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Graph-Regularized Dual Lasso For Robust Eqtl Mapping, Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang

Computer Science Faculty Research & Creative Works

Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and …

Rna Profiles Of Porcine Embryos During Genome Activation Reveal Complex Metabolic Switch Sensitive To In Vitro Conditions, Olga Østrup, Gayla R. Olbricht, Esben Østrup, Poul Hyttel, Philippe Collas, Ryan A. Cabot

Mathematics and Statistics Faculty Research & Creative Works

Fertilization is followed by complex changes in cytoplasmic composition and extensive chromatin reprogramming which results in the abundant activation of totipotent embryonic genome at embryonic genome activation (EGA). While chromatin reprogramming has been widely studied in several species, only a handful of reports characterize changing transcriptome profiles and resulting metabolic changes in cleavage stage embryos. The aims of the current study were to investigate RNA profiles of in vivo developed (ivv) and in vitro produced (ivt) porcine embryos before (2-cell stage) and after (late 4-cell stage) EGA and determine major metabolic changes that regulate totipotency. The period before EGA was …

Nona-Arginine Facilitates Delivery Of Quantum Dots Into Cells Via Multiple Pathways, Yi Xu, Betty Revon Liu, Han Jung Lee, Katie Shannon, Jeffrey G. Winiarz, Tien-Chun Wang, Huey-Jenn Chiang, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Semiconductor quantum dots (QDs) have recently been used to deliver and monitor biomolecules, such as drugs and proteins. However, QDs alone have a low efficiency of transport across the plasma membrane. In order to increase the efficiency, we used synthetic nona-arginine (SR9), a cell-penetrating peptide, to facilitate uptake. We found that SR9 increased the cellular uptake of QDs in a noncovalent binding manner between QDs and SR9. Further, we investigated mechanisms of QD/SR9 cellular internalization. Low temperature and metabolic inhibitors markedly inhibited the uptake of QD/SR9, indicating that internalization is an energy-dependent process. Results from both the pathway inhibitors and …

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 …