Genetics and Genomics Commons^™

Integration Of Breast Cancer Gene Signatures Based On Graph Centrality, Jianxin Wang, Gang Chen, Min Li, Yi Pan

Computer Science Faculty Publications

Background: Various gene-expression signatures for breast cancer are available for the prediction of clinical outcome. However due to small overlap between different signatures, it is challenging to integrate existing disjoint signatures to provide a unified insight on the association between gene expression and clinical outcome.

Results: In this paper, we propose a method to integrate different breast cancer gene signatures by using graph centrality in a context-constrained protein interaction network (PIN). The context-constrained PIN for breast cancer is built by integrating complete PIN and various gene signatures reported in literatures. Then, we use graph centralities to quantify the importance of …

Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer

Mark R Segal

Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …

Adding Upstream Sequence And A Downstream Reporter To The Bile Acid Inducible Promoter Of Clostridium Scindens Vpi 12708, Bryan Patrick Mason

Masters Theses & Specialist Projects

Bile acids in the small intestines of animals serve to breakdown fats and fatsoluble vitamins. Most of the bile acids are reabsorbed into the enterohepatic circulation, but approximately five percent of these bile acids pass into the large intestine. These bile acids are swiftly deconjugated by the bacterial population, and then subjected to further intestinal bacterial chemical modifications. The most significant of these modifications are 7α-dehydroxylations which form secondary bile acids (deoxycholate and lithocholate). Much research has illuminated the 7α-dehydroxylation pathway: of particular interest is the bile acid inducible operon, for which Clostridium scindens VPI 12708 serves as the model …

Identification Of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests, Yuanyuan Xiao, Mark Segal

Mark R Segal

The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. Here, we propose a novel algorithm, based on random forest methodology, to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived from DNA motif data) and transcription factor binding to gene promoters (as derived from tiling microarrays). We extend the random forest approach to model a multivariate response as represented, for example, by time-course gene expression …

Chess, Chance And Conspiracy, Mark Segal

Mark R Segal

Chess and chance are seemingly strange bedfellows. Luck and/or randomness have no apparent role in move selection when the game is played at the highest levels. However, when competition is at the ultimate level, that of the World Chess Championship (WCC), chess and conspiracy are not strange bedfellows, there being a long and colorful history of accusations levied between participants. One such accusation, frequently repeated, was that all the games in the 1985 WCC (Karpov vs Kasparov) were fixed and prearranged move by move. That this claim was advanced by a former World Champion, Bobby Fischer, argues that it ought …

Caenorhabditis Briggsae Methods, Scott Everet Baird, Helen M. Chamberlin

Biological Sciences Faculty Publications

Caenorhabditis briggsae is being developed in parallel to C. elegans as a model system, primarily for the study of evolution. Like C. elegans, C. briggsae is a protandrous hermaphrodite and like C. elegans, its genome has been sequenced. From this point, these two model systems diverge. The development, behavior, and physiology of C. elegans have been characterized through tens of thousands of genetic and molecular studies. Genetic and molecular characterizations of C. briggsae are relatively few. Experimental resources in C. elegans include a high density recombination map that is well integrated with the genome sequence. The C. briggsae …

The Genetics Of Ray Pattern Variation In Caenorhabditis Briggsae, Scott Everet Baird, Cynthia R. Davidson, Justin C. Bohrer

Biological Sciences Faculty Publications

Background: How does intraspecific variation relate to macroevolutionary change in morphology? This question can be addressed in species in which derived characters are present but not fixed. In rhabditid nematodes, the arrangement of the nine bilateral pairs of peripheral sense organs (rays) in tails of males is often the most highly divergent character between species. The development of ray pattern involves inputs from hometic gene expression patterns, TGFβ signalling, Wnt signalling, and other genetic pathways. In Caenorhabditis briggsae, strain-specific variation in ray pattern has provided an entrée into the evolution of ray pattern. Some strains were fixed for a derived …

Drawing Lines In The Sand: Even Skipped Et Al. And Parasegment Boundaries., James B. Jaynes, Miki Fujioka

