Biology Research Currently in Progress

Tom Langen, PhD (UC San Diego)
Department Chair of Biology and  Professor, Clarkson University Department of Biology
Clarkson Strategic Theme: Environment 
Aim:  To use science to improve conservation and management of nature in human-dominated landscapes.
Methods: Fieldwork on species, habitat assessments, computer modeling using Geographical Information Systems (GIS).
Applications:  Adaptive Management of natural resources, conservation of threatened species and habitats, infrastructure design.
Broader impacts:  Environmental quality, conservation of threatened species, improved infrastructure design and management, conservation education and capacity building.

Dr. Langen conducts research on the environmental impact of roads, on the effectiveness of public-private partnerships for wetland restoration, and on habitat management and conservation of birds and other animals. His road-related research has included the impacts of winter road management on roadside vegetation and lakes in the Adirondack Park, predictive modeling of hotspots of road mortality of amphibians and reptiles, design and functioning of wildlife barriers and passageways for turtles, and the impact of highways on habitat connectivity in Costa Rican National Parks. He leads professional development workshops in Latin America and North America on the environmental impact of roads and other infrastructure. Dr. Langen’s wetland research focuses on the environmental, economic, and social benefits and costs of wetland restoration to private landowners. His research on habitat management in birds focuses on cooperative projects between landowners and conservationists for threatened species such as the golden-winged warbler or spruce grouse.  Dr. Langen’s teaching interests include how to best apply problem-based learning and inquiry approaches to improve teaching in ecology and conservation biology, and how to design undergraduate summer research internship programs to best achieve program objectives.

Michael Twiss, PhD (Université du Québec, Canada)
Professor, Clarkson University Department of Biology
Clarkson Strategic Theme: Environment (Water)
Aim:  To conduct fundamental research that addresses water quality issues in the Great Lakes and St. Lawrence River during all seasons of the year.
Methods:  Involve field work working on coastal research vessels and ships, as well as remote water quality sensing stations.
Applications:  Adaptive Management of water resources, refinement of water quality criteria, understanding long-term changes in surface water quality.
Broader impacts:  Water security, graduate student education, international (Canada/USA) relations, environmental policy.

Twiss focusses on interactions of microbes with chemicals (nutrients, toxic substances) in the water column of lakes,  rivers, and wetlands and the use of advanced technologies for assessing phytoplankton community structure and health. Studies focus on the Laurentian Great Lakes and St. Lawrence River ecosystems, and involves research both in the field and laboratory. Connections to government policy and constituencies is made possible by direct participation in scientific societies (International Association for Great Lakes Research) and science advisory boards (International Joint Commission).

Thomas Lufkin, PhD (Cornell University)
Clarkson Chair and Professor of Biology, Clarkson University Department of Biology
Clarkson Strategic Theme: Biotechnology 
Aim:  Understand how human stem cells can be used for tissue and organ regeneration. 
Methods: Human somatic cells are reprogrammed to cells of the intervertebral disc in cell culture.
Applications: Regenerative medicine of degenerated or injured intervertebral discs.
Broader impacts:  Development of methods of regenerating spinal discs to treat vertebral column degeneration associated with aging. 

Our research is in the novel area of Regenerative Medicine and Stem Cell Biology with a focus on the molecular mechanisms controlling vertebral column development and an emphasis on early embryogenesis and embryonic stem cell commitment to specific differentiation pathways, but from a novel Systems Biology point of view. We are committed to understanding how the vertebral column degenerates with aging, and how this process can be reversed using stem cell based approaches. We use both mouse and zebrafish as model animals. In particular we are working on understanding the gene regulatory networks (GRNs) that govern normal embryonic development of the vertebral column and intervertebral disc (IVD). We are investigating the role of transcriptional regulators in the restriction of pluripotent embryonic stem cells into specific lineages that in turn comprise functional pre and postnatal vertebral elements with the goal of applying this knowledge to regenerative medicine using patient- specific induced pluripotent stem (iPS) cells and adult mesenchymal stem cells.

