Cores & Centers 2017-04-07T20:40:15+00:00

Zilkha Neurogenetic Institute Cores & Centers

Established in 2003, the Zilkha Neurogenetic Institute provides a home for a program of interdisciplinary research that builds on USC’s existing strengths in neuroscience, molecular epidemiology and genetics, as well as the clinical expertise of the physician-scientists in the School’s clinical departments.

Faculty associated with the ZNI represent a sampling of the broad and interactive biomedical research effort being conducted at USC. More than 30 faculty members from 17 USC departments, institutes, divisions and centers are affiliated with ZNI. These investigators have active federal grants from 12 different institutes across the National Institutes of Health, the National Science Foundation, Department of Defense, the Department of Public Health Services, foundations and industry partners.  ZNI is home to 285 building occupants, including 34 postdoctoral fellows and 56 graduate students.

Scientists at ZNI are from the Departments of Biochemistry & Molecular Biology, Cell & Neurobiology, Molecular Microbiology & Immunology, Neurology, Neurosurgery, Ophthalmology, Otolaryngology, Physiology & Biophysics, Psychiatry & the Behavioral Sciences and Preventive Medicine, the division of Biostatistics, the Alzheimer Disease Research Center, the Institute for Neuroimaging and Informatics as well as the Eli & Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, to which the ZNI is physically connected via bridges on all floors.

An organized research unit of the Keck School of Medicine at the University of Southern California, the ZNI is housed in a five-story, 125,000 sq ft building on the Health Sciences Campus, a state-of-the-art facility that allows basic and clinical neuroscientists to concentrate and collaborate.  Research programs at the ZNI concentrate on Alzheimer and Related Diseases, Psychiatric Genetics, Genomics, Circuits, Vascular areas, Vision/Eye and Hearing/Ear. Among other research groups, the ZNI is home to the Protein Structure Lab, the Multiphoton Center, the Center for Genomic Psychiatry and the Center for Neurodegeneration and Regeneration.  In addition to the wet-lab space on every floor, there is a vivaria, conference facilities, classroom space, common equipment areas, faculty offices and workrooms and a café. PIs have access to two shared cold-rooms, several common facility rooms, a liquid nitrogen storage room, and one autoclave/dishwasher room throughout the Zilkha Neurogenetic Institute.

The Center for Neurodegeneration and Regeneration has 3,500 sq ft laboratory space in the ZNI. There are dedicated suites/rooms for specialized procedures and techniques: (A) A neurovascular imaging suite containing one multi-photon microscope (Zeiss LSM 5MP) coupled to a Mai Tai DeepSee Ti:Sapphire and HeNe 543 laser and one multi-photon/confocal microscope (Zeiss LSM 510) coupled to a Mai Tai DeepSee Ti:Sapphire, Argon 488, HeNe 543, and HeNe 633 laser. Suite also contains a picospritzer and stimulator for analysis of CBF response to whisker stimulation. (B) TissueCyte 1000 Whole Mount Tissue Scanner (Tissue Vision) for serial two-photon tomography and 3D reconstruction of brain connectomes and angiograms. figure_2

(C) A microscopy suite containing an Olympus AX70 Research microscope equipped with a motorized stage and both bright field and epifluorescent capabilities, an Inverted Nikon Eclipse T2000-U microscope, and a Nikon TE2000-S microscope with a temperature-controlled chamber for real time cell culture imaging. (D) A blood flow suite containing laser Doppler flow meter (Transonic Systems Inc.) for quantification of CBF response to brain activation, quantitative autoradiography (MCIE Autoradiography) for quantification of regional resting CBF, a custom-designed laser speckle imaging apparatus (Thor Laser Speckle Flowmetry) for visualization of pial blood vessels and blood flow, and a custom-designed intrinsic optical signal mapping apparatus for visualization of regional brain activation.

(E) Imaging suite for neuronal (cortical activation) by voltage sensitive dye (VSD) imaging and electrophysiological recordings. (F) A behavioral suite containing a Barnes maze, rotar rod, novel object location, novel object recognition, wire grip, beam balance, and burrowing test apparatus to study murine cognitive function. (G) A cell culture room containing 4 CO2 incubators for normoxic studies, 2 CO2 chambers for hypoxic studies, two SterilGard laminar-flow hoods, and three liquid nitrogen storage tanks for cell storage (H) Adjacent molecular biology suites containing two Zeiss Palm Microbeam laser capture microscopes for single cell isolation and a multitude of molecular techniques, including centrifugation, RNA extraction, EMSA, DNA analysis, Western and Southern blot analysis, PCR thermal cylcers, immunoprecipitation of proteins, and spectrophotometric protein determination.

(I) A protein purification suite containing both FPLC (Biorad) and HPLC (Shimadzu) systems. (I) A radioisotope labeling suite specially designed for preparation of radiolabeled proteins, including 125I-, 14C-, 3H-. Suite also contains a Gamma Wallac Wizard 1470 and beta Packard Tricarb 2100TR counters for subsequent analysis of radioactivities. (I) An electrophysiology recording suite. In the main laboratory of the Center, there is a dark room and cold room as well as a crytostat and vibratome for tissue sectioning and preparation.

