The goal of the Pittsburgh Area Yeast Meeting (PAYM) is to provide a platform to discuss the latest research by members of our community who use yeast as a model system. Our research areas are broad, including transcription, chromatin and translation regulation, protein quality control and trafficking, and the impact of variant effects and cellular evolution.
The PAYM group has been operational for over 30 years, originally formed by Drs. John Woolford and Beth Jones (Carnegie Mellon University). Its expansion was spearheaded by Drs. Karen Arndt and Jeff Brodsky (2005-2019). The group is now led by Drs. Allyson O'Donnell (allyod@pitt.edu) and Matt Wohlever (wohlever@pitt.edu). We are a highly collaborative group and are often willing to share yeast resources so please reach out to Allyson and/or Matt with requests.
Currently, the members meet each month to hear about the latest discoveries from two of the more than 15 labs affiliated with this group. This local meeting allows us to foster strong connections and collaborations between groups, permits lively and in-depth discussion of research topics, and creates a supportive environment for our trainees. Even if you don’t use yeast as a model system, all are welcome to attend, and the schedule of events for Fall 2025-Spring 2026 can be found here.
In addition to presenting at the PAYM, many of our researchers use yeast as a model in teaching authentic, research-driven laboratory courses or bring yeast research into their classrooms. We are happy to discuss resources for developing course-based undergraduate research curricula with those who would like to adopt this kind of approach in their classrooms.
PAYM-Affiliated Labs
- Arndt Lab
Dr. Karen Arndt's lab studies eukaryotic gene expression with a focus on the interplay between transcription and chromatin structure. One major area of study is the elucidation of regulatory proteins and mechanisms that control the epigenetic marking of eukaryotic genomes through histone modifications. A second major area of study is the role of chromatin structure, modification, and remodeling in regulating transcription elongation and termination. The Arndt lab uses a multi-faceted approach of genetics, genomics, proteomics, mechanistic biochemistry, and protein crosslinking experiments to address these fundamental questions in eukaryotic gene regulation.
- Brodsky Lab
The lab of Dr. Jeff Brodsky focuses on understanding how misfolded proteins are recognized and destroyed in the cell, how molecular chaperones mediate protein quality control “decisions”, how cellular stress impacts protein homeostasis ("proteostasis"), and how defects in protein architecture can be corrected. Our early work contributed to the discovery of the endoplasmic reticulum associated degradation (ERAD) pathway, which we named, and ongoing studies are deciphering the mechanisms underlying this pathway in yeast, mammalian cell culture, and rodent models. The importance of ERAD is evidenced by the fact that >70 human diseases are associated with the pathway, and numerous ERAD substrates play vital roles in human physiology.
- Carvunis Lab
What makes each species unique? In the lab of Dr. Anne Ruxandra Carvunis, we study the molecular mechanisms of change and innovation in evolution. This involves thinking about how genomes change over time, what cellular processes enable these changes, and how novel molecular networks emerge. The research tools we rely on most are bioinformatics, yeast genetics and genomics. Generally, we strive to foster an interdisciplinary and collaborative research environment where researchers can develop creative approaches to describe, engineer and predict the genetic and network-level determinants of species-specificity and the emergence of new genetic elements.- Clark Lab
In the lab of Dr. Nathan Clark, we study the process of adaptive evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology. To meet these goals, we have developed a suite of computational and experimental approaches employing comparative genomics. Ultimately, our research program develops an evolutionary model in which genomic elements are shaped by their co-evolution with other elements and their environment.
