DNA barcoding of the main cultivated yams and selected wild species in the genus Dioscorea

Distinguishing yam species based on morphological traits is extremely difficult and unreliable, posing a challenge to breeders and genebank curators. Development of a molecular assay based on DNA barcoding can facilitate rapid and accurate identification of important Dioscorea species. To develop a DNA barcoding system forDioscorea species identification, the rbcL and matK loci (in unison and in combination), the non-coding intergenic spacer trnH-psbA of the chloroplast genome, and the nuclear ITS regions were investigated using criteria for developing candidate DNA barcodes. All DNA barcoding sequences were assessed for ease of PCR amplification, sequence quality and species discriminatory power. Amongst the markers investigated, the matK locus performed well in terms of species identification (63.2%), in addition to detecting high interspecific variation with mean divergence of 0.0196 (SD=0.0209). The combination of the two coding regions (rbcL + matK) was determined to be the optimal (76.2%) DNA barcoding approach as 16 out of 21 species could be defined. While the rbcL exhibited good PCR amplification efficiency and sequence quality, its species discriminatory power was relatively poor with 47.6% identification. Similarly, the trnH-psbA region had a weak discrimination efficiency of only 36.8%. While the development of more robust DNA barcoding systems is an ongoing challenge, our results indicate that therbcL + matK combination can be utilized as multi-locus DNA barcode regions for Dioscorea species identification.     

Osmotic Adjustment in Sorghum: II. Relationship to Gas Exchange Rates

Lowering of the solute potential by osmotic adjustment (OA) has been proposed to allow maintenance of leaf turgor potential (Ψ_p), stomatal conductance (g), and photosynthesis (A) at low leaf water potential. However, literature concerning the role of OA in the maintenance of g and A under water stress is limited and often contradictory. The objective of this experiment was to examine the association of OA with g and A in grain sorghum (Sorghum bicolor L. Moench). A single sorghum hybrid (cv AT×623 × RT×430) was studied under field conditions using four different water supplies. Diurnal and midday water potential, solute potential, Ψ_p, OA, g, and A were measured during preflowering and grain-filling growth stages. A second experiment was conducted under greenhouse conditions. Two sorghum genotypes (BT×623 and BT×378) differing in their g and A responses to plant water stress were compared for their OA capacity during a water deficit cycle imposed from the beginning of panicle initiation through flowering. Under both field and greenhouse conditions, g and A rapidly declined with increased water stress despite the occurrence of OA. Under greenhouse conditions, BT×623 maintained significantly higher g and A than BT×378 during the water stress cycle. However, no significant differences in OA or Ψ_p existed between the two genotypes, indicating that OA was not associated with differences observed in g and A between these genotypes. We conclude that the response of g and A to water stress was not directly associated with OA and certainly was not maintained by OA.     

Defective sarcolemmal phospholipase C signaling in diabetic cardiomyopathy

Phospholipase C (PLC) activity is known to influence cardiac function. This study was undertaken to examine the status of PLC 3 in the cardiac cell plasma membrane (sarcolemma, SL) in an experimental model of chronic diabetes. SL membrane was isolated from diabetic rat hearts at 8 weeks after a single i.v. injection of streptozotocin (65 mg/kg body weight). The total SL PLC was decreased in diabetes and was associated with a decrease in SL PLC 3 activity, which immunofluorescence in frozen diabetic left ventricular tissue sections revealed to be due to a decrease in PLC 3 protein abundance. In contrast, the SL abundance of Gq was significantly increased during diabetes. These changes were associated with a loss of contractile function (±dP/dt). A 2-week insulin treatment of 6-week diabetic animals partially normalized all of these parameters. These findings suggest a defect in PLC 3-mediated signaling processes may contribute to the cardiac dysfunction seen during diabetes. (Mol Cell Biochem 261: 193–199, 2004)     

Affordability of commonly prescribed antibiotics in a large tertiary teaching hospital in Ethiopia: a challenge for the national drug policy objective

Objective

In national drug policies of many countries, ensuring availability and affordability of essential medicines is indicated among the major policy objectives. To achieve the objectives, countries with low and middle income compile such medicines into NEMLs. This study aims to determine availability and affordability of commonly prescribed antibiotics at a tertiary hospital in Ethiopia by assessing (in private and public pharmacies) 13 antibiotics constituting DU90% at the hospital.

