Caenorhabditis elegans NDX-4 is a MutT-type enzyme that contributes to genomic stability

MutT enzymes prevent DNA damage by hydrolysis of 8-oxodGTP, an oxidized substrate for DNA synthesis and antimutagenic, anticarcinogenic, and antineurodegenerative functions of MutT enzymes are well established. MutT has been found in almost all kingdoms of life, including many bacterial species, yeasts, plants and mammals. However, a Caenorhabditis elegans MutT homologue was not previously identified. Here, we demonstrate that NDX-4 exhibits both hallmarks of a MutT-type enzyme with an ability to hydrolyze 8-oxodGTP and suppress the Escherichia coli mutT mutator phenotype. Moreover, we show that NDX-4 contributes to genomic stability in vivo in C. elegans. Phenotypic analyses of an ndx-4 mutant reveal that loss of NDX-4 leads to upregulation of key stress responsive genes that likely compensate for the in vivo role of NDX-4 in protection against deleterious consequences of oxidative stress. This discovery will enable us to use this extremely robust genetic model for further research into the contribution of oxidative DNA damage to phenotypes associated with oxidative stress.     

Species composition and seasonal abundance of zooplankton in two Ethiopian Rift Valley lakes — Lakes Abiata and Langano

The composition and annual cycle of the zooplankton of two Ethiopian Rift Valley soda lakes is described. Lake Langano has a conductivity of 1 400 to 1800 µS cm^–1 and a permanent mineral turbidity. Lake Abiata is more concentrated (conductivity 19 000 to 23 000 µS cm^–1) and more alkaline but less turbid; it is characterised by dense phytoplankton blooms, mainly cyanophytes.The zooplankton assemblage is typically tropical, with relatively few species of Cladocera and Copepoda. There was a marked difference in zooplankton between the two lakes, Lake Abiata showing much higher concentrations and greater wet season/ dry season differences. The species composition was also different. Lake Abiata lacked Cladocera, and calanoid copepods occurred only during the wet season with lower conductivities. These two phenomena were attributed to high sodium bicarbonate concentration and to dense cyanophyte blooms. Eleven species of rotifers occurred in Lake Abiata, including six Brachionus spp. but B. rubens was the only rotifer found in Lake Langano. The seasonal variation of the zooplankton is discussed in relation to seasonal fluctuations in conductivity and Chl a concentration.     

Chloroplast Genome Sequence Variations and Development of Polymorphic Markers in Coffea arabica

Plant Molecular Biology Reporter - Coffee is a popular beverage in the world and a valuable agricultural export commodity for several developing countries. Coffea arabica is one of the widely...     

Comparison of the Kato-Katz and FLOTAC techniques for the diagnosis of soil-transmitted helminth infections

Decisions on individual or community treatment and evaluation of chemotherapy based control programs depend on parasitological diagnostic techniques. The aim of this study was to compare the accuracy of a single Kato-Katz thick smear and a single FLOTAC for the determination of the prevalence and intensity of soil-transmitted helminth infections. A total of 271 faecal specimens were collected from schoolchildren in Ethiopia, and microscopically examined using the Kato-Katz method (41.7 mg stool per slide) and the FLOTAC technique. The combined results from the Kato-Katz and FLOTAC methods were used as diagnostic 'gold' standard for reference in the analysis. Agreement between the two methods showed kappa values of 0.74, 0.73 and 0.28 for Ascaris lumbricoides, Trichuris trichiura and hookworm, respectively. A single FLOTAC revealed significantly more infections than a single Kato-Katz for each of the three soil-transmitted helminths (p<0.01). The sensitivities of a single Kato-Katz for diagnosis of T. trichiura, A. lumbricoides and hookworm infections were 76.6%, 67.8% and 19.6%, respectively, while the sensitivity of FLOTAC was 100% for all the three soil-transmitted helminth species. A single Kato-Katz yielded considerably higher mean faecal egg counts (FECs) (729.1, 145.2 and 60.7 eggs per gram of stool (EPG) for A. lumbricoides, T. trichiura and hookworm, respectively) compared with a single FLOTAC (142.5, 54.5 and 14.6 EPG, respectively) (p<0.05). Our study confirms that a single FLOTAC is more sensitive than a single Kato-Katz for the diagnosis of soil-transmitted helminth infections, but results in lower FECs. Further standardization and validation are still required in different epidemiological settings with varying levels of intensity of infections before recommending FLOTAC for large-scale community diagnosis.     

Cattle brucellosis in traditional livestock husbandry practice in Southern and Eastern Ethiopia,and its zoonotic implication

Background  

Cattle brucellosis has significant economic and zoonotic implication for the rural communities in Ethiopia in consequence of their traditional life styles, feeding habits and disease patterns. Hence, knowledge of brucellosis occurrence in traditional livestock husbandry practice has considerable importance in reducing the economic and public health impacts of the disease.     

Local increase of arginase activity in lesions of patients with cutaneous leishmaniasis in Ethiopia

Background

Cutaneous leishmaniasis is a vector-borne disease that is in Ethiopia mainly caused by the parasite Leishmania aethiopica. This neglected tropical disease is common in rural areas and causes serious morbidity. Persistent nonhealing cutaneous leishmaniasis has been associated with poor T cell mediated responses; however, the underlying mechanisms are not well understood.

