Capabilities & Resources

  • Cellular Phenotyping Laboratory

    The STDOI Cellular Phenotying Laboratory located on the UTRGV Brownsville campus utilizes a Perkin Elmer Operetta system.  This fully integrated High Content Screening (HCS) System offers brightfield, widefield and a Nipkow-spinning disc confocal option, with easy switching between modes.  The widefield option offers high-throughput imaging of 2D cultures; and the true hardware based confocality option provides variable height Z-axis sectioning capability for the high quality imaging of both 2D and 3D cellular structures such as in vitro organoides.  The Operetta system also has a temperature/CO2 controlled chamber and integrated brightfield illumination suitable for live cell imaging applications.  The laboratory also houses two Zeiss microscopes, an Axio Imager D2 upright and an Axio Observer D1 inverted microscope.  The Axio Imager D2 upright microscope provides excellent optical quality for both transmitted light and fluorescence imaging applications for both fixed and live cells.  The Axio Observer D1 inverted microscope is designed for live cell observation, manipulation and analysis.  An Oxytherm System is available for assessing cellular oxygen consumption and expulsion; and a Lonza 4-D Nucleofector X System for the transfection of cells; a BD CytoFLEX flow cytometry system for cell analysis.  Additionally, the laboratory houses two Sanyo CO2 incubators and a Sanyo fridge/freezer unit for storage of cell culture reagents only.  Contact John Blangero, Ph.D., at john.blangero@utrgv.edu or (956) 956-882-7522 for information.

  • Genetic Epidemiology

    STDOI provides exceptional resources and expertise to conduct genetic epidemiologic investigations of complex diseases (i.e. diabetes, obesity) influenced by genetic and environmental factors.  Next generation sequencing technologies have enabled STDOI researchers to obtain complete information on human genetic variation to enhance understanding of the genetic basis of complex diseases such as cardio-metabolic, infectious, neurodegenerative, and psychiatric disorders.  STDOI researchers develop and apply statistical genetic analytical tools to complex diseases across a wide range of large data sets from large families across global populations.  Standard statistical genetic analytical methods used include disease gene localization using both association and novel advanced linkage methods, causal variant prioritization using Bayesian quantitative trait nucleotide analysis, quantitative genetic analysis of heritabilities and genetic correlations in studies using either families or unrelated individuals based on empirical kinship analysis, novel endophenotype/biomarker discovery using methods appropriate for both common and rare disorders, gene-by-enviroment interaction analyses, and many other types of genetic/genomics analysis.  A wide variety of software, statistical and mathematical packages, and pedigree data management and pedigree drawing packages are available to carry out various types of genetic analysis and STDOI's own SOLAR (Sequential Oligogenic Linkage Analysis Routines) suite of computer applications is available, which has been optimized for the parallel compute system on MEDUSA at the STDOI Genomic Computing Center (GCC).  STDOI researchers have applied expertise in all aspects of modern genomic analysis including complex disease gene discovery, biomarker/endophenotype discovery, advanced high dimensional genomic analysis for transcriptomics, metabolomics, methylomics, and microbiomics, together with clinical data, functional genomics, and bioinformatics.  In-house statistical genetic and genetic epidemiologic experts are available to discuss study design, sample size, power calculation, methodological and analytical approaches that suit specific experimental scenarios, and interpretation of data.  Contact Ravindranath Duggirala, Ph.D., at ravindranath.duggirala@utrgv.edu or (956) 665-6456 for information.

  • Genomics Computing Center

    The STDOI Genomics Computing Center (GCC) on the UTRGV Brownsville campus is a 1,000 square-foot machine room that houses the high performance computing cluster, MEDUSA, which consists of a M&A Technology 10,944 Core High Performance Computer Cluster with Opteron processors, a 10-Gbps connection between racks and a Hitachi 1Pb Distributed File Storage System using the Lustre File System, and a 40-Gbps connection to the processors.  The GCC represents one of the world’s largest high performance clusters dedicated to human genomics.  Additionally, there are eight Dell Poweredge C6145 server chasses with 128 Opteron CPU cores per chassis (total of 1,024 cores), 512Gb per chassis, and 20TB per chassis.  The backup system includes two Dell R730 Servers for backups, a Dell 6020 Tape Library with 6 LTO-6 drives (used for backups), a Dell 6020 Tape Library with 4 LTO-6 drives, and a Dell MD3460 Disk Array with 110TB RAID 5 disk space.  All systems are connected via a 10Gb/s network link.  An uninterruptible power supply (UPS) and generator system guarantee protection against power outages and the machine room temperature is continuously monitored..

    In addition to MEDUSA, UTRGV's STDOI San Antonio Annex hosts two storage servers with 24 cores, 64Gb of RAM, and 66Tb of disk storage per server.  One of these two storage servers serves the home directories for users, and the second storage server acts as a repository for static data.

