Mycobacterium bovis WGS from South African wildlife
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB63553 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11879729.fastq.gz | Fastqsanger.gz | |||
| ERR11879730.fastq.gz | Fastqsanger.gz | |||
| ERR11879732.fastq.gz | Fastqsanger.gz | |||
| ERR11879733.fastq.gz | Fastqsanger.gz | |||
| ERR11879735.fastq.gz | Fastqsanger.gz |
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Project description:Mycobacterium bovis WGS from South African wildlife species and neighboring livestock
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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. Keywords: comparative genomic indexing analysis
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Project description:Bovine tuberculosis (bTB), caused by Mycobacterium bovis (Mycobacterium tuberculosis complex), is a zoonotic disease that affects cattle and wildlife worldwide. In some regions of Spain, Iberian red deer (Cervus elaphus hispanicus) can serve as reservoir of infection, thus increasing the risk of human and cattle exposure and infection. Mesenteric lymph nodes are naturally infected with M. bovis in Iberian red deer, in which the digestive route of infection is particularly important in Mediterranean Spain. In this study we characterized the differential expression of inflammatory and immune response genes in mesenteric lymph nodes of Iberian red deer naturally infected with M. bovis using a Ruminant Immuno-inflammatory Gene Universal Array (RIGUA) and real-time RT-PCR. Of the 600 genes that were analyzed in the microarray, 157 showed ? 1.2 fold changes in expression in infected or uninfected deer and 17 genes displayed an expression fold change greater than 1.7 with a P-value ? 0.05 and were selected for further analysis. These genes included tight junction proteins (Z02 and occluding), IL-11R, bactenecin, CD62L, CD74, desmoglein, IgA and IgM that constitute new findings and suggest new mechanisms by which M. bovis may modulate host inflammatory and immune responses. Identification of genes differentially expressed in animals and tissues naturally infected with M. bovis contributes to our basic understanding of the mechanisms of pathogenesis and protective immunity to mycobacterial infections and may have important implications for future functional genomic and vaccine studies to aid in the control of bTB in deer and other wildlife reservoir species. Mesenteric lymph node RNA from four different uninfected Iberian red deer stags and two Iberian red deer stags infected with Mycobacterium bovis. Infected animals were naturally infected with M. bovis. All animals were hunter-harvested and the tissues retrieved 2-6 hrs after animal hunting.
2007-10-17 | E-GEOD-6083 | biostudies-arrayexpress
Project description:Bovine tuberculosis (bTB), caused by Mycobacterium bovis (Mycobacterium tuberculosis complex), is a zoonotic disease that affects cattle and wildlife worldwide. In some regions of Spain, Iberian red deer (Cervus elaphus hispanicus) can serve as reservoir of infection, thus increasing the risk of human and cattle exposure and infection. Mesenteric lymph nodes are naturally infected with M. bovis in Iberian red deer, in which the digestive route of infection is particularly important in Mediterranean Spain. In this study we characterized the differential expression of inflammatory and immune response genes in mesenteric lymph nodes of Iberian red deer naturally infected with M. bovis using a Ruminant Immuno-inflammatory Gene Universal Array (RIGUA) and real-time RT-PCR. Of the 600 genes that were analyzed in the microarray, 157 showed ≥ 1.2 fold changes in expression in infected or uninfected deer and 17 genes displayed an expression fold change greater than 1.7 with a P-value ≤ 0.05 and were selected for further analysis. These genes included tight junction proteins (Z02 and occluding), IL-11R, bactenecin, CD62L, CD74, desmoglein, IgA and IgM that constitute new findings and suggest new mechanisms by which M. bovis may modulate host inflammatory and immune responses. Identification of genes differentially expressed in animals and tissues naturally infected with M. bovis contributes to our basic understanding of the mechanisms of pathogenesis and protective immunity to mycobacterial infections and may have important implications for future functional genomic and vaccine studies to aid in the control of bTB in deer and other wildlife reservoir species. Keywords: disease state analysis
2007-10-17 | GSE6083 | GEO