Pro- and Anti-Inflammatory Cytokines against Rv2031 Are Elevated during Latent Tuberculosis: A Study in Cohorts of Tuberculosis Patients,Household Contacts and Community Controls in an Endemic Setting

Tuberculosis (TB) is among the leading causes of morbidity and mortality. The causative agent, Mycobacterium tuberculosis (Mtb), has evolved virulent factors for entry, survival, multiplication and immune evasion. Rv2031 (also called alpha crystallin, hspX, 16-kDa antigen), one of the most immunogenic latency antigens, is believed to play a key role in long-term viability of Mtb. Here, we report the dynamics of pro-inflammatory (IFN-γ, TNF-α) and anti-inflammatory (IL-10) cytokines against Rv2031 using whole blood assay in human cohorts in a TB endemic setting. Cytokine responses to ESAT-6-CFP-10 were also measured for comparison. Blood samples were collected from smear positive pulmonary TB patients and their contacts at baseline, 6 and 12 months, and from community controls at entry. At baseline, 54.4% of controls and 73.2% of contacts were QFT-GIT test positive. Baseline IFN-γ, TNF-α and IL-10 responses to Rv2031 were significantly higher in controls compared to contacts and untreated patients (p<0.001). Furthermore, untreated patients had significantly higher TNF-α and IL-10 responses to Rv2031 compared to contacts (p<0.001). In contacts and treated patients, IFN-γ, TNF-α and IL-10 responses to Rv2031 significantly increased over 12 months (p<0.0001) and became comparable with the corresponding levels in controls. There was a positive and significant correlation between Rv2031 and ESAT-6-CFP-10 specific cytokine responses in each study group. The fact that the levels of IFN-γ, TNF-α and IL-10 against Rv2031 were highest during latent TB infection may indicate their potential as markers of protection against TB. Taken together, the findings of this study suggest the potential of IFN-γ, TNF-α and IL-10 against Rv2031 as biomarkers of the host response to Mtb during convalescence from, and the absence of, active tuberculosis.     

Griffithsin, a potent HIV entry inhibitor, is an excellent candidate for anti-HIV microbicide

BACKGROUND: The predominant mode of HIV-1 transmission is by heterosexual contact. The cervical/vaginal mucosa is the main port of HIV entry in women. A safe and effective topical microbicide against HIV is urgently needed to prevent sexual transmission. Hence, we evaluated griffithsin (GRFT), a 12.7 kDa carbohydrate-binding protein, both native and recombinant GRFT, potently inhibited both CXCR4-and CCR5-tropic HIV infection and transmission in vitro. METHODS: The antiviral efficacy of native and recombinant GRFT against CXCR4-and CCR5-tropic HIV and SHIV strains and SIVmac251 was evaluated by in vitro assays. We also evaluated the time course of antiviral activity and stability of GRFT in cervical/vaginal lavage as a function of pH 4-8. RESULTS: Griffithsin blocked CXCR4-and CCR5-tropic viruses at less than 1 nm concentrations and exhibited a high potency. GRFT was stable in cervical/vaginal lavage fluid and maintained a similar potency of anti-HIV activity. GRFT is not only a highly potent HIV entry inhibitor, but also prevents cell fusion and cell-to-cell transmission of HIV. CONCLUSIONS: The in vitro efficacy of GRFT revealed low cytotoxicity, high potency, rapid onset of antiviral activity and long-term stability in cervical/vaginal lavage. GRFT is an excellent candidate for anti-HIV microbicide development.     

Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations—a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina’s sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.     