    A wide variety of software (for word processing, graphics, spreadsheets, statistical analysis, etc.) is available.  Programming and scripting languages provided include FORTRAN, C, C++, Java, Tcl, Perl, and Python.  Statistical and mathematical packages available include Gauss, Maple, Matlab, S-PLUS, and R.  The PEDSYS database system is used for management and analysis of genetic, demographic, epidemiological and laboratory data for all of the projects in our department.  Software available for genetic analysis includes PAP, S.A.G.E., MENDEL, FISHER, LINKAGE, CRI-MAP, PREST, Merlin, GeneHunter, Morgan, SimWalk2, Loki, PLINK, and our own SOLAR.  The pedigree drawing package entitled Pedigree-Draw and Madeline are also available.  Contact John Blangero, Ph.D., at john.blangero@utrgv.edu or (956) 956-882-7522 for additional information.

  • High Throughput Sequencing Center

    STDOI established a High Throughput Sequencing Center on the UTRGV Brownsville campus equipped with two Illumina HiSeq 2500 v4 sequencing systems capable of outputting 500 Gb of sequence per flow cell, or 1 Tb each per run (6 days).  These sequencing instruments are supported by a cBot instrument for cluster generation.  Dedicated servers for preliminary sequence quality control and sequence data transfer are available, although direct connection to our high performance parallel cluster, MEDUSA, is also available.  Two external 12 TB OWC Mercury Elite Pro Qx2 RAID Solutions are also available for additional, temporary data storage.  An Illumina MiSeq is available for targeted sequencing applications.  This system can generate up to 15 Gb of output per run (~55hrs).  An Applied Biosystems 3730xl DNA Analyzer, capable of outputting 920,000bp of sequence or per day is available for conventional DNA sequencing applications.  Contact Joanne Curran, Ph.D., at joanne.curran@utrgv.edu or (956) 882-7532 for additional information.
  • Metabolomics Laboratory

    The STDOI Metabolomics Laboratory located in the STDOI San Antonio Annex houses a LECO Pegasus 4D Comprehensive Two-dimensional Gas Chromatograph Time-of-Flight Mass Spectrometer (GC×GC-ToFMS) for untargeted metabolomic profiling using a two-dimensional gas chromatography approach.  GC×GC-ToFMS is a sophisticated separation technique that is well suited to the analysis of complex samples for volatile and semi-volatile small molecules.  GC×GC is used to separate the individual components in a sample, and mass spectrometry is used to identify the individual components by comparison of a component's spectrum against spectra contained in libraries (NIST, Wiley, etc.) as well as quantify the amount of the component in the sample.  Two-dimensional GC offers enhanced resolution, greater dynamic range, and larger peak capacity over conventional a one-dimension GC.

    LECO’s Pegasus 4D is a state-of-the-art instrument that includes computer hardware and software for operation and troubleshooting of the instrument, record keeping, data receiving, archiving, and analysis, including signal deconvolution by the ChromaTOF software package.  Two different modulator options are available in the laboratory, an electric chiller cryogen-free modulator and a cryogenic modulator utilizing liquid nitrogen.  The modulators can be swapped depending on need, permitting us to optimally analyze a variety of different types of samples.  The GC×GC-ToFMS is equipped with a GERSTEL Multipurpose Autosampler (MPS) with dual heads for automated sample preparation, including derivatization, incubation and the capability for automated inlet liner exchanges.  Utilization of the dual head set-up increases throughput and improves consistency through automation.  The instrument is also equipped with a CIS-4 cryo-focusing inlet with TDU thermal desorption for the introduction of non-liquid samples including direct thermal desorption and stir-bar sorptive extraction (SBSE).  STDOI technology is sensitive and reliable requiring only small sample volumes (≤100 ml).  Cost per sample is reasonable ($100 or less) and throughput is >100 samples per month.

    The STDOI San Antonio Annex is also outfitted for processing of blood samples from ongoing San Antonio Family Study recruitments, DNA extractions, and sample storage.  A Beckman Coulter AC T diff2™ Hematology Analyzer is available for cell counting and a Hematron for aliquoting samples for long term storage.  The laboratory contains a -80 freezer, -30 freezer, 4C refrigerator and a 150L liquid nitrogen dewar for sample and reagent storage.

    Contact Harald H. H. Göring, Ph.D., at harald.goring@utrgv.edu or (210) 585-9771 for additional information.  The research group located at the STDOI San Antonio Annex is headed by Professor Göring and includes Dr. Pete Stevens Ph.D. (email: peter.stevens@utrgv.edu), a Senior Research Scientist and experienced metabolomics expert, and several technical and doctoral staff members.

  • Molecular Genetics Laboratory

    The STDOI Molecular Genetics phenotyping laboratory located on the UTRGV Brownsville campus is equipped with an Illumina iScan and autoloader to allow 24 hour runs without user intervention for high-throughput genotyping allowing processing of up to 96 multi-sample BeadChips per day.  The iScan System is a cutting-edge, dedicated array scanner that supports rapid, sensitive, and accurate imaging of Illumina's array-based genetic analysis products.  A Tecan Freedom Evo liquid handling platform is available for automation of all Illumina post-PCR protocols.  A Life Technologies QuantStudio 12K Flex instrument is available for genotyping and gene expression analyses.  This highly adaptable real-time PCR system is capable of accommodating multiple interchangeable blocks (96- and 384-well plates, TaqMan LDA cards, and OpenArray plates) to run numerous molecular assays (real-time qPCR, digital PCR, allele-specific gene expression, single variant genotyping, and miRNA).  Throughput capacity is fully scalable and supported by an AccuFill System for automatically loading of OpenArray plates.  Additionally, an ABI 7900 HT Sequence Detection system is also available for real-time PCR, TaqMan genotyping and gene expression assays.  For phenotyping, a Luminex LX200 and ACE Clinical Chemistry Analyzer are available.  An Eppendorf epMotion 5075T CleanCap robot is available to support all instruments.

