CBISCenter for BioteChnology and interdisCiplinary studies

Focused collaboration on the frontiers of life sciences, physical science, and engineering

Industry Partners Program

Join Our Research PowerhouseCompanies looking for solutions to cutting-edge biotechnology

problems are finding their way to RPI’s unique Center for

Biotechnology and Interdisciplinary Studies (CBIS). In operation

since 2004, CBIS offers one of the most advanced biotechnology

research facilities in the nation. What sets us apart is our collabora-

tive focus on innovation and discovery in biotechnology and medicine

at the interface of life sciences, physical sciences, and engineering.

218,000 square feet in the Center

13,009 square feet of support labs

27,350 square feet of core facilities

31,240 square feet of open research labs

31,775 square feet of office space

5,830 square feet of conference and seminar space

33 principal investigator laboratories

150 Ph.D. students

50 postdoctoral students

25 visiting research scientists CBIS

Our interdisciplinary research teams perform fundamental, applied,

and translational research. CBIS is a powerhouse of basic research

and its application to solving real-world problems in healthcare and

biotechnology. The combination of diverse research constellations

and advanced technological tools enables ground-breaking work in:

• BiocatalysisandMetabolicEngineering: Biologics,

bioengineered drugs, high-throughput assays

• TissueEngineeringandRegenerativeMedicine: Acellular

scaffolds for tissue engineering and drug delivery, 3D cell

printing, stem cell bioengineering

• BiocomputationandBioinformatics: Healthcare analytics,

green industrial enzymes, molecular dynamics

• AdvancedMaterials: Bio-nano materials, biofilms, anti-infection

compounds and coatings

DEEpAkVAshishTh,ph.D.Director,CenterforBiotechnologyandinterdisciplinarystudiesp:518-276-2296e:vashid@rpi.edu

Center for Biotechnology and interdisciplinary studies rensselaer polytechnic institute 110 8th street, troy, ny 12180 usa

p: 518-276-2877f: 518-276-4233e: cbisbiopartners@rpi.edu

> Core faCilities page 4

> industry partners page 10

> ConferenCe faCilities page 14

GlEnnM.MonAsTERsky,ph.D.operationsDirector,CenterforBiotechnologyandinterdisciplinarystudiesp:518-276-2877e:monasg@rpi.edu

Inside

CBIS

Fromcomplexbiologicalnetworkstonanoscaleassembliesthatmimicbiologicalprocesses,morethan200CBis

scientistsandengineersareworkingtouncoverthemolecularbasisofbiologicalmechanismsanddisease,using

biologicalsystemsasthebasisfornewtherapeutics,anddevelopingnewcellularnichescriticalintissueregeneration.

Cores

TherearenineCoreFacilitiesatCBisledbyDirectorsholdingaph.D.intheirrespectiveareasandengagedinresearchactivities.ouruniquefacilities,combinedwithhighly-skilledstaff,createtheidealenvironmentforindustrycollaborations.

The AnalyticalBiochemistryCore facility provides state-of-the-art instrumentation for physical and/or chemical characterization of biological samples and nano-materials.

FeATuReS:• Jasco815spectrometerwithBiologic

stoppedflow for rapid kinetics in fluorescence and CD mode.

• spexFluorologTau3spectrometer for steady state anisotropy and lifetime measurements.

• BeckmanAnalyticalUltracentrifugeXl-iequipped with uV-Vis detection system and Rayleigh interference optics.

• WyattTechnologyDynaproTitanBatchDynamiclightscattering to measure particle dimension in the nm range.

• TADifferentialscanningCalorimeterQ100 for measuring temperatures and heat flows associated with thermal transitions in materials.

• TAThermogravimetricAnalyzerQ50 for measuring weight changes in a mate-rial as a function of temperature (or time) under controlled atmosphere.

• perkinElmerMicroBetaTrilux liquid scintilation and luminescence counter.

• MicroCalVp-iTC. The isothermal titration calorimeter measures the heat involved in binding reactions.

• BrukernanostarsmallAngleX-Rayscatteringprovides information about particle sizes and shapes in liquids, powders, and bulk solutions.

