Directory - Jane Coffin Childs Memorial Fund

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Xingjie Pan, Ph.D. HHMI-Jane Coffin Childs Fellow

Harvard University

Project Title: Reconstruct cell trajectories and communications in brain development

During mammalian development, coordinated cell differentiation and migration convert a simple neural tube into a brain with more than a hundred anatomical regions and probably more than a thousand cell types. How do these cell types emerge? How do cells migrate to their destined locations? How do cells communicate with each other? These are some fundamental problems in brain development.

As a postdoctoral fellow in Xiaowei Zhuang’s lab at Harvard, I develop new methods to systematically study these problems in mouse brain development. I develop new computational methods to connect cells from MERFISH spatial transcriptomics measurements into trajectories and determine cell-cell communication pathways activated in each cell. The reconstructed trajectories will allow me to comprehensively map the differentiation, maturation, and migration of individual cells. I will identify which cell-cell communication pathways are functionally crucial for generating each cell type. Then I will develop high throughput imaging-based screen methods to validate the discoveries.

Niranjan B. Pandey, Ph.D. Jane Coffin Childs Fellow

Massachusetts Institute of Technology /
Massachusetts Institute of Technology

Project Title: Isolating mammalian homologues of MAT alpha1 and STE12

Scott R. Panzer, Ph.D. Jane Coffin Childs Fellow

Yale University

Project Title: CYSPID: a database of properties and relationships among cytoskeletal proteins on the World Wide Web

Claude A. Paoletti, Ph.D. Jane Coffin Childs Fellow

Stanford University

Project Title: Identification and purification of deoxyribonucleases of E. coli

William N. Pappano, Ph.D. Jane Coffin Childs Fellow

Johns Hopkins University

Project Title: Molecular analysis of long-range Hh signaling in vivo

Frederic Paques, Ph.D. Jane Coffin Childs Fellow

Brandeis University

Project Title: Genetic and molecular study of genetic recombination

Sang-Hyun Park, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: Controlling the flow of intracellular information: understanding the role of scaffolding proteins in signaling

Jung-Un L. Park, Ph.D. HHMI - Jane Coffin Childs Fellow

University of California, Berkeley

Project Title: Redesigning RNA-guided DNA integration system using protein engineering

CRISPR-Cas systems have revolutionized genetic engineering and led to novel genetic medicines. As powerful as these systems are, they have some disadvantages such as their large size and a lack of orientation bias which limits their therapeutic usage. CRISPR-associated transposons (CASTs) are mobile genetic elements that use CRISPR-Cas systems for RNA-guided transposition. CASTs may represent the next generation of genome editors due to their enhanced features relative to CRISPR-Cas. Yet, CASTs still require further optimization to realize this potential.

Dr. Jung-Un Park will engineer novel forms of CASTs to optimize properties for genome editing in Dr. David Savage’s lab at the University of California, Berkeley. Using structural biology, biochemistry, and protein engineering approaches, Dr. Park will enhance the activity of individual CAST proteins, as well as tune the functional association between different CAST proteins. Ultimately, Park’s research will provide vast insight into genome editing and may result in the next generation of gene editing technologies.

Park’s interest in CAST biology stems from his graduate work in Dr. Elizabeth Kellogg’s lab at Cornell University. There, he solved structures for CAST that informed on both RNA-guided and RNA-independent transposition. Park will leverage his extensive knowledge of CAST structural details to optimize this system for genome editing during his postdoctoral work.

Eunyong Park, Ph.D. Jane Coffin Childs - HHMI Fellow

Rockefeller University

Project Title: Molecular mechanism of chloride ion transport by CLC protein family

My current research focus is on understanding molecular mechanisms of CLC proteins, ubiquitous membrane proteins that transport chloride ions across membranes. The CLC proteins are involved in various biological processes including regulation of membrane potential, electrolyte/fluid transport across epithelia, and control of intravesicular pH. Mutations in CLC genes cause many hereditary disorders in humans. An interesting aspect of the CLC family is that a common structural architecture seems to be used for both active and passive ion transport. Some CLCs are chloride channels, which provide a passive pore for chloride ion conduction, whereas others function as secondary active transporters that exchange two chloride ions for one proton. Despite recent advances in our understanding of their mechanisms, fundamental questions remain unanswered, especially regarding how exactly CLC transporters couple the transfer of chloride and proton ions and what leads to the mechanistic difference between the channels and transporters. In the MacKinnon lab, I use structural and functional approaches to address these questions.

