Genetic analysis of HIV-1 subtypes in Nairobi, Kenya

Background

Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution.

Objective

In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.

Methodology

69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database.

Results

Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.

Conclusion

Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.     

A GRK5 polymorphism that inhibits beta-adrenergic receptor signaling is protective in heart failure

Beta-adrenergic receptor (betaAR) blockade is a standard therapy for cardiac failure and ischemia. G protein-coupled receptor kinases (GRKs) desensitize betaARs, suggesting that genetic GRK variants might modify outcomes in these syndromes. Re-sequencing of GRK2 and GRK5 revealed a nonsynonymous polymorphism of GRK5, common in African Americans, in which leucine is substituted for glutamine at position 41. GRK5-Leu41 uncoupled isoproterenol-stimulated responses more effectively than did GRK5-Gln41 in transfected cells and transgenic mice, and, like pharmacological betaAR blockade, GRK5-Leu41 protected against experimental catecholamine-induced cardiomyopathy. Human association studies showed a pharmacogenomic interaction between GRK5-Leu41 and beta-blocker treatment, in which the presence of the GRK5-Leu41 polymorphism was associated with decreased mortality in African Americans with heart failure or cardiac ischemia. In 375 prospectively followed African-American subjects with heart failure, GRK5-Leu41 protected against death or cardiac transplantation. Enhanced betaAR desensitization of excessive catecholamine signaling by GRK5-Leu41 provides a 'genetic beta-blockade' that improves survival in African Americans with heart failure, suggesting a reason for conflicting results of beta-blocker clinical trials in this population.     

Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations

The feasibility of constructing an overlapping part-chromosome substitution library between the Landsberg erecta (Ler) and Columbia (Col ) ecotypes of Arabidopsis thaliana was investigated using computer simulations. Such a library can be used effectively in the fine mapping of quantitative trait loci (QTLs) in this species, with donor tracts of Col inserted into the recurrent background of Ler and vice versa. The study was based on the known RFLP profiles of Ler and Col ecotypes, and of some selected recombinant inbred lines (RILs) that have already been extracted from their cross by self pollination. It was shown that homozygous substitution lines can be produced for a large segment of the genome (>80%) by crossing just 11 RILs with their respective recurrent/recipient parents and selecting the desired recombinants from the F₂ or Bc₁ generation or their selfed progenies. In the case of four RILs, however, at least two rounds of backcrossing were deemed necessary to remove the unwanted donor tracts from the background genotype prior to selfing/selection. The simulations also provided valuable information on the scale of the breeding programme and show that a resource of up to 59 substitutions can be produced within a short period of 4-5 generations.Contributed equally;     

<Emphasis Type="Italic">Nocardioides dilutes</Emphasis> sp. nov. Isolated from Soil in Bigeum Island,Korea

A short coccoid-rod-shaped, nonmotile actinobacteria strain MSL-11^T was isolated from soil in Bigeum Island, Korea. A polyphasic study was undertaken to establish the taxonomic position of this strain. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain MSL-11^T forms an evolutionary lineage within the radiation of the genus Nocardioides. The cell wall peptidoglycan of strain MSL-11^T contained ll-diaminopimelic acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H₄). Strain MSL-11^T had a cellular fatty acid profile containing straight-chain, branched, unsaturated, and 10-methyl fatty acids, with iso-C_16:0 as a major fatty acid component detected. The DNA G + C content of the strain was 71.8 mol%. Comparative 16S rRNA gene sequencing revealed that the strains constituted a distinct subclade within the genus Nocardioides, displaying a 16S rRNA gene sequence similarity of about 95.68% with Nocardioides jensenii DSM 20641^T. On the basis of both phenotypic and phylogenetic evidence, the strain is separated from previously described Nocardioides species and should be assigned to represent a novel species of the genus Nocardioides, for which the name Nocardioides dilutes sp. nov. is proposed. The type strain is strain MSL-11^T (= KCTC 19288^T = DSM 19318^T).     

