Digital Commons Network^™

Estimating Gene Signals From Noisy Microarray Images, Pinaki Sarder, Arye Nehorai, Paul H. Davis, Samuel L. Stanley Jr.

Biology Faculty Publications

In oligonucleotide microarray experiments, noise is a challenging problem, as biologists now are studying their organisms not in isolation but in the context of a natural environment. In low photomultiplier tube (PMT) voltage images, weak gene signals and their interactions with the background fluorescence noise are most problematic. In addition, nonspecific sequences bind to array spots intermittently causing inaccurate measurements. Conventional techniques cannot precisely separate the foreground and the background signals. In this paper, we propose analytically based estimation technique. We assume a priori spot-shape information using a circular outer periphery with an elliptical center hole. We assume Gaussian statistics …

An Improved String Composition Method For Sequence Comparison, Guoquing Lu, Shunpu Zhang, Xiang Fang

Biology Faculty Publications

Background: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector (CV) methods, which use the frequencies of nucleotide or amino acid strings to represent sequence information, show promising results in genome sequence comparison of prokaryotes. The existing CV-based methods, however, suffer certain statistical problems, thereby underestimating the amount of evolutionary …

Antiretroviral Pre-Exposure Prophylaxis Prevents Vaginal Transmission Of Hiv-1 In Humanized Blt Mice, Paul W. Denton, Jacob D. Estes, Zhifeng Sun, Florence A. Othieno, Bangdong L. Wei, Anja K. Wege, Daniel A. Powell, Deborah A. Payne, Ashley T. Haase, J. Victor Garcia

Biology Faculty Publications

Background: Worldwide, vaginal transmission now accounts for more than half of newly acquired HIV-1 infections. Despite the urgency to develop and implement novel approaches capable of preventing HIV transmission, this process has been hindered by the lack of adequate small animal models for preclinical efficacy and safety testing. Given the importance of this route of transmission, we investigated the susceptibility of humanized mice to intravaginal HIV-1 infection.

Methods and Findings: We show that the female reproductive tract of humanized bone marrow–liver–thymus (BLT) mice is reconstituted with human CD4þ T and other relevant human cells, rendering these humanized mice …

Optimal Data Partitioning And A Test Case For Ray-Finned Fishes (Actinopterygii) Based On Ten Nuclear Loci, Chenhong Li, Guoqing Lu, Guillermo Orti

Biology Faculty Publications

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative …

New Genus And Species Of Aporocotylidae (Digenea) From A Basal Actinopterygian, The American Paddlefish, Polyodon Spathula, (Acipenseriformes: Polyodontidae) From The Mississippi Delta, Stephen A. Bullard, Scott D. Snyder, Kirsten Jensen, Robin M. Overstreet

Biology Faculty Publications

Acipensericola petersoni n. gen., n. sp. (Digenea: Aporocotylidae) infects the heart of the American paddlefish Polyodon spathula (Walbaum, 1792) in the Mississippi Delta. It has robust, spike-like body spines arranged in ventrolateral transverse rows; a bowl-shaped anterior sucker centered on the mouth and having minute spines on the inner anteroventral surface only; a pharynx; an inverse U-shaped ceca extending to near the posterior body end; intercecal testes comprising a pre-ovarian testicular column plus a single testis posteriorly; an extensively lobed ovary located medially and immediately posterior to the testicular column; a spherical ootype that is intercecal and post-ovarian; a Laurer’s …