Public Health Lab Academy

Dr. Raj Agrawal
The Agrawal Laboratory uses biochemical and structural biology approaches to study structure and function of the ribosome, the protein synthesizing machinery of the cell, and cellular organelles. Our research probes the structures of bacterial and human ribosomes, including mitochondrial ribosomes, in order to understand the mechanism of protein synthesis and antibiotics/drugs action. REU students will gain hands-on experience in techniques of ribosome biochemistry, 3D cryo-EM, molecular modeling and interpretation. Currently, there are three major projects in the Agrawal Lab:

• Structural aspects of protein synthesis in mammalian mitochondria
• Translational Control by Fragile X Mental Retardation Protein
• Alternative ribosomes in mycobacteria

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.

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. Jan Conn

Dr. Conn's research aims to broaden and deepen the field of vector biology by combining and integrating these disciplines to be of practical value in moving the field of malaria eradication forward.

This integrated approach has advanced our understanding about the relative roles in pathogen transmission of anopheline species complex members, species boundaries, population structure and replacement, and the increasing effects of landscape modification on malaria transmission in the Neotropics. Specifically, outcomes from her extensive fieldwork in Venezuela, Brazil, Peru, Panama, and Colombia demonstrate the need for an increased focus on the quantification of entomological parameters locally, and on the underlying broad-scale ecological processes, together with local adaptation, that influence malaria transmission.

Sample projects include:

Exploring mosquito feeding patterns, infectivity, and malaria transmission patterns in Peru.

Dr. Keith Derbyshire/Dr. Todd Gray
The Derbyshire-Gray Laboratory is a friendly, fun, research environment, enriched with stimulating seminars and discussions on the role of research in public health. The REU student will receive daily mentoring, as needed, and be involved in all regular group activities. Contributions of data to publications will merit co-authorship.

The REU student will be exposed to a variety of E. coli and mycobacterial genetic tools. Experience will be gained in culturing mycobacteria, as well as in molecular protocols of targeted mutagenesis, nucleic acid prep, RNA- and DNA-deep sequencing, qRT-PCR, western blotting, cell fractionation and fluorescent-protein-reporter design and microscopy.

Potential projects include examining the higher-order activities of mycobacterial communities using our collection of M. smegmatis mutants, and characterizing the mycobacterial small proteome by knocking out small proteins and assessing the phenotype.

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. Anil Ojha
My lab investigates the molecular basis of persistence of one of the deadliest bacterial pathogens, Mycobacterium tuberculosis (Mtb), which kills over a million people every year. Mtb is the causative agent of human tuberculosis (TB), which has inflicted mankind since the prehistoric era. But even in the age of modern medicine, the only possible treatment of TB is a 6-9 month regimen of three specialized anti-TB antibiotics. This lengthy and complicated treatment is in sharp contrast to a week-long mono-drug treatment for most other bacterial infections.

We are focused on addressing unmet challenges in TB control. Our investigations are addressing questions like: a) what makes Mtb the toughest of all bacterial species, with an ability to tolerate virtually all kinds of stress, and b) how we can shorten the TB treatment?

We are testing a hypothesis that the extraordinary persistence of Mtb against antibiotics is facilitated by the pathogen’s ability to grow in organized multicellular structures, called biofilms. We have developed various molecular tools to visualize the location of drug tolerant persisters inside the biofilms. Using these tools, we are asking how localization and frequency of these persisters are perturbed in vitro and in animal models in genetically defined mutants of biofilms. Using a high-throughput analysis of transposon-insertion mutants, we have performed genome-wide mapping of loci required for either development of biofilm architecture or physiological adaption to the microenvironment within. In one of the potential projects, a student joining my laboratory will investigate in detail one of the loci to identify whether it is required for development of biofilms, or for adaption within biofilms. The techniques in addressing these questions would involve making isogenic deletions in a Mtb strain, tagging the strain with a fluorescent reporter, and analyzing biofilm growth of the deletion mutant by confocal laser scanning microscopy.

In another project, we are investigating the molecular principles of drug resistance in zinc-starved Mtb caused by ribosome hibernation. The REU student joining my lab will also have opportunity to identify new factors involved in the regulation of ribosome hibernation. The potential project will involve ribosome purification and analysis, in vitro translation, genome-wide analysis of transcriptomic responses to ribosome hibernation by RNAseq analysis.

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).

Dr. Joseph Wade
We use genome-scale approaches to study gene regulation and gene function in bacteria, as well as the biology of CRISPR-Cas immunity systems. My laboratory is particularly interested in the regulation of transcription initiation, transcription termination, and regulation by non-coding RNAs. We recently showed that much of the transcription occurring in bacterial cells initiates inside of genes rather than in the intergenic regions. The regulation of these intragenic transcripts, and their potential functions in gene regulation, are being investigated. A novel regulator of transcription termination which is required for proper transcription of ribosomal RNA, and its assembly into mature ribosomes was also discovered. Lastly, we are mapping the binding of transcription factors across the Escherichia coli and Salmonella enterica genomes. This research has identified many unexpected binding sites for transcription factors in the E. coli genome, as well as potential virulence genes in S. enterica.
Students will gain experience in bacterial genetics, basic molecular biology, and genomic methods such as ChIP-seq and RNA-seq, as well as bioinformatic analysis of genome-scale datasets. Our laboratory also networks with other REU mentors to collaborate on diverse research projects. Sample projects include:

• Determining mechanisms of ribosomal RNA regulation;
• Determining the mechanism of CRISPR-Cas immunity in E. coli; and
• Identifying regulators of intragenic transcripts in E. coli.