• BrukerD-8DiscoverpowderDiffrac-tometercapable of performing In-Plane Grazing Incidence Diffraction (IP-GID), High Resolution and X-Ray reflectance. Ther-mally controlled stage for measurements between –100 to +350 degrees C.

• hitachiUV-visspectrophotometer has a dual beam for accurate absorbance measurement.

Analytical Biochemistry & Nanobiotechnology Research CoreDR.JoElMoRGAnAnalytical Biochemistry Research Core Director p: 518-276-4170 | e: morgaj3@rpi.edu

Ph.D., 1989, California Institute of Technology

DR.MARiMARD.lopEz

Core Director, Center for Biotechnology and Interdisciplinary Studies Ph.D., 1991, university of Valencia Consejo Superior de Investigaciones Cientificas CSIC, Madrid

p: 518-276-4416e: lopezm4@rpi.edu

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• Bruker13cm7ThorizontalBoreMRiscanner. The MRI is impacting fields including tissue engineering/regenera-tion, neuroscience, and transgenic animal investigations, since it provides information about changes induced at the organ or animal level.

• scancoMedicalVivaCT40 is a high speed in vivo micro CT scanner ideal for resolving dense tissues, including bone and contrast enhanced structures such as vasculature. It is equipped with a micro-focus X-ray source capable of 5 μm spot size and 50-70 kVp, 8W (160 μA) and can achieve 10 μm nominal resolution. It can

cover a maximum scan length of 145 mm and has a field-of-view up to 20-38 mm. Animals or tissue can be up to 80 mm in diameter and up to 200 mm in length. The system includes software capable of data acquisition, online/offline reconstruction, 2D & 3D analysis and reconstruction, 3D visualization and animation, and archiving.

• Bruker14T(600Mhz)Wide-BoreMulti-channelheteronuclearMicroimagingscanner/spectrometer. Microimaging/MRS provide exceptional sensitivity for imaging and MRS (spatial resolved NMR spectroscopy) studies of small animals, tissue samples, and materials approaching

μm range resolution for many resonator/gradient combinations (far exceeding resolution limits achievable by standard horizontal bore imaging systems).

• BrukerUltraflexiii-MAlDiToF/ToFMassspectrometer used to acquire mass spectrometric data directly from a cryostat section of a tissue. Spectra are obtained in a measuring grid across the tissue area with high lateral resolution. Peaks can be correlated with underlying tissue architecture without any geometrical distortion, enabling true Molecular Histology.

FeATuReS:

DR.sCoTTA.MCCAllUMBioImaging & NMR Research Core Director p: 518-276-2856 | e: mccals@rpi.edu

Ph.D., 1999, university of Virginia

BioImaging Research Core

The BioResearchCore(BRC) is a state-of-the-art rodent housing and research facility designed to provide a carefully controlled environment. The facility includes nine barrier and three quarantine holding rooms and six procedure rooms for both ABSL-1 and 2 work. One holding room is equipped with a light lock for total control of light for variable or reversed day-night lighting conditions. FeATuReS:• Rodents are housed in HePA-filtered,

individually ventilated cage racks. They are provided environmental enrichment and sterile food, water, and bedding, maintain-

ing specific pathogen-free standards. Quarantine holding areas are used for animals with unknown health status or restricted pathogens. Micro isolation units are also available.

• Procedure rooms are equipped with either chemical fume hoods or biosafety cabinets. Materials are available for rodent survival surgery, blood and tissue collection, euthanasia, and necropsy.

• The BehavioralRoom provides space and equipment for analysis of rodent activ-ity, arousal, learning, memory, anxiety, depression, etc.

• BRC staff are skilled in animal husbandry and technical animal procedures and provide training and support for developing and executing protocols for biomedical research and engineering models.

• BRC staff members have performed many specialized procedures such as major and minor survival surgery, orthopedic testing, in vivo MRI and fluorescence imaging support, behavioral testing, and cardiovascular physiology.

DR.RoBERTA.WAniEWskiBioResearch Core Directorp: 518-276-4835 | e: wanier@rpi.edu

Ph.D., 1980, George Washington university

BioResearch Core

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DR.JoElMoRGAnMicrobiology Research Core Directorp: 518-276-4170 | e: morgaj3@rpi.edu

Ph.D., 1989, California Institute of Technology

Microbiology Core

The MicrobiologyCore at Rensselaer can facilitate bacterial growth, harvesting, and processing on a small, medium and large scale.

