30th Annual Conference
"Frontiers in Biocatalytic Science"
October 14, 2023
The University of Iowa
Pharmacy Building, Iowa City, IA
Edgar Valencia-Morales, Ph.D., Microbial Viability Lab Lead, Bayer's Crop Sciences Division Chesterfield, MO
"Multiple Applications of qPCR for microbial CFU evaluation and identification"
As part of Bayer’s sustainability strategies, we have started evaluating the use of microorganisms to improve Plant health and yield. An important component of this strategy is our capacity to show that our products containing microbes have them in the desired titers and that they do not affect the chemical components in the formulations. It is also important to show that the microbial populations are stable and that there are no pathogens or nuisance microbes present. For microbial evaluation, most of our analysis depend on the traditional plating methods. These methods, in essence simple, have several disadvantages such as: its low throughput, incapacity to distinguish between close related species and time required to obtain the results. Therefore, a faster and more efficient method for microbial analysis is highly desirable.
Among the alternative methods we have evaluated, we think that qPCR is our best option. We would like to show and discuss some of our current advances, challenges and future plans using qPCR for microbial evaluation and identification.
Kristan S. Worthington, Ph.D., Associate Professor of Biomedical Engineering, Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, IA
"Light-based Manufacturing in Retinal Engineering: Fundamentals, Constraints, and Considerations for Cell Delivery Scaffolds and In Vitro Models"
The use of light to make materials with controllable mechanical and physical properties is a powerful tool in biomedical engineering. Furthermore, understanding the ways in which biological systems interact with these materials is critically important to their employment in medical devices and tissue engineering systems. In this seminar, Dr. Worthington will share examples of light-based manufacturing across several application areas, with a primary focus on retinal regenerative engineering. Technical points of emphasis will include the impact of scaffold structure on cell orientation and packing, use of high-resolution 3D printing to achieve sub-cellular control of structure, the role of stiffness and surface chemistry in directing cell fate, and techniques for increasing manufacturing speed and affordability. She will also discuss important regulatory, global, environmental, and economic considerations that have emerged throughout these research projects.
Isaac Cann, PhD., Professor, Department of Animal Sciences, Division of Nutritional Sciences, Center for East Asian and Pacific Studies and the Carl R. Woese Institute for Genomic Biology University of Illinois Urbana-Champaign (UIUC), Urbana, ILL
"Polysaccharide degradation in the human gut and its potential applications in biotechnology and human health "
Human diets contain diverse polysaccharides, including starch, arabinoxylans, arabinans and pectin. The human genome codes for the enzymes required to hydrolyze starch, from which we derive most of our energy. In contrast, our genomes are devoid of the genes encoding the enzymes that target degradation of the other foregoing polysaccharides. These complex carbohydrates in our diets, therefore, escape degradation in the stomach and flow to the colonic environment known to be inhabited by diverse microbiota. The microorganisms present in the colon are dominated by four different bacterial phyla, namely the Bacteroidota, Bacillota, Actinobacteria and Proteobacteria. In addition, organisms belonging to the archaeal domain of life are found in the human colon. The combined genetic material of the colonic microorganisms, i.e., the colonic microbiome, encodes a large collection of genes, including those that orchestrate complete hydrolysis of the polysaccharides escaping degradation in the stomach. Thus, the colonic microbiome endows the human host with a significant genetic versatility that had hitherto been overlooked. My presentation will look at how one of the major groups of polysaccharide-degrading bacteria senses polysaccharides flowing into the colon to efficiently deploy their enzymes for hydrolysis and to further capture the component sugars for metabolism. Using arabinoxylan as a model, I will present how we use transcriptomics, biochemical and structural approaches to look at some of the enzymes that have been evolved by these human colonic bacteria to completely depolymerize this complex polysaccharide. I will further look at how the microbial enzymes involved may be harnessed for the production of value-added products and how our understanding of these processes can lead to rational manipulation of the diet and the microbiome for benefits in the fields of personalized nutrition and health.
