Digital Commons Network^™

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 …

Complex Dynamics Of Coral Gene Expression Responses To Low Ph Across Species, Veronica Z. Radice, Ana Martinez, Adina Paytan, Donald C. Potts, Daniel J. Barshis

Biological Sciences Faculty Publications

Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges (‘Ojo’; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2‐year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef‐building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities …

Advancing The Understanding Of Clinical Sepsis Using Gene Expression–Driven Machine Learning To Improve Patient Outcomes, Asrar Rashid, Feras Al-Obeidat, Wael Hafez, Govind Benakatti, Rayaz A. Malik, Christos Koutentis, Javed Sharief, Joe Brierley, Nasir Quraishi, Zainab A. Malik, Arif Anwary, Hoda Alkhzaimi, Syed Ahmed Zaki, Praveen Khilnani, Raziya Kadwa, Rajesh Phatak, Maike Schumacher, M. Guftar Shaikh, Ahmed Al-Dubai, Amir Hussain

All Works

Sepsis remains a major challenge that necessitates improved approaches to enhance patient outcomes. This study explored the potential of machine learning (ML) techniques to bridge the gap between clinical data and gene expression information to better predict and understand sepsis. We discuss the application of ML algorithms, including neural networks, deep learning, and ensemble methods, to address key evidence gaps and overcome the challenges in sepsis research. The lack of a clear definition of sepsis is highlighted as a major hurdle, but ML models offer a workaround by focusing on endpoint prediction. We emphasize the significance of gene transcript information …

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).

Differences In Pathogenesis-Related Protein Expression And Polyphenolic Compound Accumulation Reveal Insights Into Tomato-Pythium Aphanidermatum Interaction, Seham A. Soliman, Abdulaziz A. Al-Askar, Sherien Sobhy, Marwa A. Samy, Esraa Hamdy, Omaima A. Sharaf, Yiming Su, Said I. Behiry, Ahmed Abdelkhalek

Publications

Plant diseases significantly reduce crop yields, threatening food security and agricultural sustainability. Fungi are the most destructive type of phytopathogen, and they are responsible for major yield losses in some of the most crucial crops grown across the world. In this study, a fungus isolate was detected from infected tomato plants and molecularly identified as Pythium aphanidermatum (GenBank accession number MW725032). This fungus caused damping-off disease and was shown to be pathogenic. Moreover, the expression of five pathogenesis-related genes, namely PR-1, PR-2, PR-3, PR-4, and PR-5, was quantitatively evaluated under the inoculation of tomato with …

Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …

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 …

7-Deazaguanines In Dna: Functional And Structural Elucidation Of A Dna Modification System, Samanthi Herath Gedara, Andrew Gustafson, Dirk Iwata-Reuyl, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ₀ and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray …

Cytotoxicity And Reproductive Impairment In Rainbow Trout Cell Lines Exposed To Microcystis Aeruginosa Extracellular Metabolites, Keira Harshaw

Electronic Theses and Dissertations

Current trends in cyanobacterial harmful algal blooms (cHABs) demonstrate increasing risks to human health and the health of aquatic ecosystems around the globe. Expansion of algal blooms, both geographically and temporally, serve to place increasing numbers of freshwater species, including fish, in peril. Microcystis aeruginosa, one of the most common species of bloom-causing cyanobacteria, is capable of producing a vast diversity of biologically active compounds, however Microcystis studies are often dominated by microcystins. How non-microcystin metabolites contribute to Microcystis toxicity, particularly in freshwater fish, has been the subject of a limited, but growing, body of research. To contribute to …

A Comparison Of Computational Approaches For Intron Retention Detection, Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li

Big Data Mining and Analytics

Intron Retention (IR) is an alternative splicing mode through which introns are retained in mature RNAs rather than being spliced in most cases. IR has been gaining increasing attention in recent years because of its recognized association with gene expression regulation and complex diseases. Continuous efforts have been dedicated to the development of IR detection methods. These methods differ in their metrics to quantify retention propensity, performance to detect IR events, functional enrichment of detected IRs, and computational speed. A systematic experimental comparison would be valuable to the selection and use of existing methods. In this work, we conduct an …

Subomiembed: Self-Supervised Representation Learning Of Multi-Omics Data For Cancer Type Classification, Sayed Hashim, Muhammad Ali, Karthik Nandakumar, Mohammad Yaqub

Computer Vision Faculty Publications

For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of omics data show various aspects of samples. Integration and analysis of multi-omics data give us a broad view of tumours, which can improve clinical decision making. Omics data, mainly DNA methylation and gene expression profiles are usually high dimensional data with a lot of molecular features. In recent years, variational autoencoders (VAE) [13] have been extensively used in embedding image and text data into …

Critical Dynamics In Biological Boolean Networks Follows From Symmetric Response To Input Genes, Hamza Çoban, Alkan Kabakçioğlu