    The STDOI Complex Disease Genetics Laboratories house an EnSpire multimode plate reader with combined fluorescence, luminescence and absorbance capabilities; an Agilent TapeStation 2200 for quality control analysis of DNA, RNA, and protein by small-scale gel electrophoresis; a G:Box Chemi XRQ gel imaging and analysis instrument with fluorescent and chemiluminescent imaging capabilities; a Beckman Coulter AcT diff2 Hematology Analyzer for the measurement of 18 blood cell parameters; a Genesis BPS Rapid Seal II SE340 for aliquoting samples for long term storage; and a BioTek 405 plate washer for cell-based and microsphere-based assays.  All instruments are supported by ABI 9700 dual 384 head thermocyclers, and MJ Research PTC-200 96 well thermocyclers. The pre- and post-PCR and gene expression laboratory areas contain dedicated equipment including PCR workstations, single and multi-channel pipettes, bench-top and micro-centrifuges, centrifuges, water baths, hybridization ovens, refrigerators and freezers.  All major equipment is connected to uninterrupted power supply (UPS) units to maintain operation against brief power outages prior to the backup generator power supply providing longer term electrical support.

    Contact Matthew Johnson, Ph.D., at matthew.johnson@utrgv.edu for additional information.

  • National Lab Opossum Resource

    The STDOI laboratory opossum resource consists of more than 20 genetic stocks and strains of Monodelphis domestica, which STDOI investigators have been developing since 1979.  This and other marsupial species give birth to infants that are at the developmental stage of a 6-week human embryo.  Therefore, experimental manipulations can be conducted ex utero throughout most of embryonic and all of fetal development.  The colony has a steady state of 1,500 animals post-weaning, and produces several thousand progeny annually.  It is the world’s largest laboratory animal resource of any marsupial species.  Current active research projects focus on genetic and dietary regulation of blood cholesterol levels, genetic and dietary influence on susceptibility to non-alcoholic fatty liver disease and NASH, pathological effects of Zika virus infection during embryonic and fetal development as well as in juveniles and adults, and behavior particularly as affected by experimental perturbations during development.  The resource is available for collaborative use by investigators from UTRGV and other institutions.  Collaborative research involving outside investigators is conducted within our facility.  In addition, we provide breeding nuclei, experimental animals, and biological materials to investigators around the world; along with advice on maintaining, breeding, and experimentally manipulating these animals.

    Contact John VandeBerg, Ph.D., at john.vandeberg@utrgv.edu for additional information.

  • Biorepository

    The South Texas Diabetes and Obesity Institute maintains an extensive biorepository of samples collected from its long-term family studies. Tens of thousands of samples from individuals participating in the San Antonio Mexican American Family Studies, the Jirel Population Studies, the Posse Family Health Studies and other projects are stored in -80 freezers in a “freezer farm” located at the STDOI-Brownsville and in freezers housed in the STDOI-Edinburg laboratories. Over $200 million in NIH funding supported the studies that generated the samples over the past 30 years.

    Contact Sarah Williams-Blangero, Ph.D., at sarah-williams-blangero@utrgv.edu for additional information.

  • Stem Cell Biology Program

    The STDOI Stem Cell Biology program based on the UTRGV Edinburg campus develops in vitro cell-based models of human inherited disorders to understand the cellular and molecular mechanisms involved and underlying genetic component influencing disease phenotype.  STDOI uses state of the art induced pluripotent stem cell (iPSC) technology to generate disease specific target cells which otherwise can be difficult to obtain without invasive surgery or which only become available post-mortem.

    Many STDOI research programs focus on common complex disease genetics and gene identification utilizing large family based studies.  STDOI houses a large repository of blood derived immortalized cell lines (lymphoblastoid cell lines) established from > 2000 Mexican American participants of its San Antonio family heart study (SAFHS).  A transgene integration free methodology developed in-house (Kumar et al., 2016) is used to reprogram these human adult somatic cells including blood primary cells and lymphoblastoid cell lines into iPSC lines.  In house iPSC reprogramming methodology achieves a high reprogramming efficiency, 100% reprogramming success and generates foot print free bonafide iPSCs.  

    The STDOI stem cell biology laboratory is well equipped for iPSC reprogramming, differentiation of the generated iPSCs into target cell types (i.e. cells of neural lineage, cardio-myocytes and hepatocytes).  Generated iPSC lines and differentiated target cell types are validated by immunocytochemistry and differential gene expression analysis of the pluripotency and target cell type specific markers.  Contact Satish Kumar, Ph.D., at satish.kumar@utrgv.edu or (956) 665-6477 for information.