J. Bennett Johnston Health and Environmental Research Building The J. Bennett Johnston Health and Environmental Research (JBJ) Building, located on Tulane Avenue, is a seven story, state-of-the-art facility which houses the Center for Bioenvironmental Research and other Tulane research activities. The 184,000 square foot building is designed to encourage interdisciplinary collaboration. The laboratories are configured in 360 square foot modules. Modular design permits economical reconfiguration of the lab space as research activities and needs change.

Access Grid The JBJ Building houses a state-of-the-art conference room equipped with Access Grid videoconferencing capabilities. Located on the 5th floor and headed by the Center for Infectious Diseases, Access Grid materials include video, audio and large visual display, as well as internet set up, all which facilitate large group-to-group interactions. The conference room holds up to 50 individuals. An adjoining room that seats an additional 15 persons contains closed-circuit viewing capabilities.

Tropical Medicine Dr. Dawn Wesson Located in the J. Bennett Johnston Health and Environmental Research Building (JBJ, Rms. 535 and 577) on Tulane Avenue, Dr. Wesson currently supervises approximately 1,350 square feet of laboratory space, partitioned into three areas: a general laboratory, a contained insectary and a field laboratory. The main laboratory is 500 square feet dedicated to clinical research activities. Storage space for biological samples at 4, -20 and -85°C, as well as cryopreservation in liquid nitrogen, is available within the lab or associated equipment hallways. Standard laboratory equipment includes water baths, analytical balances, pH meters, fume hoods, etc. Ultrapure (18 megaohm) water is provided by a Nanopure dual-cartridge deionizer (Barnstead), which is fed by an in-house distilled water source. There is access to an adjacent 575-square-foot laboratory, which is used for all insect identifications, specimen processing, data entry and storage and maintenance of field collection gear.

Dr. Nirbhay Kumar Office: Dr. Kumar has an administrative office (~400 sq. ft) in the Tidewater Building (2 blocks from his research labs). In addition he also maintains a research office (Rm. 504; ~250 sq. ft.) next to his labs in the JBJ Building. These offices are equipped with Dell computers with internet connections.

Laboratories and computers: Dr. Kumar’s labs in the JBJ Building are housed on the 5th floor in rooms 517 (1019 sq. ft.), 520 (688 sq. ft.), and 564 (200 sq. ft.). All the freezers, refrigerators and equipment are connected to Emergency Power supply outlets to ensure uninterrupted power supply. All the molecular biology, biochemical studies, and immunology are carried out in Rooms 517 and 520. Room 564 is dedicated to cell culture and immunology research. The labs are equipped with adjustable benches next to the desk area for students and post-doctoral fellows. All the sitting desks are equipped for hard-wired and wireless internet connections. Computers on these desks are also connected for periodic downloading of research data on a Buffalo drive located in the Dr. Kumar’s office in the Tidewater Building for safety of data and as a back-up option.

Insectaries: Dr. Kumar’s laboratory maintains state-of-the-art brand new insectaries (Rms. 518- 519, 669 sq. ft.) with temperature – humidity and –light control options for breeding colonies of An. gambiae and An. Steophensi in dedicated chambers. These are used for malaria infection and transmission studies. These insectaries have multiple physical barriers for safe handling and are approved by the Tulane Bio-safety Office and USDA. In addition, Millipore Water purification units supply best quality water for maintaining Anopheles colonies. Infected mosquitoes are housed in self-contained incubators and are handled in a separate room equipped with six dissecting microscopes, centrifuge and circulating water baths for mosquito infection by membrane feeding, built within the general insectary area. In JBJ Building, there are separate insectary facilities for work with Aedes and Culex mosquitoes, including insectaries in certified BSL3 labs.

Animal Facilities: Research on animals is supported by the department of vivarial sciences and research and is located on the 7th floor of the building. These AALAC approved facilities use state- of-the-art procedures to maintain germ-free environment for high quality research. In addition, all the investigators have access to use of non-human primates for research at the Tulane Primate Research Center.

Major Equipment: Dr. Kumar’s lab is equipped with all the needed equipments for any aspect of malaria research involving cell culture, immunology, biochemical and molecular biology approaches.

