Public Health Lab Academy

Dr. Sherry Fay

The Wadsworth Center’s Nuclear Chemistry Laboratory (NCL) program has two objectives:  mandated radiological surveillance in NYS and research in radiological sciences. The surveillance program assesses exposure of the population to ionizing radiation and involves monitoring of the environment around nuclear power plants for fission products, as well as monitoring of drinking water supplies for natural radioactivity. Programs focusing on radiological emergency response relate to potential accidents or terrorism threats involving radioactivity. Research in radiological sciences is primarily related to the development of new and more sensitive methods to detect ionizing radiation in environmental, food, and bioassay samples, such as alpha and gamma spectrometry and liquid scintillation counting. Potential projects include determination of Ra-228 detection limits using surface level gamma spectrometry or optimization of electrodeposition for alpha spectrometry source preparation.

Dr. Nilesh Banavali
I use computational and structural biology techniques to answer questions related to structure and function of macromolecular machinery. The present focus is to resolve the details of ribosome structure, function, and dynamics by using single particle cryo-electron microscopy (cryo-EM). The research will be performed in close collaboration with the Agrawal Laboratory, and will allow the students to experience single particle cryo-EM data collection at our local 300 KV electron microscope. The project will involve applying computational techniques to improve structural resolution for flexible regions in cryo-EM density maps.

The Wadsworth PHAGES (Public Health Academy for Genomics Exploration and Study) program is a research opportunity where interns partner with a team of research labs focused on Bacterial Drug Resistance and Molecular Genetics. Interns will participate in microbiological research, initially undertaking a phage discovery project aimed at isolating novel bacterial viruses from the environment. In the second phase of the internship, students will engage in primary research within one of the PHAGES laboratories, exploring the molecular secrets of microbes relevant to human health and disease.

Dr. Alex Ciota
The Arbovirus Laboratory's unique facilities allow for extensive experimentation in a range of natural invertebrate and vertebrate hosts. Dr. Ciota’s primary research areas include arbovirus evolution and mosquito-virus interactions, with a focus on West Nile virus in Culex spp. mosquitoes and Zika virus in Aedes spp. mosquitoes. Specific studies include understanding WNV microevolution both within and among hosts and vectors, defining how specific interactions between viral and vector genomes influence transmissibility in distinct environments, defining the role of replicase fidelity on viral fitness and evolution, and identifying how unique microbial signatures influence vectorial capacity. The overarching goal of these studies is to gain a better understanding of the factors that shape patterns of arbovirus transmission and ultimately to influence novel public health interventions. Sample projects include:

Characterizing the replicative fitness and transmissibility of Zika virus; and
​Evaluating the role of microbial interactions in West Nile virus transmissibility.

Dr. Pallavi Ghosh
Mycobacterium abscessus (Mab) causes broncho-pulmonary infection and acute respiratory failure in patients with chronic lung damage. Cystic fibrosis (CF) patients are particularly vulnerable to Mab infections. M. abscessus infections are incredibly difficult to treat due to three primary reasons:

1. Mab is highly resistant to most FDA approved antibiotics such as rifampicin, isoniazid, ethambutol, tetracyclines and streptomycin, making them unavailable for therapy.
2. Mab displays initial susceptibility to some antibiotics (e.g. macrolides) but becomes resistant after extending the testing period. Exposure to antibiotics induces transcription of drug resistance genes resulting in delayed resistance.
3. There is a poor correlation between in vitro antibiotic susceptibility and in vivo efficacy, a part of which may be attributed to the ability of Mab to form biofilms.

The focus of the lab is to decipher the molecular mechanisms involved in this extreme drug resistance using a combination of bacterial genetics, biochemistry and high throughput genomic analysis to decipher mechanisms of drug resistance. Specifically, we are involved in obtaining a systems-level understanding of changes that accompany exposure of M. abscessus to antibiotics, identifying effectors that confer unique profiles of drug resistance, screening small molecule libraries for inhibitors of identified targets and studying the role of biofilm formation on antibiotic resistance of M. abscessus.

Dr. Erica Lasek-Nesselquist
My research focuses on understanding microbial genome evolution and developing new bioinformatics approaches for the analysis of large datasets. I routinely perform molecular analyses with next-generation sequence data to determine phylogenetic relationships among microbes and assess transmission dynamics of various pathogens, detect mutations associated with drug resistance, and characterize variation in microbial populations. A potential project in collaboration with Dr. Pascal LaPierre is MinION sequencing to assess Legionella diversity in natural environments.

Dr. Nicholas Mantis 
The long-term goal of my laboratory is to develop countermeasures against infectious diseases and potential bioterrorism agents, particularly those that afflict the human gastrointestinal tract. At present, our efforts are focused on two primary agents, ricin toxin and Salmonella enterica.
Ricin is one of the most potent toxins known to date and can be lethal following injection or ingestion. The toxin has a track record of being used as a biothreat agent, yet we currently do not have an antidote or vaccine. My laboratory is working on identifying antibodies, as well as small chemicals, that can neutralize the toxin and that may prove useful as therapeutics.
Salmonella enterica is a gram-negative bacterium that is primarily associated with food borne illness in the United States, but is responsible for more serious diseases, namely typhoid fever, in developing countries. The bacterium causes disease by gaining entry into the epithelial cells that line the gastrointestinal tract. We are studying how certain types of antibodies called secretory IgA, produced by the immune system, are capable of preventing Salmonella enterica infections. My laboratory believes that by understanding how secretory IgA works, a more effective vaccine against not only Salmonella, but other enteric infections like Shigella flexneri and Vibrio cholerae can be designed.
Students will learn techniques that include: assays of cytotoxicity and neutralization; culturing human epithelial cell and human/mouse macrophage cells; enzyme-linked immunosorbant assays; immunofluorescence microscopy; assistance with collection and analysis of mouse tissues; protein and DNA electrophoresis; polymerase chain reaction and DNA cloning.

