Prevalence of hepatitis B, hepatitis C and human immunodeficiency viruses, and evaluation of risk factors for transmission: Report of a population screening in Nigeria

Background. Hepatitis B virus (HBV), hepatitis C virus (HCV) and HIV are common blood-borne infections unevenly distributed across regions in Nigeria. Few population-based prevalence studies have been done in Nigeria.Objective. To determine the prevalence of HBV, HCV and HIV and risk factors for infection with these viruses in a Nigerian population.Methods. Hepatitis B surface antigen, anti-HCV and HIV were assayed in 1 498 healthy adult participants. A structured questionnaire was used to assess risk factors for viral acquisition. Bivariate analysis was used to compare differences in sociodemographic characteristics. Significant risk factors were identified by stepwise logistic regression. A p-value <0.05 was considered significant.Results. The prevalences of HBV, HCV and HIV were 8.8%, 10.0% and 12.9%, respectively, with urban/rural disparity. HBV/HCV positivity was higher among males than females. The reverse was true for HIV. Age was significantly associated with being HBV-, HCV- or HIV positive. Communal use of a toothbrush was significantly associated with HBV positivity in the final model (odds ratio 2.46, 95% confidence interval 1.45 - 4.18).Conclusions. The prevalence of HBV, HCV and HIV infection is high in Nigeria, with urban/rural disparity. HCV may be more of a public health concern than HBV in some communities. Population-based studies are required to provide vital data to inform optimal national control strategies

Callus induction and plant regeneration via leaf segments of three accessions of African rice (Oryza glaberrimaStued.)

A study conducted with the aim of developing a protocol for callus induction and plantlet regeneration in vitro from leaf segments of three accessions of African rice (O. glaberrimaSteud.) indigenous to Ghana. Leaf segments of the accessions namely, Guame, N/4 and SARI 1 were assessed for callus induction and plantlet regeneration ability on different concentrations of plant growth regulators, incorporated into Murashige and Skoog, (1962) (MS) basal medium. Frequency of callus induction which was achieved on MS medium supplemented with (0-10) mg/l 2,4-D differed significantly (p≤0.05) among the accessions, as well as among the levels of 2,4-dichlorophenoxyacetic acid (2,4-D) tested. Highest callus induction frequency was exhibited at a concentration of 6 mg/l 2,4-D for all three accessions.Sub-culturing of callus on regeneration medium, which consisted of MS supplemented with (1:0-5) mg/l NAA:BAP resulted in no plantlet regeneration in all tested accessions. Instead, prolific root formation was observed

Microfluidic Microcirculation Mimetic as a Tool for the Study of Rheological Characteristics of Red Blood Cells in Patients with Sickle Cell Anemia

Sickle cell disorder (SCD) is a multisystem disease with heterogeneous phenotypes. Al- though all patients have the mutated hemoglobin (Hb) in the SS phenotype, the severity and frequency of complications are variable. When exposed to low oxygen tension, the Hb molecule becomes dense and forms tactoids, which lead to the peculiar sickled shapes of the affected red blood cells, giving the disorder its name. This sickle cell morphology is responsible for the profound and widespread pathologies associated with this disorder, such as vaso-occlusive crisis (VOC). How much of the clinical manifestation is due to sickled erythrocytes and what is due to the relative contributions of other elements in the blood, especially in the microcapillary circulation, is usually not visualized and quantified for each patient during clinical management. Here, we used a microfluidic microcirculation mimetic (MMM), which has 187 capillary-like constrictions, to impose deformations on erythrocytes of 25 SCD patients, visualizing and characterizing the morpho-rheological properties of the cells in normoxic, hypoxic (using sodium meta-bisulfite) and treatment conditions (using hydroxyurea). The MMM enabled a patient-specific quantification of shape descriptors (circularity and roundness) and transit time through the capillary constrictions, which are readouts for morpho-rheological proper- ties implicated in VOC. Transit times varied significantly (p < 0.001) between patients. Our results demonstrate the feasibility of microfluidics-based monitoring of individual patients for personalized care in the context of SCD complications such as VOC, even in resource-constrained setting

Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n=20, 26%), followed by the Ghana genotype (n=16, 21%). A sub-clade of the Cameroon genotype, which emerged ~22 years ago was likely to be involved in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be MDR than other genotypes after controlling for treatment history. We identifed a clade of four related Beijing isolates that included one MDR-TB isolate. It is a major concern to fnd the Cameroon and Ghana genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing genotype in Bamako remains worrying, given its high transmissibility and virulence

Prevalence of hepatitis B, hepatitis C and human immunodeficiency viruses, and evaluation of risk factors for transmission: Report of a population screening in Nigeria