FeATuReS:•ThreenewBrunswickBio-Flow

Fermentors(two 30 L and one 15 L, working volume).

• Cepaz41ContinuousFlowCentrifuge

• incubatorsandshakers

• highspeed/high-CapacityCentrifuges

• Ultracentrifuges

• Frenchpress

• Microfluidizer

• sonicator

• klettfor measuring DNA concentrations in cell cultures.

• nanodropfor measuring absorbances of small volume (2 μL) solutions.

• GETyphoonTrio+ Flatbedscannerfor imaging fluorescently labeled blots, gels, multiwell trays, and even tissue sections with up to 10μm lateral resolution. A phosphor screen can be used to retain signal from beta particles, X-rays, and gamma rays.

• TissueCultureFacility includes biosafety cabinets, refrigerators, water baths, centri-fuges, and incubators for routine tissue culturing needs.

• The Amaxanucleofector for high-efficiency, non-viral transfection to deliver DNA and RNA to both cytoplasm and nucleus of cells and bacteria, including difficult primary cell lines.

• RochelightCycler480 is a high- throughput real-time PCR for a broad range of genomics applications, including array validation, gene knockdown studies, SNP analysis, and genotyping.

• FlowCytometryFacilities includes a BD FACS Aria and BD-LSRII for high-throughput cell counting and sorting of up to four different cell types based on size and 10+ fluorescent markers.

FeATuReS:

DR.sERGEypRyshChEpCell & Molecular Biology Research Core Directorp: 518-276-3456 | e: pryshs@rpi.edu

Ph.D., 2001, International Sakharov environmental university

Cell & Molecular Biology Core

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DR.sERGEypRyshChEpMicroscopy & Cellular Imaging Research Core Directorp: 518-276-3456 | e: pryshs@rpi.edu

Ph.D., 2001, International Sakharov environmental university

Microscopy & Cellular Imaging

The MicroscopyCore at Rensselaer offers advanced state-of-the-art imaging capabilities.

FeATuReS:• ConfocalandMultiphotonzeisslsM

510METs,nlo. The confocal and multi-photon are designed to collect 3D images of thick fluorescently labeled samples. The MeTA spectral detection system can distinguish multiple (5+) fluorescent signals in a single specimen. environmental control (temperature, CO2, humidity) is available.

• TheolympusTotalinternalReflec-tionFluorescence(TiRF) microscope is ideal for imaging fluorescent structures in the immediate vicinity of the coverslip (~100nm) with minimal background, and is well suited to live samples.

• TheAsylumMFp-3DBioAtomicForceMicroscope(AFM) scans topographical features on the nano-meter scale, and measures forces associated with single molecule measurements.

• TheMMiopticalTweezers-laserMicrodissection.The optical tweezers measure piconewton forces and single molecule interactions. Laser microdissec-tion isolates tissue, cells, and even subcel-lular structures including chromosomes for protein, RNA or DNA analysis.

NMR CoreDR.sCoTTA.MCCAllUMNMR Core Director p: 518-276-2856 | e: mccals@rpi.edu

Ph.D., 1999, university of Virginia

The nuclearMagneticResonance(nMR)Coreis used for solution structure determination of small molecules (proteins, carbohydrates and macromolecular complexes) at atomic resolution.

NMR is also used to elucidate protein fold-ing and aggregation mechanisms/kinetics, structural informatics/gene discovery, and structure activity relationships.

FeATuReS:• Bruker800and600Mhz

spectrometer.Both equipped with a cryogenically cooled probe for ultra-high sensitivity. Both feature a sample changer, allowing data collection on 24 samples during unattended operation. Include TopSpin software to acquire, process and analyze NMR data.

• Bruker600MhzWide-Boresolid-statenMRspectrometer.The Solid-State NMR is a vital tool for characterization and development of new materials, devices, and molecular systems, including:› Synthesis and assembly of molecular

machines at the interface of biology and nanotechnology.

› Polymers employed as membranes in fuel cells.

› Membrane proteins, which constitute over 30% of all eukaryotic proteins, but <0.5% of known protein structures.

