Speaker: Brad "Buddy" Gersey, Ph.D.

Time & Date: 12:00pm, Wed., May 22, 2019

Room: ELEN 231

Abstract

A complex and changing spectrum of galactic cosmic and solar particle radiation is present in space and also continually bombards the Earth’s upper atmosphere. Components of this cosmic radiation spectrum interact in different ways with the atmosphere producing secondary radiation. The measureable amount of radiation exposure caused by this primary and secondary radiation in the atmosphere increases with increasing altitude. In Low Earth Orbit (LEO) as well as at common commercial aircraft altitudes, the radiation dose received by astronauts, flight crew members or frequent flyer passengers can be significant from a radiation protection and safety standpoint. Awareness of this radiological safety issue by the aerospace scientific community, individuals associated with the air travel industry, as well as the general public has led to a host of studies over a period of decades which have been designed to measure, model and predict the radiological environment and risks posed during air and space travel. Presented in this seminar are results from flight dosimetry studies performed by researchers at the National Aeronautics and Space Administration (NASA) Center for Radiation Engineering and Science for Space Exploration (CRESSE) at Prairie View A&M University, Prairie View, Texas. Also presented are examples of how flight dosimetry results are integrated into both human radiation safety programs and cancer epidemiology studies.

Speaker Bio

Dr. Brad Gersey is considered an expert in micro-dosimetry and interacts with all major academic and governmental groups in the field of radiation research. He has taken micro-dosimetry measurements in radiation facilities all over the world, including the NASA Space Radiation Laboratory at Brookhaven National Laboratory, the Los Alamos Neutron Science Center at Los Alamos National Laboratory and the HiMAC facility at NIRS in Chiba, Japan. He has also conducted collaborative radiation dosimetry research aboard a multitude of flight platforms including the ER2, DC9, high altitude balloons, Virgin Galactic SpaceshipTwo, and the NASA Zero Gravity Plane (The Vomit Comet). He has included underrepresented STEM students in his research, including work at all these facilities and platforms. He also advised students performing micro-dosimetry experiments on the NASA “Vomit Comet” micro-gravity vehicle. The results obtained by the students were presented at an international conference on space dosimetry on the International Space Station.

Speaker: Anna Joy, Ph.D.

Time & Date: 12:00pm, Wed., May 8, 2019

Room: ELEN 231

Abstract

Genomic studies of bulk tissue give insight into pathways, gene regulatory networks and epigenetic modifications that play a role in disease. Yet it is clear that every tissue is comprised of diverse cell types that work together to drive biological processes and behaviors. Studies of bulk tissue miss rare cells that are important in disease and gives population averages that obscure genomic features present in a subset of cells. Recent advances in single cell genomics allows us to sequence DNA and study RNA expression and epigenetic modifications in individual cells. It has had a substantial impact on our understanding of development, the immune system, CNS and cancer. We are in the process of bringing single cell technologies to the Center for Computational Systems Biology at Prairie View A & M. I will discuss various single cell RNAseq technologies and technical challenges with single cell isolation, library preparation and data analysis. I will also outline capabilities we plan to acquire that will distinguish our center from other single cell labs.

Speaker Bio

Dr. Anna Joy is a Research Associate Professor in the Center for Computational Systems Biology. Her research focus is to understand mechanisms of tumorigenesis, progression and therapy resistance in Glioblastoma brain tumors for discovery of novel drug targets and treatment biomarkers. She has elucidated an unexpected role for a member of the PI3K/AKT tumor driver pathway that has consequences for pathway inhibitors. She is also developing a biomarker that shows promise in identifying Glioblastoma patients that will have an exceptional response to nitrosoureas and is working to understand the biology underlying this phenomenon.