General: Six -20°C freezers, -80°C Revco freezer, liquid nitrogen tanks, water baths (10), stirrer- hotplates (12), pH meters, table-top high speed centrifuges (4), micro-centrifuges (8), balances (3), etc. Cell Culture: Biosafety cabinets, 37°C and CO2 incubators, water baths, microscopes (light and inverted), dedicated centrifuge, etc. Immunology: ELISA plate washers, ELISA reader, fluorescence reader, IFA microscopes with digital photographic capability, cell harvester, etc. Molecular biology and Protein Chemistry: Bacterial shaking incubators, sonicators, microfluidizer, PCR thermal cyclers (3), electro-porator (BioRad), dozens of protein and DNA/RNA gel boxes and power supply units, fraction collector, peristaltic pumps, hybridization chambers, speed vac, gel dryers, GelDoc system, dark room with automatic X-ray film processor, chemical fume hoods (3), NanoDrop 2000, shaking water baths, incubators for bacterial and yeast culture plates maintained at different temperatures, homogenizer, light box for viewing gels, microwave oven and hot air oven, Strata UV X-linker, vacuum oven, spectrophotometer, rockers, shakers, radioactivity counters, gradient makers, etc.

Other Resources: There are core facilities providing genomic, proteomic and structural biology research support. In addition, shared instrumentation facility is open to all researchers for use of several centrifuges, spectrophotometers and FACS analysis. The SOM also maintains core services supporting efficient procurement of reagents and supplies from vendors such as Fisher, Sigma, and Invitrogen.

Dr. Hong-Wei Deng Laboratory: Dr. Deng, and all other major investigators for this project are members of the Tulane Center for Bioinformatics and Genomics (CBG), which is an integrated research entity staffed with one Endowed Chair, one full professor, four associate professors, eight tenure track assistant professors, two research assistant profs, and approximately 40 postdoctoral researchers, graduate students, visiting scholars, research coordinators, technicians and database managers, who have expertise in diverse study areas such as the statistical genetics, molecular and cellular genetics, quantitative and population genetics, functional genomics, proteomics, epigenetics/epigenomics and bioinformatics. Four additional tenure track assistant/associate professors will be recruited to strengthen/complement the current research of the center. These faculty and staff are engaged in research ranging from basic in vitro cell line studies, in vivo mice studies, human clinical and translational research, to clinical patient care in musculoskeletal diseases and related health problems.

The research dry labs of the CBG occupy approximately 750 sq. ft., including two computer labs equipped with twelve computers, and a computer room housing two workstations. Software packages for biostatistics, bioinformatics, statistic and genetics, such as SAS and/or R, R Bioconductor, and Plink, are installed on these computers. The CBG has access to a controlled computer room housing our computing servers and cluster. The CBG has full access to the Biostatistics Data Center, which is housed in the Department of Biostatistics and Bioinformatics, providing data entry and management services for researchers within and beyond the Tulane community. In addition, the CBG has access to the Tulane School of Public Health and Tropical Medicine (SPHTM) computer lab, which is located in the same building as that of CBG and is designed for training and education.

The research wet labs of the CBG occupy approximately 5,000 sq. ft. The research labs house the major equipment needed for basic, clinical, and translational research on musculoskeletal diseases. The basic wet labs at CBG house the major equipment for experiments of, e.g., large scale genotyping, DNA re-sequencing, transcriptome gene expression profiling, proteomics, and molecular and cellular functional studies. DNA/RNA/protein extraction and cell isolations (e.g. isolating monocytes from peripheral blood samples) are routine procedures that are conducted in our research labs, as exemplified by our ongoing projects and our previous publications.

Clinical: The CBG has two clinical recruitment sites, one located in New Orleans and the other in Baton Rouge (~1 hour drive from New Orleans). The New Orleans recruitment site is located on the 11th floor of the Tulane University School of Public Health Building, with a total area of 2,660 sq. ft. This site has 3 full-time and 5 part-time employees (including study subject recruiters, phlebotomists, research assistants, and lab technicians)/ The Baton Rouge site is located in the Baton Rouge Medical Center (affiliated with Tulane Medical School), with a total area of 5,100 sq.ft. The site has two full-time and 7 part-time employees (including study subject recruiters, phlebotomists, research assistants, and lab technicians).