› Insoluble and plaque forming protein aggregates such as those involved in Alzheimer’s and Parkinson’s diseases.

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DR.DMiTRiV.zAGoREVskiProteomics Core Director p: 518-276-2149 | e: zagord@rpi.edu

Ph.D., 1981, Institute of Organoelement Compounds – Academy of Sciences, uSSR

Proteomics Core

The proteomicsCore is equipped with a number of state-of-the-art mass spectrometers.

FeATuReS:•BrukerUltraflexiiiMAlDiToF/ToF. › Determination of molecular mass

within a range from 20 Da to 300,000 Da in real time.

› An excellent ion transmission in linear mode (important for protein MW measurement).

› A very high resolution in reflectron mode (up to 20,000).

› A high mass accuracy (up to 5 ppm). › A high sensitivity (fmol range for peptides). › Several fragmentation modes.

•shimadzuQp5050-Quadrupole GasChromatograph-Mass spectrometer. › Analyses of volatile low-molecular

weight (up to 800 Da) compounds (gases, PCBs, drugs, antibiotics, steroids, etc.) by electron ionization and chemical ionization.

› Analyses of mixtures. › Quantitative analyses.

•ThermoElectronFinniganTsQQuantumUltraMassspectrometer is coupled with a micro-flow agilent 1200 HPLC system. The triple quadrupole system performs highly selective reaction monitoring (H-SRM) to analyze complex samples quickly and efficiently. It is ideal for determination of masses in complex mixtures and quantitative analyses. It offers:

› Great versatility with mass range (m/z 30–1500). › Resolution up to 7,500 at m/z 508. › eSI ionization mode. › excellent for quantitative

measurements by LC/MS and LC/MS/MS analyses.

› Xcalibur software for instrument control and data analysis.

•ThermoscientificlTQoRBiTRApXl-linearTraporbitrapMassspectrom-eter is coupled with a nano-flow agilent

1200 HPLC system, offering: › Analysis of proteins and peptides,

their mixtures and other samples, by electrospray ionization.

› High resolution and accurate mass measurements (up to 2 ppm).

› Intact protein analysis and top-down proteomics. › Data-dependent MS/MS scans with high mass accuracy. › Protein identification (peptide mass

mapping/sequencing). › Post-translational modification location. › Xcalibur software for instrument

control and data analysis.

•proteomeDiscoverer is a flexible and expandable platform to analyze qualitatitive and quantitative proteomics data.

ThermolTQorbitrapXlisahigh-resolution,high-massaccuracyinstrumentthatisusedtodetermineelementalcompositionandstructuralcharacteristicsofavarietyofcompounds.Thisinstrumentwasemployedfordetectionandidentificationofnicotinein1,100yearoldMayanpottery.8

Stem Cell CoreDR.BRiGiTTEl.ARDUiniStem Cell Research Core Directorhttp://stemcells.rpi.edu | p: 518-276-2847 | e: arduib@rpi.edu

Ph.D., 2005, Ohio State university

The stemCellResearchCore provides comprehensive support for basic stem cell research with tissue engineering and regenerative medicine applications. Our state-of-the-art multi-laboratory facility sup-ports collaborative projects involving cell biology, biomedical engineering, chemical engineering and informatics research.

We offer consultation for academic and industry partners regarding the design and performance of investigations, including the selection of cell types, phenotypic analysis, and imaging strategies.

The laboratory is a fully-equipped aseptic cell culture facility that supports hypoxic studies and rapid workflow development including automated liquid handling, high-content and time-lapse imaging, and specialized algorithms for data analysis.

FeATuReS:• high-ContentimagingwithThermo

scientificCellomicsArrayscanVTi.The ability to accommodate slides and multiwell plates, obtain fluorescent and bright-field images, and efficiently analyze large data sets removes bottlenecks and speeds time to results. This system is ideal for high-throughput screens, cell-based assays, and numerous other applications.

• Real-TimeDataimagingwitholympusVivaView. A vital complement to endpoint data analyses, this powerful live imaging system makes it possible to collect fluo-rescent and bright-field time-lapse images of cells in stable environmental conditions.