Time & Date: 12:00pm, Wed., April. 24, 2019

Room: ELEN 231

Abstract

Control of postnatal testis development before puberty and maintenance of adult testis spermatogenesis function involves the coordinated actions of genetic, molecular, and endocrine, factors. The net result of these factors is the continual proliferation and differentiation of testes spermatogonia during the establishment and maintenance of spermatogenesis. Studies in mice reveal that complex gene networks are involved in spermatogonia proliferation and differentiation during normal spermatogenesis. These studies have led to advances in vitro and in vivo manipulation of spermatogonia in mice. Recently, the role of small non-coding RNA species has come to the forefront in the regulation or fine-tuning of gene expression in the testes. Small non-coding RNAs microRNA (miRNA) are present in spermatozoa, testes, and epididymis and thus underscore the complex transcriptional control and cell-cell communication required for spermatogenesis, and sperm transport and function. Human, goat, and pig testes express miRNAs, and in humans, the miRNAs expression profile is dependent on the clinical status of spermatogenesis. The molecular roles of miRNAs are unknown but are likely important during the establishment and maintenance of spermatogenesis. The gene networks and molecular mechanisms controlling the continual proliferation and differentiation of spermatogonia in the pre-meiotic and post-meiotic goat testes are mostly unexplained. There is a need to characterize these gene networks to provide insight into the (1) in vivo mechanisms controlling continual spermatogonia proliferation and differentiation, (2) factors necessary for identification, isolation and subsequent in vitro manipulation of spermatogonia, (3) development of molecular markers for the potential fertility of individual animals and (4) identification of therapeutic, reversible targets for male contraceptives. Therefore the objectives of the current study were to (1) identify gene networks important to establish spermatogenesis function of the testes using mRNA- and miRNA-sequencing, (2) corroborate the temporal and spatial expression of candidate gene networks by qPCR and (3) immunohistochemistry.

We observed an enrichment of genes or gene networks involved in the lysosome, endocytosis, apoptosis, cell junctions, focal adhesions, protein digestion and absorption amongst others. Interestingly the protein digestion and absorption pathway identified in juvenile goat testes our RNA sequencing experiments are best described for its role in the intestinal epithelium during protein digestion. Not only does it involve the transport of small peptides and amino acids but also the metabolism of non-digestible peptides and proteins by commensal bacteria. Since we had identified a testis microbiome, we decided to look closer at the protein digestion and absorption pathway by IHC. To date, we demonstrated that the temporal and spatial expression of SLC16A10, SLC15A1, and SLC7A8, solute carrier proteins involved in the transport of small peptides and amino acids across the plasma membrane, decrease from 2-month to 4-month testes. RNA sequencing experiments showed a similar temporal pattern. Spatially, the expression was confined to cells within or immediately surrounding the seminiferous tubules. We are continuing to define the difference in pre-meiotic and meiotic goat testes, and that also may be essential to maintain spermatogenesis in post-pubertal testes.

Speaker

Dr. Lewis, Research Scientist in the Animal Systems group in the Cooperative Agricultural Research Center and International Goat Research Center, is a reproductive physiologist and molecular biologist. He trained in the molecular, endocrine, and cellular fetal/maternal interactions during implantation at Texas A&M University and the genetic basis for male genitourinary birth defects at Baylor College of Medicine. He has been at PVAMU since 2013.

On April 16, 2019, Dr. Tesfamichael Kebrom joined the Center for Computational Systems Biology (CCSB) and the Cooperative Agricultural Research Center (CARC), a Research Scientist for Plant Systems Biology. Research Scientist for Plant Systems Biology is a joint appointment between the Center for Computational Systems Biology (CCSB) in the Roy G. Perry College of Engineering and the Cooperative Agriculture Research Center (CARC) in the College of Agriculture and Human Sciences. Dr. Kebrom will closely collaborate with other researchers in both CCSB and CARC to develop Plant Systems Biology research program and apply for external research funding to sustain the program. Both CCSB and CARC provides support for Dr. Kebrom to establish initial research program. This appointment clearly illustrates both CCSB and CARC recognize their mission: to promote collaborative research, beyond the boundaries. Both Dr. D'Souza (Dean, CAHS) and Dr. Obiomon (Dean, COE) supported this joint appointment, stating "this aligns with the vision of the College of Engineering and the College of Agriculture and Human Sciences."

