Abstract

Shoot branches develop from buds that are formed in the axil of leaves. The buds either grow into branches or become dormant depending on internal and environmental factors that affect their growth. The dormancy and outgrowth fates of buds, thus shoot branching, determine resource use efficiency and yield of crops. In addition, the dormancy and outgrowth of axillary buds influence many other aspects of crop production, for example, forage and pasture crop production and post-harvest potato sprouting and shelf life. My research focuses on understanding the physiological, genetic, and molecular mechanisms regulating dormancy and outgrowth of axillary buds and developing agronomic and breeding strategies to improve crop production. In our previous studies, we identified several physiological and developmental factors that control buds through partially distinct molecular mechanisms. We hypothesize that those partially distinct molecular mechanisms may converge on activating a few key genes that directly control the growth of buds. In this seminar, I will present our research findings and recent progress in identifying these key genes.

Speaker Bio

Dr. Tesfamichael Kebrom is a research scientist with a joint appointment at the Center for Computational Systems Biology (College of Engineering) and the Cooperative Agricultural Research Center (College of Agriculture and Human Sciences) at Prairie View A&M University (PVAMU). He received B.Sc. in Plant Sciences from the University of Asmara in Eritrea, M.Phil. (Master of Philosophy) in Crop Physiology from the University of Reading in England, and Ph.D. in Molecular & Environmental Plant Sciences from Texas A&M University. His research focuses on identifying the molecular and physiological basis of shoot elongation and branching in crop plants.

Abstract

Genomic resources for sorghum have grown rapidly in the last 20 years with the development of plant genomics technologies. However, the regulatory mechanisms of many important agronomic traits in sorghum remain unknown. The availability of a large mutant population is an important genetic resource for functional genomic studies . In this seminar, a large sequence-index sorghum mutant population will be presented. We have established Pedigreed Mutant Library in the sorghum inbred line BTx623 by mutagenizing the seeds with ethyl methane sulfonate (EMS). This library has 6,400 M4 seed pools and possesses a great diversity of mutant phenotypes. Our sequencing effort identified mutations in 97% of sorghum genes to support the gene function study. Furthermore, we have established an effective bioinformatic pipeline to identify the causal mutations through bulk-segregant-analysis (BSA) of the whole genome sequencing data of the pooled mutants selected from F2 populations. The sorghum mutant library will be a useful resource for create new traits for breeding and promising targets for genome editing.

Speaker Bio

Dr. Yinping Jiao is an Assistant Professor at the department of Plant and Soil Science, Texas Tech University since 2020. Her research group investigates the genetic diversity and regulatory mechanisms of important agronomical traits in sorghum (Sorghum bicolor), with the goal of facilitating breeding. Before joining Texas Tech, she did postdocs at Cold Spring Harbor Laboratory and USDA-ARS working on maize (Zea mays) and sorghum functional genomics. During this time, she was involved in the construction of a high-quality maize reference genome using single-molecule technologies. She did her PhD in Plant Genetics and Breeding at China Agriculture University, investigating genetic diversity in maize populations.

Abstract

Vascular inflammation critically regulates endothelial pathophenotypes, yet causative mechanisms remain incompletely defined, particularly in pulmonary arterial hypertension (PAH). Immune dysregulation and metabolic reprogramming are recognized tenets of PAH pathogenesis, but a unifying theory connecting the two has not been established. Across in vitro and in vivo discovery platforms, we found that endothelial induction of the nuclear receptor coactivator 7 (NCOA7) tempered the generation of proinflammatory sterols by bolstering lysosomal acidification and constraining endothelial cell immunoactivation. Conversely, reduced NCOA7 promoted lysosomal dysfunction, resulting in sterol- and bile acid-driven inflammation and endothelial cell phenotypes consistent with PAH. In vivo, mice deficient for Ncoa7 or treated with a NCOA7-dependent inflammatory bile acid demonstrated worsened hemodynamic and histological indices of PAH. In parallel, an unbiased, metabolome-wide association study from the multicenter PAH Biobank cohort (N=2,666) identified the same NCOA7-dependent sterol and bile acid metabolite plasma signature as significantly associated with PAH mortality. Furthermore, the common variant intronic SNP rs11154337 in NCOA7 was found to control NCOA7 levels, lysosome activity, sterol and bile acid production, and EC immunoactivation in isogenic, CRISPR-Cas9, SNP-edited, iPSC-derived ECs, indicating a potentially widespread genetic predisposition to NCOA7 deficiency. Correspondingly, SNP rs11154337 was associated with PAH severity, as reflected by six-minute walk distance and mortality in a single-center PAH cohort (N=93). In a second validation, multi-center PAH cohort (N=826), SNP rs11154337 was further associated with mortality. Our work establishes a genetic and metabolic paradigm that links lysosomal biology and sterol and bile acid processes with EC inflammation. This paradigm carries broad implications not only on molecular diagnostic and therapeutic development in PAH but also in other vascular disorders dependent upon acquired and innate immune regulation.