Ecological Flexibility in Boutourlini’s Blue Monkeys (Cercopithecus mitis boutourlinii) in Jibat Forest, Ethiopia: A Comparison of Habitat Use, Ranging Behavior, and Diet in Intact and Fragmented Forest

Comparisons of the behavior and ecology of primates living in intact and fragmented forest are critical to the development of conservation strategies for the many primate taxa threatened by habitat loss. From July 2009 to April 2010, we investigated the habitat use, ranging behavior, and diet of two groups of Boutourlini’s blue monkeys (Cercopithecus mitis boutourlinii), a subspecies endemic to western Ethiopia, whose habitats had experienced different levels of disturbance at Jibat Forest. Forest Group occupied primarily continuous tree-dominated forest with little human disturbance whereas Fragment Group inhabited a heavily degraded 2- to 3-km² forest fragment nearly surrounded by farmland and connected tenuously to the continuous forest by a narrow corridor of riverine forest. Mean daily path lengths for both groups were nearly identical (Forest Group: 799 m; Fragment Group: 783 m) and exhibited little seasonal variability. The mean home range areas of Forest Group and Fragment Group were 72.0 and 61.2 ha, respectively. Forest Group (N?=?2232 feeding records) fed mostly on fruits (52.5 %), though they also ate animal prey (14.7 %), young leaves (11.1 %), shoots (8.7 %), and flowers (7.3 %). In contrast, fruits accounted for only 17.0 % of Fragment Group’s diet (N?=?2903 feeding records), with shoots (29.8 %), young leaves (17.1 %), animal prey (13.1 %), seeds (9.6 %), and flowers (6.8 %) also making substantial contributions to their diet. Only Fragment Group engaged in crop raiding, consuming seeds from barley and wheat extensively (33–41 % of diet) during 2 mo. Fragment Group (N?=?33) ate more plant species than Forest Group (N?=?24), though both groups exploited a small number of plant species relative to other subspecies of blue monkeys. Our study revealed that, like most other blue monkey subspecies, Boutourlini’s blue monkeys are quite flexible in the habitats they occupy as well as in their foraging habits. Despite this ecological flexibility, the long-term conservation of Boutourlini’s blue monkey is far from assured given its limited distribution, the rapidly growing human population, and the high rates of forest clearance in western Ethiopia.     

Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea

The amount and distribution of genetic variation was investigated in 48 sorghum landrace accessions, representing 13 regions of origin and three adaptation zones (lowland, intermediate and highland elevation) in Ethiopia and Eritrea. Assaying 11 enzymes systems, 23 putative loci were scored for a total of 27 alleles. Nineteen loci were monomorphic and fixed for the same allele, while the remaining 4 loci, each with 2 alleles, were polymorphic across the 48 accessions. The results show significant differences in allele frequencies among the accessions, regions of origin and the adaptation zones. However, all measures of genetic variation used show that the accessions maintained much lower levels of variation than the corresponding mean values for self-pollinating crop plants, confirming previous conclusions that sorghum is depauperated in allozymic variation. The total gene diversity was 0.25, which partitioned 59% within and 41% among accessions. The latter was largely due to variation among accessions within the adaptation zones (38%), while only 3% was due to variation among accessions between the adaptation zones. Similarly, most of the total gene diversity was found within the regions of origin (80%) and within the adaptation zones (97%). Both the dendrogram constructed from NEI's unbiased genetic distance and the plot of the first two principal components distinguished three groups of regions. The level of gene flow was low among accessions, regions of origin and among accessions within adaptation zones, but high among adaptation zones. The results are discussed with emphasis on genetic resources conservation and utilization.     

Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) analysis

Genetic diversity within the forest Coffea arabica L. gene pool in Ethiopia has not been extensively examined with molecular markers. In the present study, a total of 75 polymorphic RAPD bands generated by twelve random primers were used to assess genetic diversity among 144 genotypes representing 16 C. arabica populations. The number of polymorphic bands detected with each primer ranged from 2 to 9 with a mean of 6.25 bands per primer. Banding patterns ranged in percentage polymorphism from 37% to 73% with an overall mean of 56% for the populations analyzed. The amount of genetic variation among populations estimated by Shannon-Weaver diversity index was (H = 0.30). The within population and between populations differentiation values were 0.65 and 0.35, respectively. Genetic differentiations within and between zones of sample collection sites were 0.80 and 0.20, respectively. Within population average similarities estimated by simple matching coefficients ranged from 0.72 to 0.85, with an overall average of 0.78. In the cluster analysis that used individual samples as operational taxonomic units, most of the representatives of the same population failed to cluster before they joined members of other populations. Nevertheless, most of the populations were clustered on the basis of their geographic closeness and an east west differentiation was observed at approximately 75% similarity. The results obtained provide information on how to select sites for in situ conservation of C. arabica germplasm.     

