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2023 Pilot Grants

Posted by on Tuesday, November 28, 2023 in featured.

In the space below, find our stories about the pilot grants that were awarded in Summer of 2023. We are excited to be able to support work in 11 labs with this funding call!

Jamisha Francis is a new Ph.D. student in the lab of Maria Hadjifrangiskou. Her pilot grant topic is Does the urobiome or recurrent infection affect UPEC pathogenic potential evolution?

Francis hopes to accomplish two aims with this grant. First, she will investigate the effects of A. schaalii on uropathogenic E. coli (UPEC) evolution, metabolism, and biofilm formation. She will use electron and confocal laser scanning microscopy to visualize the interactions. 

She will then define the evolution of UPEC during an acute urinary tract infection. The Hadjifrangiskou lab frequently uses a murine urinary tract infection model to discover UTI dynamics. Francis will rely on this method to investigate UPEC  evolution over time and use next generation sequencing to identify mutations. 

According to Francis, “this work is significant, because it will be the first to determine how uropathogens respond to the presence of urinary microbiota and how such interactions influence pathogen evolution. Our findings therefore have the potential to change current paradigms in UPEC pathogenesis and open avenues for probiotic therapy discoveries.”

Francis’ past experiences leave her well-equipped to tackle such a project. She earned her B.S. (cum laude) in Biology from the University of the Virgin Islands with a minor in Psychology. She then completed a M.S. in Microbe-Host Interactions here at Vanderbilt where she studied Streptococcus agalactiae pathogenicity. In 2022, she also spent some time with Pfizer in Pearl River New York where she gained skills in isolating genomic DNA, next generation sequencing, and analysis of sequence data. This year, she even earned a Scientific Leadership Certificate from the Owen Business School Executive Education Program. 

We’re excited to see where this research goes!

Neil Kelley, Assistant Professor in the Department of Earth and Environmental Sciences, will embark on a project titled “Finding and Digitizing ‘Forgotten Gems’ of Triassic Marine Reptile Evolution.” This project focuses on exploring previously collected but understudied fossils to gain critical insights into the early evolution of reptiles in Mesozoic oceans.

Over the 2023 / 2024 academic year, Kelley plans to visit collections in Boston, California, and Canada, where he will study Triassic ichthyosaur and thalattosaur fossils. The institutions involved in the project include the Museum of Comparative Zoology at Harvard University, the University of California Museum of Paleontology, the California Academy of Sciences, and the Royal Tyrell Museum of Natural History. Kelley also aims to involve Samir Cancel-Matos, a first-year PhD student in EES, in this venture, providing him with exposure to key questions in marine reptile evolution and practical experience in working with museum collections.

Goals and Hypotheses:

While many paleontological endeavors prioritize fieldwork for new discoveries, Kelley’s proposal takes a unique approach by using museum collections filled with overlooked and neglected fossils. The primary goals include lost and forgotten fossils and creating digital assets, such as 3D models through photogrammetry and microCT scanning, to share these valuable resources with the international scientific community.

William R. Kenan, Jr. Chair of Biological Sciences, professor Brandt Eichman, is researching the atomic-level molecular structures and mechanisms of enzymes involved in genome maintenance. This project investigates the fundamental processes of DNA replication and repair; essential for the proper functioning and evolution of all living organisms.

“One ongoing project involving a structural evolution approach is aimed at understanding how DNA repair proteins serve as self-resistance mechanisms for the production of DNA-damaging toxins by antibiotic-producing bacteria,” said Eichman. This research not only contributes to understanding cellular function but also addresses the broader implications of specialized DNA repair proteins in secondary metabolite production, particularly in antibiotic-producing bacteria.

Understanding the self-resistance mechanisms of DNA repair proteins can pave the way for novel biological and biochemical insights, potentially leading to the discovery of new mechanisms in enzyme function. Moreover, this research has implications for increasing the yield of natural products from re-engineered producing organisms, offering promising avenues for the development of antimicrobial and anticancer drugs.

Goals of the Research:
The overarching goal is to decipher the molecular structures of enzymes involved in genome maintenance, providing a framework to understand the outcomes of evolution at the amino acid and structural levels. By combining structural information with phylogenetic and genomic analysis, the team seeks to explore how genes related to genetic information exchange evolve and impact cellular function


Gianni Castiglione, Assistant Professor of Biological Sciences, is set to lead an innovative research project titled “Exploring Metabolic Evolution in Horses (Equus) using Seahorse Assays.” Representing a new direction for the Castiglione lab, this study delves into the metabolic networks of horses, aiming to unravel how these majestic creatures have evolved to cope with oxygen-starved environments during endurance running. 