Speaker Bio

Stephen Chan, MD, PhD, is the Vitalant Chair in Vascular Medicine and Professor of Medicine (Cardiology) at the University of Pittsburgh School of Medicine. He serves as the Director of the Vascular Medicine Institute, a multi-disciplinary research institute with 40 primary and associated investigators and with $25M of yearly research expenditures. Dr. Chan also leads a basic science and translational research laboratory studying the molecular mechanisms of pulmonary vascular disease and pulmonary hypertension (PH) – a disease where reductionistic studies have primarily focused on only end-stage molecular effectors. To capitalize on the emerging discipline of “network medicine,” the Chan laboratory utilizes a combination of network-based bioinformatics with unique experimental reagents derived from genetically altered rodent and human subjects to accelerate systems-wide discovery in PH. In doing so, Dr. Chan’s published work was the first to identify the systems-level importance of microRNAs as a root cause for pulmonary hypertension, controlling metabolism, inflammation, and vascular stiffness. Dr. Chan’s recent work also delves into the computational biology of -omics datasets in order to predict unique pathogenic pathways important in PH. Dr. Chan has served as Chair of the NIH Respiratory Integrative Biology and Translational Research (RIBT) study section, holds multiple grants from the NIH, is an elected member of the American Society for Clinical Investigation, and holds an Established Investigator Award from the American Heart Association.

Abstract

Most breast cancer (BC) fatalities are due to a metastasis and not the primary tumor. Breast cancer brain metastasis (BCBM) confers an especially grave prognosis, and patients often experience rapid declines in self-sufficiency and neurocognitive function with death typically ensuing in less than a year. There are limited effective treatment options for these patients and improved models of breast cancer brain metastasis (BCBM) are needed to elucidate tumor pathobiology and discover and test effective therapeutics. Brain organoids are self-organizing 3D structures that can be generated from pluripotent stem cells (PSC) and contain many of the morphological, functional and molecular features of the developing human brain. We are developing and characterizing a 3D, cell culture, BCBM model consisting of forebrain organoids invaded with BC cells. We will show that BC cells invade into the interior of forebrain organoids and the neural TME has a large impact on BC cell growth. Outgrowth of micrometastasis to macrometastasis is the rate limiting step of the metastatic cascade. We hypothesize that our BCBM model can be used to study molecular mechanisms driving this process and lead to therapeutics that block development of macrometastasis.

Immunotherapy has revolutionized treatment for some tumors and, although not as successful in GBM, a thorough understanding of immune evading mechanisms may lead to more effective treatments. We have developed a method to probe the immune environment using RNAseq of bulk tumor tissue. We show there are 7 immune subtypes with distinct clinical outcomes, molecular features, infiltration of immune cell types and expression of genes involved in immunosuppression mechanisms. Our in silico analysis suggests that one subtype suppresses the immune system by downregulating machinery necessary for Tcells and Natural Killer Cells to recognize and attack the tumor and identifies therapeutics that may block this immunosuppression. Our results indicate that this approach can identify physiologically relevant immune subtypes, investigate tumor immunosuppression mechanisms and predict which immunotherapy will be effective for a GBM patient.

Speaker Bio

Dr. Joy is a Research Associate Professor in the Center for Computational Systems Biology at Prairie View A & M University. She received her Ph.D. in Chemistry from Arizona State University. During her postdoctoral fellowship at Barrow Neurological Institute she studied the molecular features and pathobiology of brain tumors and continued these studies at as Associate Scientist at Barrow Neurological Institute and the Translational Genomics Research Institute. She joined the Center for Computational Systems Biology at Prairie View at the end of 2018.

The major focus of Dr. Joy’s research includes (1) Identify glioblastoma subtypes and their molecular drivers then develop biomarkers to guide personalized treatment, (2) Understand the role of the three forms of a tumor driving protein called AKT in glioblastoma and (3) Leverage public proteomic and genomic databases to investigate the topology of tumor promoting pathways in Glioblastoma tumors.

Abstract

Crop residues account for approximately 5.5 billion dry tons of agricultural waste and more than one-third of food produced is unconsumed. Loss of food and nutrients at a time of heightened global food demand and agricultural waste contributing to agricultural greenhouse gas emissions need to be mitigated as we continue to address the global population increase. Cold plasma is a novel treatment technology that has shown promising effects on increasing the shelf-life of stored food and feed products and processing and treating biomass. Optimization of such treatment technologies to reduce agricultural waste for industrial bioprocessing and microbiological contaminates in food and feed products can help address the agricultural and food waste. This requires evaluating reactive gas species kinetics, physical properties, mechanical properties, and quality parameters of stored commodities. This presentation will discuss some of the issues with farm-stored grains and oilseeds, and outlines methods for their prevention, detection, control and increased utilization.

Speaker Bio

Dr. Janie McClurkin Moore is an Assistant Professor in the Biological and Agricultural Engineering Department at Texas A&M University in College Station. She is a native of Columbus, Ohio. She received her B.S. in BioEnvironmental Engineering from North Carolina A&T State University and her M.S. and Ph.D. in Agricultural and Biological Engineering from Purdue University. She oversees the Post-Harvest Engineering and EDucation (PHEED) research team. Dr. Moore’s current research centers around three different areas 1) oxidative depolymerization of lignocellulosic biomass, 2) the inactivation of mold and mycotoxin in stored grains and 3) innovative instruction strategies for Biological and Agricultural Engineering students. She was the Montague Center for Teaching Excellence Fellow in 2020, and received the President’s Citation from the American Society of Agricultural and Biological Engineering in 2021.