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Full-Text Articles in Life Sciences
The Brain Transcriptome Of The Wolf Spider, Schizocosa Ocreata, Daniel Stribling, Peter L. Chang, Justin E. Dalton, Christopher A. Conow, Malcolm Rosenthal, Eileen Hebets, Rita M. Graze, Michelle N. Arbeitman
The Brain Transcriptome Of The Wolf Spider, Schizocosa Ocreata, Daniel Stribling, Peter L. Chang, Justin E. Dalton, Christopher A. Conow, Malcolm Rosenthal, Eileen Hebets, Rita M. Graze, Michelle N. Arbeitman
School of Biological Sciences: Faculty Publications
Objectives: Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a …
Transcriptome Prediction Performance Across Machine Learning Models And Diverse Ancestries, Paul Chukwuebuka Okoro, Ryan Schubert, Xiuqing Guo, W. Craig Johnson, Jerome I. Rotter, Ina Hoeschele, Yongmei Liu, Hae Kyung Im, Amy Luke, Lara R. Dugas, Heather Wheeler
Transcriptome Prediction Performance Across Machine Learning Models And Diverse Ancestries, Paul Chukwuebuka Okoro, Ryan Schubert, Xiuqing Guo, W. Craig Johnson, Jerome I. Rotter, Ina Hoeschele, Yongmei Liu, Hae Kyung Im, Amy Luke, Lara R. Dugas, Heather Wheeler
Biology: Faculty Publications and Other Works
Transcriptome prediction methods such as PrediXcan and FUSION have become popular in complex trait mapping. Most transcriptome prediction models have been trained in European populations using methods that make parametric linear assumptions like the elastic net (EN). To potentially further optimize imputation performance of gene expression across global populations, we built transcriptome prediction models using both linear and non-linear machine learning (ML) algorithms and evaluated their performance in comparison to EN. We trained models using genotype and blood monocyte transcriptome data from the Multi-Ethnic Study of Atherosclerosis (MESA) comprising individuals of African, Hispanic, and European ancestries and tested them using …
Gene Expression Associated With Disease Resistance And Long-Term Growth In A Reef-Building Coral, Emma R. Kelley, Robin S. Sleith, Mikhail V. Matz, Rachel M. Wright
Gene Expression Associated With Disease Resistance And Long-Term Growth In A Reef-Building Coral, Emma R. Kelley, Robin S. Sleith, Mikhail V. Matz, Rachel M. Wright
Biological Sciences: Faculty Publications
Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However, little is known about the mechanisms and trade-offs of pathogen resistance in reef-building corals. Here, we measure pathogen resistance in Montastraea cavernosa from FGBNMS. We identified individual colonies that demonstrated resistance or susceptibility to Vibrio spp. in a controlled laboratory environment. Long-term growth patterns suggest no trade-off between disease resistance and calcification. Predictive (pre-exposure) gene expression highlights …
Rna In Situ Hybridization For Detecting Gene Expression Patterns In The Abdomens And Wings Of Drosophila Species, Mujeeb Olushola Shittu, Tessa Steenwinkel, William Dion, Nathan Ostlund, Komal Raja, Thomas Werner
Rna In Situ Hybridization For Detecting Gene Expression Patterns In The Abdomens And Wings Of Drosophila Species, Mujeeb Olushola Shittu, Tessa Steenwinkel, William Dion, Nathan Ostlund, Komal Raja, Thomas Werner
Michigan Tech Publications
RNA in situ hybridization (ISH) is used to visualize spatio-temporal gene expression patterns with broad applications in biology and biomedicine. Here we provide a protocol for mRNA ISH in developing pupal wings and abdomens for model and non-model Drosophila species. We describe best practices in pupal staging, tissue preparation, probe design and synthesis, imaging of gene expression patterns, and image-editing techniques. This protocol has been successfully used to investigate the roles of genes underlying the evolution of novel color patterns in non-model Drosophila species.