Role of Tuberin in Neuronal Degeneration

One of the tuberous sclerosis complex (TSC) gene products, tuberin is assumed to be the functional component, being involved in a wide variety of cellular processes. Here, we report for the first time that tuberin dysfunction may represent a mechanism for neuronal damage in Alzheimer’s disease (AD), Parkinson’s disease with dementia (PD/DLB), and a mouse model of PD. Tuberin was hyperphosphorylated at Thr1462 in post-mortem frontal cortex tissue of both AD and PD/DLB patients and in mice treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride (MPTP). Both PTEN and Akt phosphoactivation corresponded to the hyperphosphorylation patterns of tuberin suggesting that the PTEN–Akt pathway might be the mechanism of tuberin phosphorylation. Our data provide new information regarding the possible role of tuberin dysfunction in major neurodegenerative disorders, such as AD and PD, whereby inhibition of tuberin function may trigger an onset of neuronal cell death.     

Evaluation of Iron in Serum and Urine and their Relation with Thyroid Function in Female Goitrous Patients

In many developing countries, women are at high risk of goiter and iron deficiency anemia (IDA). Iron deficiency adversely affects thyroid metabolism and may decrease the efficiency of thyroid hormones in areas of endemic goiter. The aim of the present study was to compare the level of iron (Fe) in biological samples (serum and urine) and serum thyroid hormones, thyroid stimulating hormone (TSH), free triiodothyronine (FT3), and free thyroxin (FT4) of goitrous female patients (GFPs; n = 69) with those of nongoitrous women as control subjects (n = 117), age range 21–45 years. The biological samples were analyzed for Fe concentration using flame atomic absorption spectrophotometer, prior to microwave-assisted wet acid digestion. The validity and accuracy of the method was checked by the certified sample and with those obtained by conventional wet acid digestion method on the same CRM and real samples. The overall recoveries of Fe in serum and urine were found in the range of 97.2–98.6% of certified values. The results of this study showed that the mean values of Fe in serum and urine samples of GFPs were significantly reduced as compared to control subjects (p = 0.002 and p = 0.015, respectively). The mean values of FT3 and FT4 were found to be lower in GFPs than in the age-matched healthy control women; in contrast, high mean values of TSH were detected in GFPs (p = 0.003). There was a positive correlation between serum Fe concentration and TSH (r = 0.85, p = 0.01), FT3 (r = 0.95, p = 0.003), and FT4 levels (r = 0.98, p = 0.007) in GFPs. It was observed that iron deficiency is prevalent in GFPs, so the need of Fe supplementation will be required to improve the efficacy of thyroid metabolism in goitrous women.     

Synthetic methods for the preparation of ARQ 501 (beta-Lapachone) human blood metabolites

ARQ 501 (3,4-dihydro-2,2-dimethyl-2H-naphthol[1,2-b] pyran-5,6-dione), a synthetic version of beta-Lapachone, is a promising anti-cancer agent currently in multiple Phase II clinical trials. Promising anti-cancer activity was observed in Phase I and Phase II trials. Metabolism by red blood cells of drugs is an understudied area of research and the metabolites arising from oxidative ring opening (M2 and M3), decarbonylation/ring contraction (M5), and decarbonylation/oxidation (M4 and M6) of ARQ 501 offer a unique opportunity to provide insight into these metabolic processes. Since these metabolites were not detected in in vitro incubations of ARQ 501 with liver microsomes and were structurally diverse, confirmation by chemical synthesis was considered essential. In this report, we disclose the synthetic routes employed and the characterization of the reference standards for these blood metabolites as well as additional postulated structures, which were not confirmed as metabolites.     