According to Castiglione, “horses, with their exceptional endurance, present a unique opportunity to explore how the body adapts to extreme physiological demands. Our research suggests that HIF-1 is hyperactive in horse cells and muscle tissues, revealing potential insights into enhanced glycolysis. This not only expands our understanding of equine physiology but may also shed light on how horses have evolved to thrive in oxygen-deprived conditions.”

Goals and Hypotheses:
Building on their prior research in avian metabolic adaptation related to flapping flight, the Castiglione lab is now turning its attention to Equus, investigating the physiological adaptations that enable horses to achieve unparalleled endurance running. The research focuses on understanding how horses cope with periods of oxygen starvation during their demanding physical activities and if the transcription factor HIF-1 plays a central role in their hypoxic response.


Owen Hale, under the guidance of Dr. Megan Behringer, assistant professor of biological sciences, is spearheading a research project to understand the diversity of uroprotective traits in bladder commensal bacteria. This endeavor holds promising implications for uncovering novel insights into urinary tract health and the adaptive landscape of uropathogenic Escherichia coli (E. coli).

According to Behringer, “the complexity of interactions between uropathogenic E. coli and commensal lactobacilli is a fascinating puzzle that we aim to solve through cutting-edge techniques such as RB-TnSeq.” 

A crucial aspect of the research involves understanding the tradeoffs associated with resistance mutations. By validating knockout phenotypes identified by RB-TnSeq and measuring the fitness of select mutants in coculture with each Lactobacillus strain, the team aims to explore potential tradeoffs in resistance mutations.

Hale plans to apply for an NIH F31 fellowship for further support in completing the project. Additionally, the research groups of Dr. Behringer and Dr. Sysoeva are part of a consortium developing an application for an NIH Program Project grant, reflecting the collaborative and impactful nature of their work.

Project Objectives:
The adaptive landscape of uropathogenic E. coli is intricately linked to the native bladder microbiota, predominantly composed of lactobacilli associated with urinary health. The project seeks to unravel the mechanisms by which lactobacilli inhibit E. coli growth and explore the adaptive gene loss landscape in the presence of different commensal Lactobacillus species.


Lantana Grub, graduate student in Maulik Patel’s lab, will work on an exploration of mitochondrial DNA (mtDNA) epigenetics. Grub and the Patel Lab are diving into the role of N6-methyldeoxyadenosine (6mA) in eukaryotes, particularly in the model organism C. elegans. Eukaryotes, including humans, trace their origins back to an ancient endosymbiotic event, marking the birth of the mitochondria, which have retained their semi-autonomous status over billions of years. The retention of a small but essential mtDNA has long intrigued scientists, and the Patel Lab aims to unravel this mystery by investigating the presence and function of 6mA, an epigenetic modification commonly found in prokaryotes.

“Ultimately, this research will provide essential information about how mtDNA epigenetics is affected by environmental stress and the role it has in adaptation to metabolic stress.” said Patel.

The project led by graduate student Grub, will also get valuable assistance from rising junior Marleigh Carter, an undergraduate in the Molecular and Cellular Biology program at Vanderbilt. 

Goals and Hypotheses: 
Leveraging Nanopore sequencing, the team aims to identify 6mA sites in wildtype C. elegans with unparalleled single-base resolution. This cutting-edge technique will unveil the distribution of 6mA sites, offering critical insights into its potential functions, such as marking sites of replication initiation.


In a quest to unveil the dietary secrets of Smilodon fatalis, (the sabertooth cat), graduate student Jay Pardo and Professor Larisa DeSantis embark on a research project titled “The Changing Menu of Sabertooth Cats: Dietary Ecology of Smilodon During Glacial and Interglacial Periods of the Pleistocene.”

Rancho La Brea, home to the largest collection of S. fatalis specimens globally, provides a rich archaeological backdrop for this investigation. By leveraging previously collected stable isotopes and dental microwear data, the team aims to select individuals spanning glacial and interglacial periods, as well as the arrival of humans.

The study is poised to address a pivotal evolutionary question: How did the arrival and expansion of human populations in North America influence the interactions between Smilodon, an apex predator, and its prey? The integration of sulfur isotopes in the analysis of Smilodon’s mandibular bones promises to shed light on the potential changes in home range sizes and the utilization of coastal habitats in response to environmental and anthropogenic factors.

According to Pardo, “the ESI pilot grant allows me to conduct a comprehensive study on the dietary ecology of Smilodon. This funding allows me acquire cutting-edge technology for dental microwear and stable isotopes lab work analyses. The significance of this funding extends beyond my research and will contribute to the broader scientific community’s understanding of prehistoric ecosystems and ecological dynamics."


A team of researchers led by Dr. Kate Snyder, with guidance from advisor Prof. Nicole Creanza, is set to unravel the intricate melodies of bird song and its evolutionary implications. The project, funded by a Pilot Research Grant in Evolutionary Studies, delves into the relatively unexplored realm of female bird song and its connection to complex reproductive behaviors.

