LC‐MS/MS‐based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma

Associating changes in protein levels with the onset of cancer has been widely investigated to identify clinically relevant diagnostic biomarkers. In the present study, we analyzed sera from 205 patients recruited in the United States and Egypt for biomarker discovery using label‐free proteomic analysis by LC‐MS/MS. We performed untargeted proteomic analysis of sera to identify candidate proteins with statistically significant differences between hepatocellular carcinoma (HCC) and patients with liver cirrhosis. We further evaluated the significance of 101 proteins in sera from the same 205 patients through targeted quantitation by MRM on a triple quadrupole mass spectrometer. This led to the identification of 21 candidate protein biomarkers that were significantly altered in both the United States and Egyptian cohorts. Among the 21 candidates, ten were previously reported as HCC‐associated proteins (eight exhibiting consistent trends with our observation), whereas 11 are new candidates discovered by this study. Pathway analysis based on the significant proteins reveals upregulation of the complement and coagulation cascades pathway and downregulation of the antigen processing and presentation pathway in HCC cases versus patients with liver cirrhosis. The results of this study demonstrate the power of combining untargeted and targeted quantitation methods for a comprehensive serum proteomic analysis, to evaluate changes in protein levels and discover novel diagnostic biomarkers. All MS data have been deposited in the ProteomeXchange with identifier PXD001171 ( http://proteomecentral.proteomexchange.org/dataset/PXD001171 ).     

Attitudes of local people towards the mountain nyala (Tragelaphus buxtoni) in Munessa,Ethiopia

Due to their direct dependence on wildlife products for subsistent use, people living in poverty are often viewed as being in conflict with wildlife conservation. We studied the attitudes of local people towards mountain nyala (Tragelaphus buxtoni) in Munessa, Ethiopia. A household survey (n = 214) was used to examine the socio‐economic characteristics and beliefs of local people from three peasant associations and one village. Generally, the study revealed that local people had positive attitudes towards mountain nyala, its conservation and population increase, which is consistent with our predictions. For example, a greater percentage of the respondents had positive (62.5%) rather than negative (37.5%) attitudes towards mountain nyala and its conservation. Moreover, the larger proportion of the respondents had positive (66.67%) rather than negative (33.3%) attitudes towards an increase in mountain nyala population. However, compared to socio‐economic characteristics, beliefs towards mountain nyala were more powerful and consistent predictor of attitudes and explained much of the variances of the two groups of the dependent variables. Thus, informing local communities about the value of mountain nyala (e.g. recreational and economic) through conservation education, advocating the need for sustainable utilization and introducing an economic benefit sharing may improve positive attitude and increase participation of local people in conservation and management of the mountain nyala population in Munessa.     

Helicobacter pylori-selective antibacterials based on inhibition of pyrimidine biosynthesis

We report the discovery of a class of pyrazole-based compounds that are potent inhibitors of the dihydroorotate dehydrogenase of Helicobacter pylori but that do not inhibit the cognate enzymes from Gram-positive bacteria or humans. In culture these compounds inhibit the growth of H. pylori selectively, showing no effect on other Gram-negative or Gram-positive bacteria or human cell lines. These compounds represent the first examples of H. pylori-specific antibacterial agents. Cellular activity within this structural class appears to be due to dihydroorotate dehydrogenase inhibition. Minor structural changes that abrogate in vitro inhibition of the enzyme likewise eliminate cellular activity. Furthermore, the minimum inhibitory concentrations of these compounds increase upon addition of orotate to the culture medium in a concentration-dependent manner, consistent with dihydroorotate dehydrogenase inhibition as the mechanism of cellular inhibition. The data presented here suggest that targeted inhibition of de novo pyrimidine biosynthesis may be a valuable mechanism for the development of antimicrobial agents selective for H. pylori.     

A new species of Coreopsis (Compositae — Heliantheae) from Mexico

Coreopsis crawfordii is described and illustrated. It is also compared with themorphologically similar species, C. pringlei and C. rudis , also from Mexico, and a key to all the species of Coreopsis known from Mexico is provided.     