Modulation Of Bacterial Fitness And Virulence Through Antisense Rnas, Jess A. Millar, Rahul Raghavan
Modulation Of Bacterial Fitness And Virulence Through Antisense Rnas, Jess A. Millar, Rahul Raghavan
Biology Faculty Publications and Presentations
Regulatory RNAs contribute to gene expression control in bacteria. Antisense RNAs (asRNA) are a class of regulatory RNAs that are transcribed from opposite strands of their target genes. Typically, these untranslated transcripts bind to cognate mRNAs and rapidly regulate gene expression at the post-transcriptional level. In this article, we review asRNAs that modulate bacterial fitness and increase virulence. We chose examples that underscore the variety observed in nature including, plasmid- and chromosome-encoded asRNAs, a riboswitch-regulated as RNA, and as RNAs that require other RNAs or RNA binding proteins for stability and activity. We explore how as RNAs improve bacterial fitness …
Intragenic Dna Methylation Regulates Insect Gene Expression And Reproduction Through The Mbd/Tip60 Complex, Guanfeng Xu, Hao Lyu, Yangqin Yi, Yuling Peng, Qili Feng, Qisheng Song, Chengcheng Gong, Xuezhen Peng, Subba Reddy Palli, Sichun Zheng
Intragenic Dna Methylation Regulates Insect Gene Expression And Reproduction Through The Mbd/Tip60 Complex, Guanfeng Xu, Hao Lyu, Yangqin Yi, Yuling Peng, Qili Feng, Qisheng Song, Chengcheng Gong, Xuezhen Peng, Subba Reddy Palli, Sichun Zheng
Entomology Faculty Publications
DNA methylation is an important epigenetic modification. However, the regulations and functions of insect intragenic DNA methylation remain unknown. Here, we demonstrate that a regulatory mechanism involving intragenic DNA methylation controls ovarian and embryonic developmental processes in Bombyx mori. In B. mori, DNA methylation is found near the transcription start site (TSS) of ovarian genes. By promoter activity analysis, we observed that 5′ UTR methylation enhances gene expression. Moreover, methyl-DNA-binding domain protein 2/3 (MBD2/3) binds to the intragenic methyl-CpG fragment and recruits acetyltransferase Tip60 to promote histone H3K27 acetylation and gene expression. Additionally, genome-wide analyses showed that the peak …
Disruption Of Cellular P-Bodies During An Adenovirus Infection, La`Quita Randolph, Kevin Neubrecht, Kasey A. Karen
Disruption Of Cellular P-Bodies During An Adenovirus Infection, La`Quita Randolph, Kevin Neubrecht, Kasey A. Karen
Graduate Research Showcase
Adenovirus has made major contributions in medicine by serving as a model DNA virus to study other viruses, such as human papillomavirus (HPV). Adenoviruses are a diverse family of nonenveloped, double-stranded DNA viruses that are ubiquitous to animals and humans. There are over 67 serotypes of human adenoviruses that can cause a variety of illnesses including, gastroenteritis, conjunctivitis and respiratory infections. Adenovirus can cause these infections by invading host cells and producing an environment that is favorable for viral replication. During the early phases of infection, adenovirus expresses various viral proteins such as E4 11k, which has multiple functions. One …
Fast And Pervasive Transcriptomic Resilience And Acclimation Of Extremely Heat-Tolerant Coral Holobionts From The Northern Red Sea, Romain Savary, Daniel J. Barshis, Christian R. Voolstra, Anny Cárdenas, Nicolas R. Evensen, Guilhem Banc-Prandi, Maoz Fine, Anders Meiborn
Fast And Pervasive Transcriptomic Resilience And Acclimation Of Extremely Heat-Tolerant Coral Holobionts From The Northern Red Sea, Romain Savary, Daniel J. Barshis, Christian R. Voolstra, Anny Cárdenas, Nicolas R. Evensen, Guilhem Banc-Prandi, Maoz Fine, Anders Meiborn
Biological Sciences Faculty Publications
Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were …