of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and eviden... more of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
Characterization of the high confidence novel genes. Table S13. Phylogenetic analysis of represen... more Characterization of the high confidence novel genes. Table S13. Phylogenetic analysis of representative novel genes. Figure S3. Characterization of the novel transcripts. (PDF 232 kb)
Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental se... more Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental set level
Background: Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chi... more Background: Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chickens caused by the oncogenic Gallid herpesvirus type 2 (GaHV-2; MDV). Like several human lymphomas the neoplastic MD lymphoma cells overexpress the CD30 antigen (CD30) and are in minority, while the non-neoplastic cells (CD30) form the majority of population. MD is a unique natural in-vivo model of human CD30 lymphomas with both natural CD30 lymphomagenesis and spontaneous regression. The exact mechanism of neoplastic transformation from CD30 expressing phenotype to CD30 expressing neoplastic phenotype is unknown. Here, using microarray, proteomics and Systems Biology modeling; we compare the global gene expression of CD30 and CD30 cells to identify key pathways of neoplastic transformation. We propose and test a specific mechanism of neoplastic transformation, and genetic resistance, involving the MDV oncogene Meq, host gene products of the Nuclear Factor Kappa B (NF-κB) family and CD3...
As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche... more As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche and plays a central role in comparative and evolutionary genomics. However, the chicken genome’s coding sequences, intron/exon structures, and potential protein products from each gene in different tissues are not conclusively identified experimentally. We present here Chickspress (http://geneatlas.arl.arizona.edu/), a tissue specific expression atlas for chicken. We are experimentally annotating the chicken genome by directly determining expressed sequences within the genome. Using RNASeq, proteomics and proteogenomic mapping we are analyzing 15 tissues each from two Red Jungle Fowl (male and female) and displaying this on a genome browser. Users are able to view quantitative, tissue-specific expression at both the transcript and protein level. Moreover, we also display novel transcripts identified via RNASeq and novel peptides identified via proteogenomic mapping. Moreover, we are add...
Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Gen... more Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annotate the Chicken Genome. Prepared by J. Smith, D.W. Burt, and the Avian RNAseq Consortium. 89 Noncoding RNAs in the Chicken Genome. Prepared by J. Hertel, M. Fasold, A. Nitsche, I. Erb, P. Prieto, D. Kedra, C. Notredame, T.E. Steeves, P.P. Gardner, and P.F. Stadler. 91 Genome Sequencing in Birds and Evolutionary Inferences from Avian Genome Sequences. Prepared by H. Ellegren. 94 The Use of Avian BAC Libraries and Clones. Prepared by M.N. Romanov and D.K. Griffin. 96 Comparative Genomics. Prepared by D.M. Larkin, M. Farré, and J. Damas. 100 Avian Cytogenetics Goes Functional. Prepared by D.K. Griffin, M.N. Romanov, R. O’Connor, K.E. Fowler, and...
... Authors would like to thank Juliet Tang of LSBI and Wil-liam Monroe of EM center for their te... more ... Authors would like to thank Juliet Tang of LSBI and Wil-liam Monroe of EM center for their technical assistance. REFERENCES 1. Carter DR, Beaupré GS, Giori NJ, Helms JA (1998) Mechanobiology of skeletal regeneration. Clin Orthop 355 Suppl: S41-S55 2. Pauwels F. 1980. ...
ASME 2008 Summer Bioengineering Conference, Parts A and B, 2008
ABSTRACT In the United States, it is estimated that in 2008 approximately 1.2 million people will... more ABSTRACT In the United States, it is estimated that in 2008 approximately 1.2 million people will suffer a new or recurrent myocardial infarction. In 2005, the latest full year for which statistics are available, 16 million Americans (7.3% of the population) had some form of coronary heart disease. Loss of myocardium as a result of myocardial infarction increases wall stress locally and globally and triggers adaptive responses at the molecular, cellular, and tissue levels. These adaptive responses can lead to left ventricular dilation and congestive heart failure. Accurate non-invasive evaluation of myocardial structural degeneration (damage) and left ventricular remodeling following an infarct would have both prognostic and therapeutic value clinically.
Veterinary immunology and immunopathology, Jan 15, 2005
The Harderian gland (HG), a sero-mucous secreting organ in the eye orbit, has long been recognize... more The Harderian gland (HG), a sero-mucous secreting organ in the eye orbit, has long been recognized as immunologically important in chickens. During experimentation to characterize immune components of the gland, proteomics analysis revealed the presence of hematopoietic prostaglandin D synthase (H-PGDS). Extraction of total RNA followed by RT-PCR produced cDNA of 597 base pairs. DNA sequencing revealed nucleic acid and predicted amino acid sequences that were 99% aligned with the one published sequence for chicken H-PGDS of the spleen. Alignment with murine, rat, and human H-PGDS were 69, 69, and 66%, respectively. Ocular vaccination of chickens with a Newcastle Disease/Infectious Bronchitis vaccine (Mass.-Ark. Strain) induced an increase in H-PGDS expression determined by real-time PCR. Furthermore, immunohistochemistry of frozen HG sections showed positive stained cells for both H-PGDS and mast cell tryptase in the sub-epithelial cell layers of the HG ducts. Based on the potent va...
