Bioinformatics Program – Bruce Luxon, Ph - UTMB Research ...

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CORE LABORATORIES


Core Program

(Link to Brief Description)

Web Page Link

Director or Manager

Department

Bioinformatics Program

http://www.bioinfo.utmb.edu/




Bruce Luxon, PhD

Dean of
Medicine

Biomedical Imaging Network


Massoud Motamedi
PhD

Microbiology &
Immunology


Optical Microscopy Core
(OMC)

www.utmb.
edu/oil

Leoncio Vergara,
Adrianna Paulucii



Biomolecular Resource
Facility

(BRF)

http://www.utmb.edu/brf/




Alex Kurosky, PhD

Dean of
Medicine

Protein Chemistry Section


Alex Kurosky, PhD


Biosynthesis & Biomarker
Core

http://www.utmb.edu/brf/cores/ProteinSynth
esis/index.html


Bo Xu, PhD

BRF

Peptide Synthesis Core

http://www.utmb.edu/brf/cores/PeptideSynth
esis/index.html


Stefan Serabyn

BRF

Protein Chemis
try Core

http://www.utmb.edu/brf/cores/ProteinChemi
stry/index.html


J. Stephen Smith

BRF

Proteomics Section


John Wiktorowicz, PhD

BRF

Separations

Technology
Core

http://www.utmb.edu/brf/cores/SeparationsT
echnology/index.html


John Wiktorowicz, PhD

BRF

Proteomics Bioinformatics
Cor
e

http://www.utmb.edu/brf/cores/ProteomicsBi
oinformatics/index.html


Kizhake Soman
, PhD

BRF


Mass Spectrometry Core

http://www.utmb.edu/brf/cores/MassSpectro
metry/index.html


Tony Haag, PhD

BRF

Biostatistics

http://www.utmb.edu/biostat/


Dan Freeman,
PhD

Preventive
Medicine &
Community
Health (PMCH)

Environmental Exposure
Facility

http://intranet.utmb.edu/scehm/inhalation_to
xicology.htm


Bill Ameredes, PhD

Sealy Center for
Environ
-
mental
Health &
Medicine

Flow Cytometry and Cell
Sorting

http://microbiology.utmb.edu/core/flowcore/


Jiaren Sun
, PhD

Microbiology &
Immunology

Institute for Translational
Research (ITS)

http://www.its.utmb.edu/


Allan Brasier


ITS Clinical Research Center
Core
and Imaging Laboratory


http://www.its.utmb.edu/

http://www.its.utmb.edu/resources/translatio
nal_technologies.html

Melinda Sheffield
-
Moore, PhD

Thomas Wood, PhD


Research Histopathology
Core

http://www.utmb.edu/pathology/researcht
ab/research_histopath_home.htm

Judy Aronson, MD

Pathology





Research Technology
Support

(RTS)

http://research.utmb.edu/rts/default.shtm



Jamie Svrcek

Research
Services

Sealy Center for Cancer Cell
Biology (SCCCB)
Cores

http://www.utmb.edu/scccb/default.asp



Robert Ullrich, PhD

Surgery

Transgenic Mouse Facility

http://www.utmb.edu/scccb/mouse/

Maki Wakamiya,

PhD

SCCCB

Nude Mouse Laboratory


Mark Hellmich,
PhD

SCCCB


Real Time PCR Core

http://www.utmb.edu/scccb/pcr/index.htm

.

Lisa Elferin
k, PhD

Nonggao He, PhD

SCCCB


UTMB Tumor Bank

http://www.utmb.edu/scccb/htbc/htbc.htm

.

Nonggao He, PhD

SCCCB

Biostatistics Shared Service

http://www.utmb.edu/Cancer/biostatcor
e/


TBN

Cancer Center


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Core Program

(Link to Brief Description)

Web Page Link

Director or Manager

Department

The Oncology Clinical Trials
Office (OCTO)

http://www.utmb.edu/cancer/


A
vi Markowitz
, MD

(DIR)

Cheryl Proctor (Mgr)

Cancer Center

Rodent

in vivo

Assessment
Core (RIVA)

None

Kelly Dineley
, PhD

Pharmacology

Sealy Center for Molecular
Medicine Cores


Allan Brasier, MD

DOM

Molecular Genomics

http://www.scmm.utmb.edu/genomics/

Thomas Wood, PhD

Sealy Center
for Molecular
Medicine

Recombinant DNA Lab

http://www.scmm.utmb.edu/cores/rdl/rdl.htm


Thomas Wood, PhD

Sealy Center
for Molecular
Medicine

Sealy Center for Structural
Biology (SCSB) Cores


http://scsb.u
tmb.edu/

Wayne Bolen,
Ph.D., Director

Dean of
Medicine


Computational Biology

http://scsb.utmb.edu/facilities/cb.htm


Wayne Bolen, PhD
,
Director

David Power, Manager

SCSB


Cryo Electron Microscopy

http://cryoem.utmb.edu/

Michael Sherman, PhD

SCSB


Solution Biophysics

http:/
/sbl.utmb.edu/

Luis Holthauzen, PhD

SCSB

NMR Spectroscopy

http://nmr.utmb.edu/

Tianzhi Wang, PhD

SCSB



X
-
ray Crystallography

http://xray.utmb.edu/

Mark White, PhD

SCSB

Synthetic Organic Chemistry

http://www.utmb.edu/cet/cores/synthchem.a
sp


Richard Hodge, PhD

Se
aly Center for
Environmental
Health and
Medicine/NIESH
Center

Tissue Culture Core Facility

http://microbiology.utmb.edu/tccf/index.html


Rolf Konig, PhD

Microbiology
&
Immunology


RESTRICTED CORES


Galveston National
Laboratory

http://www.utmb.edu/gnl/


James W. LeDuc,
Ph.D.

Galveston

National
Laboratory
(GNL)

Aerobiology

None

J
ohnny Peterson,
PhD

GNL

Assay Development

None

Nigel Bourne, PhD

GNL

Experimental Pathology

None

David Walker,
M
D

GNL

Imaging

None

Massoud Motamedi,
PhD (acting
)

GNL

Immunology

None


GNL

Insectary Services

None

Stephen Higgs, PhD

GNL

Preclinical Studies

None

Slobodan Paessler,
PhD

GNL

Regulatory Services

None

David Bea
sley, PhD

GNL

Shope BSL 4 Core Lab

http://www.utmb.edu/cbeid/safety.shtml


Alexander Freiberg,
PhD

IHII

Sealy Center for
Environmental Health &
Medicine


Istvan Boldogh,
DM
&B, PhD

NIEHS Center

Pepper Center Cores

http://www.utmb.edu/scoa/pepper/coreStruc
Elena Volpi, MD,
Sealy Center on

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ture.asp




PhD; James S.
Goodwin, MD

Aging

OAIC
Tracking and
Evaluation


Jean Freeman, PhD

Pepper Center

OAIC Administrator

http://www.utmb.edu/scoa/pepper/index.asp


Tony DiNuzzo, PhD

Pepper Center

Clinical Research
Resource Core


Glenn Ostir, PhD

Co
-
Leader: Elizabeth
Protas, PhD, PT

Pepper Center

Muscle Biology Resource
Core


Elena Volpi, MD,
PhD; Co
-
Leader John
Papaconstantinou
PhD

Pepp
er Center

Pilot/Exploratory Studies
Core


Blake Rasmussen
PhD; Co
-
Leaders
Melinda Sheffield
-
Moore, PhD and
James Goodwin, MD

Pepper Center

Research and Career
Development Core


Ken Ottenbacher,
P
hD; Co
-
Leaders:
Kyriakos Markides,
PhD and James
Goodwin, MD

Pepper Center





Resources: Core Facilities


The Biomedical Informatics Program

has labs and offices in the Dockside Building, the Basic Science Building,
Children’s Hospital, John Sealy Hospital, and the Medical Research Building. Staff includes the Program Directo
r (Prof.
Luxon), an administrative assistant, 7 faculty members (as well as their staff), 7 senior staff, and 5 regular and junior sta
ff.
We also have several casual BioIT Team members drawn from the institutional IT force on an
ad hoc

basis when special
skills are required that are not otherwise available within the Team.