Damien Samways, PhD (University of Bristol, United Kingdom)
Associate Professor, Clarkson University Department of Biology

Clarkson Strategic Theme: Biotechnology
Aim:  To understand how ion channel proteins conduct the movement of ions into and out of cells, and examine the potential for using these receptor proteins as endogenous drug transporters for the targeted delivery of therapeutics
Methods: I use patch clamp electrophysiology and fluorescence cell imaging to monitor the movement of ions across the cell’s outer plasma membrane.
Applications:  Identification of new therapeutic targets for rational drug design
Broader impacts:  Better understanding of how the structure of proteins impart their function, identification of novel drug targets, improved drug design, improve drug delivery 

Dr. Samways works on the role of ion channels in regulating cell signaling processes in response to neurotransmitters and other chemical mediators. Traditionally, the focus of his research has been the structure and function of ion channels largely expressed in neurons, and here he has made valuable contribution to the understanding of how a number of these proteins open and conduct cations, particularly Ca2+, into cells. More recently, the presence of certain ion channel types in cancer cells, and their potential capacity to carry therapeutic drugs, has encouraged Dr. Samways to consider the function of these proteins in a broader context. Dr. Samways’ teaching interests are in the sphere of cellular and molecular physiology and pharmacology. Much of Dr. Samways research has involved investigating how individual amino acid alterations affect the function of ion channels. Relating to this, he is currently building the first exhaustive graphical database of all amino acid alterations tested for an entire ion channel family, the P2X receptors. In addition to serving as a fun and intuitive tool for instructors teaching molecular pharmacology, the database will also provide a much needed and efficient means for researchers to navigate the enormous body of mutational data available for these ion channels.

Kenneth Wallace PhD (Ohio State U.)
Associate Professor, Clarkson University Department of Biology

Clarkson Strategic Theme: Biotechnology
Aim:  To understand the role of regulatory cells within the developing intestinal stem cell compartment and the impact of nanoparticles on development of the digestive system and whole organism.
Methods: Molecular genetics, cell biology, Developmental biology, proteomics, microscopy
Applications:  Regulation of stem cells and methods to produce biologically compatible nanoparticles.
Broader impacts: Repair and protection of digestive organs damaged by disease or environmental insults. 

Project 1: Dr. Kenneth Wallace (Biology) works to develop an understanding of control of stem cells within the developing digestive system.  Throughout the life of the digestive system, there is rapid turnover of cells that line the opening where food passes to be digested.  Within humans, cells divide move up the folds and die within three to five days. Dr. Wallace is investigating development of cells that play a role in controlling the rapid division.  Control of cell division needs to be tightly controlled or tumors and cancer may result.  Also during cancer development, new cancer cells develop that function to control proliferating cells similar to normal cells.  Understanding how and when normal control cells develop will allow for identification of cancer cells controlling proliferation and provide information as how to interrupt their development and function.  Dr. Wallace utilizes the zebrafish vertebrate model system to investigate the role of digestive epithelial cells that regulate proliferation.

Project 2: Nanoparticles are currently being used in a multitude of commercial products and are also being manufactured for a number of additional industrial processes.  This results in a substantial increase in exposure of all types of organisms to manufactured nanoparticles including humans.  While we are experiencing increased exposure, less is known about health affects.  Dr. Kenneth Wallace (Biology), in collaboration with Dr. Silvana Andreescu (Chemistry) is investigating the affects of nanoparticle exposure using the high throughput vertebrate model system of zebrafish embryos to rapidly screen and assay biological affects of a number of manufactured nanoparticles within the whole organism.  Similarities in response to toxic chemicals between zebrafish and mammals allows for faster and less costly screening of a number of combinations of nanoparticles.  Previous exposure studies use high concentrations of nanoparticles to see an affect on the whole organism.  Electrochemical probes developed in this investigation will enable determination of more subtle physiological changes occurring at more relevant environmental nanoparticle exposure.  One outcome of this work will be a better understanding of how to modify nanoparticles to minimize their toxicity in biological systems.