Both clinical sites house an outpatient reception area, a waiting area, and multiple dedicated private interview offices for subject enrollment, exams rooms that are fully equipped for clinical examination, phenotyping and phlebotomy.

The clinical recruitment site at New Orleans is within a five minute walking distance from the research wet labs of the CBG. Therefore, research specimens collected at that site can be immediately hand delivered on ice to the labs of the CBG for downstream processing. In addition, due to the short distance (~ 1 hour drive) between the clinical site at New Orleans and that at Baton Rouge, subjects recruited at the Baton Rouge site can easily visit the New Orleans site for specimen donation.

Computer: Sequencing-based genomic/epigenomic research requires high-performance computing and high capacity for data storage. The exceptional computing facility is housed within the Tulane SPHTM Tidewater office building and is readily accessible through intra- and internet at Tulane University and surrounding universities.

The CBG has more than 40 desktops and 16 laptops (IntelCore 2 Duo and Quad Core CPUs 3-8 GB memory, 250-500 GF hard drives, MS Windows 7 Enterprise), two powerful computational servers (2-4 Intel/AMD Quad/twelve Core CPUs, 64-256 GB memory), and an in-house cluster (being able to run 64 jobs simultaneously). In particular, CBG recently acquired a Dell PowerEdge R815 Rack Server with four AMD Opteron 6168 twelve-core processors and 256 GB memory (extensible to 512 GB), which is ideal for handling and processing the next-generation sequencing- based genomic and epigenomic data. The CBG has full access to the powerful Louisiana Optical Network Initiative, a state-of-the-art fiber optics network connecting Louisiana and Mississippi research universities and providing powerful distributed supercomputer resources.

For data storage, the CBG team has two Dell PowerVault NX3000 storage servers, each equipped with 12 TB storage space. The office computers are automatically backed up to the departmental/university level and off-site backup facility approximately every four days. In addition, the center has over 180 TB storage space in dedicated internal/external hard drives.

A large variety of software for daily operation, programming, data management, and biostatistics, statistical genetics, and bioinformatics analyses are available to the CBG team. Basic software packages for daily operation such as word processing, e-mail communication and web publishing, and for programming are in use on most desktop and laptop computers. Examples of these packages include Microsoft Office 2007/2010 Pro (Word for word processing, Excel for spreadsheet, and PowerPoint for presentation), Microsoft Access and MySQL (Database), and toolkit for print, web, and mobile publishing (Adobe Design Premium including Acrobat, Illustrator, InDesign, Photoshop, Dreamweaver and Flash). Available programming languages include C, C+ +, Pascal, FORTRAN 77, Fortran 90, Perl/Bioperl, and Python/Biophyton, which are often- employed for computational purposes, simulation studies in biostatistics and bioinformatics, and data handling.

General analytical packages such as SAS (Cary, NC), S-Plus (Insightful Corp., Seattle, WA), and R (http://www.r-project.org) are in use for routine biostatistical and bioinformatics analyses. They contain a variety of tools for routine analyses, such as evaluation of the appropriateness of analytical procedures (e.g., PROC UNIVARIATE in SAS for both graphical and analytic assessments of the normality of data), establishment of relationship between independent variables and dependent variables (e.g., linear regression by PROC REG in SAS, generalized linear regression including logistic regression by glm in R), and mixed model analyses (e.g., PROC MIXED in SAS).

A variety of statistical and bioinformatical programs for analyzing genomic, functional genomic, epigenomic, and proteomic data are either regularly used or have been installed and are ready for use. Examples of these programs include:

 For Genomics studies: PLINK, FBAT, QTDT, MERLIN, SOLAR, MULTIMAP, IMPUT, MACH, PHASE, STRUCTURE, EIGENSTRAT, Mendal, RareCover, Panther, PhD-SNP SVM-Profiel, MutPred, nsSNPAnalyzer, SIFT, SNAP, PolyPhen-2, Condel, MaxEntScan, RAVEN, F-SNP, FastSNP, WinBUGS/OpenBUGS, CNV-seq, Gorilla, Trait-omatic, Novoalign, MAQ, ELAND, PbShort, ssahaSNP, CMDS, Integrative Genomics Viewer (IGV), etc.