Background. Hepatitis B virus (HBV), hepatitis C virus (HCV) and HIV are common blood-borne infections unevenly distributed across regions in Nigeria. Few population-based prevalence studies have been done in Nigeria.Objective. To determine the prevalence of HBV, HCV and HIV and risk factors for infection with these viruses in a Nigerian population.Methods. Hepatitis B surface antigen, anti-HCV and HIV were assayed in 1 498 healthy adult participants. A structured questionnaire was used to assess risk factors for viral acquisition. Bivariate analysis was used to compare differences in sociodemographic characteristics. Significant risk factors were identified by stepwise logistic regression. A p-value &lt;0.05 was considered significant.Results. The prevalences of HBV, HCV and HIV were 8.8%, 10.0% and 12.9%, respectively, with urban/rural disparity. HBV/HCV positivity was higher among males than females. The reverse was true for HIV. Age was significantly associated with being HBV-, HCV- or HIV-positive. Communal use of a toothbrush was significantly associated with HBV positivity in the final model (odds ratio 2.46, 95% confidence interval 1.45 - 4.18).Conclusions. The prevalence of HBV, HCV and HIV infection is high in Nigeria, with urban/rural disparity. HCV may be more of a public health concern than HBV in some communities. Population-based studies are required to provide vital data to inform optimal national control strategies

Urine Proteome Analysis May Allow Noninvasive Differential Diagnosis of Diabetic Nephropathy

AbstractObjective: Chronic renal insufficiency and/or proteinuria in type 2 diabetes may stem from chronic renal diseases (CKD) other than classic diabetic nephropathy (DN) in over one third of cases. We interrogated urine proteomic profiles generated by SELDI-TOF/MS with the aim to isolate a set of biomarkers able to reliably identify biopsy-proven DN and to establish a stringent correlation with the different patterns of renal injury. Research design and methods: Ten mug urine proteins from 190 subjects [20 healthy subjects (HS), 20 normoalbuminuric (NAD) and 18 microalbuminuric (MICRO) diabetic patients, and 132 patients with biopsy-proven nephropathy (65 DN, 10 diabetics with non-diabetic CKD (nd-CKD) and 57 non-diabetic patients with CKD)] were run by CM10 ProteinChip array and analysed by supervised learning methods (CART analysis). Results: The classification model correctly identified 75% NAD, 87.5% MICRO and 87.5% DN when applied to a blinded testing set. Most importantly, it was able to reliably differentiate DN from nd-CKD in both diabetic and non-diabetic patients. Among the best predictors of the classification model, we identified and validated 2 proteins, ubiquitin and ss2-microglobulin. Conclusions: Our data suggest the presence of a specific urine proteomic signature able to reliably identify type 2 diabetic patients with diabetic glomerulosclerosis

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and ~40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for \u3ci\u3eCamelus dromedarius\u3c/i\u3e

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF\u3e300 bp and ~40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism

Evolution of virulent genotypes and an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

Background: Bamako, Mali, has a well-structured hierarchyfor tuberculosis (TB) case management. However, in recent yearsBamako has been faced with an emerging threat from multidrugresistant TB (MDR-TB). Here we present insights into the genomicepidemiology of TB and the evolutionary mechanisms driving theemergence of MDR-TB in Bamako.Methods & Materials:Isolates recovered from tuberculosispatients from local reference centers and the University Teach-ing Hospital at Point G, in Bamako, Mali between 2006 and 2012(n = 208), were tested for antimicrobial susceptibility at the MRCUnit The Gambia. A subset of 76 isolates were analysed using wholegenome sequencing. A time dated phylogenetic tree was recon-structed using BEAST. Lineage and resistance conferring mutationswere inferred using PhyResSe.Results:Patients included 21 females and 55 males agedbetween 3 to 78 years, among whom 12(16%) were infectedby MDR-TB. Most patients 61(80%) were new cases and among15 retreatment cases 9(60%) were MDR-TB. The phylogeny wasreconstructed from 8508 variant core genome sites. The dom-inant lineage was the Euro-American super lineage, lineage 4.Within lineage 4, the Cameroon genotype was the most preva-lent genotype (n = 20, 26%) followed by the Ghana genotype (n = 16,21%). Cameroon genotype isolates diverged from a common recentancestor∼161 years ago to form three clusters, one of whichemerged∼22 years ago and is likely to be involved in on-goingtransmission. Seven Ghana genotype isolates were MDR-TB repre-senting over half all MDR-TB in this dataset (7/12). Ghana genotypeisolates were more likely to cause MDR-TB than other genotypesafter controlling for treatment status (OR = 5.6, p-value = 0.043).The MDR-TB Ghana genotype isolates formed a clade that divergedapproximately 30 years ago, in which thekatGSer315Thr mutationwas conserved. Other Euro-American genotypes included the sixLAM, two H37Rv-like and one Uganda. Four patients were infectedwith closely related Beijing strains and five patients were infectedwith non-MDRMycobacterium africanum2