Detecting and Characterizing Genomic Signatures of Positive Selection in Global Populations

Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or multiple mutation events remains unanswered except for the fact that there exist a handful of genes such as those that confer lactase persistence, affect skin pigmentation, or cause sickle cell anemia. We have developed a long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended haplotype homozygosity (XP-EHH), for locating signals across the entire allele frequency spectrum. Our method also locates the founder haplotypes that carry the advantageous variants and infers their corresponding population frequencies. This presents an opportunity to systematically interrogate the whole human genome whether a selection signal shared across different populations is the consequence of a single mutation process followed subsequently by gene flow between populations or of convergent evolution due to the occurrence of multiple independent mutation events either at the same variant or within the same gene. The application of our method to data from 14 populations across the world revealed that positive-selection events tend to cluster in populations of the same ancestry. Comparing the founder haplotypes for events that are present across different populations revealed that convergent evolution is a rare occurrence and that the majority of shared signals stem from the same evolutionary event.     

Cross-correlation analysis of invasive mango mealybug and its associated natural enemies in relation to meteorological factors: implications for biological control

Damage caused by invasive downey snow line mealybug, Rastrococcus iceryoides Green (Hemiptera: Pseudococcidae) has been reported to vary between 30% to complete crop loss where no control measure is applied. The current studies seek to determine factors influencing R. iceryoides population outbreaks, parasitoid – host and predator–prey relationships as well as predict optimal management strategies through weather modelling over a period of 28 months from 2008 to 2010 in Tanzania. The highest incidence of R. iceryoides was recorded during the dry season coinciding with the major mango fruiting season. The relationship between R. iceryoides and the parasitoid was positive but not significant, which implies the influence on outbreaks was negligible probably due to low percent parasitism (<12%). However, the predator abundance was directly and significantly related to that of R. iceryoides. Average temperature, average relative humidity, rainfall, and R. iceryoides abundance were autocorrelated to each other. Cross-correlation coef?cients vary significantly from ?0.286 to 0.589 for the pair-variable between R. iceryoides, temperature, relative humidity, rainfall, parasitism and predators. Our findings showed that temperature was the key climatic variable that significantly influenced R. iceryoides outbreaks while rainfall was significantly negatively associated with the pest. Time series analyses show R. iceryoides population increased 4 months after an increase in average temperature in all the sites, 11 months after rainfall and 11 months after relative humidity in Kibaha and Dar es Salaam, respectively. Our findings revealed that R. iceryoides is an excellent target for classical biological control. Thus, the importation of promising co-evolved parasitoid specific to R. iceryoides from the aboriginal home is crucial in formulating an efficient and sustainable management approaches against the invasive mealybug pest in mango agro-ecosystems.     

Y chromosome lineage- and village-specific genes on chromosomes 1p22 and 6q27 control visceral leishmaniasis in Sudan

Familial clustering and ethnic differences suggest that visceral leishmaniasis caused by Leishmania donovani is under genetic control. A recent genome scan provided evidence for a major susceptibility gene on Chromosome 22q12 in the Aringa ethnic group in Sudan. We now report a genome-wide scan using 69 families with 173 affected relatives from two villages occupied by the related Masalit ethnic group. A primary ten-centimorgan scan followed by refined mapping provided evidence for major loci at 1p22 (LOD score 5.65; nominal p = 1.72 × 10⁻⁷; empirical p < 1 × 10⁻⁵; λ_S = 5.1) and 6q27 (LOD score 3.74; nominal p = 1.68 × 10⁻⁵; empirical p < 1 × 10⁻⁴; λ_S = 2.3) that were Y chromosome–lineage and village-specific. Neither village supported a visceral leishmaniasis susceptibility gene on 22q12. The results suggest strong lineage-specific genes due to founder effect and consanguinity in these recently immigrant populations. These chance events in ethnically uniform African populations provide a powerful resource in the search for genes and mechanisms that regulate this complex disease.     