Methodology/Principal Findings

We have recently shown in an experimental model of cutaneous leishmaniasis that arginase-induced L-arginine metabolism suppresses antigen-specific T cell responses at the site of pathology, but not in the periphery. To test whether these results translate to human disease, we recruited patients presenting with localized lesions of cutaneous leishmaniasis and assessed the levels of arginase activity in cells isolated from peripheral blood and from skin biopsies. Arginase activity was similar in peripheral blood mononuclear cells (PBMCs) from patients and healthy controls. In sharp contrast, arginase activity was significantly increased in lesion biopsies of patients with localized cutaneous leishmaniasis as compared with controls. Furthermore, we found that the expression levels of CD3ζ, CD4 and CD8 molecules were considerably lower at the site of pathology as compared to those observed in paired PBMCs.

Conclusion

Our results suggest that increased arginase in lesions of patients with cutaneous leishmaniasis might play a role in the pathogenesis of the disease by impairing T cell effector functions.     

Inference of population structure of Leishmania donovani strains isolated from different Ethiopian visceral leishmaniasis endemic areas

Background

Parasites'' evolution in response to parasite-targeted control strategies, such as vaccines and drugs, is known to be influenced by their population genetic structure. The aim of this study was to describe the population structure of Ethiopian strains of Leishmania donovani derived from different areas endemic for visceral leishmaniasis (VL) as a prerequisite for the design of effective control strategies against the disease.

Methodology/Principal Findings

Sixty-three strains of L. donovani newly isolated from VL cases in the two main Ethiopian foci, in the north Ethiopia (NE) and south Ethiopia (SE) of the country were investigated by using 14 highly polymorphic microsatellite markers. The microsatellite profiles of 60 previously analysed L. donovani strains from Sudan, Kenya and India were included for comparison. Multilocus microsatellite typing placed strains from SE and Kenya (n = 30) in one population and strains from NE and Sudan (n = 65) in another. These two East African populations corresponded to the areas of distribution of two different sand fly vectors. In NE and Sudan Phlebotomus orientalis has been implicated to transmit the parasites and in SE and Kenya P. martini. The genetic differences between parasites from NE and SE are also congruent with some phenotypic differences. Each of these populations was further divided into two subpopulations. Interestingly, in one of the subpopulations of the population NE we observed predominance of strains isolated from HIV-VL co-infected patients and of strains with putative hybrid genotypes. Furthermore, high inbreeding irreconcilable from strict clonal reproduction was found for strains from SE and Kenya indicating a mixed-mating system.

Conclusions/Significance

This study identified a hierarchical population structure of L. donovani in East Africa. The existence of two main, genetically and geographically separated, populations could reflect different parasite-vector associations, different ecologies and varying host backgrounds and should be further investigated.     

Endosperm Protein Quality and Kernel Modification in the Quality Protein Maize Inbred Lines

Twenty-two selected quality protein maize (QPM) lines, including 13 lines developed in India (DMRQPM series) and nine lines released by CIMMYT, Mexico (CML series), were evaluated for their endosperm protein content and quality, besides kernel modification in terms of vitreousness. Endosperm protein contents in 13QPMlines were on par or better than that of the normal maize ‘checks’ (Trishulata and Parkash). The QPM endosperm proteins showed significantly higher % tryptophan as well as EF-1α (a multifunctional protein with a positive and highly significant correlation with lysine content in the endosperm) contents, in comparison with the normal maize genotypes. Evaluation of kernel modification revealed considerable scope for accumulation of endosperm modifiers in some of the QPM lines. Positive and highly significant correlation was revealed between tryptophan and EF-1α contents in the endosperm proteins, whereas the correlations between the quality parameters with kernel modification in the QPM genotypes were found to be non-significant. The study led to the identification of some promising QPM lines, such as DMRQPM-37, DMRQPM-44, CML176, CML142 and CML149, which could be effectively deployed in the QPM breeding programmes.     

Characterization of Coffea chloroplast microsatellites and evidence for the recent divergence of C. arabica and C. eugenioides chloroplast genomes.

Comparative sequencing of >7 kb of highly variable chloroplast genome regions (atpB-rbcL, trnS-trnG, rpl22-rps19, and rps19-rpl2 spacers; introns in atpF, trnG, trnK, and rpl16) with microsatellites known from other angiosperms was carried out in Coffea. Samples comprised 8 diploid species of Coffea, 5 individuals of tetraploid C. arabica representing geographically distant wild populations from Ethiopia, 2 commercial cultivars of C. arabica, and Psilanthus leroyi and Ixora coccinea as outgroups. Phylogeny reconstruction using maximum parsimony and Bayesian inference resulted in congruent topologies with high support for C. arabica and C. eugenioides being sisters. Partitioned analyses showed that all regions except the atpB-rbcL spacer resolved this sister-group, although this was often unsupported. The large sequence data set further shows that chloroplast genomes of C. arabica and C. eugenioides each possess apomorphies, indicating that not C. eugenioides but an ancestor or close relative of C. eugenioides is the maternal parent of C. arabica. Seven variable chloroplast microsatellites were characterized in Coffea. Most microsatellites are poly(A/T) stretches, whereas one in the trnS-trnG spacer has an (AT)n motif. Most strikingly, all individuals of C. arabica possess identical sequences, suggesting a single chloroplast haplotype. This can be explained by a recent origin of C. arabica in a unique allopolyploidization event, or by severe bottleneck effects in the evolutionary history of the species. Reconstruction of the evolution of microstructural mutations shows much higher levels of homoplasy in microsatellite loci than in other parts of spacers and introns. Microsatellites are inferred to evolve by insertion and deletion of 1 to 3 motif copies in one step.