Alan Christian, PhD (Miami University)
Professor, Clarkson University Department of Biology

Clarkson Strategic Theme: Environment
Aim: Investigate pure and applied life history, ecology, evolution research in freshwater ecosystems, especially freshwater mussels, and to investigate the effects of natural and anthropogenic perturbations (e.g. land use land cover change, urbanization, restoration) on freshwater organisms, populations, communities, and ecosystems.    
Methods: Population genetics/molecular ecology/conservation genetics, microbial community structure, ecological stoichiometry, geochemistry and biogeochemistry analysis including stable isotopes and water chemistry, field monitoring, surveys, and experiments, stream habitat geomorphological and habitat characterization and assessment, Geographic Information Systems analyses, and parametric and non-parametric statistical techniques.
Applications: Conservation biology and environmental impact assessments of aquatic ecosystems and restoration projects
Broader impacts: My research spans local, state, regional, and international borders and is relevant, timely, contributes new knowledge, and helps move both science and conservation management forward.  While maintaining a focus freshwater mussel ecology and conservation, my work and that of my students contributes, locally and internationally, in the study of pure and applied watershed environmental issues.  My research portfolio is aligned with the mission of generating, communicating, and activating knowledge to solve environmental problems while integrating human, natural, and built system impacts on watersheds.  As is expected, my research is translated to practice supporting best management practices and the evolution of new modalities for restoration and aquatic system monitoring.  In sum my research addresses critical issues of aquatic ecosystem function in urbanized and rural communities facing emerging threats of global change as well as loss of ecosystem services such that my research also acts to ensure a more sustainable, just, and equitable future. 

Shantanu Sur MBBS, PhD (Indian Institute of Technology)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Biotechnology, Materials Science
Aim: (a) Study cell-biomaterials interactions with a goal to develop novel materials for biomedical applications. (b) Airborne pathogen detection from a portable real-time air quality monitoring system.
Methods: Study molecularly designed biomaterials on in vitro model systems; assay methods include spectroscopy, molecular biology techniques (western blot and PCR, transfection), fluorescence microscopy (confocal), live-cell imaging, calcium imaging, flow cytometry, in situ hybridization;  materials characterization by mass spectroscopy, circular dichroism, X-ray scattering, electron microscopy; develop mathematical models to understand cell dynamics; quantitative PCR and next generation sequencing for identification and quantification airborne pathogens.
Applications: Designed materials for regenerative or cancer therapy; targeted delivery of proteins and drugs in the lungs using microparticles; air quality monitoring to predict the risk for airborne infections. 
Broader Impacts: Advancement in health by development of novel diagnostic and therapeutic strategies.
One major goal in our lab is to find out design principles to tune supramolecular biomaterials for specific biomedical applications, focusing mainly at the interactions at the cell-biomaterials interface. We are especially interested in tailoring the biophysical properties of the supramolecular assemblies such as stiffness, nanostructure, molecular arrangement and cohesion to elicit desired cell response. On a collaborative endeavor, we are studying how the properties of peptide-based materials control cell proliferation, differentiation, migration, response to growth factors, and programmed cell death. Taking advantage of this materials platform and using live imaging studies, we seek to extend our fundamental understanding on the dynamic behavior of cells, especially how the microenvironment partakes in tumor cell invasion. We are also interested to understand how the supramolecular properties can be harnessed to target cancer cells and deliver chemotherapeutic agents. Targeted drug delivery to lungs using microparticles is another area of interest in our lab. We are currently working in collaboration to develop core-shell microparticles for tuberculosis (TB) therapy that will be deliverable via respiratory route to deep lung tissue and target macrophages to deliver anti-TB drugs to reduce bacterial load in these cells. On a different direction our lab has started a collaborative venture to build and characterize a portable aerosol biosampler that will provide information on the airborne pathogen load along with a real-time data of particle size distribution in air. Our lab’s primary objective here is to optimize techniques for DNA extraction, qPCR, and next-generation sequencing (NGS) data analysis to develop a sensitive and reliable method to identify and determine relative abundance of pathogens in aerosol samples. We are currently working on deploying this system is hospital environment where the pathogen analysis of collected aerosol particles is expected help in the risk assessment for healthcare-acquired infections transmitted or dispersed through air.