• The core serves as the nysTEMRens-selaerCenterforstemCellResearch(RCsCR)under the direction of Glenn Monastersky, Ph.D. (PI, NYSTeM award).

neuralstemCellColony 9

Industry PartnersCBIS encourages industry partners to take advantage of our unique interdisciplinary capabilities. CBIS can assist in identifying and executing research pathways to solve critical biotechnology chal-lenges affecting:

• Humanhealth • Bioprocessing • Energysecurityandsustainability • Biotechnologyandpublicpolicy

CBIS is uniquely equipped to integrate the rigor of Fundamental (Basic) research with the relevance of Translational (Applied) research to solve problems across many biotechnology fields. As one of the nation’s top biotechnology research centers, we also are unique in our integration of cross-disciplinary research involving chemistry, biology, engineering, physics, and mathematics.

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FundamentalResearchFundamental (or “Basic”) research is performed to develop general knowledge and an understanding of nature and its laws.1 Fundamental research in biomolecular and cellular sciences and engineering is a core strength at CBIS.

TranslationalResearchTranslational research applies fundamental research to specific opportunities, seeking to find real-world solutions to known problems or to revolutionize entire fields through advances in understanding of processes and technologies. This is where CBIS’ unique intersection of research disciplines is particularly critical. We offer capabilities in biocatalysis and metabolic engineering, computational biology and bioinformatics, tissue engineering and regenerative medicine, systems biology, microscale systems, high-throughput technologies, bioprocessing, and bioimaging.

TargetedResearchprogramsultimately, CBIS looks to deliver critical breakthroughs to society in key areas, such as biologics, stem cell biotechnology, nanoscale therapeutics, drug discovery, biomanufacturing, and biomass conversion. Our objective is to provide a clear path from the lab to the real world while ensuring that ethical and responsible research is maintained.

1 Donald Stokes, Pasteur’s quadrant: Basic Science and Technological Innovation (1997).

BreakthroughCapabilities

CBisisopeningpathwaystoinnovation,discovery,andcommercialdevelopmentsindiagnostics,therapeutics,medicaldevices,andregenerativemedicine.someexamplesinclude:

• syntheticheparin• Antimicrobialcoatings• integratedCT/MRi• Detoxificationchemotherapy• Biomedicine-on-Demand• 3Dcellulararraychip(toxicology)• Functionalizedacellularmatricesfor

tissueengineeringanddrugdelivery• implantablesensors• Environmentally-friendlyindustrialenzymes

CombinedCT-MRiscanner Alzheimer’sAntibodies

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WhyBecomeanindustrypartner?

The CBIS Industry Partner program enables your enterprise to tap advanced research capabilities to:

• Solve R&D or product manufacturing challenges• Identify enabling technologies to improve operational efficiencies• Develop breakthrough technologies and products

By using research resources that most companies cannot afford on their own, CBIS industry partners accelerate time to discovery, trial, and market introduction of critical products, procedures, and services.

From pharma-therapeutics to tissue regeneration, from breakthrough diagnostic technologies to medical devices, CBIS offers industry partners access to knowledge and technology with which to make truly significant advances.

ResearchAgreements

The Office of Technology Commercialization (OTC) at Rensselaer Polytechnic Institute is responsible for managing intellectual property generated from research conducted at the university. Like all u.S.-based research universities, Rensselaer is subject to the Bayh-Dole Act, which requires ownership of research at facilities funded by the federal government to remain with the funded institution. However, in recognition of the interests of commercial partners, the OTC has been recently reorganized to facilitate access to valuable intellectual property stemming from basic, applied, and demonstration research. Licensing agree-ments can have the same legal and commercial benefits of ownership and we are developing innovative, streamlined contract processes to make it easier to meet the needs and time lines of our industry partners.

howitWorksWeofferthreelevelsofparticipationintheCBisindustrypartnersprogram:

Bio1:CoreUse

• Discounted access to short courses.

• Discounted partner rates on equipment usage fees and laboratory testing assistance.

• Participation in annual conference with ample networking opportunities with faculty and other industry partners.

• Sponsorship of a graduate student, whose research will be presented at the annual conference.

Bio2:Consultancy

• Active participation in the nation’s most exciting interdisciplinary biotechnology research frontiers.

• Access to consulting assistance for basic or applied research and demonstration projects.