Our mission is to provide expertise, training, access to high
-
end hardware and software, and analytical support in BMI to
researchers. This includes high
-
level multivariate analysis, d
ata mining, developing analytical software and web
-
based
relational databases, and data management. Hardware, software, and web and data management support services are
provided through our BioIT Team. We collaborate with a wide range of scientific and cl
inical projects which use
genomics, all forms of proteomics, metabolomics, kinomics, and systems biology in their research. Our efforts are
strongly focused on systems biology and signaling pathways with a special emphasis on the incorporation of clinical

data
into these analyses for greater translational impact. The BMI Bio
-
IT Team is responsible for EMR data extractions and
the i2b2 operation at UTMB. We have also added a substantial research effort in network visualization for analysis of
biomedical d
ata, with translation of the results to the design of decision
-
support systems and improving the computer/user
interface. We are finished the development of our Next Generation Sequencing (NGS) bioinformatics support core which
will go into full service l
ate spring 2011.

We are exceptionally well
-
equipped for computationally demanding projects. We recently added a dedicated Dell Linux
cluster with 17 state
-
of
-
the
-
art Intel Xeon 5650 nodes giving a total of 192 processors with 408 GB RAM running the
RedH
at Linux OS. This substantially improves our computational support for NGS bioinformatics as well as all other
computationally intensive efforts. We also have a Sun Microsystems SunFire 4800 server with 12 UltraSparc III 1050MHz
CPU and 24GB RAM as our d
ata mining server, as well as a number of unix and PC workstations for data analysis. Most
BMI faculty and staff also have a high
-
end Dell laptop for their personal use. We have nearly 50TB of disk space
contained within a highly
-
scaleable storage area n
etwork system (SAN). The SAN is a level 5 RAID hot
-
swappable disk
system with a robotic tape backup. The SAN, the Oracle RDBMS, and web services are controlled by a SunFire V880
server with 4x1050MHz CPU and 8GB of RAM. We have virtually every kind of p
eripheral equipment necessary for state
of the art BMI operations. We use Splus as our primary statistics engine, MatLab as our modeling engine, and Oracle 10g
as our primary RDBMS. MS SQLserver, MySQL, PHP, .NET, and SAS and R are also available and wid
ely used. Web
content is served via Apache and Tomcat, as is our locally
-
written GUI to the RDBMS. We are fully integrated over a 1
gigabit Ethernet LAN with full WiFi capability. For projects with computational demands beyond our capabilities we have
fu
ll access to the Texas Advanced Computing Center (TACC) at UT Austin. TACC is one of the largest and most
advanced HPC centers in the world.


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We routinely perform graphical 2 and 3D visualization of genomics and proteomics data, a wide range of univariate
and
multivariate statistical analyses, and various cluster and data reduction analyses. We have a number of site licenses for
important software suites such as MatLab (including the Bioinformatics Toolbox, SimuLink, and SimBiology), the
Affymetrix Microar
ray Suite 5.0/GCOS, and a number of concurrent licenses for the Ingenuity Pathways Analysis suite
with full access to their knowledge bases. We have licenses for several major proteomics packages including Nonlinear’s
Progenesis and Progenera, Genologic’s

Proteomics and Genomics LIMS, Ciphergen’s ProteinChip 3.2 with Biomarker
Wizard, Ciphergen Express 3.0 (CE) and Biomarker Patterns 4.0 for SELDI MS proteomics and biomarker discovery. We
have phylogeny programs including PAUP and BEAST. For classificati
on and biomarker discovery projects we have the
CART (Classification and Regression Trees), RandomForests and MARS (Multivariate Adaptive Regression Splines)
packages from Salford Systems as well as Support Vector Machines and other machine learning softwa
re. For NGS
bioinformatics analysis and data mining we have an increasingly large base of installed software on our Dell Linux cluster
including the state of the art CLC Genomics Server, CLC Genomics Workbench, and the CLC Bioinformatics database
from CLCb
io.



Biomedical Imaging Network

is a single institutionally
-
based cost recovery center that will provide the expertise and
resources needed to effectively integrate and utilize imaging sciences and technology with basic and tran
slational
research within UTMB and Texas.


Currently, the Biomedical Imaging Network will provide resources and services for two major areas: 1) optical microscopy
and cellular imaging and 2) small animal imaging. The optical Microscopy core is equipped w
ith a wide range of
instruments that can be used for advanced cellular imaging; live cell imaging and intravital optical microscopy. The
Animal Imaging core is equipped with Inveon Micro
-
PET
-
CT
-
SPECT imaging system; Visualsonics whole
-
body high
resolution

ultrasound imaging for small animals; high resolution optical endoscopy using in vivo fluorescence confocal
imaging and optical coherence tomography for small and large animal studies; and IVIS 200 bioluminescent and
fluorescence whole
-
body imaging workst
ation. The Biomedical Imaging Network is directed by Dr. Massoud Motamedi.
Dr. Gracie Vargas and Dr. Rinat Esenaliev are available to provide technical expertise for advanced optical microcopy and
ultrasound imaging, respectively.


The Optical Microscop
y and Cellular Imaging Core

assists with high
-
resolution imaging and analysis of specimens,
including those exposed to infectious agents and/or treated with toxic substances. Agents with infectivity can be accepted
up to biosafety level 2, and fixed specim
ens lacking infectivity will be accepted for any infectious agent authorized on the
UTMB campus. The OIC is equipped with a Zeiss LSM 510 UV META laser scanning confocal microscope, a large format
fluorescence microscope (Zeiss Axiophot 2) with attached hi
gh
-
resolution digital camera and a SLM 4800S life
-
time
spectrofluorometer. The confocal microscope includes: an Axiovert 200M microscope; dry, water
-
, and oil
-
immersion high
-
resolution objectives for fluorescence and Normarski differential interference con
trast observation; Ar, dual HeNe, and UV
lasers; fluorescence filter sets for DAPI, FITC, TRITC, INDO
-
1, and SNARF; a scanning module with visible and UV
acousto optical tunable filters, two independent fluorescence channels (2 PMTs), a 32
-
PMT array; and a

stage incubator.
This instrument is equipped for high
-
resolution detection of cellular and infectious agent
-
specific proteins and in particular
for monitoring changes in their volume distribution relative to changes in physiologic parameters. A high
-
speed

computer
(Dell 530 work station with dual 1.8 GHz xeon processors) work station with two monitors and software for physiology,
scan and 3
-
D imaging supports the image analysis activities within the OIC.


