Biology subjects

Mulder, N.

Publications and source records attributed to Mulder, N..

12 recordsLinked to original sources

bioRxiv2025

Changes in the Anopheles arabiensis transcriptome and gut microbiota profiles associated with Microsporidia MB

Microsporidia MB is an endosymbiotic microbe found in Anopheles mosquito populations. This symbiont can block Plasmodium transmission in mosquitoes, and it can spread through mosquito populations and be sustained over generations by vertical and horizontal transmission. These characteristics make Microsporidia MB a potential candidate for symbiont-based malaria vector control. However, the mechanistic basis of interactions between Microsporidia MB and Anopheles arabiensis is poorly characterized. We investigated how the presence of Microsporidia MB affects transcriptomics profiles and the gut microbiota composition and diversity in non-blood-fed and blood-fed (24, 48 and 72 hours post blood meal) An. arabiensis mosquitoes. We observed that mosquito infection with Microsporidia MB upregulated farnesoic acid O-methyltransferase, a gene linked to juvenile hormone biosynthesis in the non-blood-fed mosquitoes. In addition, blood feeding in Microsporidia MB positive mosquitoes was associated with an activation of immune-related genes 24 hours after a blood meal, where several genes including the lipopolysaccharide tumor necrosis factor gene were upregulated. Interestingly, we also observed that Microsporidia MB positivity was associated with a microbiota shift to favor the proliferation of microbes including Pseudomonas and Serratia 24 hours post blood meal. There were indications of immune system activation in Microsporidia MB positive mosquitoes up to 48 hours after a blood meal where factors such as the peptidoglycan recognition SC2-like and lysozyme c-1 were upregulated. Notably, an upregulated immune system at this time point was associated with downregulation of genes associated with metabolism and the restoration of Serratia, Pseudomonas and other key microbes to relative abundances similar to those recorded in non-blood-fed mosquitoes. At the 72-hour time point, Microsporidia MB positive mosquitoes exhibited a downregulation of genes associated with immunity, including cecropins and defensins, while metabolic processes were predominantly upregulated. Our results provide insights into the effect of Microsporidia MB infection on the An. arabiensis gene expression and gut microbiota profiles. This work will contribute to mechanistic insights into symbiont-mediated malaria transmission blocking.

systems biology↗

bioRxiv2025

Defining the minimal structural requirements of DivIVA in filamentous Actinomycetota

The morphogenetic protein DivIVA exhibits diverse functions across bacterial phyla. In Bacillota, DivIVA is primarily involved in cell division, whereas in Actinomycetota, it plays a central role in coordinating polar growth. Due to its essential nature, gaining insight into DivIVA function is challenging. Here we report on the functionality of truncated DivIVA proteins, using a unique divIVA deletion mutant created in cell wall-deficient Kitasatospora viridifaciens L-forms. DivIVA comprises an N-terminal domain, two coiled-coil regions separated by an intercoil linker, and a C-terminal domain. Deleting either the intercoil or the C-terminal region impacted branching dynamics. We also created a minimized variant wherein both were deleted simultaneously, containing the N-terminus and fused coiled-coils, resembling DivIVA from unicellular bacteria. Expression of this minimized variant resulted in severe growth defects. Cells exhibited a strong increase in hyphal width and cell wall thickness, accompanied by frequent tip bursting. Finally, we successfully introduced chimeric DivIVA from the unicellular actinobacterium Mycolicibacterium smegmatis with an N-terminal domain of Kitasatospora viridifaciens, demonstrating functional conservation within the phylum. In contrast, a chimeric DivIVA from Bacillus subtilis could not support growth, underscoring that polar growth is encoded within Actinomycetota-specific amino acid motifs encoded in the first and second coiled-coil. These findings enhance our understanding of the structure-function relationship for DivIVA and present new opportunities to study polar growth. ImpactDivIVA is essential for polar growth in Actinomycetota. In Streptomycetaceae, this membrane-binding protein localizes at growing hyphal tips and along lateral hyphal walls where new branches emerge. Due to its essentiality, the structural relationship of DivIVA between unicellular and multicellular species remains elusive. Using a Kitasatospora viridifaciens L-form divIVA deletion mutant, we expressed truncated DivIVA variants to identify essential regions. Deleting two large unstructured domains produced a minimized variant containing the N-terminus and fused coiled-coils, resembling DivIVA from unicellular bacteria. This strongly impacted morphogenesis, increasing hyphal width and cell wall thickness, and leading to hyphal tip bursting. Finally, we successfully substituted DivIVA of K. viridifaciens with that from Mycolicibacterium smegmatis. Furthermore, Bacillus subtilis DivIVA could not facilitate reversion, showing that polar growth depends on amino acid motifs unique to Actinomycetota. These findings enhance our understanding of the structure-function relationship of DivIVA and offer new opportunities to study polar growth.

