Computational Analysis of Some Enzymes Involved in Synthesis of Secondary Metabolites in Camellia Sinensis

Tea is one of the most popular beverages worldwide, native to Southeast Asia but currently cultivated in over 35 countries. Studies on its chemical composition reveal that polyphenol metabolites account for 25% to 35% of the total dry weight. Tea has many health benefits owing to secondary metabolites whose level of expression in various tea clones determine tea flavor. The flavor (taste and aroma) and the color of processed tea are used to assess its quality and therefore a detailed analysis of key enzymes involved in the synthesis of secondary metabolites is necessary.  Enzyme PAL (phenylalanine ammonia-lyase) a key enzyme in the phenylpropanoid pathway, playing an important role in the plant development and defense. C4H (cinnamte-4-hydroxylse) an important enzyme in allocating significant amounts of carbon from phenylalanine into the biosynthesis of several metabolites, It maintains activities of the metabolic flux for the operation of the flavanoid pathway. 4CL (4-coumarate: COA ligase) the last enzyme in the general phenylpropanoid pathway that provides precursors for the biosynthesis of a large variety of plant natural products like COA thiol esters of 4-coumarate and other hydroxycinnamate. FLS (flavonol synthase) a key enzyme in flavonol synthesisthat determines the final content of flavonols which play an important role in defense related functions and as potent antioxidants. ANS (anthocyanidin synthase) an enzyme in the biosynthetic pathway to anthocyanin. This study employed a computational approach in the analysis of some of these enzymes to gain insight into the mechanism of synthesis of these bioactive secondary metabolites. Biological databases were used to retrieve amino acid sequences of these key enzymes. Consensus conserved regions in these sequences were identified from highly identical homologs which were useful in modeling the enzymes' three dimensional structures.  A total of 5 key enzymes were analyzed and pockets and cavities in their structures; hence the putative substrate binding sites determined, which gave insight into the enzymes-substrate as well as enzyme cofactor interactions. The preferred orientations of the interactions between substrates and/or co-factors with the enzymes were also simulated through molecular docking.  Analysis of these enzymes revealed unique enzyme structures and very specific substrate and co-factor preference. This analysis offers a platform for optimization of selective expression of these key enzymes through gene expression assays that can potentially alter the quality yield of tea clones. Keywords: camellia sinensis, Secondary metabolites, Conserved regions, Pockets and cavities, Molecular dockin

Computational Design of Novel Candidate Drug Molecules for Schistosomiasis

Schistosomiasis is a parasitic disease that leads to chronic ill-health. Infection is acquired from infested freshwater containing the larval forms (cercariae) of blood flukes, known as schistosomes. The three main species of the parasite that infect humans are Schistosoma haematobium, S.japonicum, and S.mansoni. Schistosomiasis affects at least 230 million people worldwide. The infection is prevalent in tropical and sub-tropical areas, in poor communities without potable water and adequate sanitation. The disease is considered as one of the Neglected Tropical Diseases and so far praziquantel is the only drug used for treatment. Should the parasites develop resistance to praziquantel, treatment would be problematic.  This study incorporated a computational approach to design novel compounds with unprecedented potential as candidate drug compounds for the disease. The Schistosoma mansoni fatty acid binding protein was selected as a suitable drug target for its crucial role in the dependence of the parasite on its host for fatty acids. Screening for potential lead compounds was done using molecular docking software.  Identified lead compounds were analyzed and optimized in silico for their ADMET properties then re-evaluated for suitability of their binding energies. Eight novel compounds with good predicted ADMET properties were designed and found to interact with the S.mansoni fatty acid binding protein with favorable binding energy, showing potential to inhibit this protein. This study opens up new possibilities in antischistosomal drug inquiry and potentiates efficacy studies of such compounds against schistosomiasis. Keywords: computational design, antischistosomal drug inquiry, binding energy, lead optimization, ADMET properties

HIV-1 subtype and viral tropism determination for evaluating antiretroviral therapy options: an analysis of archived Kenyan blood samples