Optical Imaging Laboratory

has

d
igital imaging sys
tems that include confocal and wide
-
field optical microscopes:
last
generation
Zeiss LSM 510 confocal microscope and spectral imager,
capable of multicolor three dimensional fluorescence
imaging for colocalization; fluorescence resonance energy transfer (F
RET), and multispectral analysis

of single cells or
thick specimens.
An advanced semiautomatic wide field imaging system is
capable of quantitative time lapse studies
combining multiple microscopy modes simultaneously. The u
pright wide field imaging system

is equipped with color and
monochrome digital CCD cameras, ideal for studies of fixed samples using color bright field, phase contrast, DIC and
multicolor fluorescence.
Image processing and analysis:
The facility has 4 PC stations equipped with Metamorph

and
Image J imaging, and other graphical software.
Fully assisted or independent operation:
depending on user needs, we
provide complete support for microscopy sessions as well as image processing and analysis; however we also allow more
experienced users

to perform their own experiments

and observations. The lab is a
vailable 24 hours a day, 7 days a
week. Online services are available via
our website under “
support and customization.” Training, supervision and
consulting:
We offer training on microscopy a
nd digital imaging.
Other equipment and services are available u
pon request.
For example, we can install perfusion systems, temperature recording and control, micromanipulators and patch clamp
recording setups.




The Biomolecular Resource Facility (BRF)
,
A. Kurosky, Director, is a UTMB
-
designated core facility providing research
support targeted to the analysis of biomolecules, especially proteins and peptides. Originated in 1975, the facility has
grown consid
erably to meet the analytical needs of UTMB investigators. The BRF is composed of 7 core laboratories
whose services are briefly outlined below. A more complete description of BRF services can be found at

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www.utmb.edu/b
rf
.


The BRF overarching philosophy is to provide, at reasonable cost, biomedical researchers with a
relevant menu of analytical services that will enhance their funded research projects and the quality of their publications.
Importantly, the BRF puts con
siderable effort into obtaining major state
-
of
-
the
-
art instrumentation too expensive for
individual investigators. Researchers are encouraged to interact closely with BRF personnel to obtain maximum benefit of
services. User fees are minimal, compared with

other institutions, largely due to support from several UTMB centers, e.g.
NHLBI Proteomics Center, NIAID Clinical Proteomics Center, NIEHS Center, and the Sealy Center for Environmental
Health and Medicine. The BRF occupies 6,461 square feet, distributed

among 12 laboratories and 7 offices in the Basic
Science Building along with 588 square feet of three office suites on the 1
st

floor.


The current scientific staff includes 18
individuals (1 M.D./Ph.D., 8 PhD, 3 MS, 6 BS).



Biosynthesis & Biomarker Core



Services include

a) biosynthesis of recombinant proteins in bacteria or yeast
cultures; b) protein purification and characterization; and c) polyclonal antibody production.

Mass Spectrometry Core

-

Services are a) MALDI


TOF/TOF MS/MS analysis; b) ele
ctrospray ionization MS/MS
analysis, including liquid chromatography (LC/MS/MS); c) protein ID analysis; d) post
-
translational modification
identifications, and e) stable isotope methods (e.g. iTRAQ and
18

O).



Peptide Synthesis Core

-

Offers a) FMOC auto
mated solid phase synthesis; b) peptide purification, and c) peptide
mass analysis.

.

Protein Chemistry Core

-

Provides a) DNA sequencing; b) protein sequencing; c) amino acid analysis, and d)

carbohydrate analysis.


.

Proteomics Bioinformatics Core



Prov
ides a) nonlinear 2D gel analysis; b) Genologics LIMS for data/sample
management and access, and c) database searching.



Separations Technology Core



Provides a) HPLC analysis; b) 1D and 2D gel electrophoreses; c) fluorescence gel
staining and imaging, a
nd d) robotic gel spot picking and processing for MS analysis.






The Office of Biostatistics (OBIOS)

provides statistical support services to all faculty at UTMB, including designing
studies that minimize the effects of measurement and experimental error, identifying appropriate methods for data
analysis based on st
atistically sound designs, producing power calculations, and determining sample. OBIOS uses the
computer packages such as NCSS
®

and SAS, statistical applications with extensive data management capabilities.


Adaptation and development in
clude quanti
tati
ve research

that will produce im
proved methods and procedures to analyze
and interpret biomed
i
cal data.


This usually occurs during a long
-
term collabo
ration between a UTMB research
er and a
member of the Office of Biostatistics.


Special services are
available to assist with the conceptualization, formulation, design, and use of data gathering tools.






The Environmental Exposure Facility

provides state
-
of
-
the
-
art capabilities for conducting exposures of experimental
animals

and
in vitro

models to gas phase environmental toxicants.


A service core of the UTMB Sealy Center for
Environmental Health and Medicine, it supports all UTMB investigators and students on a fee
-
for
-
service basis.


In
addition, the facility provides a fou
ndation for inter
-
institution collaborative investigations.


The facility is housed in an 800
square foot, three
-
room suite. In addition to a room for exposure chambers, an animal housing room and a room for
conducting in
-
vitro exposure of cells in culture

make up the facility. Four 0.8 M
3

stainless steel Hinnars
-
type exposure
chambers are available for exposure of small laboratory animals to low concentrations of gas phase chemicals. The
facility is equipped for studies using organic chemical vapors, ozone

or nitrogen dioxide. The chambers receive filtered,
air
-
conditioned, building air at a rate of 30 chamber changes per hour. Regulation of gas concentration is accomplished
using mass flow controllers. Organic vapor concentrations are monitored by gas chro
matography. Concentrations of
ozone or nitrogen dioxide are determined by dedicated gas monitors. The suite is maintained under negative pressure
relative to the surrounding building spaces to insure that any exchange of air is from the building into the f
acility, which
also has safety interlocks that shut down gas and air flow in the event of a power interruption or if a smoke detector is
triggered. The in vitro exposure facility uses similar equipment to deliver gases to small glass chambers placed on til
t
tables in cell culture incubators.




The Flow Cytometry Core Facility

in the Department of Microbiology and Immunology
is located in the Medical
Research Building room 3.159. It is directed by Dr. Jiaren Sun, Associate Professo
r in the Department. Its daily operation
is managed by Mark Griffin and assisted by Dr. Lifei Hou. Mark is an expert in flow cytometry and cell sorting with many
years of experience. Lifei is a talented immunologist, highly competent in experimental design
, instrumentation, data
analysis, and assay development.

The facility is equipped with one high
-
speed cell sorter as well as three analyzers suitable for various tasks and levels of
user friendliness. The BD
LSRFortessa

and
FacsCanto

are advanced analyzers

that can detect 18 and 6 colors,
respectively. The
Fortessa

offers automatic sample loading with a 96 well plate reader that allows for walk
-
away use. The
Canto

has a carousel loader with similar convenience features. The third analyzer,
Accuri C6
, is cap
able of detecting 4

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colors, and is particularly user friendly. All analyzers are available to independent users with 24/7 access. Users can
acquire necessary hands
-
on skills either through formal or informal training or attending one of our training sessio
ns (to be
announced later). The BD
FacsAria

is available to users as an operator
-
assisted sorter, which can separate cells into
tubes, plates, or slides at high speed. Direct cloning of sorted cells into tissue culture plates is also possible under asep
tic

conditions. In addition to its cell sorting functionality, it is capable of 9
-
color analysis in its present configuration.

The flow lab can also provide assistance with protocol development and implementation, as well as data analysis and
presentation. Th
e data from the
Aria, Fortessa
and

Canto

are available campus
-
wide over the university's intranet for 1
month, such that investigators may analyze and store data in their own labs. For scheduling work, users may email
flow.cytometry@utmb.edu

or call 409
-
747
-
2011. The operator’s assistance is available 9
-
5 daily. A schedule with
instrument availability is kept on
http://microbiology.utmb.edu/core/flowcore

fo
r user planning and service reservation. The
Accuri C6

is for users requiring no assistance available on a first
-
come first
-
served basis.




The Institute for Translational Sciences (ITS) and the Clinical and Translational Scienc
e Award (CTSA)

The ITS and its collaborators work to enhance the scope of translational research at UTMB by creating an environment for
rapid translation of basic research into diagnosis, treatment and prevention of disease and to facilitate the full spect
rum of
translational research, from T1 (bench to bedside) through T4 (community research, outcomes, adoption of best
practices).