Distribution,degree of damage and risk of spread of Trioza erytreae (Hemiptera: Triozidae) in Kenya

The African citrus triozid (ACT), Trioza erytreae Del Guercio, is a destructive pest particularly on citrus, and vectors, “Candidatus” Liberibacter africanus (CLaf), which is the causal agent of the African citrus greening disease. Our study seeks to establish the distribution and host‐plant relationship of ACT across citrus production areas in Kenya. We also modelled the risk of spread using the maximum entropy modelling algorithm with known occurrence data. Our results infer that ACT is widely distributed and causes severe damage to four alternative host plants belonging to the family Rutaceae. The adults, immature stages (eggs and nymphs), galls and the percentage of infested leaves were significantly higher in shaded than unshaded trees. However, adult ACTs preferred Kenyan highlands to Victoria Lake and coastal regions. The average area under the curve of the model predictions was 0.97, indicating an optimal model performance. The environmental variables that most influenced the prediction were the precipitation of wettest quarter, precipitation of wettest month, mean diurnal range, temperature seasonality and mean temperature of the coldest quarter. The current prediction of ACT exceeded its existing range, especially in the Western, Nyanza, Central, Rift valley and Eastern regions of Kenya. The model predicted a contraction of suitable habitats for a potential spread in 2040 with an inland shift to higher altitudes in the cooler regions. The potential for further expansion to climatically suitable areas was more pronounced for the 2080 forecast. These findings provide relevant information to improve monitoring/surveillance and designing IPM strategies to limit its spread and damage.     

The potential of novel African isolates of Phthorimaea operculella granulovirus for the control of Tuta absoluta

Phthorimaea operculella granulovirus (PhopGV) is infectious for larvae of different Gelechiidae insect species, including Tuta absoluta and Phthorimaea operculella. As these are major economic pests in North and sub‐Saharan Africa as well as in the Mediterranean area, the development of locally suitable biocontrol agents is essential. We have studied five isolates of PhopGV from Tunisia (Tns16, Tu1.11 and Tu2.11), Kenya (Ken13) and Yemen (Ym14) for their biological activity and the sequence polymorphism of their granulin and ecdysteroid UDP‐glucosyltransferase (egt) genes and allocated the isolates to two different egt types. Infection experiments with neonate larvae of T. absoluta and P. operculella demonstrated their pathogenicity to both host species. The isolate PhopGV Tu1.11 was the most virulent one for T. absoluta but had a relatively low infectivity to two P. operculella populations originating from Italy and Tunisia.     

New fatty acid oxidation inhibitors with increased potency lacking adverse metabolic and electrophysiological properties

New inhibitors of palmitoylCoA oxidation were synthesized based on a structurally novel lead, CVT-3501 (1). Investigation of structure-activity relationships was conducted with respect to potency of inhibition of cardiac mitochondrial palmitoylCoA oxidation and metabolic stability. Potent and metabolically stable analogues 33, 42, and 43 were evaluated in vitro for cytochrome P450 inhibition and potentially adverse electrophysiological effects. Compound 33 was also found to have favorable pharmacokinetic properties in rat.     

CVT-4325: a potent fatty acid oxidation inhibitor with favorable oral bioavailability

New inhibitors of palmitoyl-CoA oxidation are based on the introduction of nitrogen heterocycles in the ‘Western Portion’ of the molecule. SAR studies led to the discovery of CVT-4325 (shown), a potent FOXi (IC₅₀ = 380 nM rat mitochondria) with favorable PK properties (F = 93%, t_1/2 = 13.6 h, dog).     