Results

Availability of the antibiotics in the private and public pharmacies was 92.3% and 98.5%, respectively. Average MPRs for the antibiotics were 4.1 and 2.7, respectively, in the private and public pharmacies. The days’ wages (in median prices) ranged from 0.2 for treating acute diarrhea with doxycycline to 415.8 for treating HAP in public pharmacies. Costs of a single day treatment with antibiotics purchased from the public pharmacies ranged from USD 0.1 for acute diarrhea to USD 29.7 for HAP. For the private pharmacies, the range was from USD 0.1 for toxoplasmosis to USD 54.9 for HAP. This study showed that treatments of commonly diagnosed infectious conditions at TASH remain unaffordable according to the WHO/HAI criteria.

     

The importance of avocado (Persea americana Mill.) fruits anthracnose and factors influencing the disease in Mana district,south-western Ethiopia

Anthracnose disease surveys were conducted in 25 farmers’ orchards, wholesaler and retailer shops in south-west Ethiopia. In addition, harvesting and postharvest practices, and storage conditions influencing disease development were studied with observation and questionnaire. The assessment results indicated significant variation among farmers’ orchards with the highest incidence (84.0 ± 16.7%) and severity index (26.0 ± 5.4%). Anthracnose damage of fruit was higher at retailers (76.7 ± 20.8%) than in the wholesalers shop (56.7 ± 32.5%). The total number of isolates identified was 249 and Colletotrichum gloeosporioides was the predominant pathogen proved by pathogenecity test. Among the major factors, harvesting avocado fruits with children (88%) and climbing on the tree (72%) resulted in fruit dropping that caused substantial injury and bruise. Generally, anthracnose caused by C. gloeosporioides of avocado fruit was prevalent in producer orchards that aggravated by traditional harvest and postharvest practices coupled to inadequate transportation and storage facilities at wholesaler and retailer shops with subsequent decay and loss of avocado fruits.     

Effects of livestock grazing on an Afromontane grassland bird community in the Bale Mountains of Ethiopia

Livestock grazing has been considered to be one of the major causes for biodiversity degradation worldwide. In this study, we examined this effect on Afromontane grassland birds by comparing their diversity between ungrazed and grazed grassland sites in the northern Bale Mountains, Ethiopia. We counted birds and recorded vegetation height and cover along 28 (14 in each land‐use type) 1 km transects. We used six different diversity measures (richness, evenness, Shannon diversity, taxonomic diversity and taxonomic distinctness) to express bird diversity and explored which of these measures better reveal the diversity pattern. Vegetation structure differed significantly between the two sites; the first two principal components accounted for 78% of the variation. Discriminant function analysis (DFA) showed bird diversity to differ significantly between the two sites; taxonomic diversity (Delta) contributed the most to the difference between the two sites, while species richness contributed the least. The results of ANOVA indicated that all diversity measures, except species richness, were significantly higher in the protected site compared to the unprotected site. In general, this study showed that grazing had negatively affected bird diversity in the study area and the use of taxonomic diversity measures had enabled us to reveal the impact better.     

Limited proteolysis of human von Willebrand factor by Staphylococcus aureus V-8 protease: isolation and partial characterization of a platelet-binding domain

