Physiol. Genomics -- Table of Contents (October 17 2005, 23 [2])

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Perspective:

Mingyu Liang and Beverly Ventura: Physiological genomics in PG and beyond: July to September 2005
Physiol. Genomics 23: 119-124, 2005; doi:10.1152/physiolgenomics.00212.2005 [Full Text] [PDF]

Andreas Werner and Ariane Berdal: Natural antisense transcripts: sound or silence?
Physiol. Genomics 23: 125-131, 2005; doi:10.1152/physiolgenomics.00124.2005 [Abstract] [Full Text] [PDF]

Article:

Charles Decraene, Rachid Benchaouir, Marie-Agnes Dillies, David Israeli, Sylvie Bortoli, Christelle Rochon, Philippe Rameau, Amandine Pitaval, Diana Tronik-Le Roux, Olivier Danos, Xavier Gidrol, Luis Garcia, and Geneviève Piétu: Global transcriptional characterization of SP and MP cells from the myogenic C2C12 cell line: effect of FGF6
Physiol. Genomics 23: 132-149, 2005. First published July 20, 2005; doi:10.1152/physiolgenomics.00141.2004 [Abstract] [Full Text] [PDF]

Ilaria Filesi, Francesca Gullotta, Giovanna Lattanzi, Maria Rosaria D'Apice, Cristina Capanni, Anna Maria Nardone, Marta Columbaro, Gioacchino Scarano, Elisabetta Mattioli, Patrizia Sabatelli, Nadir M. Maraldi, Silvia Biocca, and Giuseppe Novelli: Alterations of nuclear envelope and chromatin organization in mandibuloacral dysplasia, a rare form of laminopathy
Physiol. Genomics 23: 150-158, 2005. First published July 26, 2005; doi:10.1152/physiolgenomics.00060.2005 [Abstract] [Full Text] [PDF]

G. Challen, B. Gardiner, G. Caruana, X. Kostoulias, G. Martinez, M. Crowe, D. F. Taylor, J. Bertram, M. Little, and S. M. Grimmond: Temporal and spatial transcriptional programs in murine kidney development
Physiol. Genomics 23: 159-171, 2005. First published July 5, 2005; doi:10.1152/physiolgenomics.00043.2005 [Abstract] [Full Text] [PDF] [Supplementary Tables and Figures]

Simon X. Liang, Ross Summer, Xi Sun, and Alan Fine: Gene expression profiling and localization of Hoechst-effluxing CD45– and CD45+ cells in the embryonic mouse lung
Physiol. Genomics 23: 172-181, 2005. First published August 2, 2005; doi:10.1152/physiolgenomics.00059.2005 [Abstract] [Full Text] [PDF] [Supplemental Figures]

Elena Sarropoulou, Georgios Kotoulas, Deborah M. Power, and Robert Geisler: Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology
Physiol. Genomics 23: 182-191, 2005. First published July 26, 2005; doi:10.1152/physiolgenomics.00139.2005 [Abstract] [Full Text] [PDF] [Supplemental Data]

Chris J. Sullivan, Thomas H. Teal, Ian P. Luttrell, Khoa B. Tran, Mette A. Peters, and Hunter Wessells: Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats
Physiol. Genomics 23: 192-205, 2005. First published August 23, 2005; doi:10.1152/physiolgenomics.00112.2005 [Abstract] [Full Text] [PDF] [Supplemental Data]

Peter Åkerblad, Robert Månsson, Anna Lagergren, Simonetta Westerlund, Barbro Basta, Ulrika Lind, Anders Thelin, Ramiro Gisler, David Liberg, Sven Nelander, Krister Bamberg, and Mikael Sigvardsson: Gene expression analysis suggests that EBF-1 and PPAR ${gamma}$ 2 induce adipogenesis of NIH-3T3 cells with similar efficiency and kinetics
Physiol. Genomics 23: 206-216, 2005. First published August 16, 2005; doi:10.1152/physiolgenomics.00015.2005 [Abstract] [Full Text] [PDF] [Supplementary Data (Figures)]

Juan J. Loor, Heather M. Dann, Robin E. Everts, Rosane Oliveira, Cheryl A. Green, Nicole A. Janovick Guretzky, Sandra L. Rodriguez-Zas, Harris A. Lewin, and James K. Drackley: Temporal gene expression profiling of liver from periparturient dairy cows reveals complex adaptive mechanisms in hepatic function
Physiol. Genomics 23: 217-226, 2005. First published August 9, 2005; doi:10.1152/physiolgenomics.00132.2005 [Abstract] [Full Text] [PDF] [Supplemental Material]

Katharine M. Brauch, Nirish D. Dhruv, Eric A. Hanse, and Matthew T. Andrews: Digital transcriptome analysis indicates adaptive mechanisms in the heart of a hibernating mammal
Physiol. Genomics 23: 227-234, 2005. First published August 2, 2005; doi:10.1152/physiolgenomics.00076.2005 [Abstract] [Full Text] [PDF] [Supplemental Tables]

Alexandra Schumann, Sophie Nutten, Dominique Donnicola, Elena M. Comelli, Robert Mansourian, Christine Cherbut, Irène Corthesy-Theulaz, and Clara Garcia-Rodenas: Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome
Physiol. Genomics 23: 235-245, 2005. First published August 30, 2005; doi:10.1152/physiolgenomics.00057.2005 [Abstract] [Full Text] [PDF] [Supplemental Tables]

Toolbox:

Simon N. Twigger, Dean Pasko, Jeff Nie, Mary Shimoyama, Susan Bromberg, Dan Campbell, Jiali Chen, Norberto dela Cruz, Chunyu Fan, Cindy Foote, Glenn Harris, Brian Hickmann, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Nataliya Nenasheva, Rajni Nigam, Victoria Petri, Dorothy Reilly, Victor Ruotti, Eric Schauberger, Kathy Seiler, Ronit Slyper, Jennifer Smith, Weiye Wang, Wenhua Wu, Lan Zhao, Angela Zuniga-Meyer, Peter J. Tonellato, Anne E. Kwitek, and Howard J. Jacob: Tools and strategies for physiological genomics: the Rat Genome Database
Physiol. Genomics 23: 246-256, 2005. First published August 16, 2005; doi:10.1152/physiolgenomics.00040.2005 [Abstract] [Full Text] [PDF]

Cover Caption:

Cover Cover: Overview of physiological genomics in the rat and the various translational technologies available to relate rat research to human systems. Left: the traditional positional cloning process wherein 2 rats, 1 possessing the phenotype of interest and the other an unaffected control strain, are crossed. The progeny are genotyped and phenotyped, leading to the definition of quantitative trait loci linking the phenotype to specific regions of the genome. The regions are then examined for potential candidate genes, and comparative genomics is used to integrate evidence from other organisms or to translate results to the human genome. Translation of information to the human system is also becoming possible using informatic tools such as ontologies. Various ontologies are shown connecting elements of the experimental paradigm to related human data. For details, see Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, and Jacob HJ. Tools and strategies for physiological genomics: the Rat Genome Database. Physiol. Genomics 23: 246-256, 2005 First published August 16, 2005; doi: 10.1152/physiolgenomics.00040.2005.