Melissa Bates, Ph.D., FAPS, Adjunct Associate Professor of Internal Medicine, The University of Iowa and Founder and CEO, LSF Medical Solutions, Iowa City, IA
"Moving from an academia to a commercial venture: When is the time right?"
How many of us own a Fibit, Apple Watch, or another wearable device that monitors our health? The remote health device market has exploded over the past decade, largely driven by advances in the fitness, cardiovascular, and diabetes health spaces. The start of the COVID pandemic drove interest in the respiratory health market and changed clinicians' acceptance of remotely transmitted data for clinical decision-making. The pandemic also made clear that there are geographic and socioeconomic inequities in healthcare access that can be mitigated by remote technologies. This motivated us to consider re-designing research equipment from our lab, with a 20-year track record of use, for use by patients at home. In this talk, the founder of LSF Medical Solutions will discuss the ups and downs of the transition from a traditional research program to a commercial venture, discuss the local resources available for technology commercialization, and hopefully help you answer the question, "Am I ready to be an entrepreneur?"
Arnon Lavie, PhD., Professor, Department of Biochemistry and Molecular Genetics College of Medicine, University of Illinois at Chicago, Chicago, Ill and Co-founder and CEO, Enzyme by Design Inc, Chicago, ILL
"Embracing Entrepreneurship in Academia: The Thrilling Journey from Scientific Discovery to Clinical Innovation"
In this presentation, I will take you through my journey in translational science, offering insights through three illustrative vignettes. Each vignette revolves around asparaginases, a class of enzyme drugs approved for the treatment of acute lymphoblastic leukemia (ALL), the most prevalent pediatric cancer. Asparaginases have played a pivotal role in elevating the cure rates for pediatric ALL to an impressive 90%. Nevertheless, the significant side effects associated with these enzyme drugs often lead to patients not completing their prescribed courses, resulting in a decrease in cure rates by more than 20%. Furthermore, many other cancer patients, particularly adults, who could benefit from this unique drug are denied access due to its toxicity, contributing to the notably lower (~50%) cure rates for adult ALL patients. Vignette #1 delves into our enzyme engineering efforts concerning the FDA-approved Erwinia asparaginase. Our objective here was to develop a safer drug by enhancing its substrate specificity. Vignette #2 explores the controversy within the literature surrounding the significance of high substrate specificity in asparaginases. Additionally, I will share our discovery that peer-reviewed publications on this topic often exhibit significant flaws. Lastly, the third vignette centers on my experiences and lessons learned in the journey of advancing a discovery from academia to the realm of biotech startups.
Autumn Moore, Ph.D., was part of Robert Kern’s Research Group, Department of Pharmaceuticals, Medicinal and Natural Chemistry, College of Pharmacy, The University of Iowa, Iowa City, IA
"Insulin-mediated GLUT4 translocation via small molecule binding of UNC119 for the treatment of diabetes mellitus"
Type II diabetes (T2D) is a disease that is characterized by insulin resistance, hyperglycemia, and impaired insulin secretion via pancreatic b-cells. In skeletal muscle and adipose cells, T2D results in the dysregulation of downstream functions associated with the insulin signaling pathways. In this disease state, insulin is unable to bind receptors that trigger a signaling cascade that triggers GLUT4 in the vesicles to translocate to the surface of cells for glucose storage. Impaired GLUT4 translocation results in the accumulation of glucose in blood, resulting in hyperglycemia. Currently, treatments for diabetes have largely failed to control blood glucose levels through utilization of endogenous insulin or correct insulin insensitivity. As a result, a luciferase-based assay was developed to identify small molecules that could restore GLUT4 translocation in the presence of endogenous insulin in order to prevent hypoglycemia. In identifying small molecule mediators of insulin-dependent GLUT4 translocation, the X-ray crystal structure of small molecule insulin sensitizer bound to UNC119B was utilized to guide the design and synthesis of novel small molecule insulin sensitizers. Concurrently, multiple different structures that were predicted to bind UNC119B were evaluated in silico and identified synthetically tractable compounds from computational and docking analyses. Compounds C59 and 237 were amongst the most potent and efficacious agents that increased insulin-mediated GLUT4 translocation through binding of UNC119B. Issues arose in solubilizing the compounds in water due to both being comprised of aromatic and adamantyl moieties. To remedy this issue, phase solubility studies were conducted to identify the most compatible cyclodextrin to complex with C59 and 237. Of the 3 cyclodextrins tested (a, g, hydroxypropyl-b), hydroxypropyl- b -cyclodextrin increased both C59 and 237 water solubility from <1 mM to >1 mM and >4 mM, respectively.
