Current HITS Projects

Sally Assman and Phil Bevilacqua

Novel Mechanisms in Disease Resistance and RNA: Sally Assman and Phil Bevilacqua

The Problem: Fungi infect nearly all crops and lead to loss of vast amounts of global food supply annually. 

The Idea: Discover and harness RNA-based mechanisms to combat this biotic stress.

The Risk: The feasibility and efficacy of these mechanisms to kill fungi is unproven and needs to be established in vivo before application to crops.



Marco Archetti

Covid-19 Therapy Using Synthetic Defective Interfering Miniviruses: Marco Archetti

The Problem: We still need therapies for Covid-19. Remedesivir has proven ineffective and is contra-indicated in severe cases. And even if vaccines prove effective, we’ll need drugs for at-risk groups and populations with infrastructure that limits virus distribution.

The Idea: Use synthetic defective interfering (DI) particles as a self-promoting, evolution-proof therapy that replicates 3 times faster than SARS-CoV-2 in infected cells and reduces the amount of virus by 50% in 24 hours. This method could be applied to other viruses as well. 

The Risk: The use of DIs as antivirals was suggested in the 80s but never pursued. Initial attempts were made for influenza, which is not a good system. Since synthetic DIs are unproven as therapeutic agents, in the eyes of funding bodies this is a high-risk proposition.

Collaborators:  Suresh Kuchipudi and John Liechty



Erika Ganda

Real-Time and Comprehensive Antimicrobial Resistance Profiling: Erika Ganda

The Problem: Antimicrobial resistance (AMR) is a global threat and is estimated to account for 10 million deaths per year by 2050. Current methods for resistome tracking are labor-intensive or prohibitively expensive for broad surveillance purposes.

The Idea: Develop a real-time resistome profiling system based on the RNase Hdependent PCR (rhAMR). Use highly parallel multiplexed amplicon generation to enrich for AMR genes and sequence such genes using the pocket-sized sequencer Nanopore MinION. If successful, this method will revolutionize the surveillance and fight against AMR.

The Risk: Combining rhPCR with nanopore chemistry is a new approach  to AMR that has not been previously attempted.

Collaborator: Jasna Kovac



Tony Pedley

Reveal the Compositional and Structural Determinants of Functional Protein Condensates: Tony Pedley

The Problem: To date, no one has uncovered the compositional and structural determinants of the purinosome – a metabolon that is presently the only enzymatically active protein condensate.

The Idea: Develop novel chemical and microscopy methodologies to uncover the stoichiometry and folding states of enzymes that enable functional purinosomes in live cells. Ultimately, our research aims to reveal a fundamental, comprehensive and transformative understanding of the organization, regulation, and function of protein condensates.

The Risk: Advanced imaging reagents and technologies have never been established to study the compositional and structural determinants of functional protein condensates. Thus, this project faces a number of hurdles before it is ready for a conventional funding mechanism.

Collaborators:  Stephen Benkovic, Xin Zhang, Ruobo Zhou



Michael Axtell

Using Host-Induced Gene Silencing To Fight Striga: Michael Axtell

The Problem: Striga (Witchweed) is a parasitic plant that has a devastating impact on maize and sorghum crops in Africa.

The Idea: Use advanced Host-Induced Gene Silencing to engineer transgenic maize that can silence Striga mRNA.

The Risk: A single previous study, using a more rudimentary approach and with flawed methodology, had disappointing results.


Kevin Hockett

Demonstrating and Manipulating Mushroom Devomes: Kevin Hockett

The Problem: Our understanding of the role of microbes in the development of the common edible mushroom, Agaricus bisporus, is in its infancy.

The Idea: Use next-generation sequencing and physiology coupled to high throughput cultivation or serial enrichment to demonstrate and manipulate the devome (developmental microbiome) to alter mushroom development. In this way, establish A. bisporus as a model for studying the devomes of both cultivated and wild mushrooms.

The Risk: The critical microbes involved may not be either identified or isolated, and thus require complementary subtractive, additive, and passaging approaches that should each contribute to our understanding.

Collaborators: Carolee Bull and John Pecchia


Vanessa Macias

Developing Transgenic Mosquitos To Study Virus Interactions: Vanessa Macias

The Problem: Small RNA biology controls interactions between mosquitoes and viruses and may contribute to the evolution of new human viral diseases, but our understanding of the mechanisms involved is limited.

The Idea: Genetically engineer the genome of the mosquito species Aedes aegypti to express recombinant tagged proteins and synthetic piRNAs, addressing existing hurdles in small RNA study and creating a suite of transgenic mosquitoes that could revolutionize study of mosquito-virus interactions.

The Risk: The project involves genetic engineering techniques that have previously rarely been attempted, and never in mosquitoes; NIH NIAID reviewers have repeatedly dubbed this effort innovative, but overly ambitious.


Rudolf Schilder

Seamless Microchip-Brain Interfaces In Invertebrates: Rudolf Schilder

The Problem: The most advanced computers have yet to match the complexity displayed by the human brain when performing simple tasks; scientific understanding is still restricted and even state-of-the-art approaches have serious limitations.

The Idea: Develop a microchip for use in moth brains that mimics biological synapses, enabling seamless brain-chip interfaces that open up new possibilities for measuring and stimulating brains; if successful, this could be the foundational work on feasibility of brain-chip interfaces in invertebrates and revolutionize brain science.

The Risk: The feasibility and efficacy of in vivo chip implementation is unproven and faces a number of potential hurdles before being ready for traditional funding mechanisms.

Collaborator: Jean-Michele Mongeau