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IMCI Seminar Series – Spring 2023

IMCI Seminar Series – Spring 2023

Tuesday | February 14th | 12:30 p.m.
Aurora Room (ISUB) or join us on Zoom Passcode 028591

Jennifer Maynard 
ZD Bonner Professor of Chemical Engineering
University of Texas at Austin

Join us at 12:00 p.m. for coffee and treats before the presentation.

“Outsmarting pathogens with protein engineering: Lessons from pertussis, cytomegalovirus and coronavirus”

There is growing interest in development of antibodies to provide instant immunity that protects susceptible individuals against infectious diseases, especially pathogens for which no vaccine is yet available. However, many of these pathogens, especially those that manifest as highly transmissible or latent infections, express complex arrays of virulence factors and are adept at avoiding the immune system. Some organisms have developed strategies to selectively destroy anti-pathogen antibodies, while others create decoys that trick the host immune system into generating antibodies that are at best non-protective and, at worst, enhance pathogenesis. Design of pathogen-resistant antibodies can present novel therapies and in turn guide development of protective vaccines for these challenging pathogens. This talk will provide an overview of our progress engineering antibodies and antigens resistant to specific immune defense mechanisms used by pathogens including B. pertussis, human cytomegalovirus, and SARS-CoV-2.

Tuesday | March 7th | 12:30 p.m.
Aurora Room (ISUB) or join us on Zoom Passcode 028591

Cailin O’Connor 
Professor – Logic and Philosophy of Science
Director – Philosophy, Political Science, and Economics MA Program
University of California, Irvine

Join us at 12:00 p.m. for coffee and treats before the presentation.

“Interdisciplinarity Can Aid the Spread of Better Methods”

Why do bad methods persist in some academic disciplines, even when they have been clearly rejected in others? What factors allow good methodological advances to spread across disciplines? In this work, we investigate some key features determining the success and failure of methodological spread between the sciences. We introduce a model that considers factors like methodological competence and reviewer bias towards one’s own methods. We show how self-preferential biases can protect poor methodology within scientific communities, and lack of reviewer competence can contribute to failures to adopt better methods. We further argue, however, that input from outside disciplines, especially in the form of peer review and other credit assignment mechanisms, can help break down barriers to methodological improvement.

Standards of Evidence Working Group

Working Group Leader: Bert Baumgaertner

Group Members: Florian Justwan, Kendal Mitton, Chenangnon Tovissode

Originated: January 2023


This working group uses both modeling and empirical investigations to understand the role that evidentiary standards play when individuals evaluate claims. We are interested in the systematic ways standards of evidence differ across various types of claims (e.g. political vs scientific) and the determinants of these systematic differences, including base rates (priors) vs likelihoods, in-group vs outgroup, confirmation vs disconfirmation, prospective vs retrospective, and general public vs political elites.

Mathematical Immunology

Working Group Leader: Tanya Miura

Group members: Esteban Hernandez Vargas, Rodolfo Blanco Rodriguez

Originated: November 8, 2022


The Mathematical Immunology Working Group will develop mathematical models to explain the roles of immune responses during respiratory viral infections.

PIPP Molecular Modeling (MoMo)

Working Group Leader: Marty Ytreberg

Group Members: Jonathan Barnes, Jagdish Patel, America Chi

Originated: December 15, 2022


MoMo will brainstorm ideas to participate in the pandemic preparedness proposal that will be led by University of Texas, Austin.

Paul Rowley Awarded Modeling Access Grant

Title: Using molecular modeling to assess structural conservation of KP4-Like proteins and their potential as antifungals

Project Team: Paul Rowley, Jonathan Barnes

Start Date: May 2022

KP4 protein has been used as a potent antifungal drug to reduce the spoilage of commodity crops. While the potential of KP4 has not been fully realized due to its narrow spectrum of activity, there are at least 500 more KP4-like (KP4L) homologs that we have identified that are encoded by fungal genomes. The central hypothesis is that these proteins represent an untapped resource of novel antifungal proteins that could be leveraged against important fungal diseases. To that end, we propose to initiate a molecular modeling project to determine if the low sequence homology of KP4L proteins to KP4 translates into structural conservation. This work will complement empirical studies that are underway in the Rowley lab. We anticipate that this project will be completed and published before the end of 2022.

Molecular dynamic simulations previously collected by Dr. Jagdish Patel from a prior MAG demonstrated that three KP4L proteins adopt a stable structure similar to the structural model of KP4 that was determined by X-ray crystallography. This MAG would follow up this work by using AlphaFold2 and molecular dynamics simulations to predict the structure of 20 KP4L proteins that represent the known diversity of these proteins. Furthermore, the application of in silico mutagenesis by FoldX will enable us to draw conclusions about the structural plasticity of these proteins and their ability to tolerate mutations. In silico mutagenesis will be complemented by site-saturated empirical mutagenesis to determine the accuracy of the computational models and to identify amino acids that are critical for the toxicity of KP4L proteins.