Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 5 of 5
Full-Text Articles in Life Sciences
Genomic And Gene Regulatory Signatures Of Cryptozoic Adaptation: Loss Of Blue Sensitive Photoreceptors Through Expansion Of Long Wavelength-Opsin Expression In The Red Flour Beetle Tribolium Castaneum, Magdalena Jackowska, Riyue Bao, Zhenyi Liu, Elizabeth C. Mcdonald, Tiffany A. Cook, Markus Friedrich
Genomic And Gene Regulatory Signatures Of Cryptozoic Adaptation: Loss Of Blue Sensitive Photoreceptors Through Expansion Of Long Wavelength-Opsin Expression In The Red Flour Beetle Tribolium Castaneum, Magdalena Jackowska, Riyue Bao, Zhenyi Liu, Elizabeth C. Mcdonald, Tiffany A. Cook, Markus Friedrich
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Recent genome sequence analysis in the red flour beetle Tribolium castaneum indicated that this highly crepuscular animal encodes only two single opsin paralogs: a UV-opsin and a long wavelength (LW)-opsin; however, these animals do not encode a blue (B)-opsin as most other insects. Here, we studied the spatial regulation of the Tribolium single LW- and UV-opsin gene paralogs in comparison to that of the five opsin paralogs in the retina of Drosophila melanogaster.
Results
In situ hybridization analysis reveals that the Tribolium retina, in contrast with other insect retinas, constitutes a homogenous field of ommatidia that have seven …
Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman
Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.
Results
Here we report an online codon-preserved alignment tool (OCPAT) that generates …
Wide Diversity In Structure And Expression Profiles Among Members Of The Caenorhabditis Elegans Globin Protein Family, David Hoogewijs, Eva Geuens, Sylvia Dewilde, Andy Vierstraete, Luc Moens, Serge Vinogradov, Jacques R. Vanfleteren
Wide Diversity In Structure And Expression Profiles Among Members Of The Caenorhabditis Elegans Globin Protein Family, David Hoogewijs, Eva Geuens, Sylvia Dewilde, Andy Vierstraete, Luc Moens, Serge Vinogradov, Jacques R. Vanfleteren
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
The emergence of high throughput genome sequencing facilities and powerful high performance bioinformatic tools has highlighted hitherto unexpected wide occurrence of globins in the three kingdoms of life. In silico analysis of the genome of C. elegans identified 33 putative globin genes. It remains a mystery why this tiny animal might need so many globins. As an inroad to understanding this complexity we initiated a structural and functional analysis of the globin family in C. elegans.
Results
All 33 C. elegans putative globin genes are transcribed. The translated sequences have the essential signatures of single domain bona fide …
Whole Genome Expression Profiling Reveals A Significant Role For Immune Function In Human Abdominal Aortic Aneurysms, Guy M. Lenk, Gerard Tromp, Shantel Weinsheimer, Zoran Gatalica, Ramon Berguer, Helena Kuivaniemi
Whole Genome Expression Profiling Reveals A Significant Role For Immune Function In Human Abdominal Aortic Aneurysms, Guy M. Lenk, Gerard Tromp, Shantel Weinsheimer, Zoran Gatalica, Ramon Berguer, Helena Kuivaniemi
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Abdominal aortic aneurysms are a common disorder with an incompletely understood etiology. We used Illumina and Affymetrix microarray platforms to generate global gene expression profiles for both aneurysmal (AAA) and non-aneurysmal abdominal aorta, and identified genes that were significantly differentially expressed between cases and controls.
Results
Affymetrix and Illumina arrays included 18,057 genes in common; 11,542 (64%) of these genes were considered to be expressed in either aneurysmal or normal abdominal aorta. There were 3,274 differentially expressed genes with a false discovery rate (FDR) ≤ 0.05. Many of these genes were not previously known to be involved in …
A Proteome-Wide Protein Interaction Map For Campylobacter Jejuni, Jodi R. Parrish, Jingkai Yu, Guozhen Liu, Julie A. Hines, Jason E. Chan, Bernie A. Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J. Dirita, Trey Ideker, Phillip Andrews, Russell L. Finley Jr
A Proteome-Wide Protein Interaction Map For Campylobacter Jejuni, Jodi R. Parrish, Jingkai Yu, Guozhen Liu, Julie A. Hines, Jason E. Chan, Bernie A. Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J. Dirita, Trey Ideker, Phillip Andrews, Russell L. Finley Jr
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a food-borne pathogen and a major cause of gastroenteritis worldwide.
Results
Using high-throughput yeast two-hybrid screens we detected and reproduced 11,687 interactions. The resulting interaction map includes 80% of the predicted C. jejuni NCTC11168 proteins and places a large number of poorly characterized proteins into networks that provide initial …