Susan Bailey, PhD (University of Ottawa, Canada)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme: Environment, Biotechnology
Aim:  To understand fundamental processes driving variation in evolutionary adaptation and diversification across organisms and environments.
Methods: Mathematical and statistical modelling, bioinformatics, microbial experimental evolution.
Applications:  Predicting how and when species of interest will evolve in response to environmental changes; modelling the evolutionary dynamics of human pathogens and cancers.
Broader impacts:  Inferring evolutionary history of populations and communities and predicting future evolutionary dynamics in a changing world. 

Dr. Bailey’s research aims to understand the fundamental processes driving evolutionary adaptation and diversification. She uses a combination of mathematical/ statistical models and microbial lab experiments with two current focuses: 1) investigating the dynamics of adaptation and diversification in spatially heterogeneous environments, and 2) identifying potential factors driving parallel or convergent evolution. By evolving the bacteria Pseudomonas fluorescens in varied environments in the lab, Dr. Bailey tests the effects of a range of genetic and environmental factors that play potentially important roles in populations living in the complex natural world, but are difficult to tease apart without controlled experiments. Replication of these kinds of evolution experiments and characterization of the varied outcomes, then allows for exploration of if, and when, evolution is predictable. Dr. Bailey uses comparative genomics to explore resulting genetic changes in her experimental bacteria populations, and other natural populations, and builds mathematical and statistical models to generate and test hypotheses describing the evolutionary dynamics underlying the observed genetic changes.

Andrew A. David, PhD (Universiteit van Stellenbosch, South Africa)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Aim: To understand the scope of biological invasions through an integrative approach that spans all levels of biology; from the genetic to the ecosystem level. 
Methods: Designing and maintaining experimental larval cultures, Light and Scanning Electron Microscopy, Field sampling and water quality measuring, Polymerase Chain Reaction and genotyping of specimens, bioinformatics, oceanographic modelling  
Applications:  Management of invasive species, coastal conservation, design of aquaculture farms, 
Broader impacts:  Improving the design of marine protected areas (MPAs), prioritizing localities for the management of invasive species, informing aquaculture farmers and shareholders on best practices for farm operations, contributing to the natural history of benthic invertebrates 

Dr. David works on a widely researched area in marine ecology; understanding dispersal and range expansion of invasive species. Anthropogenic disturbances such as introductory events and climate change are expected to significantly alter species ranges on a global scale and developing methods to predict these changes are crucial for conserving marine biodiversity. His research involves designing  culture methods to rear non-model organisms (e.g. obligate symbiotic polychaetes) in the laboratory and investigating the effects of changing temperature and salinity regimes, (as  predicted by climate change models) on their development.  Furthermore, his research uses population genetics to measure larval connectivity and gene-flow among spatially separated populations. This method is often used to detect evolutionary significant units, which are the targets of many conservation programs. His most recent research involves developing an integrated approach that combines genetic studies with high resolution transport/circulation models to predict the spread of invasive species. This method is expected to be a more powerful measure of estimating connectivity as the model rules out human-mediated movement, and therefore acts as a control for anthropogenic influences. The study is an ongoing collaborative effort with researchers from both South Africa and the United Kingdom. Dr. David’s teaching interests involve the use of active learning instruments such as data nuggets and case-based studies as a method of increasing student engagement in freshman Biology courses. 

Ginger Hunter, PhD (Duke)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Aim:  To understand how local signals are integrated across developmental space and temporal scales during patterning.
Methods: Molecular genetics, cell biology, developmental biology, microscopy, biophysical manipulations.
Applications:  Organismal development.
Broader impacts:  Development of new tools to study the dynamics of cell fate decision making, experimental and theoretical approaches to cell signaling and pattern formation.

Dr Hunter’s research focuses on how local cell behaviors and interactions are integrated across tissues during successful developmental patterning, using the fruit fly model system, Drosophila melanogaster. Specifically, this research takes an experimental approach towards understanding the mechanisms of signaling filopodia-mediated lateral inhibition; initially considering the regulation of the filopodia structure as well as the dynamics of Notch-mediated cell fate change during lateral inhibition. Collaborative efforts have helped to develop a mathematical model of long-range lateral inhibition, which contributes to guiding the experimental framework focussed on understanding the molecular mechanisms at the interface of cell shape and signaling. Dr Hunter takes genetic, cell biological, and biophysical approaches to ask (1) how cells engage in lateral inhibition via filopodia; (2) what are the dynamic cell responses as a function of distance; (3) what is the role of cell shape and behavior during lateral inhibition.