microbiology↗

bioRxiv2023

Assessing HLA imputation accuracy in a West African population

The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We therefore sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes dataset (1kg-All), 1000 Genomes African dataset (1kg-Afr), 1000 Genomes Gambian dataset (1kg-Gwd), H3Africa dataset and the HLA Multi-ethnic dataset. HLA-A, HLA-B and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA and Minimac4, and concordance rate was used as an assessment metric. Overall, the best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in West African populations. Author SummaryFor studies that associate a particular HLA type to a phenotypic trait for instance HIV susceptibility or control, genotype imputation remains the main method for acquiring a larger sample size. Genotype imputation, process of inferring unobserved genotypes, is a statistical technique and thus deals with probabilities. Also, the HLA region is highly variable and therefore difficult to impute. In view of this, it is important to assess HLA imputation accuracy especially in African populations. This is because the African genome has high diversity, and such studies have hardly been conducted in African populations. This work highlights that using HIBAG imputation tool and a larger population-specific reference panel increases HLA imputation accuracy in an African population.

bioinformatics↗

bioRxiv2023

Pan-genome study underling the extent of genomic variation of invasive Streptococcus pneumoniae in Malawi

AbstractStreptococcus pneumoniae is a common cause of acute bacterial infections in Malawi. Understanding the molecular mechanisms underlying its invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes in S. pneumoniae by comparing the gene pool of isolates from carriers nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. Our analysis involved 1,477 pneumococcal isolates from Malawi, comprising 825 samples from carriers (nasopharyngeal swab) and 652 from patients (368 from blood and 284 from cerebrospinal fluid). We identified 56 serotypes in the cohort. While most serotypes exhibited a similar prevalence in both carriage and disease groups, serotypes 1 and 5, the most abundant serotypes in the entire cohort, were significantly more commonly detected in specimens from patients compared to the carriage group. This difference is presumably due to their shorter nasopharyngeal colonization period. Furthermore, these serotypes displayed genetic distinctiveness from other serotypes. A magnificent genetic difference was observed in the absence of genes from the RD8a genomic island in serotypes 1 and 5 compared to significantly prevalent serotypes in the nasopharynx. RD8a genes play pivotal roles in binding to epithelial cells and performing aerobic respiration to synthesize ATP through oxidative phosphorylation. The absence of RD8a from serotypes 1 and 5 may be associated with a shorter duration in the nasopharynx, theoretically due to a reduced capacity to bind to epithelial cells and access free oxygen molecules required for aerobic respiration (essential to maintain the carriage state). Serotypes 1 and 5, significantly harbor operons that encode phosphoenolpyruvate phosphotransferase systems, which might relate to transporting carbohydrates, relying on phosphoenolpyruvate as the energy source instead of ATP. In conclusion, serotypes 1 and 5 as the most prevalent invasive pneumococcal strains in Malawi, displayed considerable genetic divergence from other strains, which may offer insights into their invasiveness and potential avenues for further research. Author summaryDespite introducing the pneumococcal conjugate vaccine in 2011, Streptococcus pneumoniae remains a major cause of bacterial infection in Malawi. Whilst some pneumococcal strains harmlessly colonize the nasopharynx, others find their way into normally sterile sites, such as lungs, blood, and nervous system, resulting in serious illness. Our study identified specific pneumococcal serotypes as the most invasive in Malawi, characterized by a short colonization period and significant genetic distinctiveness from other strains. This genetic divergence notably included the absence of several genes associated with aerobic respiration and the presence of genes facilitating ATP-independent carbohydrate transport. The presence or absence of these genes may underlie their heightened invasiveness and shorter colonization period. This hypothesis positions these genes as potential candidates for future therapeutic research. We propose that the specific gene gain and/or loss in invasive versus other serotypes may be linked to the development of invasive pneumococcal diseases. Impact StatementOur research applied pan-genomics principles to comprehensively assess diversity within the pneumococcus genome, with the primary objective of identifying pneumococcal virulence genes for advancing vaccine design and drug development. Within this study, we identified Serotypes 1 and 5 as the predominant and highly invasive pneumococcal strains in Malawi, characterized by a short nasopharyngeal colonization period, suggesting their potential for rapid infection of sterile sites within the human body such as blood and the central nervous system. These serotypes exhibited significant genetic divergence from other serotypes in Malawi, notably lacking key genes within the RD8a operon while harboring transporters functioning independently of ATP. Its important to note that these findings are based on computational analysis, and further validation through laboratory experiments is essential to confirm their biological significance and potential clinical applications. The implications of our research offer potential avenues for more effective pneumococcal disease prevention and treatment, not only in Malawi but also in regions facing similar challenges.