The ITS is the academic home of UTMB’s CTSA, designed to facilitate translational research as a rigorous discipline,
develop
translational research training programs, conduct early phase translational research and extend translation to
later phases, and interface with a national consortium of CTSA institutions. We have organized our CTSA as 12 “Key
Resources”, aggregations of e
stablished university core laboratories and existing and new intellectual resources.

Because of their importance to translational research, several of UTMB’s core laboratories and centers of excellence are
administered in partnership with the ITS and CTSA.

These include the: Sealy Center for Molecular Medicine, General
Clinical Research Center, Bioinformatics Program, Recombinant DNA Laboratory, and Biomolecular Resource Facility.

Coordinating Core:

Assists in addressing logistical, administrative and comm
unications barriers to conducting
multidisciplinary, team
-
based research.



Serves as a single point of contact for investigators and trainees interested in translational research



Facilitates communication among multidisciplinary translational teams (MTTs)
and CTSA Key Resources



Maintains a pool of study coordinators



Communicates the availability, significance and results of trials

Novel Methodologies:

Helps inv
estigators develop novel research approaches and enables use of tools and technologies
for solvi
ng human health problems.



Facilitates integration of advanced imaging techniques for diagnosing disease and for monitoring the safety and
efficacy of new therapeutic interventions



Builds and deploys infrastructure for image acquisition, image analysis, vis
ualization & data management
software tools



Leads the “Catalysts for Innovation Leadership Council”.



Awards pilot funding for new methodologies that accelerate translational research and product development

Pilot and Collaborative Studies:

Supports pilot
projects, projects involving novel methodologies and collaborative studies
that will have a significant impact on clinical and translational research.



Provides financial support for multidisciplinary teams, individual investigators and trainees engaged in

translational research



Supports the creation of new research teams by funding projects to collect preliminary data leading to
independent funding at the equivalent of an R01 level or higher

Translational Technologies and Resources:

Facilitates acquisit
ion, understanding and the use of technologies that enable
effective translational research.



Provides expertise in sample collection, handling and processing to ensure high quality clinical data outcomes



Ensures that data is accurately managed and transla
ted



Facilitates use of standard protocols



Provides access to biorepository



Provides access to the Biomolecular Resource Facility



Assists with technology acquisition, development, data analysis, and quality assurance

Biomedical Informatics:

Provides a mul
ti
-
investigator, multi
-
institutional environment for sharing biomedical data and
establishing a deep data
-
mining collaborative infrastructure.



Provides tools and personnel to significantly improve your ability to capture and analyze data efficiently,
effe
ctively and securely


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Ensures innovation in data collection and analysis



Provides expertise in deep data mining which enables improved IP discovery



Provides clinical informatics expertise to facilitate significant new innovations

Biostatistics, Epidemiolo
gy and Research Design:
Works with investigators to enhance the efficiency and quality of
research by providing integrated statistical support. By proactively engaging in the research development process, we
help clinical and translational investigators in

research design and analysis.



Provides expertise in biostatistics, epidemiology and research design



Facilitates web
-
based collection of data to capture costs and outcomes to assure estimation of efficiency (T3)



Provides a link to the Medical Bioinformatic
s system and EMR



Improves the design and implementation of evaluation



Provides integrated study statistical analysis and sample size planning



Ensures variance minimization



Increases understanding of the impact of common cause variation.

Regulatory Knowledg
e and Support.
Expedites implementation of your research by helping you navigate the complex
regulatory environment. Our services and tools are comprehensive and researcher
-
focused and are designed to remove
institutional impediments to research.



Identif
ies and disseminates best practices and system improvements for regulatory management and compliance



Assures compliance, so that data can be used for publications, FDA applications, etc…



Protects the integrity of your research



Develops study
-
specific SOPs



Completes and manages IND applications



Facilitates translation of informed consent documents into Spanish



Registers studies at: www.clinicaltrials.gov



Complete IRB documents



Assures adherence to Data Safety Monitoring Plans / Boards

Clinical Research Ce
nter:

Provides modern equipment and experienced personnel to support your inpatient and
outpatient studies.



Offers training in clinical research



Assists with subject recruitment



Provides access to multiple clinical research sites



Hosts outpatient and in
patient stays



Schedules patients



Provides nursing and dietary support



Collects blood, saliva and tissue samples



Provides access to a metabolic kitchen and metabolic cart



Provides access to underwater weighing, exercise equipment, and DEXA imaging

Commun
ity Engagement and Research:

A
dvances population
-
based translation of science by establishing and
maintaining infrastructure to represent community interests among prospective researcher partners. We can also support
your linkages to community partners, a
nd coordinate use of relevant community assets.



Provides education in the principles of Community
-
Based Participatory Research (CBPR)



Maintains and coordinates a multidisciplinary Practice
-
Based Research Network



Facilitates relationships with community par
tners interested in participating in research opportunities



Familiarizes research teams with the work of other researchers or clinicians working with community groups



Identifies opportunities for collaboration



Disseminates the results of research to public

health and policy
-
making entities as well as community groups



Assists with preparation of NIH proposals that require community engagement components

Research Education, Training and Career Development:
Enhances trainee quality and productivity by develop
ing and
integrating activities and programs at many levels. Our goal is to support biomedical scientists with the skills to become
productive members of MTTs.



Identifies and recruits qualified students and trainees at the doctoral and postdoctoral level (
MD and PhD) and
provides them with research experiences and curricula for developing skills in translational and clinical research



Implements the ITS Translational Scholars program, to help faculty establish careers in interdisciplinary
translational and c
linical research

Ethics and Support:

Provides expertise and education in research ethics and research integrity and assists in developing
ethically sound protocols and practices that enhance subject safety and rights.



Integrates knowledge of best practic
es and engage teams in discussion of ethical issues



Increases understanding of emerging issues (e.g., incidental findings, specimen storage, re
-
identification of data,
etc.)



Ensures that your research respects the autonomy of study participants


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Assesses t
he risks and benefits of your research



Helps researchers explore the social value of their research



Helps researchers avoid the therapeutic misconception in the informed consent process



Enhances privacy and confidentiality in data registries



Assists with

protocol design, consent, and recruitment



Facilitates IRB approval process



Assists with problem
-
solving and conflict
-
resolution



Deepens partnerships between ethics and science



Maintains focus on beneficial health outcomes



Provides advice on research integ
rity

Tracking and Evaluation:

Assists researchers by providing training in program evaluation and team building



Develops evaluation processes



Enhances the tracking of team progress



Clarifies challenges and growth opportunities related to team development




The Research Histopathology Core (RHC)

occupies 2800 square feet of laboratory space in the Basic Science Building,
and provides analytical morphology related services to the research teams and educational programs at UTMB. Th
e
facility is equipped with the latest available instrumentation and operated by highly skilled personnel, who can assist with
tissue preparation, Immunohistochemistry including assay optimization, image analysis, digital photomicrography,
anatomical consu
ltation, and
Insitu

Hybridization. RHC provides an expanded service including coordinated
histopathology support services or develop special protocols to fit your research needs for investigators engaged in
research in emerging diseases. We look forward to

providing these services to fit your research needs and yield high
quality results.





Research Technology Support (RTS)
r
epairs and maintains laboratory equipment,
such as centrifuges, incubators,
physiological monitors, scales
, microscopes, etc. RTS also provides preventive maintenance and electrical safety
inspections. Through the c
omplete machine shop, with CNC capabilities, RTS also works with investigators to
fabricate
structures in Lexan, Plexiglas, standard and exotic met
als for specialized research needs.