Stefanie Kring, PhD (Clarkson University)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Aim: To increase the understanding of the St. Lawrence River ecosystem, and understanding the role of phytoplankton and zooplankton role in the algal biofuel industry  
Methods: Fieldwork that involves the measurement of phytoplankton, zooplankton, nutrients, and other water quality parameters. Laboratory experiments include the use of phytoplankton and zooplankton cultures to conduct controlled experiments that include the measurement of lipids and growth rates. 
Broader Impacts: Dr. Kring conducts research on water quality and the sustainability of algal biofuels. Phytoplankton dynamics is the common theme in all of Dr. Kring’s research. She has studied wastewater lagoons as a potential biofuel source due to their phytoplankton and zooplankton populations. She has also examined the accuracy of an in situ fluorometer for measuring phytoplankton biomass in freshwater ecosystems. Dr. Kring is currently assessing the fate and transport of mercury and methyl mercury on the north and south shores of fluvial Lake St. Francis (St. Lawrence River). 

Beatrice Hernout, PhD (University of York, England)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Aim: Assessing the effects of anthropogenic contaminants in wildlife species. 
Methods: Molecular toxicology, analytical chemistry, spatial analyses, ecological monitoring and computational biology techniques. 
Applications: Predicting the potential risks and improving environmental risk assessment for regulatory purposes. 
Broader impacts: Helping in mitigating risks and contributing to the conservation of wildlife species.
My main research aims focus on 1) assessing the exposure and bioaccumulation of chemicals in wildlife; 2) evaluating the potential adverse effects and predicting the associated risks; and 3) extrapolating risk predictions from individual to populations or communities. I have previously investigated the effects of trace metals and organic pollutants in several taxa: bats, birds, reptiles and fish. 
Current research involves the monitoring of body burdens of PAHs (Polycyclic aromatic hydrocarbons), and PCBs (Polychlorinated biphenyls) in fish from the Gulf of Mexico (using GC-MS techniques). These pollutant body burdens will be associated with the activities of hepatic enzymes (involved in the biotransformation and biodegradation of organic contaminants). These monitoring data will provide a deep insights into the effects of marine pollutants in fish from the Gulf.

Petra Kraus, PhD (University of Ulm, Germany)
Assistant Professor, Clarkson University Department of Biology
Clarkson Strategic Theme:
Aim:  Develop quality control measures for the use of human stem cells and reprogrammed pluripotent cells in regenerative medicine therapy with a focus on intervertebral disc disease. 
Methods: We have established the bovine intervertebral disc (IVD) as suitable human-related experimental animal model system for the identification of markers of the different cell lineages of the IVD and for the development of much needed quality control assays at single cell resolution to improve culture conditions towards the derivation of the different IVD cell lineages for clinical applications.
Applications: Quality control of human cells generated for regenerative medicine based therapeutic approaches with a focus on cells of degenerated or injured intervertebral discs.
Broader impacts:  Development of gene and protein markers for quality control assays with single cell resolution to ensure homogeneity of cell lineages and patient safety when receiving therapeutic cell and tissue transplants. We are committed to identifying and characterizing the different cell lines present in the adult IVD. Using advanced gene editing methodologies we are engineering visible markers for the different IVD cell lineages to establish conditions for the isolation and maintenance of homogeneous cell lines. This will help understand their individual contributions to the mature IVD and their response to transcriptional regulators in order to develop robust and safe clinical protocols for culturing these cell lines for use in human cell and tissue based regenerative medicine therapies.