- Gallagher Lab
In the age of genomics, an enormous challenge to the field is predicting phenotypes from genotypes. In the lab of Dr. Jen Gallagher, we combine classical genetics and molecular biology with bioinformatics approaches such as genomics, transcriptomics, metabolomics, and proteomics to assess how organisms respond to constantly changing environmental stresses. Current stresses being studied are glyphosate, ribosome-inactivating proteins, DNA damage, and heavy metals.- Kaplan Lab
The lab of Dr. Craig Kaplan studies mechanisms of gene expression with a focus on RNA Polymerase II (Pol II) in the budding yeast Saccharomyces cerevisiae. We employ genetic, genomic, and biochemical approaches to understand how alterations to Pol II activity affect gene expression and cotranscriptional processes. We also are interested in mechanisms of initiation and how they may have evolved to be different while still using a conserved set of factors.- McManus Lab
The lab of Dr. Joel McManus studies RNA regulatory control of gene expression. The lab develops and employs novel high-throughput assay systems to identify RNA cis-regulatory elements and structures, and then quantitates their impact on mRNA translation using massively parallel reporter systems. We computationally mine the resulting data to distill features and develop models that predict the functions of mRNA transcript leaders. Using these approaches, we study post-transcriptional regulation of human and fungal genes.- O'Donnell Lab
Research in the lab of Dr. Ally O’Donnell focuses on the α-arrestins, a relatively understudied class of protein trafficking adaptor. We use the α-arrestins to define the rules that govern selective trafficking of membrane proteins in response to nutrient and stress signaling. Our lab uses cell biological, genetic, and biochemical approaches to define conserved regulatory elements that dictate selective remodeling of membrane proteomes.
- Patton-Vogt Lab
The lab of Dr. Jana Patton-Vogt's broad interest is in membrane lipid biochemistry. Of particular interest is the production, transport, metabolism, and function of a class of phospholipid metabolites called glycerophosphodiesters. Glycerophosphodiesters, such as glycerophosphocholine (GPC) and glycerophosphoinositol (GPI), are produced through phospholipase B-mediated cleavage of their precursor phospholipids. My laboratory has characterized several novel genes defining this metabolism in S. cerevisiae, including a permease (Git1), a glycerophosphodiesterase (Gde1), and an acyltransferase (Gpc1). The fundamental importance of these turnover/recycling processes is illustrated by the fact that the basic components have been described in organisms spanning the biological spectrum, including pathogenic fungi and various plant species. My lab has been involved in many of those translational studies.
- Roth Lab
The lab of Dr. Frederick (Fritz) Roth has a major focus on measuring and inferring the functional and disease impacts of human protein sequence variants. Using both human and yeast cell models, we measure variants at scale to generate complete 'lookup tables' of that can provide evidence for variant interpretation that is ready even for novel clinical variants. Our disease interests are broad, but there is a strong current focus on genes related to coronary heart disease. The lab also has a strong interest in large-scale identification of protein-protein interactions, and in the impacts of protein sequence variation on those interactions. In both areas, we are keenly interested in understanding the impact of shifting environments and genetic backgrounds, both on protein interactions and on the functional and disease impacts of sequence variation.
- Wohlever Lab
The lab of Dr. Matt Wohlever studies membrane protein quality control using biochemistry and structural, molecular, and cell biology. Membrane protein homeostasis (proteostasis) is a fundamental process in cell biology, but the molecular details are largely unexplored. Failures in membrane proteostasis can lead to many diseases including cancer, cardiovascular, and neurodegenerative diseases. Our key research questions are: (1) how do quality control factors discriminate between potential substrates in a complex cellular environment, including the lipid bilayer; (2) once a substrate is recognized, what are the downstream steps that lead to resolution of proteotoxic stress; and (3) how can we leverage the resulting mechanistic insights to develop therapeutic interventions in cancer and neurodegenerative diseases?
- Woolford Lab
The lab of Dr. John Woolford investigates the mechanism of ribosome assembly, focusing on the middle-to-late nucleolar stages of large ribosomal subunit maturation. This is an especially dynamic interval, during which nascent ribosomes undergo numerous significant remodeling events, including folding and compaction of ribosomal RNA (rRNA) structure, and trafficking of assembly factors onto and off of pre-ribosomes, ultimately to enable transit of pre-ribosomes from the nucleolus into the nucleoplasm. We are tackling these questions in the following two projects: 1: Understanding the roles of ribosomal proteins and assembly factors in remodeling events, and 2: Exploring the relationship between ribosome biogenesis and the structure and function of the nucleolus, the biomolecular condensate where ribosome assembly begins. To do so, we employ multiple tools: classic and molecular genetics, proteomics, fluorescence microscopy, bioinformatics, and near-atomic resolution cryo-electron microscopy.