Jane R. Parnes , M.D. Jane Coffin Childs Fellow

Massachusetts Institute of Technology /
National Institutes of Health

Project Title: In vitro splicing of adenovirus 2 mRNA

Dawn A. Parsell, Ph.D. Jane Coffin Childs Fellow

University of Chicago

Project Title: Functional characterization of the DnaJ protein

William A. Pastor, Ph.D. Jane Coffin Childs Fellow

University of California, Los Angeles

Project Title: Mechanisms of Arabidopsis MORC homologues

Marvin R. Paule, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: Cyclic AMP in transcription of eukaryotes

James R. Paulson, Ph.D. Jane Coffin Childs Fellow

Medical Research Council (MRC),UKRI

Project Title: Structure of eukaryotic chromosomes

Gregory S. Payne, Ph.D. Jane Coffin Childs Fellow

University of California, Berkeley

Project Title: Biochemical characterization of yeast

David S. Peabody, Ph.D. Jane Coffin Childs Fellow

Stanford University

Project Title: Regulation of expression of SV40 late genes

Matthew Y. Pecot, Ph.D. Jane Coffin Childs Fellow

University of California, Los Angeles

Project Title: Specificity of neuronal wiring in Drosophila

Jason P. Pellettieri, Ph.D. Jane Coffin Childs Fellow

University of Utah School of Medicine

Project Title: Tissue homeostasis in planarians

Richard Peltz, Ph.D. Jane Coffin Childs Fellow

University of Wisconsin, Madison

Project Title: Genetic control of mitotic cycle

Harvey S. Penefsky, Ph.D. Jane Coffin Childs Fellow

University of Amsterdam

Project Title: Intermediary metabolism

Ying Peng, Ph.D. Jane Coffin Childs Fellow

Stanford University

Project Title: System biology approach to dissecting a hierarchical signaling network

Xiao Peng, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: Molecular mechanism of injury repair in 3D epithelia

Junmin Peng, Ph.D. Jane Coffin Childs Fellow

Harvard Medical School

Project Title: Identification of a Cdk5 inhibitor in neurogenesis

Stanley M. Perlman, Ph.D. Jane Coffin Childs Fellow

Harvard Medical School

Project Title: Vesicular stomatitis virus

C. Gustavo Pesce, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: Mechanism of regulation of mitochondrial abundance

Reuben J. Peters, Ph.D. Jane Coffin Childs Fellow

Washington State University

Project Title: Structure/function of isoprenoid synthases

Brant K. Peterson, Ph.D. Jane Coffin Childs Fellow

Harvard University

Project Title: Exploring and exploiting phenotypic complexity to unearth the genetic architecture of adaptation and disease

Timothy R. Peterson, Ph.D. Jane Coffin Childs Fellow

Harvard University

Project Title: Discovery of commonly prescribed drug gene targets using haploid human cell genetics

Andrew S. Peterson, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: Identification of genes which are involved in human disease

Thomas D. Petes, Ph.D. Jane Coffin Childs Fellow

National Institute for Medical Research

Project Title: Replicating chromosomal DNA

Peter A. Petillo, Ph.D. Jane Coffin Childs Fellow

Whitehead Institute

Project Title: CT-CBH1 and its carbohydrate binding properties

Matthew D. Petroski, Ph.D. Jane Coffin Childs Fellow

California Institute of Technology

Project Title: Mechanism of SCF receptor turnover

Noah L. Pettit, Ph.D. HHMI - Jane Coffin Childs Fellow

Harvard Medical School

Project Title: Neural circuit computations underlying memory-guided navigation

In adaptive behavior, we take in information from the world around us and use that information to execute certain actions to interact with the surrounding environment. For example, successful navigation requires us to remember the spatial position of a goal and transform that information into actions that will move us towards that goal. Mechanistically, it is still unclear how neural circuits perform these computations.

