GNPS - South African Tunicate Collection
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Bruker Maxis qTOF
ORGANISM(S): Tunicata (ncbitaxon:7712)
SUBMITTER: McPhail
PROVIDER: MSV000079044 | GNPS | Fri Feb 20 18:00:00 GMT 2015
REPOSITORIES: GNPS
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Project description:South African abattoir wastewater
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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. Keywords: comparative genomic indexing analysis
2007-12-19 | GSE9862 | GEO
Project description:South African peritidal stromatolites Metagenome
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Project description:Tunicates from South African Algoa bay that collected at 2018. Mainly focus on Didemnum sp. and Lissoclinum sp. The data were collected from 2020 and 2021.
2021-05-17 | MSV000087449 | GNPS
Project description:Introduction: Gallbladder cancer (GBC) is a highly aggressive malignancy with limited therapeutic options, particularly in underrepresented populations, including South Africa. Understanding the molecular landscape of GBC may provide novel insights into its pathogenesis and potential therapeutic targets. Molecular changes are known to be associated with GBC, however, there is a paucity of this information especially in African populations. Furthermore, within the tumour microenvironment, different immune cells contribute to GBC progression. We investigated gene expression patterns in GBC tumours and their association with different immune cells in a cohort of South African patients. Methods: RNA sequencing was conducted on 2 normal and 8 gallbladder cancer tissues from South African patients (Ethics: M160640) to identify differentially expressed genes. Bioinformatics tools were used for pathway analysis, while immune cell quantification was performed using the quanTIseq software and presented as median [IQR]. Verification studies were further carried out using real-time PCR on an independent cohort comprising 7 gallstone samples and 26 gallbladder tumour samples. Results: A total of 65 genes were found to be significantly differentially expressed between the gallbladder tumours and gallstone controls. We also identified 37 upregulated and 28 downregulated genes in this cohort. Among the most upregulated genes, MUC16 was confirmed to be significantly overexpressed in tumours. Normal tissues exhibited a significantly higher proportion of dysregulated genes associated with B cells (17.132 [14.866–18.483], p<0.0001) and M1 macrophages (18.943 [1.097–36.790], p<0.0001) compared to tumours. In contrast, tumours showed a greater association with dysregulated genes linked to regulatory T cells (Tregs) (14.373 [9.696–20.162]) relative to normal tissues. Pathway analysis further revealed the upregulation of defective GALNT12, defective GALNT3, defective C1GALT1C1 and termination of O-glycan biosynthesis, highlighting key mechanisms potentially involved in tumour progression. Conclusion: The study has shown the dysregulation of key genes in South African gallbladder cancer patients. Specifically, MUC16 was verified to be significantly elevated in tumour samples. Furthermore, the association of these dysregulated genes with key immune cells in this patient group may further highlight their roles in dysfunctional immune processes linked with tumourigenesis.
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Project description:RNA was extracted from all instar (insect developmental) stages for both D. noxia biotypes SA1 and SAM with the purpose to capture as many expressed transcripts as possible. South African D. noxia biotype SA1 is known to be the least virulent aphid, while its offspring, the South African D. noxia biotype SAM is the most virulent. The overall purpose of the experiment was to establish a baseline availability of transcripts to the aphids as well as help improve on current genome assemblies. Three biological replicates of 100 aphids each was collected from both biotypes SA1 and SAM that were respectively reared on preference host cultivars. Whole aphids were flash frozen in liquid nitrogen, ground to a powder with micro pistils and RNA was extracted making use of a Qiagen RNeasy kit. Library preparation for sequencing was performed using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol. The replicate samples from the SAM biotype yielded between 120 – 140 million 100bp PE reads and the replicate samples from the SA1 biotype yielded between 113 – 137 million 100bp PE reads (with a Q20 phred score above 98% for all replicates) after sequencing on the NovaSeq6000 system. De novoassembly was performed making use of the Trinity package.
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Project description:South African human gut microbiome Metagenome
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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. The genomic diversity of 33 South African, 2 Mexican and 1 Canadian Campylobacter jejuni strains from humans were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two or three replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.
2010-05-27 | E-GEOD-9862 | biostudies-arrayexpress
Project description:Time-course expression analysis profiling whole blood samples collected from healthy South African adolescents while monitoring their potential acquisition of a Mycobacterium tuberculosis infection.
2018-08-18 | GSE116014 | GEO
Project description:Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry.
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