Turkish Journal of Physics

A recent observation on an extensive collection of biological gene regulatory networks suggests that the regulatory dynamics is tuned to remain close to the order-chaos boundary in the Lyapunov sense [1]. We here investigate, from a mathematical perspective, the structural/functional constraints which give rise to such accumulation around criticality in these systems. While the role of canalizing functions in this respect is well established, we find that critical sensitivity to small input variations also follows from an over-abundance of symmetrical inputs, i.e. regulatory genes invoking identical or complementary responses on their common target. A random network ensemble constructed to have …

Multivariate Statistical Modeling For Radio-Genomics Study, Tiantian Zeng

Theses and Dissertations--Statistics

Radiogenomics is a new direction in cancer research that focuses on the associations among radiomics, genomics and clinical outcome. Currently, the major challenge for Radiogenomics lies in the effective integration of genomics and imaging data for promising clinical outcome prediction. Herein, we propose a multivariate joint model that can integrate imaging and genomic data for better predicting the clinical outcome. Specifically, we jointly consider two multivariate group lasso models, one regresses imaging features on genomic features, and the other regresses patient’s clinical outcome on genomic features. An L1 penalty term is introduced for each variable, and weight in the penalty …

Effects Of Progesterone Concentrations And Follicular Wave During Growth Of The Ovulatory Follicle On Conceptus And Endometrial Transcriptome In Dairy Cows, R S. Bisinotto, E S. Ribeiro, L F. Greco, Daniel Taylor-Rodríguez, A D. Ealy, H Ayres, F S. Lima, N Martinez, W W. Thatcher, J E P Santos

Mathematics and Statistics Faculty Publications and Presentations

Objectives were to evaluate the effects of follicular wave and progesterone concentration on growth of the ovulatory follicle, conceptus elongation, uterine IFN-τ concentration, and transcriptome of conceptus and endometrium of pregnant cows on d 17 of gestation. Nonlactating nonpregnant Holstein cows were assigned randomly to one of 3 treatments: ovulation of a first-wave follicle (FW, n = 15); ovulation of a first-wave follicle and progesterone supplementation (FWP4, n = 12); and ovulation of a second-wave follicle (SW, n = 19). Ovulation of a first- or second-wave follicle was achieved by initiating the Ovsynch protocol (d -9 GnRH, d -2 and …

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 …

Lapatinib And Poziotinib Overcome Abcb1-Mediated Paclitaxel Resistance In Ovarian Cancer, J. Robert Mccorkle, Justin W. Gorski, Jinpeng Liu, Mckayla J. Riggs, Anthony B. Mcdowell Jr., Nan Lin, Chi Wang, Frederick R. Ueland, Jill M. Kolesar

Markey Cancer Center Faculty Publications

Conventional frontline treatment for ovarian cancer consists of successive chemotherapy cycles of paclitaxel and platinum. Despite the initial favorable responses for most patients, chemotherapy resistance frequently leads to recurrent or refractory disease. New treatment strategies that circumvent or prevent mechanisms of resistance are needed to improve ovarian cancer therapy. We established in vitro paclitaxel-resistant ovarian cancer cell line and organoid models. Gene expression differences in resistant and sensitive lines were analyzed by RNA sequencing. We manipulated candidate genes associated with paclitaxel resistance using siRNA or small molecule inhibitors, and then screened the cells for paclitaxel sensitivity using cell viability assays. …

Physiological And Molecular Responses Of Eurythermal And Stenothermal Populations Of Zostera Marina L (Eelgrass) To Climate Change, Carmen C. Zayas-Santiago

OES Theses and Dissertations

As CO₂ levels in Earth’s atmosphere and oceans steadily rise, varying organismal responses may produce ecological losers and winners. Increased ocean CO₂ can enhance seagrass productivity and thermal tolerance, providing some compensation for climate warming. However, the consistency of this CO₂ effect across populations of cosmopolitan species such as Zostera marina L. (eelgrass) remains largely unknown. This study analyzed whole-plant performance metabolic profiles and gene expression patterns of distinct eelgrass populations in response to CO₂ enrichment. Populations were transplanted from Nisqually Landing and Dumas Bay, two cold water environments in Puget Sound, WA (USA) that rarely …

Elevated Atmospheric Co2 Concentration Triggers Redistribution Of Nitrogen To Promote Tillering In Rice, Juan Zhou, Yingbo Gao, Junpeng Wang, Chang Liu, Zi Wang, Minjia Lv, Xiaoxiang Zhang, Yong Zhou, Guichun Dong, Yulong Wang, Jianye Huang, Dafeng Hui, Zefeng Yang, Youli Yao

Biology Faculty Research

Elevated atmospheric CO₂ concentration (eCO₂) often reduces nitrogen (N) content in rice plants and stimulates tillering. However, there is a general consensus that reduced N would constrain rice tillering. To resolve this contradiction, we investigated N distribution and transcriptomic changes in different rice plant organs after subjecting them to eCO₂ and different N application rates. Our results showed that eCO₂ significantly promoted rice tillers (by 0.6, 1.1, 1.7, and 2.1 tillers/plant at 0, 75, 150, and 225 kg N ha⁻¹ N application rates, respectively) and more tillers were produced under higher N application rates, …

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.