• Partner benefits for up to 3 corporate units.

• Depending upon the research being performed, this level may involve the negotiation of a licensing agreement.

• All Bio 1 benefits.

Bio3:sponsoredResearch Agreements

• Access to tenured faculty and grad student support to conduct:

• Basic Research for technological development.

• Applied Research to address a particular problem.

• Demonstration Research for accelerating product development.

• This level will involve a negotiated spon-sored agreement. Further information available through Research Administration and Finance: RAFGrants@rpi.edu.

• All Bio 1 benefits.

Bioengineeredandsyntheticheparin

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BiotechnologyResearchConstellations

RPI’s biotechnology research constellations are fully integrated through CBIS. These constellations build upon the institution’s core strengths in microelectronics and microsystems engineering, advanced materials, nanotechnology, and advanced scientific computation, modeling, and simulation.

Constellations are multidisciplinary teams of senior faculty, junior faculty, graduate students, and undergraduates. each constellation is led by one to three world-class faculty members in the following research fields:

•BiocatalysisandMetabolicEngineering

• BiocomputationandBioinformatics

•IntegrativeSystemsBiology

•FunctionalTissueEngineeringandRegenerativeMedicine

ConsultationandRoadmap

CBIS is prepared to assist you at the level of need you define. The depth of expertise and critical knowledge available here enables us to consult with partners in everything from defining the problem to identifying research methodologies and conducting the research. We work collaboratively to develop a research roadmap that maximizes our unique strengths in interdisciplinary research and testing services.

ContactCBistodaytodiscussyourresearchinterests.

CenterforBiotechnologyandinterdisciplinarystudiesRensselaerpolytechnicinstitute

1108thstreet,Troy,ny12180UsA

p:518-276-2877

w:http://biotech.rpi.edu

e:cbisbiopartners@rpi.edu

proteomeprofilingandpredictionofosteoporoticandDiabeticBoneFracturesDia-beticBoneFractures 13

TheAuditorium(above)isa2,780squareft.state-of-theartfacilitywithcapacityfor153people.itisusedforindustrysymposia,ourAnnualindustrypartnersConference,trainings,andothercriticalgatherings.itincludesacontrolroomforbroadcast/webcastingandtwolargerear-projectiondisplaysthatcanbeusedseparatelyorasonelargedisplay.FoodandbeveragesmaybeservedinthesenatorWilliamh.hernstadt’57andJereneyaphernstadtGalleryareaoutsideoftheAuditorium.

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Auditorium, located on the 1st floor, next to the building entrance near the Science Center, is available for presentations, lectures, or meetings. The Auditorium is 2,780 square ft. and holds a capacity of 153 people. Food and beverages may be served in the Gallery area outside of the Auditorium.

Bruggeman Conference Center offers a spacious area of 1,150 square ft., holding a capacity of 72 people. Food and beverages may be served in the Bruggeman or outside in the lobby area.

There are three Oxbridge Rooms, each with an available built-in projector system. The 2nd floor Oxbridge Room is 350 square ft. and holds a capacity of 12 people. The 3rd floor Oxbridge Room is 448 square ft. and holds a capacity of 14 people. The 4th Floor Oxbridge Room is 492 square ft. and holds a capacity of 16 people.

Biotech Terrace is located off the 2nd floor Oxbridge Room. It is ideal for outdoor social gatherings and networking during the spring, summer, and fall months.

Two Open Window Conference Rooms are available on the 3rd floor. each room holds a capacity of 14 people with one room at 384 square ft. and the other 395 square ft. Breakout Rooms are also available. One on the 3rd floor has a capacity of 6 people at 179 square ft. A second room on the 4th floor has a capacity of 6 people at 172 square ft.

Conference Facilities

TheCenterforBiotechnologyandinterdisciplinarystudiesisproudtoofferseveralroomsforpresentations,lectures,networkinggatherings,conferencesormeetings.Eachroomoffersuniquecapabilitiesfittingitsfunction.

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CenterforBiotechnologyandinterdisciplinarystudiesRensselaerpolytechnicinstitute

1108thstreet,Troy,ny12180UsAp:518-276-2877

e:cbisbiopartners@rpi.eduhttp://biotech.rpi.edu