Life Sciences Commons^™

Integrating Evolutionary And Functional Approaches To Infer Adaptation At Specific Loci, Jay F. Storz, Christopher W. Wheat

Jay F. Storz Publications

Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests …

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelyenne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Faculty Publications

No abstract provided.

Comparative Mitogenomics Of Braconidae (Insecta: Hymenoptera) And The Phylogenetic Utility Of Mitochondrial Genomes With Special Reference To Holometabolous Insects, Shu-Jun Wei, Min Shi, Michael J. Sharkey, Cornelis Van Achterberg, Xue-Xin Chen

Entomology Faculty Publications

BACKGROUND: Animal mitochondrial genomes are potential models for molecular evolution and markers for phylogenetic and population studies. Previous research has shown interesting features in hymenopteran mitochondrial genomes. Here, we conducted a comparative study of mitochondrial genomes of the family Braconidae, one of the largest families of Hymenoptera, and assessed the utility of mitochondrial genomic data for phylogenetic inference at three different hierarchical levels, i.e., Braconidae, Hymenoptera, and Holometabola.

RESULTS: Seven mitochondrial genomes from seven subfamilies of Braconidae were sequenced. Three of the four sequenced A+T-rich regions are shown to be inverted. Furthermore, all species showed reversal of strand asymmetry, suggesting …

Differences In The Transcriptome Signatures Of Two Genetically Related Entamoeba Histolytica Cell Lines Derived From The Same Isolate With Different Pathogenic Properties, Laura Biller, Paul H. Davis, Manuela Tillack, Jenny Matthiesen, Hannelore Lotter, Samuel L. Stanley, Egbert Tannich, Iris Bruchhaus

Biology Faculty Publications

Results: The availability of two genetically very similar cell lines (A and B) derived from the laboratory isolate Entamoeba histolytica HM-1:IMSS, which differ in their virulence properties, provides a powerful tool for identifying pathogenicity factors of the causative agent of human amoebiasis. Cell line A is incapable inducing liver abscesses in gerbils, whereas interaction with cell line B leads to considerable abscess formation. Phenotypic characterization of both cell lines revealed that trophozoites from the pathogenic cell line B have a larger cell size, an increased growth rate in vitro, an increased cysteine peptidase activity and higher resistance to nitric …

A Framework For Automated Enrichment Of Functionally Significant Inverted Repeats In Whole Genomes, Cyriac Kandoth, Fikret ErçAl, Ronald L. Frank

Computer Science Faculty Research & Creative Works

Background: RNA transcripts from genomic sequences showing dyad symmetry typically adopt hairpin-like, cloverleaf, or similar structures that act as recognition sites for proteins. Such structures often are the precursors of non-coding RNA (ncRNA) sequences like microRNA (miRNA) and small-interfering RNA (siRNA) that have recently garnered more functional significance than in the past. Genomic DNA contains hundreds of thousands of such inverted repeats (IRs) with varying degrees of symmetry. But by collecting statistically significant information from a known set of ncRNA, we can sort these IRs into those that are likely to be functional.

Results: A novel method was developed to …

Genomic Profiling Of Messenger Rnas And Micrornas Reveals Potential Mechanisms Of Tweak-Induced Skeletal Muscle Wasting In Mice, Siva K. Panguluri, Shephali Bhatnagar, Akhilesh Kumar, John J. Mccarthy, Apurva K. Srivastava, Nigel G. Cooper, Robert F. Lundy, Ashok Kumar

Physiology Faculty Publications

BACKGROUND: Skeletal muscle wasting is a devastating complication of several physiological and pathophysiological conditions. Inflammatory cytokines play an important role in the loss of skeletal muscle mass in various chronic diseases. We have recently reported that proinflammatory cytokine TWEAK is a major muscle-wasting cytokine. Emerging evidence suggests that gene expression is regulated not only at transcriptional level but also at post-transcriptional level through the expression of specific non-coding microRNAs (miRs) which can affect the stability and/or translation of target mRNA. However, the role of miRs in skeletal muscle wasting is unknown.

METHODOLOGY/PRINCIPAL FINDINGS: To understand the mechanism of action of …

The Prospects For Sequencing The Western Corn Rootworm Genome, Nicholas Miller, S. Richards, T. W. Sappington

Department of Entomology: Faculty Publications

Historically, obtaining the complete sequence of eukaryotic genomes has been an expensive and complex task. For this reason, efforts to sequence insect genomes have largely been confined to model organisms, species that are important to human health and representative species from a few insect orders. This situation is set to change as a number of ‘next generation’ sequencing technologies are making largescale DNA sequencing both affordable and accessible. Sequencing the genome of the western corn rootworm, Diabrotica virgifera virgifera, is likely to become a realistic proposition within the next 2 years. In the meantime, there is an active community …

Genomic And Transcriptomic Studies In Mycobacterium Avium Subspecies Paratuberculosis, J. P. Bannantine, Adel M. Talaat

