A5081432438- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Tuberculosis Research and Epidemiology
- RNA and protein synthesis mechanisms
- HIV/AIDS Impact and Responses
- Antifungal resistance and susceptibility
- Inflammatory Bowel Disease
- Fungal Infections and Studies
- Microscopic Colitis
- Mycobacterium research and diagnosis
- Biochemical and Molecular Research
- Metabolomics and Mass Spectrometry Studies
- Viral gastroenteritis research and epidemiology
- Global Public Health Policies and Epidemiology
- Neurological disorders and treatments
- Helicobacter pylori-related gastroenterology studies
- Gut microbiota and health
- Parkinson's Disease Mechanisms and Treatments
- Bacterial Genetics and Biotechnology
- Bioeconomy and Sustainability Development
- Cellular transport and secretion
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
Stellenbosch University
2010-2024
University of Cape Town
2017-2023
South African Medical Research Council
2015-2019
South African Tuberculosis Vaccine Initiative
2015
Pacific Northwest National Laboratory
2012-2013
University Hospital of North Norway
2010
Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán
2010
University of Oslo
2010
National Research Foundation
2010
Reversible protein phosphorylation, regulated by kinases and phosphatases, mediates a switch between activity cellular pathways that contribute to large number of processes. The Mycobacterium tuberculosis genome encodes 11 Serine/Threonine (STPKs) which show close homology eukaryotic kinases. This study aimed elucidate the phosphoproteomic landscape clinical isolate M. tuberculosis. We performed high throughput mass spectrometric analysis proteins extracted from an early-logarithmic phase...
Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse pathogenesis human diseases, agriculture and climate change. Poor correlations typically observed between RNA protein expression datasets make it hard to accurately infer synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses rely on focused search sequence databases based prior knowledge for...
Abstract Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise microbial patterns that may be amenable dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome a cross-sectional study healthy rural urban Xhosa people (South Africa). Urban individuals had...
Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact further proteomic studies, and also compromises characterization clinical isolates with many specific genetic variations may not be represented selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) can merge protein databases several sources...
Although the genome of Mycobacterium tuberculosis H37Rv laboratory strain has been available for over 10 years, it is only recently that genomic information from clinical isolates used to generate hypothesis virulence differences between different strains. In addition, relationship strains displaying differing in an epidemiological setting and their behavior animal models received little attention. The potential causes variation strains, as determined by differential protein expression, have...
Due to an increase in the overuse of antimicrobials and accelerated incidence drug resistant pathogens, antimicrobial resistance has become a global health threat. In particular, bacterial resistance, both hospital community acquired transmission, have been found be leading cause death due infectious diseases. Understanding mechanisms is clinical significance irrespective or since it plays important role treatment strategy controlling Here we highlight advances mass spectrometry-based...
Abstract Background Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse pathogenesis human diseases, agriculture and climate change. Poor correlations typically observed between RNA protein expression datasets make it hard to accurately infer synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses rely on focussed search libraries based prior knowledge for...
Aspergillus fumigatus is the primary pathogen causing devastating pulmonary disease Invasive Aspergillosis in immunocompromised individuals. There high genomic synteny between A. and closely related rarely pathogenic Neosartorya fischeri clavatus genomes. We applied activity-based protein profiling to compare unique or overexpressed probe-reactive proteins of all three fungi over time minimal media growth response human serum. found 360 exclusive fumigatus, including known virulence...
In proteomics, peptide information within mass spectrometry (MS) data from a specific organism sample is routinely matched against protein sequence database that best represent such organism. However, if the species/strain in unknown or genetically poorly characterized, it becomes challenging to determine which can sample. Building customized databases merging multiple strains for given species has become strategy overcome restrictions. as more genetic publicly available and interesting...
The Escherichia coli proteome is the most extensively characterized and studied of all prokaryotic proteomes. Despite this, large scale bacterial proteomics experiments performed on E. cells grown in liquid cultures have failed to identify key virulence factors thought be important determinants establishing infections. It seems likely that many associated with host cell adhesion are exclusively expressed during growth biofilms, which can crudely mimicked solid media. This method describes a...
Abstract In proteomics, peptide information within mass spectrometry data from a specific organism sample is routinely challenged against protein sequence database that best represent such organism. However, if the species/strain in unknown or poorly genetically characterized, it becomes challenging to determine which can sample. Building customized databases merging multiple strains for given species has become strategy overcome restrictions. as more genetic publicly available and...
of immunomodulators and aminosalicylates
Abstract Background: Inflammatory bowel disease is a chronic relapsing and remitting inflammation of the bowel. Tumour necrosis factor α - antagonists are safe effective in treatment IBD. Indications outcomes with consecutive anti-TNF agent, although often used, not clear. Since data for this choice scarce, we set out to evaluate use agents patients Method: A national registry established by The South African Gastroenterology Society was used retrospective extraction agent use. Demographic,...
Parkinson's disease (PD), the fastest-growing neurological disorder globally, has a complex etiology. A previous study by our group identified p.G849D variant in