Luteolin Inhibits Proliferation, Triggers Apoptosis And Modulates Akt/Mtor And Map Kinase Pathways In Hela Cells, Ritu Raina, Sreepoorna Pramodh, Naushad Rais, Shafiul Haque, Jasmin Shafarin, Khuloud Bajbouj, Mawieh Hamad, Arif Hussain

All Works

Flavonoids, a subclass of polyphenols, have been shown to be effective against several types of cancer, by decreasing proliferation and inducing apoptosis. Therefore, the aim of the present study was to assess the anti-carcinogenic potential of luteolin on HeLa human cervical cancer cells, through the use of a cell viability assay, DNA fragmentation assay, mitochondrial membrane potential assay, cell cycle analysis using Annexin/PI staining and flow cytometry, gene expression analysis and a protein profiling array. Luteolin treatment exhibited cytotoxicity towards HeLa cells in a dose- and time-dependent manner, and its anti-proliferative properties were confirmed by accumulation of luteolin-treated cells in …

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 …

Combining Assumptions And Graphical Network Into Gene Expression Data Analysis, Demba Fofana, E. O. George, Dale Brown

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

Background

Analyzing gene expression data rigorously requires taking assumptions into consideration but also relies on using information about network relations that exist among genes. Combining these different elements cannot only improve statistical power, but also provide a better framework through which gene expression can be properly analyzed.

Material and methods

We propose a novel statistical model that combines assumptions and gene network information into the analysis. Assumptions are important since every test statistic is valid only when required assumptions hold. So, we propose hybrid p-values and show that, under the null hypothesis of primary interest, these p-values are …

Statistical Approaches Of Gene Set Analysis With Quantitative Trait Loci For High-Throughput Genomic Studies., Samarendra Das

Electronic Theses and Dissertations

Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis approaches used for different high-throughput genomic studies is provided. The analysis of gene sets is usually carried out based on …

Cancer Phylogenetic Analysis Based On Rna-Seq Data, Tingting Zhai

Theses and Dissertations--Statistics

Studying tumor evolution is a major task to understand the biological mechanism of carcinogenesis, develop new cancer therapies, and prevent drug resistance. We focus on two important questions in tumor evolution. The first question is to quantify intra-tumor heterogeneity, where multiple subclones of tumor cells with distinct transcriptomic profiles. Another question is to estimate the temporal order of alteration of key cancer pathways during tumor evolution. We present a new statistical method to 1) reconstruct the evolutionary history and population frequency of the subclonal lineages of tumor cells and 2) infer temporal order of pathway alterations in tumor evolution for …

Detecting Differentially Co-Expressed Gene Modules Via The Edge-Count Test, Anne Gratius Lin

Graduate Theses and Dissertations

Background

Gene expression profiling by microarray has been used to uncover molecular variations in many different diseases. Complementary to conventional differential expression analysis, differential co-expression analysis can identify gene markers from the systematic and granular level. There are three aspects for differential co-expression network analysis, including the network global topological comparison, differential co-expression cluster identification, and differential co-expressed genes and gene pair identification. To date, most of the methods available still rely on Pearson’s correlation coefficient despite its nonlinear insensitivity.

Results

Here we present an approach that is robust to nonlinearity by using the edge-count test for differential co-expression analysis. …

Computational Approaches For Finding Disease Related Genes And Rnas, Negin Fraidouni

Computer Science and Engineering Dissertations

Finding candidate genes that could cause specific diseases has been the subject of many studies. This is an important research task, however in the biological experimentation domain it can be very expensive and time consuming. So an alternative way is to find gene expression values from partial measurements and try to predict the rest. By using computational methods, we can statistically estimate these relationships faster and in a more efficient way, providing domain experts suggestions on what exploration of likely relationships they should be focusing. One common computational approach is to model the gene expression data as a matrix (where …

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Dan Nettleton

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Cancerous Male And Female Gene Expression, Clarissa Farmer, E. Shannon Tass

Journal of Undergraduate Research

Genetic diagnosing is becoming more popular, as well as more and more accurate. However, many genetic diseases have complex genetic effects and are still not fully understood. Transthyretin Amyloidosis (ATTR; also known as familial or hereditary amyloidosis) is a terminal genetic disease. It is caused by unstable transthyretin proteins that fold improperly, and then deteriorate. The fragmented proteins are deposited outside of the cell and build up in the tissues over time, forming insoluble oligomers. The oligomers continue to grow into Amyloid fibrils, which adversely affect many organs in the body, eventually causing their failure. In order to accurately diagnose, …