Hypervirulent in a South African tertiary hospital-Clinical profile, genetic determinants, and virulence in .

Introduction: A distinct strain of () referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in isolates from one of the largest tertiary hospitals in a South African province.

Identifying genetic loci that are associated with changes in gene expression in PTSD in a South African cohort.

The molecular mechanisms underlying posttraumatic stress disorder (PTSD) are yet to be fully elucidated, especially in underrepresented population groups. Expression quantitative trait loci (eQTLs) are DNA sequence variants that influence gene expression, in a local (cis-) or distal (trans-) manner, and subsequently impact cellular, tissue, and system physiology. This study aims to identify genetic loci associated with gene expression changes in a South African PTSD cohort.

Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions.

Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna.

Recent advances in genetic tools for engineering probiotic lactic acid bacteria.

Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities.

Coding-Complete Genome Sequences for Two Confirmed Monkeypox Cases in South Africa 2022.

The coding-complete genome sequences of monkeypox virus (MPXV) were obtained from skin lesion swabs from two human cases detected in South Africa in June 2022. Sequence analyses indicated that the genetic sequences of the viruses associated with these two cases were related most closely to the genetic sequences of other MPXVs reported during the 2022 multicountry outbreak and belong to the monkeypox hMPXV-1 clade (previously West Africa clade) and B.1 lineage.

Draft Whole-Genome Sequence of A4, a Putative Endophyte from .

We report the draft whole-genome sequence of the putative endophytic fungus Penicillium simplicissimum A4, isolated from the roots of Echium plantagineum plants. The genome was sequenced using PacBio technology with an estimated genome size of 39 Mb.

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations.

Studies of laboratory animals demonstrate extensive variation of host gut microbiomes and their functional capabilities across populations, but how does anthropogenic change impact the microbiomes of non-model species? The anthropogenic movement of species to novel environments can drastically alter animals' microbiomes; however, factors that shape invasive species gut microbiota during introduction remain relatively unexplored. Through 16S amplicon sequencing on guttural toad (Sclerophrys gutturalis) faecal samples, we determine that residence time does not impact microbiome variation between source and introduced populations. The youngest population (~ 20 years in Cape Town) has the most distinct microbiome and associated functional capabilities, whereas longer residence times (~ 100 years in Réunion and Mauritius) produce less divergent microbial compositional, phylogenetic, and predicted functional diversity and differential abundance from source populations (Durban).

Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA.

The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi.

Draft Genome Sequence of the Putative Endophytic Bacterium Pantoea agglomerans R6, Associated with Lactuca serriola from South Africa.

Here, we present the draft genome sequence (∼4.7 Mb) of the endopyhtic bacterium strain R6, which was isolated from surface-sterilized roots of (prickly lettuce).

The complete mitochondrial genome of (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors.

Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (; CGV) and griffon () vultures are also susceptible to diclofenac toxicity.

Isolation and characterization of 30 STRs in Temminck's ground pangolin () and potential for cross amplification in other African species.

Temminck's ground pangolin () is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck's ground pangolin using next-generation sequencing.

Population genetic structure of the thick-tailed bushbaby () from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species.

Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae.

Background: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla).

Genome Sequences of Three Vaccine Strains and Two Wild-Type Canine Distemper Virus Strains from a Recent Disease Outbreak in South Africa.

Canine distemper virus causes global multihost infectious disease. This report details complete genome sequences of three vaccine and two new wild-type strains. The wild-type strains belong to the South African lineage, and all three vaccine strains to the America 1 lineage.

Next generation sequencing yields the mitochondrial genome of the critically endangered (white-winged flufftail).

The mitochondrial genome of was sequenced using next generation sequencing technology. The size of the genome is reported as 16,767 bp and comprises 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The organization of the genome is comparable to that of other bird species.

Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing.

Purpose: A majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts.

Single nucleotide polymorphisms of the SLC22A2 gene within the Xhosa population of South Africa.

Human organic cation transporter 2 (hOCT2) is thought to play a critical role in the uptake, pharmacological effects and/or adverse effects of many cationic clinical therapeutics and xenobiotics. Moreover, genetic variations in hOCT2 gene, SLC22A2, are increasingly being recognized as a possible mechanism that can explain individual variation in drug response. To screen for variations in this gene, SLC22A2 was directly sequenced in 96 healthy Xhosa individuals.

Genetic polymorphisms of the organic cation transporter 1 gene (SLC22A1) within the Cape Admixed population of South Africa.

Human organic cation transporter 1 (hOCT1) is expressed primarily in hepatocytes and mediate the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for hOCT1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response of individual patients to clinical drugs which are substrates for this transporter. The aim of this study was to investigate the allele and genotype frequencies of single-nucleotide polymorphisms (SNPs) of SLC22A1 in the Cape Admixed population of South Africa.

Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1) in the Xhosa population of South Africa.

Human organic cation transporter 1 is primarily expressed in hepatocytes and mediates the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for human organic cation transporter 1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response to clinical drugs, which are substrates for this transporter. The genotypic and allelic distributions of 19 nonsynonymous and one intronic SLC22A1 single nucleotide polymorphisms were determined in 148 healthy Xhosa participants from South Africa, using a SNAPshot(®) multiplex assay.

Manual and manipulative therapy compared to night splint for symptomatic hallux abducto valgus: an exploratory randomised clinical trial.

Context: Hallux abducto valgus (HAV) is a frequent cause of great toe pain and disability, yet common treatments are only supported by mixed or equivocal research findings. Surgery often only provides modest improvement and post-surgery complications may significantly hamper outcomes, implying the need for trials testing conservative treatment, such as manual and manipulative therapy, particularly in cases where surgery may be contraindicated or premature. The purpose of this exploratory trial was to test an innovative protocol of manual and manipulative therapy (MMT) and compare it to standard care of a night splint(s) for symptomatic mild to moderate HAV, with a view gather insight into the effectiveness of MMT and inform the design of a definitive trial.

Nitric oxide synthase activity is required for development of functional nodules in soybean.

The effects of a nitric oxide synthase inhibitor (N(ω)-nitro-L-arginine) on soybean growth parameters and nodule functioning were investigated, along with soybean nodule cell viability and cysteine endopeptidase activity. N(ω)-nitro-L-arginine reduced soybean growth parameters, inhibited nodule nitrogenase activity, and caused a decrease in nodule cell viability. The negative effects of N(ω)-nitro-L-arginine were reversed by the nitric oxide donor 2,2'-(hydroxynitrosohydrazono)bis-ethanimine.

Delayed breeding affects lifetime reproductive success differently in male and female green woodhoopoes.

In cooperatively breeding species, many individuals only start breeding long after reaching physiological maturity [1], and this delay is expected to reduce lifetime reproductive success (LRS) [1-3]. Although many studies have investigated how nonbreeding helpers might mitigate the assumed cost of delayed breeding (reviewed in [3]), few have directly quantified the cost itself [4, 5] (but see [6, 7]). Moreover, although life-history tradeoffs frequently influence the sexes in profoundly different ways [8, 9], it has been generally assumed that males and females are similarly affected by a delayed start to breeding [7].

Experimental evidence of a link between breeding conditions and the decision to breed or to help in a colonial cooperative bird.

In many species mature individuals delay independent reproduction and may help others to reproduce. This behaviour is often explained through ecological constraints, although recently attention has also been paid to the variation in habitat quality. If the quality of vacant habitat influences the fitness trade-off between delaying reproduction and breeding independently, individuals should delay reproduction when conditions for breeding are poor.