The use of genetic markers to measure genomic response to selection in livestock

A method to measure genomic response to natural and artificial selection by means of genetic markers in livestock is proposed. Genomic response through several levels of selection was measured using sequential testing for distorted segregation of alleles among selected and nonselected sons, single-sperm typing, and a test with records for growth performance. Statistical power at a significance level of 0.05 was >0.5 for a marker linked to a QTL with recombination fractions 0, 0.10, and 0.20 for detecting genomic responses for gene effects of 0.6, 0.7, and 1.0 phenotypic standard deviations, respectively. Genomic response to artificial selection in six commercial bull sire families comprising 285 half-sib sons selected for growth performance was measured using 282 genetic markers evenly distributed over the cattle genome. A genome-wide test using selected sons was significant (P < 0.001), indicating that selection induces changes in the genetic makeup of commercial cattle populations. Markers located in chromosomes 6, 10, and 16 identified regions in those chromosomes that are changing due to artificial selection as revealed by the association of records of performance with alleles at specific markers. Either natural selection or genetic drift may cause the observed genomic response for markers in chromosomes 1, 7, and 17.     

Numerical simulation of the flow and concentration fields for oxygen delivery systems

The flow and concentration fields for various medical oxygen delivery devices are numerically investigated. Simulations are performed for a classical Venturi mask and two new OxyArm portable devices. The velocity and oxygen concentration fields are investigated for: (i) a constant (steady-state) inhalation and (ii) a complete respiratory cycle (unsteady). The numerical results are qualitatively compared with clinical trials. It is found that the optimal functioning of these medical devices implies a balance between oxygen delivery by advection and the mixing process that allows for reliable CO2 monitoring (capnographic capability). Also, at the typical scales associated with these devices the flow is found to be Reynolds number dependent.     

A flagellum-specific calcium sensor

The flagellar calcium-binding protein (FCaBP) of the flagellated protozoan Trypanosoma cruzi associates with the flagellar membrane via its N-terminal myristate and palmitate moieties in a calcium-modulated, conformation-dependent manner. This mechanism of localization is similar to that described for neuronal calcium sensors, which undergo calcium-dependent changes in conformation, which modulate the availability of the acyl groups for membrane interaction and partner association. To test whether FCaBP undergoes a calcium-dependent conformational change and to explore the role of such a change in flagellar targeting, we first introduced point mutations into each of the two EF-hand calcium-binding sites of FCaBP to define their affinities. Analysis of recombinant EF-3 mutant (E151Q), EF-4 mutant (E188Q), and double mutant proteins showed EF-3 to be the high affinity site (Kd approximately 9 microM) and EF-4 the low affinity site (Kd approximately 120 microM). These assignments also correlated with partial (E188Q), nearly complete (E151Q), and complete (E151Q,E188Q) disruption of calcium-induced conformational changes determined by NMR spectrometry. We next expressed the FCaBP E151Q mutant and the double mutant in T. cruzi epimastigotes. These transproteins localized to the flagellum, suggesting the existence of a calcium-dependent interaction of FCaBP that is independent of its intrinsic calcium binding capacity. Several proteins were identified by FCaBP affinity chromatography that interact with FCaBP in a calcium-dependent manner, but with differential dependence on calcium-binding by FCaBP. These findings may have broader implications for the calcium acyl switch mechanism of protein regulation.