Michelle Mi-Jeong Yoo, PhD (University of Florida)
Clarkson Strategic Theme:
Environment, Biotechnology
Aim:  To understand the impact of polyploidy on plant speciation/diversification and crop domestication.
Methods: Evolutionary “-omics” tools of genomics, transcriptomics, proteomics, and metabolomics, bioinformatics, physiological response to environmental stress, phylogenomics using target enrichment method
Applications: crop improvement, development of conservation program
Broader impacts: Predicting the target genes and networks in crop species which lead to improved yields and increased stress-tolerance capabilities; development of conservation program based on a population structure and species diversity

Dr. Yoo’s research have encompassed diverse areas of biology, including molecular evolution, phylogenetics, evolutionary developmental biology, evolutionary genomics, proteomics, metabolomics, physiology, and genetics. The primary focus of her research is on how plants adapted to their environment and how evolutionary processes, such as polyploidy, hybridization and domestication, contributed phenotypic modification and diversification of higher plants. Dr. Yoo tries to address the following questions using comparative and integrative approaches with omics technologies: 1) how human selection has shaped the evolution of spinnable cotton fibers?, 2) how polyploidy or whole genome duplication triggered the diversification of flowering plants, focusing on two model systems, cotton and Tragopogon?, 3) how polyploids better cope with environmental stresses than their diploid parents using Brassica polyploid system?, and 4) what evolutionary and molecular processes have shaped the plant diversity and trait evolution in flowering plant lineages?. The improved understanding of plant genome evolution and plant adaptation to the environment may provide effective biotechnology targets and strategies for the improvement of crop species. 

Ali Boolani, Ph.D. (Oklahoma State University)
Adjunct Associate Professor, Clarkson University Physical Therapy Program
Clarkson Strategic Theme:
Aim: To use science to better understand how physiology influences how we feel and our cognitive decline and how our moods and cognitive decline influence how we move. 

Applications: To create systems to help identify people who have mood disturbances or cognitive decline.

Broader Impact: Identifying sub-clinical mood changes through human movement, creating interventions to reduce the onset of clinical mood changes, creating better objective measures to identify sub-clinical mood states, identifying sub-clinical mood changes through changes in human physiology, identify cognitive decline through human movement and human physiology

The research in the Boolani lab is four fold: 1) Understand how human physiology influences mood and how those moods manifest themselves in human movement; 2) Develop interventions to improve moods; 3) Identify the physiological mechanisms behind cognitive decline and how they influence human movement; 4) Develop interventions to reduce cognitive decline. Currently our lab is trying to understand the influence of mitochondrial function, heart rate variability and pulmonary function on moods and cognitive decline and how these moods and this cognitive decline influences human movement. Additionally, we are trying to develop interventions to improve moods and reduce cognitive decline.

Deborah M. Brown, PhD (University of Rochester Medical Center)
Adjunct Associate Professor, Trudeau Institute
Clarkson Strategic Theme:
Aim:  To understand the immune response to viral infection in order to improve vaccines for influenza.
Methods: Mouse models of infection and immunity, flow cytometry, ELISA, influenza infection
Applications:  Vaccine design, generation of immune memory, T cell biology
Broader impacts:  Better understanding of the immune response to vaccination, improved vaccine design and development for influenza vaccines, preparing undergraduates for research careers
The overall goal of Dr. Brown’s research program is to understand how T cells are activated, differentiate into memory and provide protection against viral infections. We aim to understand how the innate immune response shapes the development of resident T and B cell memory as a prerequisite for developing vaccine strategies that induce broad protection against influenza against infection in order to facilitate novel vaccine designs for emerging infectious disease.  Project 1 utilizes synthetic small molecule activators of innate immunity as vaccine adjuvants to promote protection against lethal, highly pathogenic influenza infection. Dr. Brown’s group has demonstrated that using small molecules in combination can provide dose sparing effects of both vaccine and adjuvant and promotes an immune state that more resembles infection, unlike current vaccine strategies for influenza.  Project 2 involves understanding the signals required for differentiation of distinct T cell subsets that provide anti-viral, anti-bacterial or homeostatic immune responses, while at the same time, avoiding autoimmunity.
Dr. Brown’s teaching interests include using innovative and student based learning techniques to make a complex subject like Immunology accessible for undergraduate Biology students. In addition, Dr. Brown is actively involved in creating unique laboratory experiences and career development training for undergraduates interested in a biomedical research career.



