Physiol. Genomics -- Table of Contents (December 16 2003, 16 [1])

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Perspectives:

Sergio Kaiser and Laura K. Nisenbaum: Evaluation of common gene expression patterns in the rat nervous system
Physiol. Genomics 16: 1-7, 2003; 10.1152/physiolgenomics.00125.2003 [Abstract] [Full Text]

Call for Papers: Comparative Genomics:

Steven P. Suchyta, Sue Sipkovsky, Robert G. Halgren, Rachael Kruska, Michael Elftman, Miriam Weber-Nielsen, Michael J. Vandehaar, Lan Xiao, Robert J. Tempelman, and Paul M. Coussens: Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts
Physiol. Genomics 16: 8-18, 2003. First published October 14, 2003; 10.1152/physiolgenomics.00028.2003 [Abstract] [Full Text]

Ren Zhang and Chun-Ting Zhang: Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis
Physiol. Genomics 16: 19-23, 2003. First published November 4, 2003; 10.1152/physiolgenomics.00170.2003 [Abstract] [Full Text]

Research Articles:

M. C. K. Yang, J. J. Yang, R. A. McIndoe, and J. X. She: Microarray experimental design: power and sample size considerations
Physiol. Genomics 16: 24-28, 2003. First published October 7, 2003; 10.1152/physiolgenomics.00037.2003 [Abstract] [Full Text]

Holly Van Remmen, Yuji Ikeno, Michelle Hamilton, Mohammad Pahlavani, Norman Wolf, Suzanne R. Thorpe, Nathan L. Alderson, John W. Baynes, Charles J. Epstein, Ting-Ting Huang, James Nelson, Randy Strong, and Arlan Richardson: Life-long reduction in MnSOD activity results in increased DNA damage and higher incidence of cancer but does not accelerate aging
Physiol. Genomics 16: 29-37, 2003; 10.1152/physiolgenomics.00122.2003 [Abstract] [Full Text]

Janine Arens, Kim M. Moar, Sandra Eiden, Karin Weide, Ingrid Schmidt, Julian G. Mercer, Eckhart Simon, and Horst-W. Korf: Age-dependent hypothalamic expression of neuropeptides in wild-type and melanocortin-4 receptor-deficient mice
Physiol. Genomics 16: 38-46, 2003. First published October 14, 2003; 10.1152/physiolgenomics.00123.2003 [Abstract] [Full Text]

Emily P. Tierney, Suzana Tulac, Se-Te Joseph Huang, and Linda C. Giudice: Activation of the protein kinase A pathway in human endometrial stromal cells reveals sequential categorical gene regulation
Physiol. Genomics 16: 47-66, 2003. First published October 7, 2003; 10.1152/physiolgenomics.00066.2003 [Abstract] [Full Text] [Supplemental Tables]

Mary Beth Genter, Paul P. Van Veldhoven, Anil G. Jegga, Bhuvana Sakthivel, Sue Kong, Kristin Stanley, David P. Witte, Catherine L. Ebert, and Bruce J. Aronow: Microarray-based discovery of highly expressed olfactory mucosal genes: potential roles in the various functions of the olfactory system
Physiol. Genomics 16: 67-81, 2003. First published October 21, 2003; 10.1152/physiolgenomics.00117.2003 [Abstract] [Full Text]

Geneviève Aubin-Houzelstein, Nelly R. Da Silva, Sylvain Bellier, Pierrick Salaün, Xavier Montagutelli, and Jean-Jacques Panthier: Genetic interaction between a maternal factor and the zygotic genome controls the intestine length in PRM/Alf mice
Physiol. Genomics 16: 82-89, 2003. First published October 14, 2003; 10.1152/physiolgenomics.00106.2003 [Abstract] [Full Text]