The Rodent
In Vivo

Assessment (RIVA) Core

was established by the Center for Addiction Research to facilitate the
advancement of interdisciplinary and translation research on and off
-
campus.


We provide rodent models for analyses of
new transgenic mice

and rats, as well as a wide variety of

research tools ideal for drug discovery and evaluation of
chemical entities for therapeutic potential.


Our facilities include 12 behavioral procedure rooms equipped with state
-
of
-
the
-
art computer driven data collect
ion
apparati, three animal holding facilities and a surgical suite. Multiple assays are available, and can be adapted to many
questions. Services range from consultation and training to study design, execution, data analysis and interpretation. For
researc
hers interested in a more hands
-
on approach, we will provide appropriate orientation and training, leaving the data
collection to individual lab personnel with minimal supervision. For those preferring a less
-
involved approach, studies may
be arranged to b
e performed by RIVA personnel. We are a fee
-
for
-
service facility and will gladly provide a quote for any
level of service.






Sealy Center for Cancer Cell Biology

Cores


The Transgenic Mouse Core Facility (TMCF)
was established as a university core in 1996. It is the sole core facility
that specializes in the generation, maintenance and preservati
on of genetically engineered mice in UTMB. To date, the
TMCF generated over 80 strains of genetically engineered mice. The TMCF is supported by user cost
-
sharing, grants
funding individual investigators, and several departments including the Comprehensiv
e Cancer Center, Department of
Neurology, Department of Biochemistry and Molecular Biology, Department of Neuroscience and Cell Biology, the Mitchell
Center for Alzheimer’s disease, and Research Services.


The mission of the TMCF is to provide comprehensi
ve and flexible support to investigators who engage in genetically
engineered mouse model research, and to facilitate the growth of the mouse research and translational research in the
UTMB.



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The TMCF is available for use by all UTMB scientists. We can pr
ovide guidance and technical support at all stages of the
development of genetically engineered mouse models. We can serve as a mentor of your student, your collaborator, or
your hand.




Nude
Mouse Laboratory

was established in 1983 to serve UTMB investigators interested in establishing human cancer
xenograft lines and studying the effects of various agents on tumor growth in an
in vivo

model.


Because tumors generally
maintain their h
istology and human karyotype and because human drug sensitivity or resistance are stable when tumors
are transplanted to the nude mouse, the laboratory both enhances and promotes research related to human cancerous
tissue.


In addition, it enables investig
ators to apply for grants and contracts related to human cancer research, many of
which specifically require experimentation on nude mice.


The establishment of uncommon cancers can be facilitated by
transplantation into the nude mouse.


Finally, various a
gents and drug delivery systems may be tested using this
in vivo

model.



Specific objectives are to: assess specific therapies and drug delivery systems on the growth of different human cancers
in nude mice; provide source materials for human tumors; use
the T
-
cell
-
deficient nude mouse for immunological studies;
provide an immunocompromised
in vivo

model; assess developmental growth and gene expression of normal tissues
from other species; and facilitate the establishment of uncommon tumors resected from p
atients


Many colorectal, gastric and pancreatic cancer xenograft lines have been established and are available for analysis and
experimentation.


In addition, novel human endocrine cancers have been established that represent, in some instances,
one
-
of
-
a
-
kind tumor models.


The majority of tumors are transplanted to the subcutaneous tissue of the back or flank.


This allows for ease of analysis and measurement.


Further, tumor models are available that involve implantation into the
abdomen and mimic human
metastatic cancers with metastasis to the liver or other organs.


Injection of test agents can
be achieved by the oral, subcutaneous, intraperitoneal or intravenous routes.


Novel methods of drug delivery may be
relatively easily assessed using nude mice.




Real
-
Time PCR Core Facility

offers a full complement of real
-
time PCR (polymerase chain reaction) services including
primer and probe design and order, preparation of real
-
time PCR reactions, and data analyses for gene expression (DNA
and RNA samples)
, as well as allelic discrimination. The PCR core facility has the following major equipment available:
Applied Biosystems (ABI) PRISM 7000 sequence detector with a Dell Pentium III laptop computer; a Dell Pentium IV
desktop computer installed with the ABI

PRISM 7000 SDS (sequence detection system), PrimerExpress and file builder
software.





The UTMB Tumor Bank

is housed in the Sealy Center for Cancer Cell Biology as part of our efforts to facilitate cancer
research at UTMB. Collection of tumor tissues is a collaboration of the SCCB and the Division of Surgical Pathology. This
bank contai
ns >2,000 different specimens of various tumor
-
types, The Human Tumor Bank Core provides tissues for
cancer
-
related research approved by the Institutional Review Board (IRB) and the Biological Safety Committee for using
biohazard materials. In addition, th
is service promotes material
-
sharing and provides assistance on cancer tissue
-
related
research.





The Biostatistics Shared Resource (BSR) Facility

operates under the auspices of the UTMB Cancer Center. The BSR
serves as a centralized resource for comprehensive and high
-
quality statistical support to all aspects of cancer research,
including basic
science, translational research and clinical studies.

The Cancer Center’s BSR Facility provides the following services to cancer researchers:



Study design and determination of sample size to optimize resource utilization



Planning of
in vitro
,
in vivo

stud
ies of animal cancer models and translational studies



Design and oversight of clinical trials



Monitoring of safety/toxicity and efficacy parameters in clinical trials



Development of database and information management systems



Generation of interim stat
istical reports



Application of innovative statistical methodology in cancer research



Analysis and interpretation of final statistical data



Training and teaching through cancer specific programs at UTMB





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The Oncology Clinica
l Trials Office (OCTO)

serves as a full service, multidisciplinary resource for University
investigators and clinical study sponsors who are committed to performing the highest quality clinical studies. OCTO is a
resource that provides the necessary tools
and expertise for conducting innovative and safe clinical trial research in
compliance with required federal guidelines. The OCTO mission is to:




Facilitate patient access to oncology clinical trials by providing up to date information about ongoing clinic
al
research at UTMB



Support investigators in every aspect of oncology clinical trials research, including protocol development and
review, contract execution, financial accounting, budget negotiations, compliance reporting and trial
maintenance



Serve as li
aison between PI’s and clinical sponsors





Sealy Center for Molecular Medicine Cores




The

Molecular Genomics (MG) Core Laboratory

provides services, technical support and advice to UTMB
investigators in the area of genomic analysis. The MG Core provides gene expression analysis through the use

of
Affymetrix gene chips and real time arrays, SNP analysis (both association
-
based studies and discrimination
assays), real time quantitative RT
-
PCR, miRNA analysis, DNA sequence analysis and high resolution melt
analysis.







The

Recombinant DNA Laborat
ory

provides UTMB investigators with a variety of essential services and
technical support in the area of recombinant DNA techniques.


Services include the production of plasmid DNA,
transformation and screening of recombinant plasmids, bacterial expressio
n, site directed mutagenesis,
construction of transgenic and null gene plasmids and various PCR based technologies.





The Sealy Center for Structural Biology & Molecular Biophysics (SCSB) Research Laboratories


The
SCSB

Researc
h Laboratories

aid scientists interested in elucidating the basic relationships between
macromolecular sequence, structure and function, with a goal of leveraging this information into the understanding and
treatment of disease. The basic research within S
CSB combines thermodynamic, kinetic and structural data about
biomolecules and their complexes to understand important biomedical processes. The structural and dynamical basis for
molecular recognition, signal transduction, protein folding and allosteric r
egulation is studied by X
-
ray crystallographic
<
http://scsb.utmb.edu/facilities/xray.htm
> , nuclear magnetic resonance, <
http://scsb.utmb.edu/facili
ties/nmr.htm
>

and
cryo
-
electron microscopic <
http://scsb.utmb.edu/facilities/cryoem.htm
>

techniques, advanced computational tools,
<
http://scsb.
utmb.edu/facilities/cb.htm
>

and solution thermodynamics <
http://scsb.utmb.edu/facilities/thermo.htm
> .