of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and eviden... more of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
Characterization of the high confidence novel genes. Table S13. Phylogenetic analysis of represen... more Characterization of the high confidence novel genes. Table S13. Phylogenetic analysis of representative novel genes. Figure S3. Characterization of the novel transcripts. (PDF 232 kb)
Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental se... more Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental set level
Background: Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chi... more Background: Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chickens caused by the oncogenic Gallid herpesvirus type 2 (GaHV-2; MDV). Like several human lymphomas the neoplastic MD lymphoma cells overexpress the CD30 antigen (CD30) and are in minority, while the non-neoplastic cells (CD30) form the majority of population. MD is a unique natural in-vivo model of human CD30 lymphomas with both natural CD30 lymphomagenesis and spontaneous regression. The exact mechanism of neoplastic transformation from CD30 expressing phenotype to CD30 expressing neoplastic phenotype is unknown. Here, using microarray, proteomics and Systems Biology modeling; we compare the global gene expression of CD30 and CD30 cells to identify key pathways of neoplastic transformation. We propose and test a specific mechanism of neoplastic transformation, and genetic resistance, involving the MDV oncogene Meq, host gene products of the Nuclear Factor Kappa B (NF-κB) family and CD3...
As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche... more As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche and plays a central role in comparative and evolutionary genomics. However, the chicken genome’s coding sequences, intron/exon structures, and potential protein products from each gene in different tissues are not conclusively identified experimentally. We present here Chickspress (http://geneatlas.arl.arizona.edu/), a tissue specific expression atlas for chicken. We are experimentally annotating the chicken genome by directly determining expressed sequences within the genome. Using RNASeq, proteomics and proteogenomic mapping we are analyzing 15 tissues each from two Red Jungle Fowl (male and female) and displaying this on a genome browser. Users are able to view quantitative, tissue-specific expression at both the transcript and protein level. Moreover, we also display novel transcripts identified via RNASeq and novel peptides identified via proteogenomic mapping. Moreover, we are add...
Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Gen... more Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annotate the Chicken Genome. Prepared by J. Smith, D.W. Burt, and the Avian RNAseq Consortium. 89 Noncoding RNAs in the Chicken Genome. Prepared by J. Hertel, M. Fasold, A. Nitsche, I. Erb, P. Prieto, D. Kedra, C. Notredame, T.E. Steeves, P.P. Gardner, and P.F. Stadler. 91 Genome Sequencing in Birds and Evolutionary Inferences from Avian Genome Sequences. Prepared by H. Ellegren. 94 The Use of Avian BAC Libraries and Clones. Prepared by M.N. Romanov and D.K. Griffin. 96 Comparative Genomics. Prepared by D.M. Larkin, M. Farré, and J. Damas. 100 Avian Cytogenetics Goes Functional. Prepared by D.K. Griffin, M.N. Romanov, R. O’Connor, K.E. Fowler, and...
... Authors would like to thank Juliet Tang of LSBI and Wil-liam Monroe of EM center for their te... more ... Authors would like to thank Juliet Tang of LSBI and Wil-liam Monroe of EM center for their technical assistance. REFERENCES 1. Carter DR, Beaupré GS, Giori NJ, Helms JA (1998) Mechanobiology of skeletal regeneration. Clin Orthop 355 Suppl: S41-S55 2. Pauwels F. 1980. ...
ASME 2008 Summer Bioengineering Conference, Parts A and B, 2008
ABSTRACT In the United States, it is estimated that in 2008 approximately 1.2 million people will... more ABSTRACT In the United States, it is estimated that in 2008 approximately 1.2 million people will suffer a new or recurrent myocardial infarction. In 2005, the latest full year for which statistics are available, 16 million Americans (7.3% of the population) had some form of coronary heart disease. Loss of myocardium as a result of myocardial infarction increases wall stress locally and globally and triggers adaptive responses at the molecular, cellular, and tissue levels. These adaptive responses can lead to left ventricular dilation and congestive heart failure. Accurate non-invasive evaluation of myocardial structural degeneration (damage) and left ventricular remodeling following an infarct would have both prognostic and therapeutic value clinically.
Veterinary immunology and immunopathology, Jan 15, 2005
The Harderian gland (HG), a sero-mucous secreting organ in the eye orbit, has long been recognize... more The Harderian gland (HG), a sero-mucous secreting organ in the eye orbit, has long been recognized as immunologically important in chickens. During experimentation to characterize immune components of the gland, proteomics analysis revealed the presence of hematopoietic prostaglandin D synthase (H-PGDS). Extraction of total RNA followed by RT-PCR produced cDNA of 597 base pairs. DNA sequencing revealed nucleic acid and predicted amino acid sequences that were 99% aligned with the one published sequence for chicken H-PGDS of the spleen. Alignment with murine, rat, and human H-PGDS were 69, 69, and 66%, respectively. Ocular vaccination of chickens with a Newcastle Disease/Infectious Bronchitis vaccine (Mass.-Ark. Strain) induced an increase in H-PGDS expression determined by real-time PCR. Furthermore, immunohistochemistry of frozen HG sections showed positive stained cells for both H-PGDS and mast cell tryptase in the sub-epithelial cell layers of the HG ducts. Based on the potent va...
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