Department of Biochemistry and Molecular Biology Faculty Papers

The pair-rule segmentation gene even skipped (eve) is required to activate engrailed stripes and to organize odd-numbered parasegments (PSs). The protein product Eve has been shown to be an active repressor of transcription, and recent models for Eve function suggest that activation of engrailed is indirect, but these models have not been fully tested. Here we identify the forkhead domain transcription factor Sloppy-paired as the key intermediate in the initial activation of engrailed by Eve in odd-numbered parasegments. We also analyze the roles of the transcription factors Runt and Odd-skipped in this process. Detailed analysis of engrailed and pair-rule gene …

The Hyperthermophilic Archaeon Sulfolobus: From Exploration To Exploitation, Stan J.J. Brouns, Thijs J.G. Ettema, Kenneth M. Stedman, Jasper Walther, Hauke Smith, Ambrosius P.L. Snijders, Mark Young, Rolf Bernander, Phillip C. Wright, Betina Siebers, John Van Der Oost

Biology Faculty Publications and Presentations

In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will …

Systematic And Population Genetic Analyses Of Northern Vs Southern Yellow Lady's Slippers (Cypripedium Parviflorum Vars Parviflorum, Pubescens, And Makasin): Inference From Isozyme And Morphological Data, Lisa Ellen Wallace

Dissertations, Theses, and Masters Projects

No abstract provided.

Comparative Mapping Of Arabidopsis Thaliana And Brassica Oleracea Chromosomes Reveals Islands Of Conserved Organization, Stanley P. Kowalski, Tien-Hung Lan, Kenneth A. Feldmann, Andrew H. Patterson

Law Faculty Scholarship

The chromosomes of Arabidopsis thaliana and Brassica oleracea have been extensively rearranged since the divergence of these species; however, conserved regions are evident. Eleven regions of conserved organization were detected, ranging from 3.7 to 49.6 cM in A. thaliana, spanning 158.2 cM (24.6%) of the A. thaliana genome, and 245 cM (29.9%) of the B. oleracea genome. At least 17 translocations and 9 inversions distinguish the genomes of A. thaliana and B. oleracea. In one case B. oleracea homoeologs show a common marker order, which is distinguished from the A. thaliana order by a rearrangement, indicating that the lineages of …

Micronuclear Genome Organization In Euplotes Crassus: A Transposonlike Element Is Removed During Macronuclear Development, Scott Everet Baird, Gina M. Fino, Susan L. Tausta, Lawrence A. Klobutcher

Biological Sciences Faculty Publications

After mating, hypotrichous ciliated protozoa transform a set of their micronuclear chromosomes into thousands of short, linear DNA molecules that form the macronuclear genome. To examine micronuclear genome organization in the hypotrich Euplotes crassus, we have analyzed two cloned segments of micronuclear DNA as well as the macronuclear DNA molecules that are derived from them. E. crassus was found to display a number of features characteristic of other hypotrich genomes, including (i) clustering and close spacing of the precursors of macronuclear DNA molecules, (ii) the frequent occurrence of internal eliminated sequences within macronuclear precursors, (iii) overlapping macronuclear precursors, (iv) lack …

Characterization Of Chromosome Fragmentation In Two Protozoans And Identification Of A Candidate Fragmentation Sequence In Euplotes Crassus, Scott Everet Baird, Lawrence A. Klobutcher

Biological Sciences Faculty Publications

Following the sexual cycle, hypotrichous ciliated protozoans fragment a set of their micronuclear chromosomes to generate the thousands of short, linear DNA molecules present in the transcriptionally active macronucleus. We have used a hybrid selection procedure to examine macronuclear DNA molecules for subtelomeric length heterogeneity to determine whether chromosome fragmentation occurs at unique or multiple sites. The results suggest that multiple, but closely spaced, chromosome fragmentation sites are used by Oxytricha nova. In contrast, Euplotes crassus uses unique chromosome fragmentation sites in a reproducible manner to generate the ends of macronuclear DNA molecules. Additional studies compared DNA sequences in …