The SCSB Research Laboratories are Research Cores requiring serious time investment by resear
chers. Accordingly,
each Laboratory offers training in use of instrumentation, software and
experimental
design, along with workshops on
specific topics.

Graduate students and post docs may take the instruction provided by
SCSB
in conjunction with
academi
c courses in NMR
, X
-
ray Crystallography, CryoEM, or Molecular Biophysics

offered
by SCSB faculty
through the
GSBS. Unless researchers have the appropriate expertise in their own laboratories most projects will require the expertise
provided by collaboratin
g with the Center, either
with
a
SCSB f
aculty member or one of the
Laboratory

managers.

To
initiate a research project in the Center please contact
a SCSB faculty member
, the
specific Laboratory

manager
,
or the
Center Director, Wayne Bolen.





The Computational Biology Research Laboratory
in SCSB provides modern computational resources to researchers
and to students who are in need of large
-
scale computing power. The power house of the
Laboratory

is a 30 processor
Linux cluster, which provides parallel
-
processing capabilities with a total of 84 billions floating point operations per second,
42 GB of memory and 1.6 TB of storage space. The cluster also provides centralized file
-
server capabilities as well as a
tape l
ibrary with 400 GB of storage space to archive and secure data. Peripheral devices include a scanner, B&W and
color printers, plus tape drives. All computing resources are connected to the UTMB network, and thus other workstations
within the campus can eas
ily access the resources of the
Laboratory
. An account request form is available online
<
mailto:tdpower@utmb.edu?subject=SCSB%20Cluster%20Account%20Request
>.

(Manager, David P
ower)


The Cryo Electron Microscopy Research Laboratory
, on the first floor of the Medical Research Building, has laboratory

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11


space featuring a BSL
-
3 room for viral and pathogen work. The Laboratory has three JEOL cryo
-
electron microscopes,
used for imaging

of macromolecular complexes, cell organelles and other biological systems. The high
-
resolution
JEM2200FS is located in the BSL
-
3 facility and permits structural imaging of pathogens. Unique to the core is the W. M.
Keck Center for virus imaging with BSL
-
3

containment, the only cryo
-
EM facility in the U.S. designed for high
-
resolution
structural studies of wild type infectious agents. The JEM2100 is available for imaging of non
-
pathogenic targets. A lower
resolution JEM1400 microscope is available for preli
minary screening.

Image data are stored in a local database that is
archived remotely. Microscope scheduling, for qualified users, is available online.




The NMR Spectroscopy Research Laboratory.
L
ocated in its own two
-
story bu
ilding (Bldg. 73) at the Universit
y of
Texas Medical Branch the SCSB NMR Research Laboratory
includes
a
state
-
of
-
the
-
art high field Varian VNMR system
800MHz (with a HCN Cold Probe),
a
VNMR system 750MHz
,

and

an

Inova 600 MHz NMR spectrometer
with 31P NMR
capability. Both

the 800 and 750 MHz instruments are capable of HCN triple
-
resonance experiments with 2H decoupling.
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool in studies involving structural biology, proteomics,
metabolomics, metabon
omics, nutrition, toxicology, analysis of biological fluids, functional genomics, structure/activity
relationship, drug discovery and development, macromolecule structure/function analysis and small molecule structural
analysis.

The NMR techniques used i
n such studies include: relaxation measurements, chemical shift mapping,
hydrogen exchange, conformational exchange, transfer NOE, Saturation Transfer Difference(STD), dynamics and 3D
solution structure determination. Spectrometer scheduling, for quali
fied

users,is available online.





The Solutions Biophysics Research Laboratory
, located on the fifth floor of MRB,

is equipped with a Beckman
Analytical Ultracentrifuge XL
-
A to monitor the hydrodynamic properties of biomacromolecule
s and protein
-
protein
interactions, a GE Health Sciences' Biacore T100 SPR high
-
throughput system for measuring the kinetics of protein
-
protein and protein
-
ligand interactions, a Johnson and Johnson ThermoFluor, high
-
throughput ligand screening system for
the discovery of protein
-
ligand interactions, a MALDI Mass Spectrometer for use in monitoring the quality of
biomacromolecules samples, a MicroCal Isothermal Titration Microcalorimeter, and various spectroscopic instruments.

High throughput analyses are f
acilitated by an epMotion 5075 Solution Robot for sample preparation. Solution biophysics
and thermodynamics techniques are used both as primary research tools and to guide structural studies.




X
-
ray Crystallography Laboratory

in the SCSB provides complete facilities for crystallization studies of macromolecules.

The
Laboratory

houses a Rigaku Crystalmation® robotics system, consisting of an Alchemist
-
II for preparation of crystal
screens, a PHOENIX, for fast reliable and effic
ient screening of crystallization conditions, and a DT Minstrel/Gallery 160
for automated imaging of crystallization trays. Two x
-
ray area detector systems are available for the collection of X
-
ray
diffraction data, each with an ultra
-
fine
-
focus high
-
brill
iancy x
-
ray generator and focusing multilayer optics. These are
suitable for protein crystals from 50 microns in size with cell dimensions up to 400 Å and are equipped cryogenic sample
cooling systems.

The Crystallographic Computation Lab provides high
-
pe
rformance Linux stereographics workstations for
crystallographic structure solution, refinement, and analysis or CryoEM reconstructions.

Diffractometer and robotics
scheduling, for qualified users, is available online.




Sealy Center for Environmental Health and Medicine (SCEHM)

The Synthetic Organic Chemistry Core

provides an on
-
site, cost
-
efficient, full
-
service, chemical synthesis facility to
synthesize defined DNA lesions, bioconjugates an
d small organic molecules that are unavailable or commercially
expensive.


The SOCC is part of the SCEHM and the NIEHS CET at UTMB and has been in operation since March 1998.


Since then it has synthesized more than 800 different organic synthesis products

for a number of researchers and
research cores on and off campus.


SOCC synthesis projects include modified nucleosides and oligonucleotides, metal
chelators, steroid analogs, modified peptides, enzyme substrates and inhibitors, bioconjugates, as well as
hard to find
organic analytical standards and reagents. The lab is a shared chemical synthesis facility also open to researchers who
need assistance with chemical syntheses, wish to use the lab’s resources, or need technical supervision and/or training of
technicians on research synthesis projects.


The 1200 sq ft lab, located in room 2.130 of Ewing Hall, houses equipment
for multi
-
step organic chemical syntheses from mg to 100g scales, modified DNA syntheses, HPLC analyses and
purification, photochemical r
eactions, flash chromatography, rotary evaporation, distillations, sublimations, titrations,
temperature controlled and high pressure reactions.





The Tissue Culture Core Facility
is a division of the Department of Microbiology
and Immunology. The core supports
UTMB investigators in a time
-

and cost
-
efficient manner. The facility provides products for tissue culture, molecular
biology, and immunology research from multiple vendors. Other services include heat in
-
activation of ser
um, mycoplasma
detection and eradication, tissue culturing, and cryogenic preservation and repository of cells.






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RESTRICTED CORES


The Galveston National Laboratory (GNL)


The Galveston National Laboratory (GNL) is an academic research center at the University of Texas Medical Branch in
Galveston, Texas.


