This course is designed for experienced teachers of Advanced Placement Biology who are looking to enrich their courses with knowledge of research and science practices currently being conducted in science labs at Rice and beyond.
Participants will engage with Rice University faculty and others in an in-depth discussion of topics and documents commonly taught in AP Biology. They will explore the connections between AP courses and college-level courses and examine new research in their field. Readings and documents will be provided during class.
Agenda (subject to change):
Overview of the Week
8-9 a.m. - Robert Dennison, lead consultant
Engineering diagnostic and therapeutic gut bacteria
9- 11:30 a.m. - Jeff Tabor, Ph.D., Rice University
The human gut contains trillions of bacteria that play key roles in health. Engineered gut bacteria have promise to serve as next-generation diagnostics and therapeutics for a wide range of diseases. Here, I will focus on our recent work to use the methods of synthetic biology to engineer gut bacteria to diagnose gastrointestinal diseases. In particular, we are engineering bacterial two-component histidine kinase signal transduction systems as sensors of gut disease biomarkers. We are linking them to genetic circuits and genetic reporter systems to develop novel diagnostics. We have focused on inflammation (colitis) and are beginning to target colon cancer.
Dr. Jeff Tabor is an Associate Professor of Bioengineering at Rice University. He earned his Ph.D. at UT-Austin in 2006 studying the design and evolution of synthetic biological systems with Andy Ellington. There he led a team that engineered E. coli to function as a high-resolution photographic film. He went on to be an NIH postdoctoral fellow with Chris Voigt at UCSF. Here, he re-programmed the bacterial film to function as a parallel computer capable of performing the challenging image processing task of edge detection. He started his lab at Rice in 2010. Here, he has focused on using light to control gene expression (optogenetics) and engineering diagnostic and therapeutic gut bacteria.
His work has been covered in numerous international media outlets including the New York Times, and he has received several national awards including the NSF CAREER and ONR Young Investigator.
Epigenetics and brain development
1-3:30 p.m. - Laura Lavery, Ph.D., Baylor College of Medicine
Our DNA encodes the information of life, yet the cells in our body are different depending on the system of the body in which they function. This diversification is essential for complex organisms like humans. So how does this happen? Epigenetic mechanisms, such as methylation of DNA, regulate our DNA to set unique patterns of gene expression in our cells, which in turn create the necessary cell types. In the mammalian brain, there is a unique form of methylation that marks our DNA after we are born up until 25 years of life. My talk will focus on this form of methylation, termed “mCH”, and what we are learning about its function and mechanism in the brain.
Dr. Laura Lavery earned her Ph.D. with David Agard, Ph.D., at the University of California, San Francisco where she studied the structure and function of an essential chaperone protein that helps the other proteins in our cells fold so they can perform their native functions. She is currently a postdoctoral researcher in the lab of Huda Zoghbi, MD, at Baylor College of Medicine studying the mechanism and impact of a unique form of DNA methylation in our brains.
8-11:30 a.m. - Adrienne Correa, Ph.D., Rice University
The session will look at Dr. Correa’s lab’s work which applies interdisciplinary approaches to quantify how microorganisms influence hosts and ecosystem-level processes, particularly under environmental stress. Their primary research interests include the diversity and evolutionary histories of marine microorganisms; the context-dependent roles of dinoflagellate symbionts, bacteria and viruses in host health and disease; and the influence of microbes on ecosystem function and persistence. We will also use several hands-on tools (2-D Reef Replicas, giant printouts of coral reef bottom, which quadratic measuring tools and coral ID guides), to experience firsthand the science practices used in their research.
Dr. Adrienne Correa is an assistant professor in Ecology and Evolutionary Biology at Rice University.
Genome Editing using CRISPR-Cas9: Microbial Immunity to Curing Diseases
1-3:30 p.m. - Mithil Chokshi, Doctoral Student, Rice University
This lecture will focus on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) protein Cas9. From its evolution in bacteria and early use by yogurt companies to editing human genome precisely, CRISPR has led the recent revolution in Biological Sciences and beyond. Before the origins of CRISPR, gene editing was carried out by other technologies, namely Transcription Activator-like Effector Nucleases (TALENs) and Zinc Finger Nucleases (ZFNs). While these technologies accomplished gene editing successfully, CRISPR still became the juggernaut because of its ease of design and application. However, there are still major improvements to be made to increase the levels of mutation correction that can be achieved, to reduce its off-target activity, and to efficiently deliver it in vivo without any deleterious effects. We will look at the potential it holds in probing scientific inquiries that have been around for decades which can now be studied better and do a case study with a few examples of its application to human diseases. From the discovery of DNA’s 3D structure in the 1960s to engineering it at such great detail, biological engineering has taken exponential leaps comparable to celebrated human feats like stepping on the moon and innovations in computing.