Differential and dynamic localization of topoisomerases in Bacillus subtilis

Visualization of topoisomerases in live Bacillus subtilis cells showed that Topo I, Topo IV, and DNA gyrase differentially localize on the nucleoids but are absent at cytosolic spaces surrounding the nucleoids, suggesting that these topoisomerases interact with many regions of the chromosome. While both subunits of Topo IV were uniformly distributed throughout the nucleoids, Topo I and gyrase formed discrete accumulations, or foci, on the nucleoids in a large fraction of the cells, which showed highly dynamic movements. Three-dimensional time lapse microscopy showed that gyrase foci accumulate and dissipate within a 1-min time scale, revealing dynamic assembly and disassembly of subcellular topoisomerase centers. Gyrase centers frequently colocalized with the central DNA replication machinery, suggesting a major role for gyrase at the replication fork, while Topo I foci were frequently close to or colocalized with the structural maintenance of chromosomes (SMC) chromosome segregation complex. The findings suggest that different areas of supercoiling exist on the B. subtilis nucleoids, which are highly dynamic, with a high degree of positive supercoiling attracting gyrase to the replication machinery and areas of negative supercoiling at the bipolar SMC condensation centers recruiting Topo I.     

Biology-based mapping of vector-borne parasites by geographic information systems and remote sensing

Application of growing degree day-water budget analysis and satellite climatology to vector-borne parasites will be reviewed to demonstrate the value of using the unique thermal-hydrological preferences and limits of tolerance of individual parasite-vector systems to define the environmental niche of disease agents in the landscape by modern geospatial analysis methods. Applications of geospatial modeling will be illustrated by examples on fascioliasis, malaria, leprosy and leishmaniasis.     

Variants of the SFTPA1 and SFTPA2 genes and susceptibility to tuberculosis in Ethiopia

Lungs are the central organ affected and targeted by Mycobacterium tuberculosis and immune processes in the lung are of critical importance in the pathogenesis of tuberculosis. A major lung defense against invading pathogens is provided by surfactant protein A, a multi-chain protein encoded by the SFTPA1 and SFTPA2 genes. Here, we investigated polymorphisms in the SFTPA1 and SFTPA2 genes for association with tuberculosis in 181 Ethiopian families comprising 226 tuberculosis cases. Four polymorphisms, SFTPA1 307A, SFTPA1 776T, SFTPA2 355C, and SFTPA2 751C, were associated with tuberculosis (P=0.00008; P=0.019, P=0.029 and P=0.042, respectively). Additional subgroup analysis in male, female and more severely affected patients provided evidence for SFTPA1/2-covariate interaction. Finally, out of five intragenic haplotypes identified in the SFTPA1 gene and nine identified in the SFTPA2 gene, 1A ³ was most significantly associated with tuberculosis susceptibility (P=0.026). These findings suggest that SFTPA1 and SFTPA2 modify the risk of tuberculosis susceptibility and that this risk is influenced by additional covariates.     

Limnological and ecological characteristics of tropical highland reservoirs in Tigray, Northern Ethiopia

The semi-arid highlands of Northern Ethiopia (Tigray) have numerous small reservoirs that have been created by microdams in an attempt to provide water supply for irrigation and livestock drinking. Although the reservoirs have substantial added value to residents, their use as water resource is jeopardized by eutrophication and a high occurrence of blooms of toxic cyanobacteria. So far, there is no systematic information available on the limnological and aquatic ecological characteristics of these dams. We carried out a standardized survey of 32 reservoirs and assessed a wide set of morphometric, abiotic and biotic variables. The sampling was performed during two seasons, September–October 2004 (end of the wet season/start of the dry season) and April–May 2005 (towards the end of the dry season). Using multivariate analysis, we revealed dominating patterns of variable associations and compared the variability in these patterns among seasons. According to standardized PCA and RDA analyses, the most important axis of variation was mainly represented by a gradient in nutrients and altitude that was also positively associated with phytoplankton biomass, suspended matter and oxygen concentration, and negatively with water transparency. For most variables, correlations between the wet and dry season were weak, which suggests that individual reservoirs behaved rather differently in their response to seasonal changes. Nevertheless, a Mantel correlation (r = 0.32; P = 0.035) showed a weak but significant overall concordance in the variable association patterns among seasons. A number of reservoirs became very shallow or fell dry in the dry season, a process that was associated with an increase in suspended matter and conductivity and a decrease in transparency. These reservoirs contained lower amounts of fish and tended to be less eutrophic than the deeper, permanent systems, as they had lower levels of phosphorus and chlorophyll-a. With multiple regression analysis, we constructed most parsimonious models in an attempt to explain the variation in key biotic variables: phytoplankton and cyanobacteria biomass, cladoceran biomass, fish biomass and the abundance of submerged vegetation. Phytoplankton and fish biomass tended to be positively related with the concentration of total phosphorus, whereas cladoceran biomass was not associated with nutrient concentrations. The positive association of fish and phytoplankton with nutrient concentrations suggests a bottom-up control, whereas the absence of an association between zooplankton and nutrient concentrations may be indicative for top-down control. The biomass of cyanobacteria was negatively related to the biomass of cladocerans (Daphnia), which likely reflects a top-down effect. Most reservoirs were turbid. The occurrence and abundance of macrophytes tended to be positively related to water transparency and was negatively associated to TP and the amount of livestock frequenting the reservoirs. However, macrophytes were not limited to clear-water reservoirs. Handling editor: L. M. Bini     

