The following are the latest faculty funding:

• Michael Gebhardt, PhD, NIH R35 (MIRA) grant: Exploring post-transcriptional regulators in Acinetobacter baumannii. 
  Project Summary: Bacterial gene expression can be regulated at nearly every conceivable point across the central dogma of molecular biology where DNA is transcribed into RNA, which is in turn translated into proteins. Following transcription, mRNA transcripts are subject to regulation by so-called post-transcriptional regulators, which includes both RNA-binding proteins (RBPs) as well as short (50-500 nt), non-coding RNA transcripts, referred to as small RNAs, or sRNAs. The post-transcriptional regulation networks comprised by the sRNAs and associated RBPs are thought to allow bacteria to rapidly respond to changing environmental conditions by enhancing plasticity within gene expression networks. Research in my lab combines large-scale, genome-wide analyses facilitated by next generation sequencing approaches with classic bacterial genetics techniques. We utilize these approaches in a complimentary fashion; we leverage the sequencing results to inform the genetics experiments, and vice versa. Ultimately, we use the data to generate and test hypotheses about novel regulatory networks and regulatory mechanisms, with a particular focus on the RNA binding proteins, sRNAs and post- transcriptional regulatory networks in the gram-negative bacterium, Acinetobacter baumannii, a notorious opportunistic human pathogen. A. baumannii is a frequent cause of ventilator associated pneumonia, skin and soft tissue infections, and other hospital acquired infections. These organisms are amongst the most problematic species in the context of antibiotic resistance, where extensively drug resistant isolates present an urgent crisis to our healthcare system, especially considering that contemporary isolates also demonstrate increased virulence properties relative to ancestral strains. In this proposal, I present two major research projects in my laboratory, which address key concerns for understanding bacterial pathogens through the lens of understanding post-transcriptional regulation. Post-transcriptional regulatory networks remain largely unstudied in A. baumannii. We previously performed experiments to identify and characterize key RNA-RNA interactions and identified hundreds of RNA-RNA interactions, suggesting the existence of a robust post-transcriptional regulatory network in A. baumannii. In this proposal, we propose to systematically dissect relevant RNA-RNA interactions that are mediated by a key RNA binding protein, called Hfq, and further characterize how this essential protein integrates RNA-mediated regulation with cellular RNA processing enzymes. Collectively, the results of these studies will provide a comprehensive picture of the sRNA regulatory landscape in a significant bacterial pathogen and will enhance our understanding about the post-transcriptional regulatory network coordinates gene expression in the context of human disease.
   
• Thomas Kehl-Fie, PhD, NIH MPI R01/University of North Carolina: Calprotectin and antibiotic activities at the infection interface.
   
• Jeremiah Johnson, PhD, NIH R01 transfer: Integration of nutrient availability, TCA cycle activity, and colonization factor expression in Campylobacter jejuni.
   
• Adam Mailloux, PhD, The American Cancer Society Catalyst Award: Hypoxia induces a state of immunogenic dormancy in cancer cells. 
   
• Wendy Maury, PhD, NIH UH2 supplement: Identifying placental tissue tropism and cellular mechanisms of Ebola Virus transmission from mother to fetus in pregnancy. 
   
• Stanley Perlman, MD, PhD, NIH R21/Loyola University-Chicago: Impacts of adaptive coronavirus evolution on viral membrane fusion.
   
• Stanley Perlman, MD, PhD, Indiana University research contract: AEGIS: Post-Acute Sequelae of COVID-19, PASC.
   
• Mary Weber, PhD, VPMA Focused Grant Revision Supplement.
   
• Li Wu, PhD, NIH R21 grant: SAMHD1-mediated regulation of innate immunity during SARS-CoV-2 infection.
  Project Summary: The COVID-19 pandemic caused by severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) remains a threat to public health, particularly in aging populations. The top priority for COVID-19 research is to improve fundamental knowledge of SARS-CoV-2 and viral pathogenesis, including studies to characterize the virus and to understand the host immunity. Our proposed study aims to better understand the molecular mechanisms underlying SARS-CoV-2 infection and innate immune regulation, which is important for controlling COVID-19 and potential future threats of other emerging coronaviruses. Sterile alpha motif (SAM) and HD-domain containing protein 1 (SAMHD1) is the unique mammalian dNTP hydrolase (dNTPase) that also regulates innate and adaptive immunity in hosts. Importantly, SAMHD1 phosphorylation negatively regulates its dNTPase activity and antiviral function. We found that SAMHD1 negatively regulates antiviral innate immune responses and inflammation through interacting with various key proteins in innate immune signaling in macrophages. SAMHD1 transcript is upregulated in SARS-CoV-2 infected primary human bronchial epithelial cells. Our preliminary data showed that SARS-CoV-2 infection of human lung epithelial cell lines or primary human airway epithelial (HAE) cultures significantly upregulated SAMHD1 phosphorylation. However, the function of SAMHD1 in regulating SARS-CoV-2 replication and innate immunity remains unclear. Our hypothesis is that SARS-CoV-2 infection increases inflammation in lung and airway epithelial cells by upregulating phosphorylation of SAMHD1, thereby reducing SAMHD1-mediated anti- inflammation effects. Our established primary HAE cultures provided a physiologically relevant in vitro model to study SARS-CoV-2 infection and cellular responses. We will also use an established mouse model of SARS-CoV-2 infection as a complementary in vivo approach in our studies. We designed two specific aims to test our hypothesis: Aim 1. To examine the role of SAMHD1 in SARS-CoV-2-induced inflammation of primary HAE cultures and SAMHD1- knockout mice; and Aim 2. To investigate the mechanisms of SARS-CoV-2-upregulated phosphorylation of human SAMHD1. Accomplishing our multidisciplinary studies will help define the mechanisms by which SAMHD1 regulates SARS-CoV-2 replication, inflammation, and antiviral innate immunity.