Mithil Chokshi joined Rice University’s esteemed Bioengineering department from the University of Pennsylvania to pursue Ph.D. His work focuses on editing the human genome in stem cells to understand and contribute to the cure of, lung diseases like Cystic Fibrosis. Since before his undergraduate career, he has worked towards raising awareness for the importance of education for children and women coming from challenged socioeconomic communities around the world. This journey has brought him recognition and teaching opportunities from prominent universities and The National Science Foundation (NSF). Recently, he taught undergraduate level courses in Bioengineering at University of Pennsylvania and Physics and Organic Chemistry to local community college students. Currently, he is working with the Houston School District schools and with the Knowledge is Power Program (KIPP) to make our educators better leaders and to lessen the education opportunity disparity in our society. In the hope to better innovate our futures, he is also helping small companies increase their research and development budgets by consulting with them about the PATH Act signed by President Obama in 2015.
Gene Therapy: Next Wave of Biologics That Harness the Power of Viruses
8-11:30 a.m. - Junghae Suh, Ph.D., Rice University
Gene therapy suffered from major clinical setbacks in the late 1990’s, putting the entire field of genetic medicine at a standstill. However, through perseverance and strategic re-thinking of how viruses and cells could be used as therapeutics, the field is currently experiencing a biotechnological revolution. In December of 2017, a virus-based gene therapy drug was approved by the FDA, making it the first of its kind for the treatment of an inherited disease. This landmark achievement is just the beginning of a new era of human therapeutics. This session will discuss the gene therapy field – where it was and where it is now. Clinically important viral vectors currently under human testing and opportunities for the next generation of improved viruses will be presented.
Dr. Junghae Suh received her S.B. in Chemical Engineering from MIT in 1999 and a Ph.D. in Biomedical Engineering from Johns Hopkins School of Medicine in 2004. She then completed a two-year postdoctoral fellowship in the Laboratory of Genetics at the Salk Institute for Biological Studies. She is currently an associate professor of Bioengineering at Rice University located in Houston, Texas. Dr. Suh works at the interface of virology, synthetic biology, and protein engineering to investigate and create virus-based materials for biomedical applications. By manipulating the “inputs” and “outputs” of viruses, she endeavors to develop platform technologies that can be used as therapeutics for a broad range of human diseases. She was awarded the NSF CAREER Award and the MDACC Ovarian Cancer SPORE Career Development Program Award for her innovative work on reprogramming viruses as therapeutic platforms. Most recently, Dr. Suh was awarded the Outstanding New Investigator Award from the American Society for Gene and Cell Therapy. Her work is currently funded by the National Institutes of Health, National Science Foundation, and the American Heart Association.
1-3:30 p.m. - Daniel Wagner, Ph.D., Rice University
This session will focus on work being done in Dr. Wagner’s lab which investigates the function of essential elements required to execute vertebrate morphogenetic programs. Morphogenesis is a collective term for the processes by which cells move and change shape to transform the relatively featureless blastoderm into a recognizable vertebrate embryo.
To investigate vertebrate morphogenetic movements, we analyze the early development of the zebrafish, Danio rerio. The zebrafish embryo provides an excellent model for studying morphogenesis since they are optically transparent, develop rapidly and mutants have been identified that display defective morphogenetic movements. They are applying genetic, molecular and embryological approaches to determine the precise nature of the mutations and the morphogenetic defects they observe. Immediate goals are to identify the genes encoded by the mutant loci and to determine in detail the defects that result from these mutations. By coupling the molecular identity of the mutants with their specific defects we will gain deep insight into the mechanisms of vertebrate morphogenesis.
Dr. Daniel Wagner is an Associate Professor in BioSciences at Rice University.
The Physical Biology of the Cell
8-11:30 a.m. - Ilya Levental, Ph.D., The University of Texas Health Science Center at Houston
We will start with a discussion of the practical scientific method and how it is applied in the laboratory. Following that, a presentation of several vignettes demonstrating the connections between simple physical principles (e.g. Brownian diffusion, phase separation) and cellular processes.
Dr. Ilya Levental began his academic career as a bioengineer at the University of Pennsylvania, with particular passion in the intersection of technology, physics, and cell biology. Following completion of his thesis on the organization and physical chemistry of the important bioactive lipid PIP2, Dr. Levental received the Alexander von Humboldt Fellowship for postdoctoral research and joined the laboratory of Dr. Kai Simons, the discoverer and leading researcher in the field of membrane rafts, at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany. There, he developed a quantitative assay for raft association and characterized structural determinants for raft targeting by the immune system and oncogenic proteins. In 2012, Dr. Levental and his wife Dr. Kandice Levental (a native Texan and long-time collaborator) started up their lab in the Department of Integrative Biology and Pharmacology at The University of Texas Health Science Center at Houston. Their lab is combining classical cell biology, biophysics, synthetic biology and computational modeling to characterize the role of membrane structure in the regulation of cell function, specifically in the context of oncogene addiction in breast cancer cell signaling. The ultimate goal of their research is to understand the principles of organization in the mammalian cell and to manipulate these systems for biomedical advancements. In the first 4 years since starting up the lab, they have published 10 senior author papers – 3 of which were highlighted as cover articles in Journal of Biological Chemistry, Nature Protocols, and PNAS.
Exploring DNA Structure: The Glow Lab from MiniPCR
1-3:30 p.m. - Robert Dennison, lead consultant
Wrapping up the week: A discussion of how to bring the week’s topics back to the AP Biology classroom.