN1 rather than variants in FLG may be involved in the susceptibility of AD in the Ethiopian population.

Is it really you,Orthotrichum acuminatum? Ascertaining a new case of intercontinental disjunction in mosses

Intercontinental disjunct distributions are a main issue in current biogeography. Bryophytes usually have broad distribution ranges and therefore constitute an interesting subject of study in this context. During recent fieldwork in western North America and eastern Africa, we found new populations of a moss morphologically similar to Orthotrichum acuminatum. So far this species has been considered to be one of the most typical epiphytic mosses of the Mediterranean Basin. The new findings raise some puzzling questions. Do these new populations belong to cryptic species or do they belong to O. acuminatum, a species which then has a multiple-continent disjunct range? In the latter case, how could such an intercontinental disjunction be explained? To answer these questions, an integrative study involving morphological and molecular approaches was conducted. Morphological results reveal that Californian and Ethiopian samples fall within the variability of those from the Mediterranean Basin. Similarly, phylogenetic analyses confirm the monophyly of these populations, showing that O. acuminatum is one of the few moss species with a distribution comprising the western Nearctic, the western Palaearctic and Palaeotropical eastern Africa. Pending a further genetic and phylogeographical study to support or reject the hypothesis, a process of long-distance dispersal (LDD) is hypothesized to explain this distribution and the origin of the species is suggested to be the Mediterranean Basin, from where diaspores of the species may have migrated to California and Ethiopia. The spore release process in O. acuminatum is revisited to support the LDD hypothesis, 2015, 180, 30–49.

A metabolomics study for the quality control of Black seed oil (Nigella sativa) based on Gas Chromatography-Mass Spectrometry

Black cumin seed oil (BCSO) is the cold-pressed oil obtained from the seeds of Nigella sativa, Ranunculaceae. Nigella sativa is widely cultivated throughout southern Europe and the middle east for culinary and medicinal purposes. Recently, attention has been focused on BCSO as an edible oil with high nutritive value and role in human health attributed to high content in unsaturated fatty acids including linoleic and oleic acids among other components [1]. BSCO is available as a dietary supplement and marketed worldwide, which prompted to study the quality differences in the oil metabolome globally and conclude an association with geographic distribution. A total of 28 samples of marketed BSCO were collected from Egypt, Libya, Saudi Arabia, Ethiopia, Syria and Europe. The oils were analyzed using GC-MS carried out on a RTX-5MS column using temperature programming from 45 to 300 ° at 5 °/min rate and fatty acid composition was determined following the reported protocol [1]. A total of 125 of oil components were identified using Kovat's index and comparison of mass spectra to NIST Mass Spectral Library. The normalised GC peak areas were measured, expressed as percentages and 14 common components were used in the Principal Component Analysis (PCA) data set. The loading plot revealed the major peaks: linoleic acid (LA 0%-33.5%), oleic acid-methyl ester (OAM 7.3%-49.6%) and oleic acid (OA 0%-12.9%) as main chemical markers contributing to the segregation. The PCA score plot showed that most Egyptian samples were segregated above the line demarcating PC2 showing high concentrations in all three components while European, Ethiopian and Syrian samples were clearly segregated below the PC2 line with much lower values.

Large differences in variability for genes associated with antimalarial drug resistance between samples from Tanzania and Ethiopia

Results A surprising finding was that a majority of Ethiopian isolates carried the wild type variant of pfmdr1. The majority of samples from different regions of Tanzania were wild type for both pfcrt and pfmdr1. Analysis of a variable linker region in pfmdr1 showed substantial variation in samples from Tanzania, but minimal variation in samples from Ethiopia. The variable part consists of consecutive NDN residues. The dominating variant in Ethiopians was 7/2/9 and 7/2/10 in Tanzania. The same pattern was seen for a variable part of the pfubp1 gene, where all Ethiopian samples were identical to 3D7. In 19 Tanzanian samples only 8 were identical to 3D7 with 5 other variants. A polymorphism at codon 1528, detected previously in Kenyan samples [2] was found in 2 Tanzanian samples. Conclusions While the presence of the mutant variant of pfcrt in the Ethiopian samples can be explained by continued use of chloroquine in Ethiopia for treatment of P. vivax, the selection of wild type pfmdr1 could be a consequence of using ACT for treatment of P. falciparum. In general, the variability in both studied genes was greater in Tanzania than in Ethiopia. There are no data yet to link the variability in pfubp1 to efficacy of ACT.

The VKORC1 Asp36Tyr variant and VKORC1 haplotype diversity in Ashkenazi and Ethiopian populations

The vitamin K epoxide reductase (VKORC1) is a key enzyme in the vitamin K cycle impacting various biological processes. VKORC1 genetic variability has been extensively studied in the context of warfarin pharmacogenetics revealing different distributions of VKORC1 haplotypes in various populations. We previously identified the VKORC1 Asp36Tyr mutation that was associated with warfarin resistance and with distinctive ethnic distribution. In this study, we performed haplotype analysis using Asp36Tyr and seven other VKORC1 markers in Ashkenazi and Ethiopian-Jewish and non-Jewish individuals. The VKORC1 variability was represented by nine haplotypes (V1-V9) that could be grouped into two distinct clusters (V1-V3 and V4-V9) with intra-cluster difference limited to two nucleotide changes. Phylogeny analysis suggested that these haplotypes could have developed from an ancestral variant, the common V8 haplotype (40% in all population samples), after ten single mutation events. Asp36Tyr was exclusive to the V5 haplotype of the second cluster. Two haplotypes V5 and V4, distinguished only by Asp36Tyr, were prevalent in both Ethiopian population samples. The V2 haplotype, belonging to the first cluster, was the second most prevalent haplotype in the Ashkenazi population sample (15.8%) but relatively uncommon in the Ethiopian origin (4.5-4.7%). We discuss the genetic diversity among studied populations and its potential impact on warfarin-dose management in certain populations of African and European origin.