Department of Biology

Lab

Simon Hall 015
812-856-0649
Hardy Lab website

Awards

Name Indiana University Provost Professor, 2023
Indiana University Trustees’ Teaching Award, 2006, 2007, 2009, 2011, 2016

Research

Research in the Hardy laboratory is focused on the molecular requirements for virus replication. We are specifically interested in what molecules are necessary for the replication of the viral genetic material and the optimal expression of viral genes within host cells. Viruses present a unique challenge to the understanding of their replication because of their obligate, intracellular, parasitic nature; that is, they can only replicate inside a host cell and require numerous cellular resources in order to proliferate. This intimate, though parasitic, relationship with the host cell means that we must look to both viral and host components to understand virus replication. For certain viruses the problems are of even greater complexity since they infect multiple host species. Many viruses, such as those causing human diseases like Dengue fever and yellow fever, are transmitted by mosquitoes. These viruses cause devastating disease in humans; however, the mosquito shows little or no adverse effects as a consequence of infection. We infer that such viruses interact with the vertebrate and arthropod hosts in very different ways.

The Hardy lab studies member of the alphavirus genus, a group of mosquito-borne viruses maintained primarily in an endemic cycle between mosquitoes and warm-blooded vertebrates. Epizootic transmission to humans may result in wide ranging symptoms from subclinical to fatal encephalitis. The broad geographic distribution of alphaviruses—viruses have been isolated on every continent—in combination with associated morbidity and mortality during human epidemics highlights their importance as a global public health problem. For example, in the spring/summer of 2006, Chikungunya virus infection caused a massive outbreak of polyarthritis in the Indian subcontinent and Indian Ocean islands of Reunion and Mauritius, infecting an estimated 1.5 million people. Problems associated with alphavirus disease are exacerbated by the absence of low-cost, effective vaccines and antiviral therapies. Thus, there is a pressing need for a deeper understanding of how these pathogens replicate and how they interact with their hosts. Our research examines the viral and host requirements viral genome replication, gene expression, and transmission.

Protein-genome interactions

One aspect of our research seeks to understand the regulation of gene expression and genome replication of plus-strand RNA viruses using Sindbis virus, the type species of the Alphavirus genus. The alphavirus genome is a positive strand of RNA, as such it functions in multiple processes during virus replication requiring different RNA-protein (vRNP) complexes to perform each function. The molecular interactions that mediate the transitions in vRNP composition and function, however, have not been elucidated. We employ in vitro and cell culture systems to analyze the viral protein and RNA requirements for formation of active RNA synthetic complexes as well as examination of how these complexes change over the course of a single infectious cycle. Recently, we have identified a group of cellular proteins (hnRNPs) that interact with viral RNA and impact the function of the genomic RNA (LaPlante et al.). Additionally, we have shown that the viral capsid protein binds to viral RNA at specific sites impacting the stability of the viral genome and consequently viral pathogenesis (Sokoloski et al.). Understanding the interplay between host and viral protein interactions with viral RNA is an area of ongoing research.

Particle composition and virus transmission

Another research area in the lab is the examination of the virus-arthropod host interaction. Alphaviruses are obligatorily transmitted by a hematophagous arthropod vector in which a lifelong persistent infection is established. Recent work from our lab has shown that virus produced from vertebrate cells is physically different from virus produced in mosquito cells. Vertebrate cells produce two distinct populations of virus separable on the basis of density, whereas mosquito cells produce a single population of virus. The more dense virus particles contain molecules derived from the host cell in which they are made, and the presence of these molecules influences the infectivity in a host specific manner. Particles lacking host components are more infectious in mosquitoes than in vertebrate cells, whereas the reverse is true for those particle possessing host components (Sokoloski et al., Liu et al.). This holds true for the infection of mosquitoes through blood feeding. We are currently attempting to understand which host derived particle components regulate host specific infectivity and the nature of the host response to infection.

Wolbachia, pathogen blocking and RNA modification

We collaborate with the lab of Dr. Irene Newton, examining the molecular mechanisms that underlie the pathogen blocking effect of Wolbachia pipientis. Wolbachia is a Gram-negative endosymbiont that infects many insect species and is maternally transmitted to offspring. One effect of Wolbachia infection is the inhibition of certain pathogens in the insect, particularly positive stranded RNA viruses such as alphaviruses. Currently, Wolbachia-infected Aedes aegypti mosquitoes are being released to reduce transmission of certain mosquito-transmitted viruses such as Dengue virus; however, the means by which Wolbachia inhibits virus replication and transmission is not understood. Through the use of a tri-partite experimental system of Drosophila-Wolbachia-Sindbis virus, in combination with Wolbachia-infected cultured mosquito cells, we have found that a host cell RNA methyltransferase (Dnmt2) is stimulated by Wolbachia and has an antiviral effect. This antiviral effect inhibits replication of alphavirus and flaviviruses and also perturbs infectivity of virus produced from Wolbachia-infected cells. Initial investigations indicate that the viral genomic RNA is hypermethylated and reduced in stability. We are currently conducting studies to define the extent and sites of methylation. This work will not only allow an understanding of Wolbachia-mediated pathogen blocking but will shed light on the role of genome modification in the epitranscriptomic control of virus replication and transmission.

Research areas

Eukaryotic Cell Biology, Cytoskeleton, and Signaling
Virology