Laboratory Facilities

Cell Receptor Signaling Lab (Associate Prof. Damien Samways; Science Center 105): Our laboratory is interested in how cells use surface receptors, particularly ion channels and G protein-coupled receptors, to sense and respond to extracellular neurotransmitters, hormones and drugs. We have a particular focus on those cell signaling mechanisms that involve the ubiquitous cytosolic second messenger, Ca2+, which plays a key role in regulating numerous cellular processes including secretion, muscle contraction, cell migration, and gene regulation. Our laboratory is equipped to use patch clamp electrophysiology, including patch clamp photometry, to study plasma membrane ion channel function. We also employ a time-lapse fluorescence imaging system to investigate Ca2+ signaling dynamics and membrane potential fluctuations in intact cells.

Developmental Genetics and Stem Cell Regulation Lab (Associate Professor Kenneth Wallace; Science Center SC172): The lab facility is designed to support research activity in the area of vertebrate intestinal development using the zebrafish model system. Specifically, we are investigating control of the developing intestinal stem cell compartment before the mature structure forms. We have a fish facility with three independently circulating racks from Aquatic Habitats. Each of the fish racks have a mix of ten, three and 1.5 liter tanks. The fish racks have automated conductivity and pH monitoring and draws water from a reverse osmosis system. We have a variety of stereomicroscopes, an epifluorescent microscope to image immunohistochemistry and RNA in situ hybridizations. We have a microinjection apparatus for embryo injections. We are equipped for genetic and molecular biology work with PCR machines, qPCR (Biorad), electrophoresis equipment, incubators and hybridization ovens.

Bioimagery rooms (SC108 and SC102): Fluorescent imagery is performed on two different inverted microscopes (Nikon and Zeiss). We have an upright Zeiss light microscope for histological observations and a stereomicroscope with both transmitted and reflected light capabilities. In SC102 we have the Leica Confocal microscope with an automated inverted DMi8.  It is equipped with four solid state scanning lasers 405/488/561/635 nm. The objectives are 10x, 20x, 40x dry and oil, 63x oil. Each lens is equipped with differential interference contrast (DIC). The scope has epi-fluorescense to identify samples before scanning. Driver/analysis software is LAS SPE 3D Visualization Basic for reconstruction and processing of 3D data.

The Limnology Laboratory (Prof. Michael Twiss, Science Center 176B):  The Limnology Laboratory is designed to support student research activity in the subject area of freshwater science, which encompasses measurements of physical, chemical, and biological conditions in surface fresh waters (rivers, lakes, and wetlands).  Both classical (e.g., water sampling bottles, microscopy, filtration apparatus) and advanced instrumentation (e.g. pigment-specific fluorometers, electronic water quality sensors) is available in this laboratory that is also equipped as a staging point for field work using coastal research vessels (

Cell-Materials Interaction Lab (Asst. Professor Shantanu Sur; Science Center 207):  This lab focuses primarily on the study of biomaterials-cell interactions using in vitro models for the development of tissue engineering scaffolds and targeted drug delivery systems. The lab has a BSL2 mammalian tissue culture set-up and a live-cell imaging facility (Nikon Biostation). Thermocyclers and gel electrophoresis equipment are available for routine gene and protein expression analysis (PCR and western blot). A multi-mode microplate detection platform with an attached imaging cytometer (SpectraMax i3x with Minimax imaging cytometer) is used for colorimetric, fluorescence, and microscopy-based assays for high throughput assessment of cell response such as viability and proliferation.

Experimental Evolution and Bioinformatics Lab (Asst. Professor Susan Bailey; Science Center 107):  We use experiments with bacteria to study evolutionary dynamics, and analyze genome sequence data to identify the underlying genetic changes that drive adaptation. In the lab, we culture bacteria in different types of media, using our biological safety cabinet for safe and sterile transfer of bacteria (bio safety levels 1 and 2). Bacteria are grown in our shaking incubators, and quantified using Petri dish plating, and optical density measures obtained with our Epoch 2 Microplate Spectrophotometer. For preservation of bacterial cultures we have an ultra-low-temperature freezer and for DNA extraction and quantification, we have a micro-centrifuge, and a nano-drop spectrophotometer.