Dr. Noah Pettit will approach this question using fruit fly interaction with wind direction in Dr. Rachel Wilson’s lab at Harvard Medical School. Dr. Pettit hypothesizes that specific cell types form a circuit that encodes wind direction, maintains it in memory, and transforms this information to influence body movement. Pettit will use multisensory virtual reality, two-photon imaging, and genetic silencing approaches to investigate this circuit at the cellular and molecular levels. These studies will provide a detailed description of how environmental perception is sensed, stored, and translated into action, thereby providing a general framework for understanding these computations in different systems and organisms.

Pettit generated expertise in the underlying neurobiology of spatial learning in Dr. Christopher Harvey’s lab at Harvard Medical School. During his graduate studies, he examined the role of Fos, a transcription factor implicated in memory and spatial learning. Pettit discovered that Fos-induced neurons are more likely to be place cells – cells that are activated when an animal experiences a certain place in its environment. Additionally, Pettit found that the place code degrades when mice voluntarily disengage from a spatial task, suggesting that the internal state exerts a strong influence on place cell activity. With this experience, Pettit will now transition to fruit flies and understanding how these animals transform and respond to external cues.

Cathie M. Pfleger, Ph.D. Jane Coffin Childs Fellow

University of California, Berkeley

Project Title: Identifying proteins involved in cell growth and division

Vanha N. Pham, Ph.D. Ludwig Cancer Research - Jane Coffin Childs Fellow

Princeton University

Project Title: Biochemical basis and function of lipid spatial localization within the brain

Dr. Vanha Pham hypothesizes that there are many molecular examples of the “Goldilocks principle” in cell biology. During her graduate research she demonstrated how the right amount of formaldehyde mediates functional epigenetic signaling, while too much leads to general toxicity. In her fellowship, Pham will investigate how lipids in the brain are organized to maintain homeostasis and the functional and disease implications that result when they are not.

Pham’s thesis research in Dr. Chris Chang’s lab at UC Berkeley, focused on the role of small molecules and metal ions in helping the body’s cells carry out chemical processes. Pham discovered that formaldehyde can block an enzyme needed to make SAM, a key molecule in one-carbon metabolism. Surprisingly, this didn’t cause widespread changes in gene regulation, but instead affected only specific spots on certain genes.

As she transitions to Dr. Joshua Rabinowitz’s lab at Princeton University, Pham will shift her studies to the interplay between proteins and lipids. Using the brain as a model system, she’ll investigate why lipids are spatially enriched in different layers of the brain using a novel approach that maps lipids and gene activity in specific parts of a tissue in combination with genetic screens.

Additionally, she will investigate what happens when certain lipid patterns are disrupted. Pham anticipates that her findings will reveal important insights on how lipids impact membrane protein function, regulate cell morphology, and modulate physiology and disease.

Michael Piechowski, Ph.D. Jane Coffin Childs Fellow

University of Wisconsin, Madison

Project Title: Bacteriophage maturation

Daniel W. Pierce, Ph.D. Jane Coffin Childs Fellow

University of California, San Francisco

Project Title: The kinesin mechanism: two heads and two directions

Vincent P. Pigiet Jr., Ph.D. Jane Coffin Childs Fellow

Karolinska Institutet

Project Title: Ribonucleotide reductase in regulation and synthesis of deoxyribonucleotide

Zachary S. Pincus, Ph.D. Jane Coffin Childs Fellow

Yale University

Project Title: Quantitative longitudinal analysis of aging in C. elegans populations

Current research: I am investigating the causes of differences in lifespan between individuals, using the nematode work Caenorhabditis elegans as a model organism.