 For Functional Genomics studies: GeneMAPP, Ingenuity Pathways Analysis (IPA), miRecords, miRanda, PicTar, TargetScan, ExprTarget, Partek Genomic Suite (PGS), ImaGene, LIMMA, BioPerf, Biophython, Bioconductors, etc.

 For Proteomics studies: ProteinLynx, ProteinExpression, TMpred, SMART, etc.

 For Epigenomics studies: MEDIPS, BATMAN, MOM, ChiPDiff, cisGenome, XSET PeakSeq, Model-based Analysis for ChIP-seq (MACS), Quantitative enrichment of sequence tags (QuEST), Site Idenificiation from Short Sequence Reads (SISSR).

The CBG team has installed and started using the MAQ, ELAND, MEDIPS, and BATMAN, which are efficient tools to analyze and visualize the epigenome-wide DNA methylation data.

Office: The PIs’ and other investigators’ offices and meeting spaces occupy approximately 5,000 sq. ft. In addition, other research personnel of CBG have additional ~2,000 sq. ft. of office space.

Scientific Environment: All key investigators of this project are from the Tulane CBG. This is a highly interdisciplinary integrated program staffed with one endowed chair, one full professor, twelve associate/assistant professors, and roughly 40 other research members. The investigators and researchers in the CBG have had extensive experiences in multidisciplinary areas related to the proposed study, including genetic epidemiology, functional genomics, statistical genetics, epigenetics/epigeomics, statistical genetics, bioinformatics, and molecular biology. During the past couple of years, the CBG researchers who originally started at their previous institute launched major initiatives and efforts into the forefront of epigenetic/epigenomic research, using state-of- the-art technologies and leading the field of genetic/genomics studies in the bone field. The close and fruitful collaboration among the CBG investigators, which is documented by over 400 publications in the past 14 years and partially testified by the NIH, funded one of the eleven SCOR (Specialized Center of Research) grants in women’s health in the US, attests to the optimistic prospects that the proposed work will be efficiently executed and successfully completed. The research wet labs of the CBG investigators are all located on the 3 rd floor of JBJ Building of Tulane Health Science Center, which create a centralized working environment where all research equipment are easily accessible and shared and where investigators can communicate and collaborate closely. In addition, the clinical space at the Tulane University SPHTM building is located within a five minute walking distance from the research wet laboratories, ensuring that all samples can be processed timely and efficiently.

Major equipment: The following listed equipment are either available in the laboratories of the investigators or are accessible to the group at Tulane CBG. Available major equipment include the following:

General Lab Equipment Major Molecular Biology and Cell Culture Equipment Genetics Equipment UV/Vis spectrophotometer Amersham Pharmacia Biotech 4 CO2 incubators MegaBACE model 500 1 fluorometer ABI Prism 3730 DNA sequencer 2 cell harvesters NanoDrop Micro-Volume UV-Vis Affymetrix GeneChip® Instrument 3 light microscopes Spectrophotometer System

Various centrifuges (2 high-speed, Illumina Genome Analyzer IIx Zeiss LSM 510 confocal ultra, 5 table-top) microscope 2 water purification systems Agilent 2100 Buianalyzer Desktop One cryostat, one microtome System Water baths ABI 7900 HT Fast Real-Time PCR Nikon inverted fluorescent System microscope coupled with both a camera and a CCD videocamera and high-resolution monitor 2 analytical balances Multiple 96-/384-well Thermal Olympus upright fluorescent Cyclers microscope coupled with a SPOT- RT 12-bit digital camera and image analysis system Autoclave Tecan RSP 150 Robotic pipette Tissue culture facility system Ice machine Hewlett-Packard (HP) 1100 DAKO auto-staining system Automated Quaternary LC3D HPLC systems 6 -80° C Freezers RoboSNiP 1600 Automated 2 laminar flow hoods Workstation (MWG Biotech AG) 10 -20° C Freezers Transgenomic WAVE System 1 tissue chopper 10 refrigerators 6750-115 Freezer mill (SPEX 2 TissueMizer homogenizers CertiPrep) Vortexes, stir plates, heating plates 2D-gel electrophoresis and blocks of various sizes and types Chemical fume hoods SYNAPT™ G2 Mass Spectrometry Liquid nitrogen