microbiology↗

bioRxiv2021

The role of copper resistance in Mycobacterium tuberculosis pathogenesis

Despite the development of new drugs and social interventions, tuberculosis remains a leading cause of mortality. This burden falls disproportionately on developing countries, particularly those where the incidence of HIV is high. In the Western Cape, South Africa, we have identified and isolated two Beijing family strains of Mycobacterium tuberculosis that, despite few differences at a genomic level, differ greatly in their severity of disease caused, providing an opportunity to study virulence in this organism. The aim of this study was to identify differences at a genomic and transcriptomic level that may identify the cause of the different virulence levels observed in the two isolates. The isolates were compared at the transcriptome level under four different growth conditions including oxidative stress. In comparing the transcriptome of the two isolates, an operon containing genes involved in the production of molybdenum cofactor that showed consistently lower levels of expression in the hypervirulent isolate was identified. A copper sensing transcriptional regulator was identified as the most probable regulator, and we found that the Cso operon which it is known to regulate was similarly differentially expressed in the strains. The production of molybdenum cofactor is effected in two ways by copper levels. Through the independent insertion of copper into molybdopterin (MPT), and destabilisation of Fe-S clusters. As MoaA3 contains a Fe-S cluster that is known to be destabilised by copper, and a number of copper sensitive genes are likewise found differentially expressed, it is likely that the strains differ in terms of their levels of resistance to copper. It is therefore hypothesised that the differences in virulence are as a result of different levels of resistance to phagosome copper overload, and the mechanism by which copper levels are linked to the production of molybdenum cofactor is described. Author summaryIn this article, we describe the differences in gene expression of two closely related strains of Mycobacterium tuberculosis isolated in the Western Cape of South Africa that differ in the severity of disease that they cause. We compared the strains at a genomic and transcriptomic level, and in doing so, we discovered a set of molybdenum cofactor genes regulated by a copper sensing transcription factor that came up in all datasets. Further genes linked to copper response were identified, providing greater evidence that the difference between the two strains was the manner in which they responded to copper stress. Phagocytes are known to exploit high levels of copper to kill intracellular bacteria, suggesting an important link between copper and disease. We conclude that resistance to copper toxicity is the most probable reason for the relative increase in virulence, and describe the regulatory relationship between copper levels and molybdenum cofactor synthesis.

microbiology↗

bioRxiv2020

Integrated Molecular Characterisation of the MAPK Pathways in Human Cancers

The mitogen-activated protein kinase (MAPK) pathways are a crucial regulator of the cellular processes that fuel the malignant transformation of normal cells. The genetic underpinnings of molecular aberrations which lead to cancer involve mutations in and, transcription variations of, various MAPK pathway genes. Here, we use datasets of 40,848 patient-derived tumours representing 101 distinct human cancers to identify cancer-associated mutations in MAPK signalling pathway genes. We identify the subset of these genes within which mutations tend to be associated with the worst disease outcomes. Furthermore, by integrating information extracted from various large-scale molecular datasets, we expose the relationship between the fitness of cancer cells after CRISPR mediated gene knockout of MAPK pathway genes, and their dose-responses to MAPK pathway inhibitors. Besides providing new insights into MAPK pathways, we unearth vulnerabilities in specific pathway genes that are reflected in the responses of cancer cells to MAPK drug perturbations: a revelation with great potential for guiding the development of innovative therapeutic strategies.

bioinformatics↗

bioRxiv2020

Microbial function and genital inflammation in young South African women at high risk of HIV infection

BackgroundFemale genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile, however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations. ResultsA total of 3,186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p<0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women nine weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women. ConclusionsBoth the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-METAP application that is available at (http://immunodb.org/FGTMetap/).

microbiology↗

bioRxiv2019

Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expression in Alzheimer’s Disease

Networks are present in many aspects of our lives, and networks in neuroscience have recently gained much attention leading to novel representations of brain connectivity. The integration of neuroimaging characteristics and genetics data allows a better understanding of the effects of the genetic variations on brain structural and functional connections. The current work uses whole-brain tractography in a longitudinal setting, and by measuring the brain structural connectivity changes studies the neurodegeneration of Alzheimers disease. This is accomplished by examining the effect of targeted genetic risk factors on the most common local and global brain connectivity measures. Furthermore, we examined the extent to which Clinical Dementia Rating relates to brain connections longitudinally, as well as to gene expression. Here we show that the expression of PLAU gene increases the change over time in betweenness centrality related to the fusiform gyrus. We also show that the betweenness centrality metric impact dementia-related changes in distinct brain regions. Our findings provide insights into the complex longitudinal interplay between genetics and brain characteristics and highlight the role of Alzheimers genetic risk factors in the estimation of regional brain connectivity alterations.