My overall scientific interest is in the control of noise in biological systems: how do organisms buffer themselves from, or exploit, stochastic events? How do individuals in a population begin to diverge from one another, and what are the consequences?

After growing up in Montana and majoring in biological sciences at Stanford University, I did my PhD training in the lab of Dr. Julie Theriot at Stanford, studying shape variability in populations of bacteria and epithelial cells. This work allowed us to devise qualitative and quantitative models of how the biochemistry of the actin cytoskeleton influences the large-scale geometry of moving cells. I am now with the lab of Dr. Frank Slack at Yale. And to the extent that postdocs permit themselves to venture outside the lab, I like to spend my time hiking and cycling.

Rachel J. Pinker, Ph.D. Jane Coffin Childs Fellow

Memorial Sloan Kettering Cancer Center

Project Title: Interaction of oncogene products with molecular chaperones

Mark H. Plitt, Ph.D. Jane Coffin Childs Fellow

University of California, Berkeley

Project Title: Exploring mechanisms for flexible learning in higher-order neural circuits

As we learn new behaviors, we still have to remember old behaviors as well. Thus there is a tension between the flexibility in learning and the stability of maintaining behaviors. Dr. Mark Plitt proposes that neural circuits resolve this tension by using neuromodulation to adaptively switch between stable and labile states. He will investigate these questions in Dr. Yvette Fisher’s lab at the University of California, Berkeley. There, Dr. Plitt will use a fly’s head direction circuit – a neuronal representation of the fly’s orientation in space – to investigate the tradeoffs between flexibility and stability. Dr. Plitt predicts that different neurotransmitters will reinforce learning and maintenance of memory. By developing this powerful model system, Dr. Plitt hopes to uncover physiological and computational principles that govern flexible learning.

As a graduate student in Dr. Lisa Giocomo’s lab at Stanford University, Plitt investigated hippocampal “place” cell remapping – a cellular process that encodes an animal’s memory-guided navigation. Specifically, Dr. Plitt demonstrated that hippocampal remapping patterns are predictably driven by an animal’s prior experience. This expertise in memory establishment will assist Dr. Plitt in investigating the tradeoff between stability and flexibility during adaptive learning.

Jessica K. Polka, Ph.D. Jane Coffin Childs Fellow

Harvard Medical School

Project Title: Mobility and maintenance of a carbon-fixing microcompartment: bioengineering applications and insights into broad mechanisms of bacterial spatial organization

I am interested in the mechanisms that guide proteins to assemble into mesoscale structures, from force-generating cytoskeletal polymers to metabolic microcompartments. While the basic principles underlying these systems underpin much of biological organization, I focus on tractable polymers found in bacteria. For example, as a graduate student in Dyche Mullins¬í lab at UCSF, I reconstituted a three-component bacterial plasmid-segregating actin system in vitro and elucidated the multiple regulatory functions of its single accessory protein. As a postdoc, I have investigated the assembly of the carboxysome, a protein organelle in cyanobacteria that we found grows like a crystal until it is rapidly coated by a layer of shell proteins. Currently, I am interested in a long-range protrusive apparatus actuated by chemical changes.

I hope that a thorough understanding of these machines can permit the rational design of self-assembling structures suited for use in nanotechnology, metabolic engineering, and drug delivery.

Samuel Pontes, Ph.D. Jane Coffin Childs Fellow

Columbia University

Project Title: Behavioral function of pattern completion in the cortex

Brian M. Pontius, Ph.D. Jane Coffin Childs Fellow

University of Oregon

Project Title: A role for unstructured, polymeric domains in increasing the kinetics of specific macromolecular association