Souradip Sinha, Ph.D. Candidate, Munir Tanas's Research Group, Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, IA
"The ATAC histone acetyltransferase complex is a key oncogenic driver in sarcomas"
Sarcomas are a heterogenous group of neoplasms originating in mesenchymal tissues and have few targeted therapies. Our lab previously found that the Hippo signalling pathway is perturbed in multiple sarcomas, and TAZ/YAP, the end effectors of the Hippo pathway, are key oncoproteins that drive oncogenesis in sarcomas. Epithelioid hemangioendothelioma (EHE) is a vascular sarcoma that is driven by two mutually exclusive gene fusions encoding the chimeric proteins TAZ-CAMTA1(TC) and YAP-TFE3(YT). Unlike full length TAZ/YAP, the fusion proteins are not inhibited by the upstream Hippo kinases.
The TC/YT fusion proteins promote hallmarks of cancer and alter gene expression patterns in sarcoma cell lines by interacting with the Ada2A-Containing (ATAC) histone acetyltransferase complex, specifically the key scaffolding proteins YEATS2 and ZZZ3, which are critical subunits of ATAC complex. YEATS2 reads acetyl-H3K27 on enhancers and promoters, and ZZZ3 binds to and reads the H3 tail. This promotes the assembly of the ATAC complex, after which the ATAC histone acetyltransferase (HAT) module can acetylate H3K9 via GCN5/PCAF which are mutually exclusive acetyltransferases. YEATS2 is emerging as a key oncoprotein in non-small cell lung cancer, ovarian cancer, head and neck cancer, and esophageal cancer.
RNA-Seq data from The Cancer Genome Atlas (TCGA) showed that high YEATS2 and ZZZ3 levels correlate with a worse overall survival in sarcomas including those lacking TAZ/YAP fusion proteins. Consistent with this observation, we have identified upregulated YEATS2 and ZZZ3 protein levels in sarcoma cell lines as compared to human tissue-matched primary cell cultures via western blot. This suggests that the ATAC complex might be important in fusion protein negative sarcomas as well.
Currently we are conducting in vitro studies with genetic knockdowns of YEATS2/ZZZ3 as well as pharmacological inhibition of the HAT module of the ATAC complex. We have observed that knockdown of YEATS2/ZZZ3 in SKLMS (leiomyosarcoma) decreases H3K9-acetyl levels and reduces colony formation on soft agar. We also found that the HAT-inhibitors PU139 and GSK4027 decrease H3K9-acetyl levels in SKLMS, via western blot analysis. However, genetic knockdowns of YEATS2/ZZZ3 did not decrease H3K9-acetyl levels in the SW872(TC) and RD (rhabdomyosarcoma) cells, suggesting that the ATAC complex might be regulating a subset of genes in these cell lines.
Future studies include performing ChIP-Seq to determine the target genes of the ATAC complex in the above-mentioned sarcoma cell lines. We are also investigating how the above mentioned HAT-inhibitors may alter hallmarks of cancer driven by the ATAC complex in sarcomas. Additionally, we are working towards determining key interactors of the ATAC complex and how this epigenetic complex is recruited to specific chromatin regions.