Faina Schwartz, Arvi Duka, Elena Triantafyllidi, Conrado Johns, Irena Duka, Jing Cui, and Haralambos Gavras: Serial analysis of gene expression in mouse kidney following angiotensin II administration
Physiol. Genomics 16: 90-98, 2003. First published October 21, 2003; 10.1152/physiolgenomics.00108.2003 [Abstract] [Full Text]

Linette Pellis, Nicole L. W. Franssen-van Hal, Jan Burema, and Jaap Keijer: The intraclass correlation coefficient applied for evaluation of data correction, labeling methods, and rectal biopsy sampling in DNA microarray experiments
Physiol. Genomics 16: 99-106, 2003. First published October 21, 2003; 10.1152/physiolgenomics.00111.2003 [Abstract] [Full Text]

D. L. Jones, J. Petty, D. C. Hoyle, A. Hayes, E. Ragni, L. Popolo, S. G. Oliver, and L. I. Stateva: Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway
Physiol. Genomics 16: 107-118, 2003. First published October 21, 2003; 10.1152/physiolgenomics.00139.2003 [Abstract] [Full Text]

Teresa L. Squire and Matthew T. Andrews: Pancreatic triacylglycerol lipase in a hibernating mammal. I. Novel genomic organization
Physiol. Genomics 16: 119-130, 2003. First published October 28, 2003; 10.1152/physiolgenomics.00167.2002 [Abstract] [Full Text]

Teresa L. Squire, Mark E. Lowe, Vernon W. Bauer, and Matthew T. Andrews: Pancreatic triacylglycerol lipase in a hibernating mammal. II. Cold-adapted function and differential expression
Physiol. Genomics 16: 131-140, 2003. First published October 28, 2003; 10.1152/physiolgenomics.00168.2002 [Abstract] [Full Text]

A. Lionikas, D. A. Blizard, D. J. Vandenbergh, M. G. Glover, J. T. Stout, G. P. Vogler, G. E. McClearn, and L. Larsson: Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage
Physiol. Genomics 16: 141-152, 2003; 10.1152/physiolgenomics.00103.2003 [Abstract] [Full Text] [Supplemental Table]

Toolbox:

William Nobis, Xiaoning Ren, Steven P. Suchyta, Thomas R. Suchyta, Adroaldo J. Zanella, and Paul M. Coussens: Development of a porcine brain cDNA library, EST database, and microarray resource
Physiol. Genomics 16: 153-159, 2003. First published October 14, 2003; 10.1152/physiolgenomics.00099.2003 [Abstract] [Full Text]

Cover Caption:

Cover

Cover: Gene discovery and the characterization of tissues based on microarray gene expression database mining and profiling. Top: portion of a Pearson correlation hierarchical tree clustering of genes and tissues using 269 "olfactorome" genes, so called based on their high relative expression in olfactory mucosa samples versus 81 different mouse tissue samples. Tissues and genes that share similar expression profiles are grouped on the same parent of their hierarchical tree branch. Each row represents a gene and each column a mouse tissue sample. Red indicates high expression, blue indicates low expression. Bottom: in vivo localization of highly expressed genes in the olfactory mucosa using in situ hybridization and immunohistochemical localization. In situ hybridization (left) demonstrates olfactory mucosa localization of Plunc mRNA, the gene with the highest relative expression in olfactory mucosa compared to all other tissues in the expression database (signal appears as punctate bright white foci). Enzyme activity measurements and immunohistochemical localization (right) confirmed high expression of Spgl1 (encoding sphingosine phosphate lyase), which had not been localized in olfactory mucosa previously. Strong staining is present within mature olfactory sensory neurons (red peri-nuclear reaction product). For further discussion, see article by Genter MB, Van Veldhoven PP, Jegga AG, Sakthivel B, Kong S, Stanley K, Witte DP, Ebert CL, and Aronow BJ. Microarray-based discovery of highly expressed olfactory mucosal genes: potential roles in the various functions of the olfactory system. Physiol Genomics 16: 67-81, 2003. First published October 21, 2003; 10.1152/physiolgenomics.00117.2003.