Raymond C. Portalier, Ph.D. Jane Coffin Childs Fellow

Princeton University

Project Title: Structure, replication and transcription of folded chromosomes

Derek A. Pratt, Ph.D. Jane Coffin Childs Fellow

University of Illinois at Urbana-Champaign

Project Title: Mechanistic studies of lypoxygenase and cylooxygenase

Leslie A. Pratt, Ph.D. Jane Coffin Childs Fellow

Harvard Medical School

Project Title: Synthesis of an intracellular starvation signal in E coli

Ludvik Prevec, Ph.D. Jane Coffin Childs Fellow

Wistar Institute

Project Title: Replication of reovirus

Ian Price, Ph.D. Jane Coffin Childs Fellow

University of North Carolina at Chapel Hill

Project Title: Secreted proteins from tardigrades as potent protectants in extreme conditions

Jane Coffin Childs Fellow Ian Price, Ph.D., studies how living things survive extreme stress. He focuses on tardigrades, microscopic animals that can survive the vacuum of space, extreme radiation, and being dried out completely for years before rehydrating and carrying on living.

For his thesis research in Wen Tang’s lab at The Ohio State University Price examined protein-RNA assemblies called germ granules in C. elegans. He discovered novel proteins that regulate germ granule assembly, demonstrated that germ granules contribute to developmentally-appropriate gene silencing, and defined the molecular interactions that scaffold germ granule assembly. This work highlighted how powerful model organisms are for discovering new biology.

As a JCC Fellow in Bob Goldstein’s lab at UNC, Chapel Hill, Price is investigating extremophile tardigrades, colloquially known as water bears. Tardigrades can tolerate drastic conditions including complete dehydration and levels of radiation that are one thousand times higher than what humans can survive. Previous work from the Goldstein lab demonstrated that a secreted protein is crucial for desiccation tolerance in tardigrades. Price suspects there are more protective secreted proteins and is searching for them to understand how they work. If some of these proteins protect other organisms too, they could be useful for preserving cells, medicines, and other medical materials.

Amy Prichard, Ph.D. Jane Coffin Childs Fellow

University of California, Los Angeles

Project Title: Keep your enemies close: How does Flock House Virus replicate on mitochondrial membranes?

Amy Prichard, Ph.D., aims to understand how viruses reorganize their host cells to protect themselves from host defenses. During her Ph.D. research, Prichard examined how a family of bacteriophage, viruses that infect bacteria, build replication compartments in bacterial cells to shield viral genome replication from host defenses. Now, as a Jane Coffin Childs Fellow, Prichard will focus on how viruses that infect animals create a different type of replication compartment and how that may also allow them to evade host defenses during infection.

Prichard’s graduate research in the labs of Joe Pogliano, Ph.D., and Elizabeth Villa, Ph.D., at UC San Diego investigated a family of bacteriophage that they named Chimalliviridae. This viral family is unique in that they form a nucleus-like replication compartment within bacteria. Prichard defined the core genes encoded by these bacteriophage, including chimallin, the namesake of this family, which is the major structural protein that forms the replication compartment. Additionally, Prichard and her colleagues revealed how chimallin self-assembles to form this subcellular compartment. Overall, her work clarified which viruses share this unique lifestyle and how these viruses protect their genome replication from the host.

During her JCC Fellowship in the lab of Lena Pernas, Ph.D., at UCLA, Prichard will investigate a different type of virus-induced subcellular compartment. Nodaviruses, such as Flock House Virus and Nodamura Virus, are unique in that they form replication compartments on the outer mitochondrial membrane. Prichard suggests that this location is an unusual “choice” for a viral replication site since mitochondria are home to an essential anti-viral signaling protein. Also, because mitochondria have their own genomes, they use cellular resources that other organelles do not, which could put them in direct competition with these viruses. Her project will examine how and why Nodaviruses replicate in this high-risk location, offering a clear example of how our cells’ organelles, such as mitochondria, can help us fight off viral infection, and how viruses attempt to subvert these defenses by hiding their replication within subcellular compartments. By better understanding the ways viruses hijack our cells, scientists can build a biological toolkit to gain new ways to prevent disease.

Gail J. Pruss, Ph.D. Jane Coffin Childs Fellow

Carnegie Mellon University /
University of Rochester

Project Title: Phage DNA encapsulation