Time & Date: 12:00pm, Wed., April. 10, 2019

Room: ELEN 231

Abstract

The major challenge to analyze genetic data, with high dimension, low sample size, is to extract disease-related information from a massive amount of redundant data and noise. Selecting key genes, eliminating redundant and irrelevant genes, has been a key step to overcome this challenge. Feature selection, as a key step for building machine learning models, is a well-developed technique to select most relative elements from big data, with high dimension, large sample size. Recently, neural network-based machine learning has outperformed other machine learning models on different tasked. Therefore, this seminar is to present how to employ neural network to construct effective and efficient feature selection methods to extract most relative elements for genetic data analysis.

Speaker

Dr. Xishuang Dong is an Assistant Professor of CRI Center for Computational Systems Biology at Department of Electrical and Computer Engineering at Prairie View A&M University (PVAMU). Dr. Dong received B.S. degree in computer science and technique (sub-field of computer engineering) at Harbin University of Science and Technology, M.S. degree in computer software and theory (sub-field of computer engineering) at Harbin Engineering University, and Ph.D. in computer application (sub-field of computer engineering) at Harbin Institute of Technology.

His research interests include: 1) machine learning based computational systems biology; (2) biomedical information processing; (3) deep learning for big data analysis; (4) natural language processing.

Time & Date: 12:00pm, Wed., Mar. 27, 2019

Room: ELEN 231

Abstract

Research on cancer initiation, progression and the associated issues of therapy and cure have thus far been overwhelmingly within the purview of biochemistry, genomics, and cell biology of cancer. This research, while providing factual and empirical knowledge, and a few limited successes, lacks organizing principles and quantitative characterizations of the various processes involved that are typically in the purview of physical sciences – physics, chemistry, computer science, mathematics and engineering. Over the past ten years, the National Cancer Institute, disappointed with the inadequate return on investment into cancer research, established multiple research centers based on physical sciences. In this talk, I plan to cover four issues: (i) Criticism of the current state of the art research; (ii) New approaches based on physical sciences; (iii) A few selected results from across the globe within the new perspective; and (iv) A list of viable projects to pursue, with specific emphasis on: a precise, functional characterization of healthy vs. cancerous tumors, the transitions from healthy to cancer states, and the transitions from localized tumors to the metastatic state. Mathematical approaches – growth models and stochastic models – will be discussed briefly. The overall purpose of the talk is to generate interest in developing a systemic view of cancer.

Speaker

Dr. Kumar is a Professor of Electrical and Computer Engineering. After receiving his Ph.D. in Theoretical Physics in 1978 from The Indian Institute of Science, Bangalore, he worked in England, Belgium, Canada and the U.S. His research spanned multiple disciplines – disordered systems, solid state electronics, mathematical approaches to various solid state and liquid state systems, superfluid 3He and spin glasses. More recently he has been studying mathematical modeling of cancer. Over the past fifteen years, he has also been involved in enhancing the STEM curriculum in middle and high schools.

Time & Date: 2:00pm, Wed., Feb. 27, 2019

Room: ELEN 231

Abstract

Many cancers are preceded by mutations or changes in normal functioning genes which are important for maintaining a balance within the body. Some of these mutations are inherited and have been shown to correlate with an increased risk of developing certain types of cancers.

BRCA genes like BRCA2 and PALB2 are important for suppressing cancer, and mutations in these genes are prominently known for the role they play in breast, ovarian, prostate and pancreatic cancers. While various studies have shown that mutations in BRCA can predispose people to different types of cancers, it remains to be determined why cancer originates in some tissues and not others. Currently it is not known if identified, pathogenic (disease-causing) mutations or variants of undetermined significance in BRCA-related genes are associated with cancers of the cervix. The cervix, as part of the female reproductive tract, is an important barrier between the body and the environment. The cells of the cervix also play a key role in secreting solutions important for progressing the menstrual cycle and creating an environment for preventing or advancing conception. Stem cells are important because they give rise to all mature, specialized cells that make up tissues of the body. BRCA mutations in stem cells have also been shown to have tissue-specific, differential effects. It is unclear whether cervical cancer stem cells are affected by these mutations. Further, existing patient studies have been unable to examine the effects of unique mutations on a large scale, as these studies are limited by the number of patients with a specific mutation taking part in a study at any one time.

Our program will use recombinant DNA to express variants in cervical cancer cell lines and investigate the effects of the mutations on stem cell renewal and differentiation.