Purified human von Willebrand factor (vWF) was digested with Staphylococcus aureus V-8 protease, and specific domains interacting with platelets were isolated and characterized. Amino acid sequence analysis and sodium dodecyl sulfate gel electrophoresis demonstrated that the digestion proceeded primarily by a single cleavage of the native 270K subunit between an internal Glu-Glu peptide bond. This produced an integral stepwise degradation of the multimers of vWF with a concomitant accumulation of bands with mobility similar to that of the smaller molecular weight vWF multimers. The immediate precursor of the final products contained equimolar amounts of 270K subunit and of two polypeptides (170K and 110K). The cleavage of the remaining 270K subunit converted vWF into two main fragments (fragments II and III). These fragments were isolated by ion exchange chromatography, characterized, and assayed for platelet binding in the presence of ristocetin. Fragment III is a dimer of 315K composed primarily of two chains of 170K. Amino acid sequence analysis indicated that it originated from the amino-terminal portion of the 270K subunit and contained 11% of the original ristocetin cofactor activity. Also, it binds to platelets at the same specific sites as native vWF and shows a platelet binding pattern similar to that of partially reduced vWF (500K). Fragment II is a dimer of 235K composed of two identical chains of 110K. Amino acid sequence analysis indicated that it originated from the carboxyl-terminal portion of the 270K subunit and lacked ristocetin cofactor activity. Also, it does not bind to platelets or inhibit the binding of 125I-vWF in the presence of ristocetin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Community Health Seeking Behavior for Suspected Human and Animal Rabies Cases,Gomma District,Southwest Ethiopia

Background

Timely presentation to appropriate health service provider of sick animals/humans from zoonotic diseases like rabies is important for early case/outbreak detection and management. However, data on community’s health seeking practice for rabies in Ethiopia is limited. Therefore the objective of this study was to determine community’s health seeking behavior on rabies, Southwest Ethiopia.

Methods

A cross-sectional survey was conducted from January 16-February 14, 2015 to collect data from 808 respondents where the respondents were selected using multistage sampling technique. Data were collected using interviewer administered structured questionnaire by trained epidemiology graduate level students. Data were entered to Epidata version 3.1 and analyzed using SPSS version 20 for windows.

Result

Eight hundred three (99.4%) respondents participated in the study. Out of 28 respondents who reported their family members’ exposure to rabies, 8 of them replied that the exposed family members sought treatment from traditional healers. More than nine in ten respondents perceived that humans and domestic animals with rabies exposure should seek help of which 85% of them suggested modern health care facilities as the preferred management option for the sick humans and domestic animals. However, among those who reported sick domestic animals, near to 72% of them had either slaughtered for human consumption, sold immediately, visited traditional healer, given home care or did nothing for the sick domestic animals.

Conclusion

Majority of the respondents had favorable perception of seeking treatment from modern health care facilities for rabies. However, significant number of them had managed inappropriately for the sick domestic animals from rabies. Hence, raising awareness of the community about management of sick domestic animals from rabies and the need for reporting to both human and animal health service providers is needed.     

Next-generation sequencing based genotyping,cytometry and phenotyping for understanding diversity and evolution of guinea yams

Key message

Genotyping by sequencing (GBS) is used to understand the origin and domestication of guinea yams, including the contribution of wild relatives and polyploidy events to the cultivated guinea yams.

Abstract

Patterns of genetic diversity within and between two cultivated guinea yams (Dioscorea rotundata and D. cayenensis) and five wild relatives (D. praehensilis, D. mangenotiana, D. abyssinica, D. togoensis and D. burkilliana) were investigated using next-generation sequencing (genotyping by sequencing, GBS). Additionally, the two cultivated species were assessed for intra-specific morphological and ploidy variation. In guinea yams, ploidy level is correlated with species identity. Using flow cytometry a single ploidy level was inferred across D. cayenensis (3x, N = 21), D. praehensilis (2x, N = 7), and D. mangenotiana (3x, N = 5) accessions, whereas both diploid and triploid (or aneuploid) accessions were present in D. rotundata (N = 11 and N = 32, respectively). Multi-dimensional scaling and maximum parsimony analyses of 2,215 SNPs revealed that wild guinea yam populations form discrete genetic groupings according to species. D. togoensis and D. burkilliana were most distant from the two cultivated yam species, whereas D. abyssinica, D. mangenotiana, and D. praehensilis were closest to cultivated yams. In contrast, cultivated species were genetically less clearly defined at the intra-specific level. While D. cayenensis formed a single genetic group, D. rotundata comprised three separate groups consisting of; (1) a set of diploid individuals genetically similar to D. praehensilis, (2) a set of diploid individuals genetically similar to D. cayenensis, and (3) a set of triploid individuals. The current study demonstrates the utility of GBS for assessing yam genomic diversity. Combined with morphological and biological data, GBS provides a powerful tool for testing hypotheses regarding the evolution, domestication and breeding of guinea yams.