“One of our goals is to understand how sexual selection for song complexity is altered in species with cooperative breeding behaviors,” said Snyder. 

Using songbirds as a model system, the team leverages the diversity of life history strategies and songs across species to investigate the evolutionary consequences of complex reproductive behaviors. Preliminary data suggests that approximately 10% of songbird species frequently exhibit cooperative breeding social behaviors, offering a rich dataset to explore the interplay between cooperative breeding, sexual selection, and the evolution of bird song.

Goals and Hypotheses:
Bird song, traditionally considered a primarily male trait, plays a crucial role in mate attraction, species recognition, and social interactions. Dr. Snyder’s research challenges existing paradigms by investigating the occurrence, functions, and selection pressures on female bird song. The project aims to understand the influence of female preferences on male song complexity and the broader implications for evolutionary processes.


Postdcotral researcher Marina Watowich of the Lea Lab, in collaboration with the Turkana Health and Genomics Project (THGP) and the Tsimane Health and Life History Project (THLHP), embarks on a journey to investigate clonal hematopoiesis of indeterminate potential (CHIP) and its potential links to cardiometabolic health across two populations undergoing rapid lifestyle transitions—the Turkana of Kenya and the Tsimane of Bolivia.

The study will integrate genomic and biometric data, focusing on two populations. Both groups are undergoing rapid transitions from traditional to urban lifestyles.

Clonal hematopoiesis, an over-representation of blood cells derived from a single clone, has emerged as a critical area of study, particularly when mutations occur in cancer-associated ‘driver’ genes. This project will explore the prevalence of CHIP and its potential role in cardiovascular diseases, stroke, and coronary heart diseases. By investigating CHIP prevalence and its association with cardiometabolic health, the team will study environmental mismatch and the molecular-level manifestations of this phenomenon. 

The team recognizes the importance of community engagement and will communicated the results of the study with respect and transparency. The project is not just a scientific endeavor; it is a collaborative effort aimed at advancing understanding and improving health outcomes.

According to Watowich, “The funding from the ESI pilot grant allows me to quantify the prevalence of specific somatic mutations among individuals from small-scale, subsistence-level societies. As one of the first datasets of its type, this will yield important insights into the rates of somatic mutations throughout aging in these populations.”

Limestone cedar glades, a distinctive and fragile ecosystem, are primarily located within the Central Basin of middle Tennessee. Dr. Elsie Quarterman, a pioneering figure in Biological Sciences at Vanderbilt, laid the foundation for understanding the ecology of these glades. The glades, characterized by Lebanon limestone and a karst topography resulting from water erosion, face seasonal variations that pose unique challenges to the flora inhabiting them.

In an effort to safeguard the unique limestone cedar glades of middle Tennessee, a team of researchers led by Alejandro Prieto, a PhD student in Earth and Environmental Sciences, is conducting a study. The project, in collaboration with advisors Dr. Jorge and Dr. Darroch,  Dr. Dennis from the Friends of Mill Ridge Park, and undergraduate student Dante Hernandez, aims to assess the impact of anthropogenic landscape changes and develop an effective management plan for the cedar glades at Mill Ridge Park in Antioch, TN.

Goals & Hypotheses:
With Mill Ridge Park transitioning into a public space, the research team aims to assess the impact of approximately 150 years of anthropogenic landscape changes on the cedar glades. The delicate nature of this ecosystem requires a multidisciplinary approach, merging expertise in ecology and geology. The goal is to survey local plant diversity, identify potential threats, and develop an effective management plan.

Hao Yin, a Postdoctoral Researcher in the Department of Earth and Environmental Sciences, will investigate the relationship between air pollution and plant phenology. As atmospheric pollution continues to rise, posing threats to both the environment and human health, understanding its impact on plant life becomes increasingly important.

According to Yin and mentor Lin Meng, over the past few decades, rapid industrialization and urbanization have led to a surge in atmospheric pollution, with pollutants such as nitrogen oxides, sulfur dioxide, ozone, carbon monoxide, and particulate matter reaching alarming levels. While the detrimental effects of these pollutants on air quality and human health are well-documented, their impact on plant life remains a lesser-explored area. The team will bridge this gap by providing a comprehensive understanding of how air pollutants influence plant phenology, contributing valuable insights to environmental conservation and agricultural management.

The study has three primary objectives: 1)Investigate potential correlations between air pollutants and plant spring phenology. 2) Identify key atmospheric pollutants with the greatest influence on spring phenology, and 3) Determine if there exists a pollutant concentration threshold that triggers substantial changes in spring phenology.

To achieve these objectives, Yin and the team will conduct field observations in diverse regions, deploying air pollutant concentration detectors to monitor major pollutants.