175 research outputs found
Nevirapine-Induced Heratotoxicity: Incidence, Risk Factors and Associated Mortality in a Primary Care ART Programme in South Africa
CROI 200
Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering
This article utilizes a recursive segmentation and cluster procedure presented as a genome-mining tool, GEMINI, to decipher genomic islands and understand their contributions to the evolution of virulence and antibiotic resistance in Pseudomonas aeruginosa
Lead exposure in adult males in urban Transvaal Province, South Africa during the apartheid era
Human exposure to lead is a substantial public health hazard worldwide and is particularly problematic in the Republic of South Africa given the country’s late cessation of leaded petrol. Lead exposure is associated with a number of serious health issues and diseases including developmental and cognitive deficiency, hypertension and heart disease. Understanding the distribution of lifetime lead burden within a given population is critical for reducing exposure rates. Femoral bone from 101 deceased adult males living in urban Transvaal Province (now Gauteng Province), South Africa between 1960 and 1998 were analyzed for lead concentration by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Of the 72 black and 29 white individuals sampled, chronic lead exposure was apparent in nearly all individuals. White males showed significantly higher median bone lead concentration (ME = 10.04 µg·g−1), than black males (ME = 3.80 µg·g−1) despite higher socioeconomic status. Bone lead concentration covaries significantly, though weakly, with individual age. There was no significant temporal trend in bone lead concentration. These results indicate that long-term low to moderate lead exposure is the historical norm among South African males. Unexpectedly, this research indicates that white males in the sample population were more highly exposed to lead
Substituted Lactam and Cyclic Azahemiacetals Modulate Pseudomonas aeruginosa Quorum Sensing
Quorum sensing (QS) is a population-dependent signaling process bacteria use to control multiple processes including virulence that is critical for establishing infection. The most common QS signaling molecule used by Gram-negative bacteria are acylhomoserine lactones. The development of non-native acylhomoserine lactone (AHL) ligands has emerged as a promising new strategy to inhibit QS in Gram-negative bacteria. In this work, we have synthesized a set of optically pure γ-lactams and their reduced cyclic azahemiacetal analogues, bearing the additional alkylthiomethyl substituent, and evaluated their effect on the AHL-dependent Pseudomonas aeruginosa las and rhl QS pathways. The concentration of these ligands and the simple structural modification such as the length of the alkylthio substituent has notable effect on activity. The γ-lactam derivatives with nonylthio or dodecylthio chains acted as inhibitors of las signaling with moderate potency. The cyclic azahemiacetal with shorter propylthio or hexylthio substituent was found to strongly inhibit both las and rhl signaling at higher concentrations while the propylthio analogue strongly stimulated the las QS system at lower concentrations
Influence of irrigated agriculture on soil microbial diversity
Organic carbon (C), bacterial biomass and structural community diversity were measured in Southern Idaho soils with long term cropping histories. The soils tested were native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation – chisel – tilled crops (ICT) and irrigated pasture systems (IP). Organic C concentration in soils decreased in the order NSB 0–5 cm > IP 0–30 cm = ICT 0–15 cm > IMP 0–30 cm > NSB 5–15 cm = NSB 15–30 cm. Active bacterial, fungal and microbial biomass correlated with soil C as measured by the Walkely Black method in positive curvilinear relationships (r2 = 0.93, 0.80 and 0.76, respectively). Amplicon length heterogeneity (LH-PCR) DNA profiling was used to access the eubacterial diversity in all soils and at all depths. The Shannon–Weaver diversity index was used to measure the differences using the combined data from three hypervariable domains of the eubacterial 16S rRNA genes. Diversity was greatest in NSB 15–30 cm soil and lowest in the IMP soil. With the exception of IMP with the lowest diversity index, the samples highest in C (NSB 0–5 cm, IP 0–30 cm, ICT 0–15 cm) reflected lower diversity indices. However, these indices were not significantly different from each other. ICT and IP increase soil C and to some extent increase diversity relative to IMP. Since soil bacteria respond quickly to environmental changes, monitoring microbial communities may be one way to assess the impact of agricultural practices such as irrigation and tillage regime
High prevalence of hookah smoking among secondary school students in a disadvantaged community in Johannesburg
Smoking of hookahs (also known as water-pipes) represents an emerging trend in tobacco use. Hookah smokers are at risk for the same diseases caused by cigarette smoking – cancer, respiratory and heart diseases, and pregnancy-related complications. Globally, the highest rates occur in the North African and East Mediterranean regions and among young people in the USA and European countries. There has been little research on hookah smoking in southern Africa
An ecoinformatics tool for microbial community studies: Supervised classification of amplicon length heterogeneity (ALH) profiles of 16S rRNA
Support vector machines (SVM) and K-nearest neighbors (KNN) are two computational machine learning tools that
perform supervised classification. This paper presents a novel application of such supervised analytical tools for microbial
community profiling and to distinguish patterning among ecosystems. Amplicon length heterogeneity (ALH) profiles from
several hypervariable regions of 16S rRNA gene of eubacterial communities from Idaho agricultural soil samples and from
Chesapeake Bay marsh sediments were separately analyzed. The profiles from all available hypervariable regions were
concatenated to obtain a combined profile, which was then provided to the SVM and KNN classifiers. Each profile was
labeled with information about the location or time of its sampling. We hypothesized that after a learning phase using
feature vectors from labeled ALH profiles, both these classifiers would have the capacity to predict the labels of previously
unseen samples. The resulting classifiers were able to predict the labels of the Idaho soil samples with high accuracy. The
classifiers were less accurate for the classification of the Chesapeake Bay sediments suggesting greater similarity within the
Bay's microbial community patterns in the sampled sites. The profiles obtained from the VI +V2 region were more
informative than that obtained from any other single region. However, combining them with profiles from the V1 region
(with or without the profiles from the V3 region) resulted in the most accurate classification of the samples. The addition
of profiles from the V9 region appeared to confound the classifiers. Our results show that SVM and KNN classifiers can
be effectively applied to distinguish between eubacterial community patterns from different ecosystems based only on their
ALH profiles
Pseudomonas aeruginosa Adaptation to Lungs of Cystic Fibrosis Patients Leads to Lowered Resistance to Phage and Protist Enemies
Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1-25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2-23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations
- …