Speaker

Dr. Victoria Mgbemena received her Ph.D. in Microbiology &Immunology in 2013 from the University of Texas Health Science Center in San Antonio. After completing her training at The University of Texas Southwestern Medical School, in 2018, she joined Prairie View’s Biology Department. Her specialties span two major fields in the biological sciences: microbiology & immunology and cancer biology (oncology). Currently, her specific interests include cancer genetics, cancer immunology, and emerging cancer immunotherapies. As a guest lecturer, postdoc and faculty, Mgbemena has worked with high school students, undergraduates, technicians, graduate students and postdocs in research and career development programs. She has a strong commitment to fostering healthy learning environments for young women and underrepresented minority students who are interested in research and health professions.

Time & Date: 12:00pm, Wed., Feb. 13, 2019

Room: ELEN 231

Abstract

Most cancers occur from nowhere, without being inherited or directly caused by a steady deficient diet (affecting the microbiome), exposure to radiation or carcinogenic toxins, or bad habit (like smoking), although such risk factors increase the chances of the “bad luck”. Tumors are heterogeneous, composed of regions with distinct characteristics, some of them malignant, some others preserving the normal features of the tissue. In spite of a very rich literature, there is not yet a comprehensive explanation of cancer development, nor a perfect therapeutic solution. Moreover, with all similarities, each human is unique and has a unique lifeline, so, although a trained pathologist can recognize the cancer type, the tumors are not identical, nor develop identically or respond identically to treatment. Therefore, instead of targeting the same alleged gene biomarker for all humans with a particular cancer form, we devised a method by which the cancer of the actual patient itself indicates us what genes are now commanding it. We call these commanders “gene master regulators” (GMRs) and identify them by profiling the gene expression in tumor biopsies or blood samples (pending on the suspected cancer type) using RNA sequencing or microarray platforms. Here, we prove that cancer nuclei and surrounding normal tissue are governed by distinct GMRs and that smart manipulation of a GMR’s expression selectively affects cancer cells. The method, consistent with our Genomic Fabric Paradigm, relies on original mathematical algorithm and software that establishes the gene hierarchy from the transcriptomic profiles of tumor biopsies based on their Gene Commanding Height (GCH). GCH is a composite measure of gene expression control and coordination with major functional pathways. We present validation of the approach using microarray data obtained in our previous NYMC laboratory by profiling human kidney, thyroid, blood, lung and prostate cancer samples. The GMR approach provides the most legitimate targets for cancer gene therapy. It is also personalized and time-sensitive because the GMR hierarchy is unique for each patients and changes slowly during cancer development.

Speaker

Dr. Iacobas, Research Professor and Director of the CCSB Personalized Genomics Laboratory, is an expert of both experimental and computational genomics. Trained as a biophysicist (PhD of the University of Bucharest, Romania), he was on faculty positions at medical schools from Romania (1981-2001) and NY (Albert Einstein College of Medicine-Neuroscience 2001-2013, New York Medical College-Pathology 2013-2017). At NYMC he founded and directed the Systems Biology Core laboratory. Dr. Iacobas was also involved in the technology development, performed analyses of the technical noise of various microarray platforms and took care of transgenic mouse colonies and genetically engineered cell cultures. His lab profiled a wide diversity of tissues and cell cultures from blood and regions of brain, spinal cord, retina, heart, liver, kidney, lung, thyroid and prostate from humans and animal (mouse, rat, rabbit, dog, chicken embryo) models of human diseases. He studied transcriptomic alterations in cancer, neurodegenerative, cardiovascular and infectious diseases, and following hypoxic or low gravity stress. His main contribution to the theoretical genomics is the introduction of the Genomic Fabric Paradigm and the development of the mathematically advanced analyses of the Relative Expression Estimate, Coordination Power, Pair-Wise Relevance and Gene Master Regulators.

Dr. Iacobas’ publications include: 3 patents in microelectrophysiology, 7 books (total 22 editions in Romanian, English, Spanish and Greek), 86 articles in peer-reviewed journals, 27 chapters in books and conference proceedings and 77 genomic experiments included in http://ncbi.nlm.nih.gov/gds.