Life Sciences Commons^™

Molecular Approaches In The Analysis Of Red Clover Rhizobium Symbiosis, Randy D. Dinkins, L. Koch, M. L. Sullivan, H. Zhu

IGC Proceedings (1997-2023)

Red clover (Trifolium pratense L.) is an important forage and pasture legume grown throughout temperate regions. Because it can form a symbiotic relationship with rhizobium, it is able to fix atmospheric nitrogen. Due to the high cost of nitrogen fertilizers, pasture legumes have been increasingly important in forage production settings. Red clover has not been a model legume primarily due to selfincompatibility and the associated high level of genomic heterozygosity, therefore it has not been a significant contributor in molecular or genetic studies and basic information on red clover legume/rhizobium symbiosis is lacking. Using recently annotated genomic resources, RNA-seq …

Multiple Rsv Strains Infecting Hep-2 And A549 Cells Reveal Cell Line-Dependent Differences In Resistance To Rsv Infection, Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor Mcbride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra

Research Symposium

Background: Respiratory syncytial virus (RSV) is the major viral driver of a global pediatric respiratory disease burden disproportionately borne by the poor¹. Thus, RSV, like SARS-CoV-2, combines with congenital and environmental and host-history-dependent factors to create a spectrum of disease with greatest severity most frequently occurring in those least able to procure treatment.

Methods: Here we apply whole genome sequencing and a suite of other molecular biological techniques to survey host-virus dynamics in infections of two distinct cell lines (HEp2 and A549) with four strains representative of known RSV genetic diversity.

Results: We observed non-gradient patterns of RSV …

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …

Light Intensity Is Positively Correlated With The Synthesis Of Condensed Tannins In Lotus Corniculatus, Sergio Arcioni, T. Bovone, F. Damiani, F. Paolocci

IGC Proceedings (1997-2023)

The importance of Condensed Tannins (CT) in forage legumes has been well documented in several studies. The role of plant genetics in this field is the acquisition of competences in order to be able to modulate CT synthesis in leaves of these species. The role of light has been investigated in this work on the increase of condensed tannin levels in leaves of two contrasting genotypes of birdsfoot trefoil (Lotus corniculatus).

Overexpressing Two Helicobacter Pylori Small Rnas From A Bacterial Pathogenicity-Related Chromosomal Region To Investigate Their Regulation Of Virulence Genes, Roxanne N. Mcpeck, Olivia F. Morgan, Andrea R. Castillo Phd

2023 Symposium

The bacterial pathogen Helicobacter pylori infects the stomachs of approximately 50% of humanity, causing symptomatic disease (e.g., stomach ulcers, gastric cancer, and MALT lymphoma) in 10-15% of the infected. Colonizing the acidic, inhospitable stomach requires H. pylori to tightly regulate gene expression despite lacking many common bacterial genetic regulatory elements. The pathogen may compensate by using abundant non-protein-coding small RNAs (sRNAs) to regulate gene expression, including of infection-intensifying virulence genes. Additionally, severe disease and cancer correlate with infection by H. pylori strains that contain a nonessential chromosomal region, the cytotoxin-associated gene pathogenicity island (cagPAI). This encodes powerful virulence …

The Investigation Of Flowering Control In Late/Rare Flowering Lolium Perenne, S. Byrne, I. S. Donnison, L. J. Mur, E. Guiney

IGC Proceedings (1997-2023)

Flowering in Lolium perenne (perennial ryegrass) results in reduced digestibility and its inhibition would enhance forage quality. Flowering regulation has been well studied in Arabidopsis thaliana (Simpson and Dean, 2002) and orthologs of Arabidopsis flowering genes underlying heading date Quantitative Trait Loci (QTL) have been identified in rice (Yano, M et al., 2000). However it is not clear yet how universally applicable such studies are to Lolium. The project goals are to characterise the gene expression profiles of late/rare flowering L. perenne plants to determine factors affecting flowering and to map the genes involved in the flowering process. Initial …

Biological Interactions In Grassland Soils And Productivity, R. Cook, R. D. Bardgett, W. R. Eason, L. Skøt, K. J. Webb

IGC Proceedings (1997-2023)

This paper describes research on interactions between grassland plant species and soil microorganisms. Both parasitic and symbiotic microorganisms modify nutrient transfers between plants and soil. Experiments are described in which nematode infection of clover increased nitrogen transfer to companion ryegrass plants. Infection of clover enhanced activity of soil bacterial and fungal communities. Legume genotypes differing only in responses to symbionts (rhizobium and arbuscular mycorrhizal fungi) and pathogens are being developed for studies of gene expression during establishing and functional symbioses. Such plants can be used in experiments as defined perturbations that will provide information on the interactions and functions of …

Lipoxin A 4 (Lxa 4 ) Promotes Reduction And Antibiotic Efficacy Against Pseudomonas Aeruginosa Biofilm, Julianne M. Thornton, Jean Walker, Prem Y.K. Sundarasivarao, Bernd Spur, Ana Rodriguez, Kingsley Yin

