A method for identifying ancient introgression between caballine and non-caballine equids using whole genome high throughput data.

Introgression is one of the main mechanisms that transfer adapted alleles between species. The advantageous variants will get positively selected and retained in the recipient population while rest of the variants undergo negative selection. When analyzing horse genome, two alleles were found in CXCL16 gene, one associated with susceptibility and one with resistance to developing persistent shedding of the Equine Arteritis Virus. The two alleles differ by 4 non-synonymous variants in exon 1 of the gene. Comparison with 3 non-caballine equids (zebras, asses and hemiones) revealed that one haplotype was almost identical to the haplotype found in non-caballines while the other had differences characteristic of 4.5 million years since a common ancestor. Based on this observation, we project that an ancient introgression event occurred between caballine and non-caballine equids. If so, we should be able to find more instances of introgression between these species. We developed a method to identify putatively introgressed segments in the horse genome. It is estimated that non-caballine equids such as zebras and asses diverged from horses between 4 and 4.5 MYA. Genomic analysis of these animals vs. equine reference genome reveals the divergence at both the nucleotide and chromosomal level. Whole genome data for the non-caballine equids when mapped to the caballine (Equus caballus) reference genome show a greater frequency of single nucleotide differences than horses have relative to the same reference. We have created a Likelihood Estimate framework that uses this difference in single nucleotide frequencies to predict whether a haplotype evolved along the caballine or non-caballine lineage. Our results demonstrated that these haplotypes are between 0.5 and 2kb in length and are detectable at a rate of several hundred loci per horse. About 1.1% of the equine genome was introgressed and 64% of the identified putative regions were associated with either structural elements, regulatory regions, or both. These regions were responsible for gene products involved in regulation of response to stimuli, signal transduction, integral components of cell membrane and important metabolism pathways such as purine metabolism and thiamine metabolism. Furthermore, these haplotypes occur at high frequency in the horse population suggesting that they are positively selected by evolution

Child with Deletion 9p Syndrome Presenting with Craniofacial Dysmorphism, Developmental Delay, and Multiple Congenital Malformations

A 4-month-old Sri Lankan male child case with a de novo terminal deletion in the p22 → pter region of chromosome 9 is described. The child presented with craniofacial dysmorphism, developmental delay, and congenital malformations in agreement with the consensus phenotype. A distinctive feature observed in this child was complete collapse of the left lung due to malformation of lung tissue. Cytogenetic studies confirmed terminal deletion of the short arm of chromosome 9 distal to band p22 [46,XY,del(9)(p22 → pter)]. This is the first reported case of a de novo deletion 9p syndrome associated with pulmonary hypoplasia. This finding contributes to the widening of the spectrum of phenotypic features associated with deletion 9p syndrome

Comic Based Learning for Students with Visual Impairments

Visual impairment can affect a student's ability to learn since their concept development when interacting with educational material is being limited. Learning activities based on images and visually rich content are mainstream learning methods, where facilitating students with visual impairments for engaged learning can be challenging. For comic books, which have shown promising results in engaged student learning, this problem is more severe. To overcome this challenge, this research presents a novel voice synthesised learning method to reduce the gap between the learning experience of a student with visual impairments compared to a mainstream learning activity. Utilising comic books, the proposed technique and the tool developed extracts semantic content, stores them in a database, and generates an audio stream in multiple languages on the user's demand. To assess the usability of the system, a survey for a selected set of students with visual impairments was carried out. The results showed a mean rating of 5.76 out of 7 for the Informative Interest. Furthermore, a concept-mapping approach was used to analyse the feedback given through the open-ended questions. From the analysis, key concepts with an emphasis on positive emotions, willingness to try again, and features to be improved, were identified

Child with Deletion 9p Syndrome Presenting with Craniofacial Dysmorphism, Developmental Delay, and Multiple Congenital Malformations

A 4-month-old Sri Lankan male child case with a de novo terminal deletion in the p22→pter region of chromosome 9 is described. The child presented with craniofacial dysmorphism, developmental delay, and congenital malformations in agreement with the consensus phenotype. A distinctive feature observed in this child was complete collapse of the left lung due to malformation of lung tissue. Cytogenetic studies confirmed terminal deletion of the short arm of chromosome 9 distal to band p22 [46,XY,del(9)(p22→pter)]. This is the first reported case of a de novo deletion 9p syndrome associated with pulmonary hypoplasia. This finding contributes to the widening of the spectrum of phenotypic features associated with deletion 9p syndrome

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016

I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power Bernie J Daigle, Jr. P3 Designing and writing software for subtractive hybridization of large eukaryotic genomes Deborah Burgess, Stephanie Gehrlich, John C Carmen P4 Tracking the molecular evolution of Pax gene Nicholas Johnson; Chandrakanth Emani P5 Identifying genetic differences in thermally dimorphic and state specific fungi using genomic comparison Stephanie Gehrlich, Deborah Burgess, John C Carmen P6 Identification of conserved genomic regions and variation therein amongst species using next generation sequencing Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch P7 Mining physiological data to identify patients with similar medical events and phenotypes Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang P8 Smart brief for home health monitoring Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber P9 Side-effect term matching for computational adverse drug reaction predictions AKM Sabbir, Sally R Ellingson P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics Yuping Lu, Charles A Phillips, Michael A Langston P11 Deep neural networks for transcriptome-based cancer classification Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui P12 Motif discovery using K-means clustering Mohammed Sayed, Juw Won Park P13 Large scale discovery of active enhancers from nascent RNA sequencing Jing Wang, Qi Liu, Yu Shyr P14 Computationally characterizing genomic pipelines and benchmarking results using GATK best practices on the high performance computing cluster at the University of Kentucky Xiaofei Zhang, Sally R Ellingson P15 Development of approaches enabling the identification of abnormal gene expression from RNA-Seq in personalized oncology Naresh Prodduturi, Gavin R Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W Klee P16 Processing RNA-Seq data of plants infected with coffee ringspot virus Michael M Goodin, Mark Farman, Harrison Inocencio, Chanyong Jang, Jerzy W Jaromczyk, Neil Moore, Kelly Sovacool P17 Comparative transcriptomics of three clinical isolates with different antibiotic resistance patterns Leon Dent, Mike Izban, Sammed Mandape, Shruti Sakhare, Siddharth Pratap, Dana Marshall P18 Metagenomic assessment of possible microbial contamination in the equine reference genome assembly M Scotty DePriest, James N MacLeod, Theodore S Kalbfleisch P19 Molecular evolution of cancer driver genes Chandrakanth Emani, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine P20 Biorepository Laboratory Information Management System Naga Satya V Rao Nagisetty, Rony Jose, Teeradache Viangteeravat, Robert Rooney, David Hain