Utilizing the unique resources of its BSL2, 3 and 4 labora
tories, the GNL’s renowned scientists work
collaboratively, both locally and internationally, tackling some of the world’s most pressing health concerns.


With
strengths in aerobiology, assay development, experimental pathology, imaging, immunology, insect
ary services and
preclinical studies, the GNL advances local discoveries on the diagnostic tests, treatments and vaccines for the infectious
diseases impacting global health like tuberculosis, SARS virus, West Nile virus, Ebola, Marburg, Plague, encephalit
is,
influenza and a host of others. The GNL was funded in part by the National Institutes of Health (NIH)/National Institute of

Allergy and Infectious Disease (NIAID) and serves as a national resource in support of NIAID’s biodefense and emerging
infecti
ous diseases research agenda standing ready to assist local, state and national public health efforts in the event of
a public health emergency.




The GNL and adjacent facilities offer more than 14,000 square feet of BSL4 space, over 29,000 square feet of BSL3
facilities and nearly 52,000 square feet of BSL2 facilities.


These facilities include typical lab spaces as well as animal
biosafety lab
space (ABSL), insectaries and aerobiology facilities.


UTMB is a registered select agent facility for CDC,
USDA and overlap agents.



The GNL’s mission is fulfilled through a system of specialized services available to researchers in biodefense and
emergin
g infectious diseases via the following Service Divisions:



Aerobiology:

The Aerobiology Services Division offers aerosolization capabilities to researchers examining BSL3
and BSL4 level bacteria and viruses via inhalational exposure. This division uses sp
ecialized equipment to
expose models to various pathogens including select agents such as anthrax, plague and Venezuelan equine
encephalitis, to allow examination of disease mechanisms and to evaluate the efficacy of potential
countermeasures.






Assay De
velopment:

The Assay Development Services Division provides assay development and drug
screening for identification of new therapeutics for researchers who study select or emerging disease agents.
Division personnel generate assays that are standardized,
reproducible and useful in medium
-

to high
-

throughput
screening. While the emphasis is on developing low
-
containment BSL2 assays, the division also designs and
tests assays suitable for BSL3 and BSL4 containment.





Experimental Pathology:

The Experimenta
l Pathology (EP) Services Division features support for tissue
-
based
studies and tissue culture needs of researchers.


EP offers routine histopathological services (tissue processing,
microtomy, cryotomy, cytospin and smear preparation, routine and special

histochemical staining),
immunohistochemistry, immunofluorescence, and
in situ
hybridization analyses.


EP Division staff provide expert
assistance in staining and tissue preparation for advanced microscopy studies (confocal or two photon
microscopy) in c
onjunction with the Imaging Services Division.


Facilities for light microscopy, digital
photomicrography, image analysis, fluorescence microscopy, and laser capture microdissection are available.


The unit’s Tissue Culture Core facility also exists as a s
ource of scientific supplies, such as media, sera and
enzymes, and serves as a safety
-
compliant shipping and receiving unit. In addition, tissue
-
based diagnostic and
etiological assessments from EP experts are available to public health entities in the eve
nt of disease outbreaks.





Imaging:

The state
-
of
-
the
-
art Imaging Services Division provides advanced optical analysis for
in vivo
whole
-
animal studies and tissue specimens at BSL2,
-
3 and
-
4 biocontainment levels.


The unit offers combined
confocal and m
ultiphoton microscopy imaging systems at the BSL2 and BSL3 levels for molecular imaging and
microscopy, an IVIS 200 system for
in vivo
small animal molecular optical imaging, a micro PET/CT whole
-
animal
imaging system, digital X
-
ray, and ultrasound equipme
nt. Also available are a full complement of gel
-
imaging
capabilities, as well as traditional X
-
ray services.




Immunology:

Immunology Support Services Division capabilities include the generation and maintenance of
knockout and transgenic mouse models fo
r immunological examinations of select and emerging disease agents.
In addition, the Division develops, from these models, primary cell lines for use in
in vitro
experiments and
provides experimental surgery services and production of human monoclonal anti
bodies.





Insectaries Services:

The Insectaries Services Division (IS) provides expert consultation and state
-
of
-
the
-
art
equipment for research into arthropod
-
borne biothreat agents and emerging infectious diseases. IS facilitates
research by biodefense

investigators who require high and maximum containment for studies with arthropod
vectors by either providing expertise and/or training for the researchers’ personnel. In addition to mosquito and
tick rearing in Arthropod Containment Level two (ACL2) faci
lities, specialized resources and equipment located
within ACL3 facilities include, membrane feeding systems, intrathoracic inoculation apparatus, chill tables,
environmental chambers, trituration apparatus, containment glove
-
boxes, microscopy and imaging
capabilities.


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Preclinical Studies:

The Preclinical Studies Services Division supports testing of vaccines, diagnostics and
therapeutics against challenges from biodefense and/or emerging disease agents. Division expertise includes
surgical implantation

of telemetric devices, as well as conducting laparoscopic, endoscopic and ultrasound
-
guided
tissue biopsies. The division’s aim is to provide real
-
time data with minimally invasive techniques. The division
accesses, as appropriate, the GNL’s other service
s, such as the animal support unit, which has facilities for both
small animals and non
-
human primates, and the services of the Aerobiology Services Division.




The services and specialized equipment these Divisions provide, amon
g others, include:



aerosolization studies of BSL
-
3 and
-
4 level pathogens in small animals and non
-
human primates;



animal model development;



host
-
pathogen studies;



vaccine, diagnostics and therapeutics testing;



screening methodology development through

in vitro

studies;



technical assistance in histological and tissue processing methods;



diagnostic expertise in the event of disease outbreaks or bioterrorism,



protocol development against arthropod vectors;



imaging expertise in the analysis of human an
d animal tissues and
in vivo

whole
-
animal imaging specialized
imaging equipment, including combined confocal and multiphoton microscopy imaging systems at the BSL
-
2 and
BSL
-
3 levels;



IVIS 200 system for
in vivo

small animal molecular optical imaging;



mic
roPET/CT whole animal imaging system;



digital X
-
ray and ultrasound equipment;



a full complement of gel imaging capabilities as well as a traditional X
-
ray film processing



a full
-
service immunology core capable of developing knockout and transgenic mouse
models for immunological
studies.





GLP study oversight



full
-
service animal care procedural and maintenance facilities



a Tecan robotic liquid handling system and other robotics instruments for assay development



a full complement of thermal cyclers, includ
ing RT
-
PCR machines, a BSL4 level flow cytometer and a BSL3 level
fluorescence activated cell sorter.


There is also a fully equipped histopathology suite, ultra
-
, super
-
, and low
-
speed centrifuges; and glassware washing and sterilization equipment and aer
osol challenge facilities allowing
the safe study of inhaled viral and bacterial pathogens via Madison chamber units and equipment capable of
facilitating nose
-
only exposure.

The University has an existing safety program that is in accordance with appropr
iate federal, state, and local regulations
for research performed safely under BSL2, BSL3 and BSL4 laboratory conditions.
UTMB is also home to the
The
National Biocontainment Training Center

which prepares infectious disease scientists to work safely in hi
gh and
maximum
-
containment environments.


Through extensive one
-
on
-
one, customized didactic training, practical
demonstration and mentored experience in the lab environment, the NBTC’s Laboratory Biosafety Training Program
provides laboratory and support s
taff training in BSL2 to 4 laboratory biosafety.


The NBTC also offers parallel fellowship
tracks for scientists and biocontainment engineers, affording individuals the unique opportunity to gain valuable
knowledge and experience working in BSL3 and BSL4 l
aboratory environments.