Rowan-Virtua Research Day

Pseudomonas aeruginosa (P aeruginosa) is an opportunistic bacterium commonly found in wound infections and airways of cystic fibrosis patients P aeruginosa readily forms biofilms which can reduce the efficacy of antibiotics used to eradicate the pathogen We have previously shown that a Specialized Pro resolving Mediator ( Lipoxin A 4 (LxA 4 is a quorum sensing inhibitor which can reduce P aeruginosa virulence In this study, we examined the direct actions of LxA 4 and RvD 2 on P aeruginosa biofilm formation and virulence gene expression The influence of LxA 4 on antibiotic efficacy and the combined effects on biofilm …

Low‐Temperature Tolerance Related Cbf And Fructosyltrans Ferase Genes In Forage Grasses, H. Hisano, K. Tamura, M. Yoshida, A. Kanazawa, T. Yamada

IGC Proceedings (1997-2023)

No abstract provided.

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Determining The Role Of Epigenetic Factors In Antifungal Drug Resistance, Abigail R. Gress, Scott D. Briggs, Nina Serratore

The Summer Undergraduate Research Fellowship (SURF) Symposium

Epigenetic factors are proteins that regulate gene expression by altering transcriptional machinery access to nucleosomes, DNA wrapped around histone proteins. Two classes of epigenetic factors are ATP-dependent chromatin remodelers and histone modifiers such as histone methyltransferases (HMTs), proteins that add methyl groups to histone tails. This study focuses on AIF4 (Antifungal-Induced Factor 4), a possible HMT induced upon neutral lipid depletion that we hypothesize is regulating antifungal drug resistance genes. Overexpression of AIF4 results in hypersensitivity to antifungal drugs. Studying epigenetic factors in the yeast Saccharomyces cerevisiae, including AIF4, can lead to better understanding of cell adaptation to their environments …

Characterizing The Role Of Aif4 In Saccharomyces Cerevisiae, Antonia L. Hur Ms., Nina Serratore Ms., Scott D. Briggs

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromatin remodelers are important regulatory mechanisms that eukaryotic cells use to modify the structure of chromatin, which is made up of DNA and proteins. DNA wraps around histone proteins to make up chromatin. When these proteins are modified, the shape of the chromatin is altered. “Loosening” the chromatin structure by chromatin modifications allows for active gene expression whereas “tightening” or compaction of chromatin results in gene repression. Therefore the modifications on chromatin modulate gene expression in all eukaryotes. It has been shown that mis-regulation of chromatin remodelers contribute to various cancers. Understanding the biochemistry behind how chromatin associating proteins modify …

Gene Set Testing To Characterize Multivariately Differentially Expressed Genes, John R. Stevens, S. Clay Isom

Conference on Applied Statistics in Agriculture

In a gene expression experiment (using oligo array, RNA-Seq, or other platform), researchers typically seek to characterize di erentially expressed genes based on common gene function or pathway involve-ment. The eld of gene set testing provides numerous characterization methods, some of which have proven to be more valid and powerful than others. These existing gene set testing methods focus on experimental designs where there is a single null hypothesis (usually involving association with a continuous or categorical phenotype) for each gene. Increasingly common experimental designs lead to multiple null hypotheses for each gene, and the characterization of these multivariately di …

Dynamic Clustering Of Cell-Cycle Microarray Data, Lingling An, R. W. Doerge

Conference on Applied Statistics in Agriculture

The cell cycle is a crucial series of events that are repeated over time, allowing the cell to grow, duplicate, and split. Cell-cycle systems play an important role in cancer and other biological processes. Using gene expression data gained from microarray technology it is possible to group or cluster genes that are involved in the cell-cycle for the purpose of exploring their functional co-regulation. Typically, the goal of clustering methods as applied to gene expression data is to place genes with similar expression patterns or profiles into the same group or cluster for the purpose of inferring the function of …

Genetic Mapping Of Gene Expression Levels: Expression Level Polymorphism Analysis For Dissecting Regulatory Networks Of Plant Disease Resistance, Kyunga Kim, Marilyn A. L. West, Richard W. Michelmore, Dina A. St. Clair, R. W. Doerge

Conference on Applied Statistics in Agriculture

The genetic basis of inherited traits has been studied through di erent approaches in many areas of science. Examples include quantitative trait locus (QTL) analysis and mutant analysis in genetics, genome sequencing and gene expression analysis in genomics. Each of these approaches is used for the investigation of complex traits, such as disease resistance, but also provides knowledge on components of complex biological systems. We introduce a novel functional genomics approach that integrates two areas, genetics and genomics, by applying QTL analysis to quantitative di erences in the mRNA abundance of trait-related genes. This approach allows comprehensive dissection of regulatory …