Chapter 1: System biology

by Elizabeth C. Plunk, Weston S. Chambers, Sean M. Richards


The discovery and development of genomics, epigenomics, transcriptomics, proteomics, and metabolmics over the past few decades has aided researchers in understanding the human body at the molecular levels. With the use of these techniques, researchers have created tools that can be used in a clinical setting for diagnosis and treatment of diseases. Understanding of the human genome was greatly facilitated by the Human Genome Project (HGP) and has led to further discovery of associations between genetics and disease. Meanwhile, studying epigenetics has led to an understanding of how external factors can alter genetic expression. Transcriptomics allow for the research to appreciate the variability of the transcriptome which is not as stable as genome s it can change based on the cell cycle, exposure, and aging. This allows for a better understanding of the cellular condition. Proteomics involves the investigation of protein profiles within a cell, organ system, or organism, and this information can be used in disease diagnosis as well as predictions on the best treatment options for an individual. Finally, metabolomics provides information on the real-time biochemical processes of cell, tissue, or organism based on metabolites measured from tissue, saliva, or urine. All the techniques discussed in this chapter have uniquely aided in the progression of understanding the human body as well as helped advance the medical field. The information gain from these tools provide insights to disease development, patients response to treatment, and ultimately refine personalized medicine. 

Elizabeth C. Plunk

Department of Environmental Medicine, University of Rochester Medical School, Rochester, NY

I am Elizabeth Plunk, and I am a graduate student in the Toxicology Training Program at the University of Rochester Medical Center. I received a Bachelor of Science degree from the University of Tennessee at Chattanooga in May of 2019. I then worked at European Biomedical Research Institute of Salerno under the guidance of Jacopo Troisi before being accepted into graduate school in the Fall of 2020. My current studies consist of characterizing microglia and neuron interactions during development after gestational and lactational exposures to environmentally relevant toxicants. 


Weston S. Chambers

Department of Biological and Environmental Sciences, University of Tennessee-Chattanooga, Chattanooga, TN, United States2

Weston S. Chambers was born and raised in Chattanooga, Tennessee. He is a graduate of the University of Tennessee at Chattanooga, and he currently is a medical student at the University of Tennessee Health Science Center College of Medicine.


Sean M. Richards

Department of Biological and Environmental Sciences, University of Tennessee-Chattanooga, Chattanooga, TN 37403 - Department of Biological and Environmental Sciences, University of Tennessee-Chattanooga, Chattanooga, TN 37403, USA; Department of Obstetrics and Gynecology  University of Tennessee Health Science Center College of Medicine Chattanooga, TN 37403 

Over the last 25 years Dr. Richards has conducted research on the exposure and effects of multiple toxicants on organisms ranging from bacteria to humans. These toxicants include herbicides, insecticides, pharmaceuticals, Bisphenol A, Poly Aromatic Hydrocarbons, Per- and Polyfluoroalkyl Substances, metals, and Poly Chlorinated Biphenyls. Dr. Richards also has experience with the laws and regulations which govern exposure to toxicants through air, soil, and water. 
Most recently, Dr. Richards has focused on metabolomics.  Specifically,  the alterations of metabolomes in response to toxicants or in populations of humans affected by endometrial cancer, congenital malformations, endometriosis, polycystic ovarian syndrome, and fetal central nervous system anomalies.  The goal of this research is to determine specific biochemical pathways associated with the affected populations. Ultimately, understanding the changes in the metabolome as a result of disease or intoxication can lead to early detection and personalized treatments.