<p>Abstract</p> <p>Background</p> <p>Infection with HIV-1 is characterized by genetic diversity such that specific viral subtypes are predominant in specific geographical areas. The genetic variation in HIV-1 <it>pol </it>and <it>env </it>genes is responsible for rapid development of resistance to current drugs. This variation has influenced disease progression among the infected and necessitated the search for alternative drugs with novel targets. Though successfully used in developed countries, these novel drugs are still limited in resource-poor countries. The aim of this study was to determine HIV-1 subtypes, recombination, dual infections and viral tropism of HIV-1 among Kenyan patients prior to widespread use of antiretroviral drugs.</p> <p>Methods</p> <p>Remnant blood samples from consenting sexually transmitted infection (STI) patients in Nairobi were collected between February and May 2001 and stored. Polymerase chain reaction and cloning of portions of HIV-1 <it>gag</it>, <it>pol </it>and <it>env </it>genes was carried out followed by automated DNA sequencing.</p> <p>Results</p> <p>Twenty HIV-1 positive samples (from 11 females and 9 males) were analyzed. The average age of males (32.5 years) and females (26.5 years) was significantly different (p value < 0.0001). Phylogenetic analysis revealed that 90% (18/20) were concordant HIV-1 subtypes: 12 were subtype A1; 2, A2; 3, D and 1, C. Two samples (10%) were discordant showing different subtypes in the three regions. Of 19 samples checked for co-receptor usage, 14 (73.7%) were chemokine co-receptor 5 (CCR5) variants while three (15.8%) were CXCR4 variants. Two had dual/mixed co-receptor use with X4 variants being minor population.</p> <p>Conclusion</p> <p>HIV-1 subtype A accounted for majority of the infections. Though perceived to be a high risk population, the prevalence of recombination in this sample was low with no dual infections detected. Genotypic co-receptor analysis showed that most patients harbored viruses that are predicted to use CCR5.</p

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Molecular detection of novel Anaplasma sp . and zoonotic hemopathogens in livestock and their hematophagous biting keds (genus Hippobosca) from Laisamis, northern Kenya.

Funder: Wellcome TrustBackground: Livestock are key sources of livelihood among pastoral communities. Livestock productivity is chiefly constrained by pests and diseases. Due to inadequate disease surveillance in northern Kenya, little is known about pathogens circulating within livestock and the role of livestock-associated biting keds (genus Hippobosca) in disease transmission. We aimed to identify the prevalence of selected hemopathogens in livestock and their associated blood-feeding keds. Methods: We randomly collected 389 blood samples from goats (245), sheep (108), and donkeys (36), as well as 235 keds from both goats and sheep (116), donkeys (11), and dogs (108) in Laisamis, Marsabit County, northern Kenya. We screened all samples for selected hemopathogens by high-resolution melting (HRM) analysis and sequencing of PCR products amplified using primers specific to the genera: Anaplasma, Trypanosoma, Clostridium, Ehrlichia, Brucella, Theileria, and Babesia. Results: In goats, we detected Anaplasma ovis (84.5%), a novel Anaplasma sp. (11.8%), Trypanosoma vivax (7.3%), Ehrlichia canis (66.1%), and Theileria ovis (0.8%). We also detected A. ovis (93.5%), E. canis (22.2%), and T. ovis (38.9%) in sheep. In donkeys, we detected ' Candidatus Anaplasma camelii' (11.1%), T. vivax (22.2%), E. canis (25%), and Theileria equi (13.9%). In addition, keds carried the following pathogens; goat/sheep keds - T. vivax (29.3%) , Trypanosoma evansi (0.86%), Trypanosoma godfreyi (0.86%), and E. canis (51.7%); donkey keds - T. vivax (18.2%) and E. canis (63.6%); and dog keds - T. vivax (15.7%), T. evansi (0.9%), Trypanosoma simiae (0.9%) , E. canis (76%), Clostridium perfringens (46.3%), Bartonella schoenbuchensis (76%), and Brucella abortus (5.6%). Conclusions: We found that livestock and their associated ectoparasitic biting keds carry a number of infectious hemopathogens, including the zoonotic B. abortus. Dog keds harbored the most pathogens, suggesting dogs, which closely interact with livestock and humans, as key reservoirs of diseases in Laisamis. These findings can guide policy makers in disease control

Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm

Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37&ndash;0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6&ndash;10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14&ndash;40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize

Comparative Assessment Of Total Phenolic Content In Selected Medicinal Plants

This study was to compare the total phenolic (TP) content in extracts from eleven plant materials collected at different geographical locations in Kenya,Nigeria, and USA. These plants have been selected because the majority of them are highly pigmented, from yellow to purple, and would therefore haveeconomic value in industries for producing antioxidants and surfactants. Two of them were collected from the industrial and domestic waste outlets. Eachanalysis was achieved using the Folin-Ciocalteau technique. The order of decreasing phenolic acid content as gallic acid concentration (mg/g dry weight)was Prunus africana (55.14) > Acacia tortilis (42.11) > Khaya grandifoliola (17.54) > Curcuma longa (17.23) > Vernonia amygdalina (14.9)> Russeliaequisetiformis (14.03) > Calendula officinalis (7.96) >Phragmites australis (control) (7.09) > Rauwolfia vomitoria (6.69) > Phragmites australis(industrial) (6.21) > Cnidoscolus aconitifolius (5.6). The TP contents of Spartina alterniflora species were below the detection limit