bioinformatics↗

bioRxiv2019

MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets

BackgroundMicrobiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focussed search libraries based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing will only target the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. We describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored databases for target-decoy searches directly at the proteome level, enabling analyses without prior expectation of sample composition or metagenomic data generation, and compatible with standard downstream analysis pipelines. ResultsWe compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome database - but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying a known sample contaminant without prior expectation. ConclusionsBy estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence search databases. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself. The pipeline source code is available on GitHub1 and documentation is provided to run the software as a singularity-compatible docker image available from the Docker Hub2.

bioinformatics↗

bioRxiv2018

GenGraph: a python module for the simple generation and manipulation of genome graphs.

BackgroundAs sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph based representation of collections of genomes as a single genome graph. Though there are currently a handful of tools that can create genome graphs and have demonstrated the advantages of this new paradigm, there still exists a need for flexible tools that can be used by researchers to overcome challenges in genomics studies.\n\nResultsWe present the GenGraph toolkit, a tool that uses existing multiple sequence alignment tools to create genome graphs. It is written in Python, one of the most popular coding languages for the biological sciences, and creates the genome graphs as Python NetworkX graph objects. The conceptual model is highly intuitive, and as much as possible represents the biological relationship between the genomes. This design means that users will quickly be able to start creating genome graphs and using them in their own projects.\n\nWe outline the methods used in the generation of the graphs, and give some examples of how the created graphs may be used. GenGraph utilises existing file formats and methods in the generation of these graphs, allowing graphs to be visualised and imported with widely used applications, including Cytoscape, R, and Java Script.\n\nConclusionGenGraph provides a set of tools for generating graph based representations of sets of sequences with a simple conceptual model in a widely used coding language. It is publicly available on Github (https://github.com/jambler24/GenGraph).

bioinformatics↗

bioRxiv2018

Genome-Wide Association Study of Brain Connectivity Changes for Alzheimer’s Disease

Variations in the human genome have been found to be an essential factor that affects susceptibility to Alzheimers disease. Genome-wide association studies (GWAS) have identified genetic loci that significantly contribute to the risk of Alzheimers. The availability of genetic data, coupled with brain imaging technologies have opened the door for further discoveries, by using data integration methodologies and new study designs. Although methods have been proposed for integrating image characteristics and genetic information for studying Alzheimers, the measurement of disease is often taken at a single time point, therefore, not allowing the disease progression to be taken into consideration. In longitudinal settings, we analyzed neuroimaging and single nucleotide polymorphism datasets obtained from the Alzheimers Disease Neuroimaging Initiative for three clinical stages of the disease, including healthy control, early mild cognitive impairment and Alzheimers disease subjects. We conducted a GWAS regressing the absolute change of global connectivity metrics on the genetic variants, and used the GWAS summary statistics to compute the gene and pathway scores. We observed significant associations between the change in structural brain connectivity defined by tractography and genes, which have previously been reported to biologically manipulate the risk and progression of certain neurodegenerative disorders, including Alzheimers disease.

bioinformatics↗

bioRxiv2017

A global perspective on bioinformatics training needs

In the last decade, life-science research has become increasingly data-intensive and computational. Nevertheless, basic bioinformatics and data stewardship are still only rarely taught in life-science degree programmes, creating a widening skills gap that spans educational levels and career roles. To better understand this situation, we ran surveys to determine how the skills dearth is affecting the need for bioinformatics training worldwide. Perhaps unsurprisingly, we found that respondents wanted more short courses to help boost their expertise and confidence in data analysis and interpretation. However, it was evident that most respondents appreciated their need for training only after designing their experiments and collecting their data. This is clearly rather late in the research workflow, and suboptimal from a training perspective, as skills acquired to address a specific need at a particular time are seldom retained, engendering a cycle of low confidence in trainees. To ensure that such skill gaps do not continue to create barriers to the progress of research, we argue that universities should strive to bring their life-science curricula into the digital-data era. Meanwhile, the demand for point-of-need training in bioinformatics and data stewardship will grow. While this situation persists, international groups like GOBLET are increasing their efforts to enlarge the community of trainers and quench the global thirst for bioinformatics training.

scientific communication and education↗