Research
Skin-penetrating gastrointestinal parasitic nematodes are a major source of "diseases of disadvantage". They infect approximately one billion people around the world, primarily in the world’s most socioeconomically depressed communities. These parasites can cause chronic gastrointestinal distress as well as stunted growth and cognitive impairment in children; in some cases, infections can be fatal for immunocompromised individuals. Current therapies are inadequate – some are toxic, drug resistance is a growing concern, and the lack of prophylactic treatments results in high reinfection rates. The development of strategies that prevent infections thus has clear relevance for global health.
One potential approach is to interfere with the parasites’ ability to find humans to infect. Most research on parasitic nematodes is focused on the host animals’ immune response to infection, or uses animal-parasitic nematodes or the free-living nematode Caenorhabditis elegans as models for human parasites. My innovative interdisciplinary approach focuses on the human parasites directly, and combines expertise in neuroscience, parasitology, molecular biology, and genetics to understand the mechanisms that underlie successful sensory-driven parasitism of humans.
My research has two specific aims:
To characterize the role of thermal cues in host seeking.
To identify the neural circuits, molecular mechanisms, and evolutionary adaptations that underlie parasite-specific thermosensory behaviors.
Aim 1: To characterize the role of thermal cues in host seeking
The infective larvae (iL3s) of skin-penetrating parasitic nematodes actively search for hosts in a poorly understood, sensory-driven process that likely involves both olfactory and thermosensory cues. The detailed thermosensory behaviors of parasitic nematodes were not well understood.
I investigated the temperature-driven behaviors of an evolutionarily diverse set of skin-penetrating iL3s, including the human-parasitic threadworm Strongyloides stercoralis and the human-parasitic hookworm Ancylostoma ceylanicum. Aided by two pre-graduate researchers, I found that skin-penetrating iL3s are highly sensitive to thermal gradients. They display two distinct modes of temperature-driven movement: positive thermotaxis towards mammalian body heat, and negative thermotaxis towards cooler temperatures. The switch between positive and negative thermotaxis is subject to experience-dependent plasticity. This plasticity may enable iL3s to optimize host seeking on a diurnal cycle, a possibility with important implications for the development of preventative interventions. Furthermore, the influence of environmental temperature on host-seeking behaviors raises the question of whether parasitic helminth infection rates will be altered by global climate change. Our observation that iL3s are capable of engaging in positive thermotaxis after experiencing a wide range of environmental temperatures suggests that worms will be able to host seek despite changing climate conditions. Recently, we discovered a new component of the sensory strategy that guides parasitic nematodes to hosts: the ability to rapidly reverse erroneous attraction to non-host heat sources. Finally, I found that temperature-driven responses are dominant in multisensory contexts. At temperatures below host body heat, when thermal drive is strong, iL3s appear to prioritize temperature-driven behaviors over chemosensory responses.
Taken together, these results suggest that skin-penetrating nematodes utilize a host-seeking strategy that a) relies on thermal. Much of this research was published in 2018 in Current Biology. For more information on reversal behaviors, please see our BioRxiv manuscript.
Aim 2: To determine the neural and genetic basis of parasite-specific behaviors
Virtually nothing was known about how parasitic worms target humans due to the lack of tools for probing neural function in these parasites. I investigated the neural basis of temperature-driven host seeking in parasitic nematodes using the skin-penetrating human threadworm Strongyloides stercoralis.
I identified the primary thermosensory neurons in S. stercoralis and characterized their responses to thermal stimuli by applying single-cell genetic targeting, cell-type specific neural silencing, and calcium imaging techniques for the first time in an endoparasitic animal. These neurons display unique thermal response properties that support the ability of parasitic worms to engage in long-distance host seeking using body heat. I identified the thermoreceptors that confer parasite-specific sensitivity to body heat, and used CRISPR-Cas9 mutagenesis of the downstream sensory transduction pathway to identify, for the first time in parasitic worms, a gene necessary for host seeking. Together, my results are the first direct evidence that the sensory neurons of parasitic worms exhibit unique neural adaptations and sensory coding strategies that allow them to target humans, a finding with important implications for efforts to develop new therapeutic strategies for nematode control.
For more on these results, please see our manuscript on BioRxiv.
Side projects: To develop computational tools for Strongyloides researchers
Due to the COVID-19 pandemic, I developed several computational projects aimed at providing accessible resources for researchers studying Strongyloides species.
Project 1: Wild Worm Codon Adapter
Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis. Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes. Platforms for generating DNA sequences codon optimized for the free-living model nematode Caenorhabditis elegans are broadly available. However, until now such tools did not exist for non-Caenorhabditis nematodes. We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes. The app includes built-in optimization for parasitic nematodes in the Strongyloides, Nippostrongylus and Brugia genera as well as the predatory nematode Pristionchus pacificus, and C. elegans. The app also supports custom optimization for any species using user-provided optimization rules. In addition, the app supports automated insertion of synthetic, native, or custom introns, as well as the analysis of codon bias in transgene and native sequences. For more information, please see our study published in G3.
The app is deployed at the following link:
https://hallemlab.shinyapps.io/Wild_Worm_Codon_Adapter/
Project 2: Strongyloides RNA-seq Browser
Soil-transmitted gastrointestinal parasitic nematodes infect approximately 1 billion people worldwide, predominantly in low-resource communities. Skin-penetrating gastrointestinal nematodes in the genus Strongyloides are emerging as model systems for mechanistic studies of soil-transmitted helminths due to the growing availability of functional genomics tools for these species. To facilitate future genomics studies of Strongyloides species, we designed a web-based application, the Strongyloides RNA-seq Browser, that provides an open source, user-friendly portal for accessing and analyzing Strongyloides genomic expression data. Specifically, the Strongyloides RNA-seq Browser takes advantage of alignment-free read mapping tools and R-based transcriptomics tools to re-analyze publicly available RNA sequencing datasets from four Strongyloides species: Strongyloides stercoralis, Strongyloides ratti, Strongyloides papillosus, and Strongyloides venezuelensis. This application permits on-demand exploration and quantification of gene expression across life stages without requiring previous coding experience. For more information, please see our study published in G3.
The app is deployed at the following link:
https://hallemlab.shinyapps.io/strongyloides_rnaseq_browser/
Project 3: Power Analysis App
The goal of this project was to generate a Shiny web app for conducing simple power analyses on user-provided data. Most online resources currently require users to provide pre-processed data in the form of individual and group averages. Excel spreadsheets with embedded lookup tables for calculating power analyses require users to be comfortable with several advanced excel features, and assumes familiarity with lookup tables. These requirements may act as a barrier for some researchers. By providing a user-friendly web-based application, I hope to encourage researchers to conduct power analyses on pilot data, when appropriate.
The app is deployed at following link:
https://asbryant.shinyapps.io/Power_Analysis_App/