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Microarray technology is an important tool in functional genomic research. It has enabled a deeper analysis of genomic diversity among bacteria belonging to the Mycobacterium avium complex (MAC). In addition, the expression of thousands of genes can be studied simultaneously in a single experiment. With the complete genome sequence of a bovine isolate of M. avium subspecies paratuberculosis, and the independent construction of DNA microarrays in our laboratories, transcriptomic studies for this veterinary pathogen are now possible. Furthermore, the bovine genome sequence project is completed and bovine arrays have been developed to examine host responses to infection with M. avium …

Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey S. Morris

Jeffrey S. Morris

A recent article published in The Annals of Applied Statistics (AOAS) by two MD Anderson researchers—Keith Baggerly and Kevin Coombes—dissects results from a highly-influential series of medical papers involving genomics-driven personalized cancer therapy, and outlines a series of simple yet fatal flaws that raises serious questions about the veracity of the original results. Having immediate and strong impact, this paper, along with related work, is providing the impetus for new standards of reproducibility in scientific research.

Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the …

Bayesian Random Segmentationmodels To Identify Shared Copy Number Aberrations For Array Cgh Data, Veerabhadran Baladandayuthapani, Yuan Ji, Rajesh Talluri, Luis E. Nieto-Barajas, Jeffrey S. Morris

Jeffrey S. Morris

Array-based comparative genomic hybridization (aCGH) is a high-resolution high-throughput technique for studying the genetic basis of cancer. The resulting data consists of log fluorescence ratios as a function of the genomic DNA location and provides a cytogenetic representation of the relative DNA copy number variation. Analysis of such data typically involves estimation of the underlying copy number state at each location and segmenting regions of DNA with similar copy number states. Most current methods proceed by modeling a single sample/array at a time, and thus fail to borrow strength across multiple samples to infer shared regions of copy number aberrations. …

Detecting Outlier Genes From High-Dimensional Data: A Fuzzy Approach, Debashis Ghosh

Debashis Ghosh

A recent nding in cancer research has been the characterization of previously undis- covered chromosomal abnormalities in several types of solid tumors. This was found based on analyses of high-throughput data from gene expression microarrays and motivated the development of so-called `outlier' tests for dierential expression. One statistical issue was the potential discreteness of the test statistics. Using ideas from fuzzy set theory, we develop fuzzy outlier detection algorithms that have links to ideas in multiple comparisons. Two- and K-sample extensions are considered. The methodology is illustrated by application to two microarray studies.

Data Sharing, Latency Variables And The Science Commons, Jorge L. Contreras

Jorge L Contreras

Over the past decade, the rapidly decreasing cost of computer storage and the increasing prevalence of high-speed Internet connections have fundamentally altered the way in which scientific research is conducted. Led by scientists in disciplines such as genomics, the rapid sharing of data sets and cross-institutional collaboration promise to increase scientific efficiency and output dramatically. As a result, an increasing number of public “commons” of scientific data are being created: aggregations intended to be used and accessed by researchers worldwide. Yet, the sharing of scientific data presents legal, ethical and practical challenges that must be overcome before such science commons …

Genetics And Genomics Of Complex Diseases;Mouse Atherosclerosis Modifier Genes And Human Gene Expression After Bariatric Surgery, Stela Z. Berisha

ETD Archive

The overall goal of our research was to study and identify genes involved in the development of complex diseases in mice and humans through integrative genetic/genomic approaches. Two complex diseases were the focus of research, atherosclerosis and type 2 diabetes. Mouse models of atherosclerosis, in which the genetic background and the environment can be controlled for, were used to identify and validate atherosclerosis modifier genes. We studied an atherosclerosis quantitative trait locus (QTL) on the distal end of chromosome 5, called Ath24, and generated interval-specific congenic mice on the atherosclerosis resistant AKR and susceptible DBA/2 apoE-deficient strains. To date we …

Identifying Protein Complexes From Interaction Networks Based On Clique Percolation And Distance Restriction, Jianxin Wang, Binbin Liu, Min Li, Yi Pan

Computer Science Faculty Publications

Background: Identification of protein complexes in large interaction networks is crucial to understand principles of cellular organization and predict protein functions, which is one of the most important issues in the post-genomic era. Each protein might be subordinate multiple protein complexes in the real protein-protein interaction networks.Identifying overlapping protein complexes from protein-protein interaction networks is a considerable research topic.

Result: As an effective algorithm in identifying overlapping module structures, clique percolation method (CPM) has a wide range of application in social networks and biological networks. However, the recognition accuracy of algorithm CPM is lowly. Furthermore, algorithm CPM is unfit to …

Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu

Faculty Publications

Motivation

Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes.

Results

We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually …

Genome3d: A Viewer-Model Framework For Integrating And Visualizing Multi-Scale Epigenomic Information Within A Three-Dimensional Genome, Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng

Faculty Publications

Background
New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

Results
We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …