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Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

Hempel RJ, Bannantine JP, Stabel JR - PLoS ONE (2016)

Bottom Line: The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease.Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes.The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix.

View Article: PubMed Central - PubMed

Affiliation: USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America.

ABSTRACT
Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

No MeSH data available.


Related in: MedlinePlus

Description of reads mapping to single and multiple locations in the B. taurus genome.A) Pie chart showing the mean number and percentage of reads that aligned to the reference genome using TopHat and Bowtie. B) Pie chart showing the mean percentage of uniquely mapped reads assigned to coding regions (i.e. known exons), untranslated regions (i.e. 3’ or 5’ untranslated regions), intronic regions (i.e. known introns), intergenic regions (i.e. areas where no known annotated genes are present), and ribosomal RNA based on alignment data from HTSeq and Piccard Tools.
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pone.0153932.g001: Description of reads mapping to single and multiple locations in the B. taurus genome.A) Pie chart showing the mean number and percentage of reads that aligned to the reference genome using TopHat and Bowtie. B) Pie chart showing the mean percentage of uniquely mapped reads assigned to coding regions (i.e. known exons), untranslated regions (i.e. 3’ or 5’ untranslated regions), intronic regions (i.e. known introns), intergenic regions (i.e. areas where no known annotated genes are present), and ribosomal RNA based on alignment data from HTSeq and Piccard Tools.

Mentions: An RNA-seq library was prepared for each animal within the three health stages, uninfected control, subclinical and clinical cows, resulting in 5 RNA-seq libraries for each group. All the libraries were sequenced within 5 lanes of one Illumina flow cell, generating an average of 122.2 million reads per lane. The average number of reads per sample was 40.7 million (Fig 1A). Alignment of the RNA-seq reads to the B. taurus genome (Ensembl UMD 3.1) yielded a mean of 36.9 million reads per sequenced library. An average of 32.1 million reads aligned to unique locations. Approximately 4.39 million reads aligned to multiple locations within the genome and were excluded from the gene expression analysis. A more detailed analysis of the reads mapping to unique locations revealed that 39% aligned to coding regions while 17.2% aligned to untranslated regions (UTR) of mRNAs (Fig 1B). Ribosomal genes accounted for 9.73% of reads and 30.3% of aligned reads mapped to intergenic regions.


Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

Hempel RJ, Bannantine JP, Stabel JR - PLoS ONE (2016)

Description of reads mapping to single and multiple locations in the B. taurus genome.A) Pie chart showing the mean number and percentage of reads that aligned to the reference genome using TopHat and Bowtie. B) Pie chart showing the mean percentage of uniquely mapped reads assigned to coding regions (i.e. known exons), untranslated regions (i.e. 3’ or 5’ untranslated regions), intronic regions (i.e. known introns), intergenic regions (i.e. areas where no known annotated genes are present), and ribosomal RNA based on alignment data from HTSeq and Piccard Tools.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4836751&req=5

pone.0153932.g001: Description of reads mapping to single and multiple locations in the B. taurus genome.A) Pie chart showing the mean number and percentage of reads that aligned to the reference genome using TopHat and Bowtie. B) Pie chart showing the mean percentage of uniquely mapped reads assigned to coding regions (i.e. known exons), untranslated regions (i.e. 3’ or 5’ untranslated regions), intronic regions (i.e. known introns), intergenic regions (i.e. areas where no known annotated genes are present), and ribosomal RNA based on alignment data from HTSeq and Piccard Tools.
Mentions: An RNA-seq library was prepared for each animal within the three health stages, uninfected control, subclinical and clinical cows, resulting in 5 RNA-seq libraries for each group. All the libraries were sequenced within 5 lanes of one Illumina flow cell, generating an average of 122.2 million reads per lane. The average number of reads per sample was 40.7 million (Fig 1A). Alignment of the RNA-seq reads to the B. taurus genome (Ensembl UMD 3.1) yielded a mean of 36.9 million reads per sequenced library. An average of 32.1 million reads aligned to unique locations. Approximately 4.39 million reads aligned to multiple locations within the genome and were excluded from the gene expression analysis. A more detailed analysis of the reads mapping to unique locations revealed that 39% aligned to coding regions while 17.2% aligned to untranslated regions (UTR) of mRNAs (Fig 1B). Ribosomal genes accounted for 9.73% of reads and 30.3% of aligned reads mapped to intergenic regions.

Bottom Line: The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease.Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes.The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix.

View Article: PubMed Central - PubMed

Affiliation: USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America.

ABSTRACT
Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

No MeSH data available.


Related in: MedlinePlus