N6-Cycloalkyl-2-substituted adenosine derivatives as selective, high affinity adenosine A1 receptor agonists

A series of new selective, high affinity A(1)-AdoR agonists is reported. Compound 23 that incorporated a carboxylic acid functionality in the 4-position of the pyrazole ring displayed K(iL) value of 1 nM for the A(1)-AdoR and >5000-fold selectivity over the A(3) and A(2A)-AdoRs. In addition, compound 19 that incorporated a carboxamide functionality in the 4-position of the pyrazole ring displayed subnanomolar affinity for the A(1)-AdoR (K(iL)=0.6 nM) and >600-fold selectivity over the A(3) and A(2A)-AdoRs.     

Seed treatment technology: An attractive delivery system for controlling root parasitic weed Striga with mycoherbicide

Coating sorghum seeds with Fusarium oxysporum (Foxy 2) for control of the root parasitic weed Striga, appears to be an attractive option for minimizing the inoculum amount, establishing the biocontrol agent in the potential infection zone of the host plants, and offering a simple, easy and economical delivery system. Our investigations resulted in the selection of appropriate seed coating materials and a suitable type and form of fungal inoculum. The coating materials tested were arabic gum (AG10%, 20%, 40%), carboxymethylcellulose (CMC1%, 2%) and pectin (LS 440, LM-5 CS) 1%, while the fungal inoculum included microconidia and fresh and dried chlamydospores produced using different substrates. Foxy 2 survived the seed treatment processing and showed excellent viability on seeds for at least 8 months of storage after coating. In general, the performance of 40% arabic gum in combination with dried chlamydospores was the best among the other types of inoculum and coating material tested. Regardless of the type and form of inoculum and coating materials tested, Foxy 2 was able to colonize all roots, even root tips and hairs of the host (sorghum), thereby meeting important criteria of a promising candidate for controlling Striga when applied as a seed treatment. The efficacy of treated sorghum seed with Foxy 2 using different coating materials in reducing S. hermonthica infestation was evaluated in pot and root chamber trials. Foxy 2 markedly reduced Striga emergence and dry weight and increased the percentage of the diseased emerged Striga shoots. However, the efficacy of seed coating varied according to the type and form of fungal inoculum as well as coating material. Coating sorghum seed with dried chlamydospore inoculum homogenized into 20% arabic gum (as adhesive) showed the highest efficacy of 81 and 77% (i.e., percent reduction in healthy emerged Striga shoots compared to the control treatment) against Striga using either sterilized or non-sterilized soil, respectively. In root chamber bioassays, the application of Foxy 2 in combination with AG40% significantly caused disease in 77% of the germinated Striga seeds and in all tubercles after 25 days of sowing. These findings provide an optimized coating protocol as an attractive delivery system for bioherbicides for root parasitic weeds.     

Characterization and risk assessment of the invasive papaya mealybug,Paracoccus marginatus,in Kenya under changing climate

The present study was conducted to characterize the newly invasive papaya mealybug Paracoccus marginatus Williams and Granara de Willink in Kenya using molecular techniques and to establish the potential risk of spread of the pest. Although abundant literature of P. marginatus outbreaks exists in other parts of the world, studies from Africa are rare. Our results revealed significant similarity between Kenyan samples with GenBank accession number KP692333.1 of P. marginatus. Phylogenetic analyses generated a tree that was paraphyletic with two clusters showing low genetic distance values for the P. marginatus sequences, which diverged from that of Planococcus citri. Our models displayed an optimal performance with mean area under the curve value of 0.82 and 0.98 for Genetic Algorithm for Rule-Set Production (GARP) and maximum entropy modelling (MaxEnt), respectively. Isothermality was the most influential variable in determining the potential distribution of P. marginatus with a 69% contribution to the models. Other variables included temperature mean diurnal range temperature seasonality, temperature annual range and annual precipitation in decreasing order of contribution. Current prediction by both models exceeded the existing range of P. marginatus, exacerbating the potential threat of the pest. GARP was more conservative in predicting suitable areas for P. marginatus, while MaxEnt showed further expansion by the year 2050. Our findings provide important information to guide biosecurity agencies in decision-making to prevent the spread and enhance control efforts of P. marginatus.