The NIEHS Center Cell Biology Core

(CBC), an established National Institute for Environmental Health Sciences
(NIEHS) Center Service Core at UTMB, developed an infrastructure of core services for member
s of the NIEHS Center
Research Cores. This core is dedicated to the development and delivery of state
-
of
-
the
-
art methods and technologies in
cell biology to assist Center investigators in their mission. The wide range of diseases studied includes cancer, d
rug
abuse, behavioral disorders, chronic inflammatory lung diseases, aging and age
-
associated diseases. Related research
ranges from studies of molecules (damaged DNA, DNA repair proteins, transcription factors, drug metabolizing enzymes)
and cells to thos
e of whole animals and human populations. The core supports investigators from the Departments of
Biochemistry and Molecular Biology, Pharmacology and Toxicology, Microbiology and Immunology, and the Sealy Center
for Molecular Sciences. In addition to stat
e
-
of
-
the
-
art equipment and methods, the key personnel of this core provide
scientific and technical expertise that greatly benefits investigators in terms of experimental design, execution and
interpretation. A particular strength of this core is to serve
as an integrating umbrella to foster collaborative arrangements
that cross departmental boundaries, and to facilitate productive interactions between basic and applied environmental
sciences.





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Pepper Center Cores

Claude D. Pep
per Older Americans Independence Center


Overview:

The focus of the UTMB Pepper OAIC through its first two funding cycles (2000
-
10) has been on age
-
related sarcopenia
and its contribution to loss of independence in older persons. The theme for the
current

cycle (2010
-
15) is ‘Translating
Biological Mechanisms of Muscle Growth and Loss to Improve Function and Recovery in Older Adults.’

The aims of the Pepper OAIC are to:

1)

Provide core support to funded translational research by UTMB investigators on muscle f
unction and functional
recovery from i
llness in older adults

2)

Stimulate the growth of additional interdisciplinary translational research projects to improve muscle function and
functional recovery from illness in older adults by funding pilot project resea
rch to generate preliminary data in
promising new areas of investigation and funding developmental projects to develop innovative technologies;

3)

Train future leaders in research in the mechanisms, prevention and treatment of muscle dysfunction and disabili
ty
in older adults;

4)

4) Recruit established investigators with expertise relevant to muscle function and functional recovery in older
adults into interdisciplinary translational rese
arch related to the OAIC focus.

5)

5) Foster collaborations between UTMB inves
tigators and investigators at other OAICs and other institutions on
studies of muscle function and functional recovery in older adults.


T
he Center focuses on translating basic discoveries on the mechanisms of muscle loss and re
-
growth with aging to
clini
cal practice to promote functional recovery and prevent disability in older adults. Observational studies will provide
crucial information for selection of appropriate in
-
hospital, post
-
discharge, and long
-
term outcomes for inclusion in clinical
trials of
geriatric patient populations.


T
he UTMB OAIC
goal is to

identify predictors of physical function and recovery from illness in hospitalized geriatric
patients, identify potential treatments to improve function and accelerate recovery, determine the effica
cy of the identified
treatments in clinical trials in geriatric patients, and Increase the number of junior and senior investigators involved in
geriatric research.


UTMB’s OAIC, is
directed by

Elena Volpi, MD, PhD
.

Dr. James Goodwi
n is the co
-
director
. F
or more information on the
current UTMB OAIC, please visit the Pepper website at:
http://www.utmb.edu/scoa/pepper/index.asp
.





Pepper Center Cores


Research Career and Development Core (RCDC)


The RCDC promotes the development of the next generation of geriatric/gerontologic research leaders through direct
financial support for salary and travel, structured mentoring, partici
pation in interdisciplinary conferences, other didactic
training, networking activities, and access to infrastructure support from the UTMB OAIC, and other OAICs as appropriate.
The RCDC also
provides career development training, supports pilot research p
rojects, and coordinates use of the
research cores by other investigators who are not receiving direct support from the Pepper Older Americans
Independence Center (OAIC).


The Core has two potential targets:



J
unior faculty and trainees in clinical and ba
sic science disciplines relevant to aging



E
stablished investigators with expertise highly relevant to aging research but not currently studying aging.


The RCDC takes different approaches to these two groups. For junior faculty, the RDC coordinates struct
ured didactic
training with the provision of appropriate mentoring. Junior faculty are assigned both research mentors and career
mentors, the one to focus on the specific goals of the research project and the other to assist with defining overall career
go
als. Mentors are selected from among senior faculty in aging research. A major theme of the training program is linked
to mechanistically driven research to evaluation of clinical outcomes. RCDC activities involving more established faculty
concentrate on
providing opportunities and support for interdisciplinary collaboration, drawing investigators from other
disciplines into ongoing studies of the OAIC.


Last Modified:
1
/
23
/201
2





15



The RCDC supports investigators
interested in developing a research portfolio in aging from
in a wide
spectrum of clinical
and basic science disciplines





Clinical Research Resource Core (CR
-
RC1)


The Clinical Research Core (CR

RC1)
is

the primary OAIC
re
source for
research
subject recruitment, tracking and
retention activities.

It supports studies related to 1) biological mechanisms underlying muscle loss and re
-
growth; and 2)
physical function and disability in both healthy community
-
dwelling older adults and those admitted to our Acu
te Care for
Elders (ACE) unit.
The Specific

Aims and functions of the CR

RC1 are to:

1.

Recruit, track and retain older adults for external projects, developmental studies and pilot studies. Older adults
included in Core activities range from healthy older adults living in the community to those hosp
italized with an
acute illness.

2.

Provide uniform and standardized health screenings, physical exams and functional status and disability
assessments for investigators of external projects, developmental studies and pilot studies. As examples, trained
staff

from our Core will perform phlebotomies, DEXA scans, muscle biopsies, and subjective and objective
assessments of physical function and disability status.

3.

Maintain a health outcomes database on older patients admitted to our ACE unit. Recruitment coordina
tors from our
Core will maintain a password protected web
-
based database on older patients admitted to our ACE unit, and made
available to OAIC investigators.

4.

Coordinate training in recruitment and retention, and functional assessments, and ensure complian
ce regarding the
regulations governing clinical investigations involving human subjects.




Muscle Biology Resource Core (MB
-
RC2)


The Muscle Biology Resource Core (MB
-
RC2)supports and promotes integrative and translational research on the
biological mechanisms underlying muscle loss and functional recovery in older adults. The specific aim
s are:

1.

Provide analytical support for funded translational research in muscle aging requiring

a.

G
enomics

b.

P
roteomics

c.

M
olecular

biology

d.

M
uscle m
orpholog
y

e.

T
racer methodologies

to measure metabolic processes in vivo

2.

Develop new translational methods to study th
e mechanisms of sarcopenia and muscle functional recovery in older
adults

3.

Simplify access of OAIC investigators to other institutional analytical core resources

4.

Train young investigators on the analytical and methodological aspects of translational muscle

research in older
adults




Pilot/Exploratory Studies Core (PESC)


The goal of the Pilot/Exploratory Studies Core (PESC) is to foster the development of innovative research designed to
foster translation of basic discoveries on t
he mechanisms of muscle loss and re
-
growth with aging to clinical practice for
the promotion of functional recovery in older adults. Specific aims

are
:

1.

Solicit and select the most meritorious research proposals for PESC funding

2.

Provide PESC investigators w
ith access to resources from other OAIC cores and institutional research
facilities/centers

3.

Identify potential opportunities for co
-
sponsorship of PESC studies

4.

Monitor the progress of PESC studies

5.

Ensure regulatory compliance, safety and protection of huma
n subjects enrolled in PESC studies

6.

Provide assistance and mentorship to develop PESC studies into independently funded grant applications