Dr. Jon Paczkowski
Quorum sensing (QS) is a process of bacterial cell-cell communication that controls virulence and biofilm formation in many bacterial species, including the pathogens Pseudomonas aeruginosa and Vibrio cholerae. QS relies on the production, accumulation, detection, and population-wide response to extracellular signal molecules called autoinducers (AI). QS allows bacteria to synchronously alter gene expression patterns that underpin collective behaviors. Two types of AI receptors exist: soluble transcription factors and transmembrane bound kinase/phosphatase proteins. Within each type of receptor, there are examples of receptors that bind and respond exclusively to one AI and there are cases in which receptors bind and respond to multiple AIs. QS is now understood to be the norm in the bacterial world. Bacteria live in heterogeneous communities and encounter mixtures of AIs produced by themselves, their kin, and their non-kin neighbors. Learning how bacteria correctly interpret these blends of AIs and elicit appropriate gene expression responses is essential to understand how bacteria communicate, and, more globally, to understand how all organisms decode environmental stimuli. QS presents a unique opportunity to understand these longstanding questions in biology.
Students will gain experience in bacterial genetics, molecular biology, and structural biology methods, such as RNA-seq and X-ray crystallography. Potential projects include:

• Determining mechanisms of ligand selectivity and specificity for receptors, such as AhyR from Aeromonas hydrophila and RhlR from Pseudomonas aeruginosa, that bind to short chain AIs, to compare to the established mechanisms of ligand selectivity for receptors, such as LasR from Pseudomonas aeruginosa, that bind to long chain AIs.
• Determining the consequences of promiscuous ligand selectivity in microbial fitness using competition assays.

Dr. Janice Pata
Cells have a surprisingly wide variety of DNA polymerases involved in genome replication. The main replicative polymerases are very fast and highly accurate, while more specialized polymerases are much slower and tend to be highly error prone. Although many of the specialized polymerases allow cells to tolerate DNA damage that would otherwise kill the cell, replication by these enzymes significantly increases the number of mutations made during genome duplication.
We are currently studying four DNA polymerases from Staphylococcus aureus to understand how they contribute to the evolution of antibiotic resistance. Two of the polymerases are required for the initiation and elongation of DNA synthesis, and are essential to cell survival. The other two are translesion polymerases and have been linked to the generation of antibiotic-resistant bacteria. Using a combination of high-throughput next-generation sequencing, biochemical assays, and X-ray crystallography, we are characterizing the mutational profile of each polymerase, and how the different polymerases switch places during replication.
An example project would be to determine the importance of specific amino acid residues in the polymerase by site-directed mutagenesis and purification of recombinant protein, and then to determine how polymerase structure and function have been altered by performing biochemical assays and co-crystallizing the protein with DNA. In collaboration with Dr. Erica Lasek-Nesselquist, students can also use computational methods to analyze the spectrum of mutations made during DNA replication to determine how differences in polymerase structure and dynamics influence the types of mutations created.

Melissa Prusinski
The Prusinski Lab primarily studies the ecology and epidemiology of tick-borne diseases, utilizing a combination of field and laboratory-based research methods to explore the dynamics of vector ecology and conduct tick-borne pathogen surveillance. Ongoing research projects include monitoring of tick populations and the prevalence of associated pathogens as they relate to incidence of tick-borne disease in people, exploring the ecology of tick and pathogen geographic range-limits, assessing the impact of environmental and climatic variables on tick populations, and vector and pathogen population genetics studies. In collaboration with the Ciota Lab and others at Wadsworth Center, we also investigate rare and emerging tick-borne pathogens of public health significance, such as those causing Powassan encephalitis and tick-borne relapsing fever. Potential areas of research for summer REU students include: prospective and retrospective studies to determine the prevalence and distribution of Ehrlichia muris eauclairensis and Borrelia mayonii in host-seeking ticks, which would lead to a better understanding of exposure risk for these emerging pathogens across New York State; examining how environmental factors like leaf litter composition and forest structure impact microclimate and tick establishment, which may help better characterize tick habitat requirements leading to improved predictions of vector distribution, epidemiological analysis of tick bite data obtained through the NYSDOH Tick Identification Service, which may aid in identification of risk groups and help to target tick-borne disease prevention efforts; or a related project in cooperation with any of our Wadsworth Center research partners.

Dr. Haixin Sui
The Sui Lab utilizes methods of electron microscopy in combination with other imaging and cellular techniques to study the structure and regulation of macromolecular complexes and organelles in their cellular functional context. The lab also develops new methods for specimen preparation and computational image processing in electron microscopy (EM). The lab’s current effort focuses on clarifying how motor complexes transport proteins and molecules in primary cilia of kidney cells in order to understand why related defects cause developmental problems and cystic diseases. The Sui Lab has a long history of hosting undergraduate researchers and will continue to provide opportunities of hands-on experience in specimen preparation, light and electron microscopy, computational image analysis, and graphical presentation. Potential projects include:

• Structure and function of RNA-protein complex in Coronaviruses (Complex isolation and electron microscopic characterization.
• Structure and function of bacterial protein nanocages (Protein expression, purification and electron microscopic characterization).
• How intraflagellar transport activity affects primary cilium structure (mainly by fluorescence live cell imaging).
• Development of thin 3D substrates for correlative light and electron microscopy of cells and tissue (in collaboration with Albany NanoTech Complex).