Efficacy of plant essential oils against two major insect pests of coffee (Coffee berry borer,Hypothenemus hampei,and antestia bug,Antestiopsis intricata) and maize weevil,Sitophilus zeamais

Coffee berry borer, antestia bug and maize weevil are serious pest of coffee and maize, respectively. Bioassays of plant essential oils were conducted with coffee berry borer, antestia bug and the maize weevil. Essential oils of Thymus vulgaris, Aloysia sp., Ruta chalepensis, Chenopodium ambrosioides and Cymbopogon nardus resulted in 80%–90% mortality of coffee berry borer, whereas essential oils of C. ambrosioides, T. vulgaris and R. chalepensis achieved 87.5%–92.5% mortality of antestia bug. Essential oils of C. ambrosioides caused significantly the highest percentage mortality of the maize weevils (95%) with “Lethal Dose” (LD₅₀) values of 2.202 ml 100 ml^?1 within 24 h after treatment, whereas essential oils of Mentha spicata, T. vulgaris and R. chalepensis resulted in 82.5%, 77.5% and 73.5% mortality, respectively. The potential of plant essential oils for the management of coffee berry borer, antestia bug and maize weevil for the small-scale farmers is discussed.     

Bacteriocin Production, Antibiotic Susceptibility and Prevalence of Haemolytic and Gelatinase Activity in Faecal Lactic Acid Bacteria Isolated from Healthy Ethiopian Infants

The objective of this study was to characterise lactic acid bacteria (LAB) isolated from faecal samples of healthy Ethiopian infants, with emphasis on bacteriocin production and antibiotic susceptibility. One hundred fifty LAB were obtained from 28 healthy Ethiopian infants. The isolates belonged to Lactobacillus (81/150), Enterococcus (54/150) and Streptococcus (15/150) genera. Lactobacillus species were more abundant in the breast-fed infants while Enterococcus dominated the mixed-fed population. Bacteriocin-producing LAB species were isolated from eight of the infants. Many different bacteriocins were identified, including one new bacteriocin from Streptococcus salivarius, avicin A (class IIa) from Enterococcus avium, one class IIa bacteriocin from Enterococcus faecalis strains, one unknown bacteriocin from E. faecalis and two unknown bacteriocins from Lactobacillus fermentum strains and the two-peptide gassericin T from Lactobacillus gasseri isolate. Susceptibility tests performed for nine antibiotics suggest that some lactobacilli might have acquired resistance to erythromycin (3 %) and tetracycline (4 %) only. The streptococci were generally antibiotic sensitive except for penicillin, to which they showed intermediate resistance. All enterococci were susceptible to ampicillin while 13 % showed penicillin resistance. Only one E. faecalis isolate was vancomycin-resistant. Tetracycline (51 %) and erythromycin (26 %) resistance was prevalent among the enterococci, but multidrug resistance was confined to E. faecalis (47 %) and Enterococcus faecium (33 %). Screening of enterococcal virulence traits revealed that 2 % were β-haemolytic. The structural genes of cytolysin were detected in 28 % of the isolates in five enterococcal species, the majority being E. faecalis and Enterococcus raffinosus. This study shows that bacteriocin production and antibiotic resistance is a common trait of faecal LAB of Ethiopian infants while virulence factors occur at low levels.