Rapid mechanisms of glucocorticoid signaling in the Leydig cell

Stress-mediated elevations in circulating glucocorticoid levels lead to corresponding rapid declines in testosterone production by Leydig cells in the testis. In previous studies we have established that glucocorticoids act on Leydig cells directly, through the classic glucocorticoid receptor (GR), and that access to the GR is controlled prior to the GR by a metabolizing pathway mediated by the type 1 isoform of 11beta-hydroxysteroid dehydrogenase (11betaHSD1). This enzyme is bidirectional (with both oxidase and reductase activities) and in the rat testis is exclusively localized in Leydig cells where it is abundantly expressed and may catalyze the oxidative inactivation of glucocorticoids. The predominant reductase direction of 11betaHSD1 activity in liver cells is determined by an enzyme, hexose-6-phosphate dehydrogenase (H6PDH), on the luminal side of the smooth endoplasmic reticulum (SER). Generation of the pyridine nucleotide cofactor NADPH by H6PDH stimulates the reductase direction of 11betaHSD1 resulting in increased levels of active glucocorticoids in liver cells. Unlike liver cells, steroidogenic enzymes including 17beta-hydroxysteroid dehydrogenase 3 (17betaHSD3) forms the coupling with 11betaHSD1. Thus the physiological concentrations of androstenedione serve as a substrate for 17betaHSD3 utilizing NADPH to generate NADP+, which drives 11betaHSD1 in Leydig cells primarily as an oxidase; thus eliminating the adverse effects of glucocorticoids on testosterone production. At the same time 11betaHSD1 generates NADPH which promotes testosterone biosynthesis by stimulating 17betaHSD3 in a cooperative cycle. This enzymatic coupling constitutes a rapid mechanism for modulating glucocorticoid control of testosterone biosynthesis. Under stress conditions, glucocorticoids also have rapid actions to suppress cAMP formation thus to lower testosterone production.     

In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water

Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence/absence calls, probes were designed for multiple virulence and marker genes (VMGs) of each pathogen, and each VMG was targeted by an average of 17 probes. Hybridization of the biochip with amplicon mixtures demonstrated that 95% of the initially designed probes behaved as predicted in terms of positive/negative signals. The probes were further validated using DNA obtained from three different types of water samples and spiked with pathogen genomic DNA at decreasing relative abundance. Excellent specificity for making presence/absence calls was observed by using a cutoff of 0.5 for the positive fraction (i.e., the fraction of probes yielding a positive signal for a given VMG). A split multiplex PCR design for simultaneous amplification of the VMGs resulted in a detection limit of between 0.1 and 0.01% relative abundance, depending on the type of pathogen and the VMG. Thermodynamic analysis of the hybridization patterns obtained with DNA from the different water samples demonstrated that probes with a hybridization Gibbs free energy of approximately -19.3 kcal/mol provided the best trade-off between sensitivity and specificity. The developed biochip may be used to detect the described bacterial pathogens in water samples when parallel and specific detection is required.     

Inhibitory and blocking monoclonal antibody epitopes on merozoite surface protein 1 of the malaria parasite Plasmodium falciparum

Merozoite surface protein 1 (MSP-1) is a precursor to major antigens on the surface of Plasmodium spp. merozoites, which are involved in erythrocyte binding and invasion. MSP-1 is initially processed into smaller fragments; and at the time of erythrocyte invasion one of these of 42 kDa (MSP-1(42)) is subjected to a second processing, producing 33 kDa and 19 kDa fragments (MSP-1(33) and MSP-1(19)). Certain MSP-1-specific monoclonal antibodies (mAbs) react with conformational epitopes contained within the two epidermal growth factor domains that comprise MSP-1(19), and are classified as either inhibitory (inhibit processing of MSP-1(42) and erythrocyte invasion), blocking (block the binding and function of the inhibitory mAb), or neutral (neither inhibitory nor blocking). We have mapped the epitopes for inhibitory mAbs 12.8 and 12.10, and blocking mAbs such as 1E1 and 7.5 by using site-directed mutagenesis to change specific amino acid residues in MSP-1(19) and abolish antibody binding, and by using PEPSCAN to measure the reaction of the antibodies with every octapeptide within MSP-1(42). Twenty-six individual amino acid residue changes were made and the effect of each on the binding of mAbs was assessed by Western blotting and BIAcore analysis. Individual changes had either no effect, or reduced, or completely abolished the binding of individual mAbs. No two antibodies had an identical pattern of reactivity with the modified proteins. Using PEPSCAN each mAb reacted with a number of octapeptides, most of which were derived from within the first epidermal growth factor domain, although 1E1 also reacted with peptides spanning the processing site. When the single amino acid changes and the reactive peptides were mapped onto the three-dimensional structure of MSP-1(19), it was apparent that the epitopes for the mAbs could be defined more fully by using a combination of both mutagenesis and PEPSCAN than by either method alone, and differences in the fine specificity of binding for all the different antibodies could be distinguished. The incorporation of several specific amino acid changes enabled the design of proteins that bound inhibitory but not blocking antibodies. These may be suitable for the development of MSP-1-based vaccines against malaria.