Stem Cell Biology and Regenerative Medicine Lab (Prof. Thomas Lufkin, Asst. Professor Petra Kraus; Science Center 203, 205): Our research is in the area of Developmental Genomics and Regenerative Medicine with a focus on the molecular mechanisms controlling vertebral column development and an emphasis on stem cell commitment to specific differentiation pathways leading to the adult organ, but from a Systems Biology point of view. In particular we are working on understanding the gene regulatory networks (GRNs) that govern normal development of the vertebral column and intervertebral disc (IVD). We are investigating the role of transcriptional regulators in the restriction of pluripotent stem cells into specific lineages that in turn comprise functional pre and postnatal vertebral elements with the goal of applying this knowledge to regenerative medicine in humans using patient-specific induced pluripotent stem (iPS) cells and adult mesenchymal stem cells.

Developmental Genetics lab (Asst. Professor Ginger Hunter; Science Center 113): This lab facility is equipped for performing experiments in developmental genetics using the fruit fly Drosophila melanogaster. We have two fly stations for routine fly pushing as well as live documentation of adult phenotypes and fluorescence sorting of genetic markers. In support of this, part of the lab space is dedicated to a small 'fly kitchen' where we prepare everything we need to keep the flies going and experiments running. We have all the support equipment to perform molecular biology based analysis (DNA analysis, protein analysis, other cloning) which we use to screen flies for new mutations and changes in protein expression, in addition to assembling DNA constructs for making transgenic flies. There is a computer workstation for data analysis and plenty of student workspace. The lab is equipped with the hood and incubators necessary to maintain and perform experiments in insect cell culture.

Ecology & Behavior lab (Professor Tom Langen; Science Center 170G): This lab facility serves as a base for fieldwork on terrestrial and wetland ecology and animal behavior research. It is fully equipped with field equipment for wildlife observation, radiotelemetry, capture and marking animals, camera-trapping, and vocal playback surveys. It has a computer work station for geospatial analysis using ArcGIS and other geospatial applications, and other work stations for data analysis. It has an extensive library for identifying organisms and planning biological surveys. 

Aquatic Ecology lab (Asst. Professor Andrew David; Science Center 132C): This lab facility is designed to support research in experimental marine and freshwater ecology and molecular taxonomy and ecology of aquatic invertebrates including DNA barcoding. It is equipped with four 10-gallon aquaria fitted with automatic CO2 injectors and water quality sensors for non-flow through acidification experiments. For genetic work, we have the latest Thermal Cycler from ABI (MiniAmp) for accurate amplification, along with all the standard equipment for DNA extraction (microcentrifuges, vortexer, heating blocks and materials for gel electrophoresis). There is a computer workstation for Bioinformatics analyses along with premium DNA alignment and editing applications installed included Geneious. There are also two Linux based laptops available as loaners for undergraduates working in the lab. The lab has extensive storage space for voucher specimens collected in the field. 

First Year Biology Lab (Stefanie Kring; SC 170D): This lab facility accommodates 16 students (4 desks x 4 seats/desk). All desks are equipped with computers that students can use for data analysis and research. Each desk has gas, water, and air for a variety of biological experiments. The lab is used for a wide range of applications from ecological studies to molecular manipulations. 

Upper Level Teaching Lab (SC 134A): This lab facility accommodates 20 students (2 desks x 10 seats/desk). All desks are equipped with gas, water, and air for a variety of biological experiments. This room is also equipped with compound and stereomicroscopes. Various equipment for molecular biology and biochemistry labs can be found here (NanoDrop, thermal cycler, water baths, centrifuges, vortexes, incubators, ice machine, gel apparatus, etc.) There is also a separate facility within this teaching lab that can be used for cell culture, with microscopes, a CO2 incubator, and two laminar flow hoods. This room also contains a water purification system. 

Upper Level Teaching Lab (SC 134B): This lab facility accommodates 24 students (6 desks x 4 seats/desk). Computers are equipped with AD Instruments software, for various anatomy and physiology experiments. Each desk is equipped with a dissection hood that can be used to dissect small animals. The lab is also used for a wide range of ecological studies.