There are 12 laboratory benches for wet work, each focusing on specific procedures: immunofluorescent detection of brain pericytes, isolation of neurovascular cells (pericytes, endothelial, astrocytes, VSMC, microglia and neurons), cranial window preparation for multi-photon microscopy, proximal ligation assay to study protein-protein interaction and distribution of BBB transport proteins, ELISA development and applications, molecular cloning and transgenic mouse manipulation, molecular mechanisms of brain angiogenesis and receptor signaling, Aβ, apoE and apoJ in vivo brain clearance studies, protein chemistry, neuroprotective effects of activated protein C (APC), stroke modeling (MCAO, proximal, distal and embolic models, photothrombotic mini-stroke, and intrastriatal NMDA model) , effects of APC treatment following various stroke models, neuroprotection and stem cell studies, stereological studies and neuronal spinogenesis, blood-brain barrier mediated clearance and pharmacokinetics, in situ brain vascular perfusion, in vitro blood-brain barrier studies, glucose metabolism/transport in AD murine models, and cholesterol and copper metabolism in AD murine models.

The Center for Genomic Psychiatry (CGP) has 3,000 sq ft of laboratory space in the ZNI. The CGP has 21 IBM-compatible PCs running 64-bit Vista/Win7 (8 of these are dedicated to laboratory equipment), two Windows 2003 Servers with RAID5 arrays, and one Dell PowerEdge R710s with 192 GB of RAM and 12 TB disk running VMWare ESXi. CGP also have a two Silicon Mechanics StorServs with ~400 TBs of useable disk space (including the 3 JBODs) running Solaris ZFS. On each floor of the Zilkha Neurogenetic Institute, there is available a shared computing facility, which is equipped with several Dell workstation PCs and Macintosh G5 computers, a color laser printer, a Xerox copy machine and a Canon fax machine. All computers in the CGP and the institute are directly connected to high-speed internet, and a 10 Gb fiber connection links that ZNI to the HPCC.

USC has a Linux cluster configuration (HPCC) that is ranked as the 5th fastest academic supercomputer in the USA and 17th fastest academic supercomputer worldwide, and 63rd fastest of all supercomputers worldwide (Spring 2011). The 1,988-node (each with 8-12 cores), 10-gigabit backbone benchmarked at 126.4 teraflops. The ZNI co-owns a dedicated “condo” of 122 nodes (1,308 cores). The CGP solely owns a 40 core server with 1 TB of RAM for high-memory compute jobs. PIs in the CGP belong to a consortium of USC researchers who purchased a high-performance 1.2 PB (~800 TB usable) DDN 10K-e disk array in 2011. ~400 TB of this space is owned by the CGP laboratory and further expansion of this device to 2.4 PB (raw) can be accommodated by upgrading the head node to a 12K-e (available now), as needed.

The USC Multi-Photon Microscopy Core is located in the Zilkha Neurogenetic Institute Room ZNI332 and it is an integral part of the university-wide Center of Excellence in Cell & Tissue Imaging that is overseen by the USC Provost’s Office of Research. Two unique multiphoton confocal microscope systems are available and dedicated to provide ultra-sensitive, deep tissue imaging of intact living organs in vivo in small animals with high spatial and temporal resolution that other intravital imaging modalities cannot achieve. The core’s current research base includes several NIH-funded investigators from four USC schools/campuses including the Keck School of Medicine, School of Pharmacy, Davis School of Gerontology, and the Herman Ostrow School of Dentistry in seven major user groups/themes, including kidney, liver, stem cells, lung & lacrimal gland, brain, cancer, and dental imaging. Research supported by this core and the state-of-the-art instrumentation aims to lead to our better understanding of the miracle of the brain, the normal functioning of the body’s organs, the discovery of disease mechanisms and biomarkers, testing novel pharmaceuticals and biomedical devices, and the application of stem cells and regenerative medicine to cure degenerative disorders, and will help to keep USC at the leading edge of biomedical research.

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The Protein Structure Center is housed across 3,400 sq ft of laboratory space and equipment rooms in the ZNI. The Center has a 700 Mhz nuclear magnetic resonance (NMR) spectroscopy machine, a custom-built 600 MHz Agilent solid-state nuclear magnetic resonance (NMR) spectrometer (the most modern and powerful instrument of its kind in LA County), three EPR machines including a state-of-the art pulsed EPR machine, and five systems that employ different optical spectroscopy methods. The Protein Structure Center also operates a JEOL transmission electron microscope (EM) capable of performing cryo experiments, a calorimeter to measure the heat of chemical reactions or physical changes to molecules, a fluorometer providing fluorescence spectroscopy, along with a computer cluster that is used to calculate and render the complex structures of the potential therapeutics involved with proteins.
The ZNI houses on its top floor, a brand new Hastings Foundation & Wright Foundation Laboratory for Biosafety, a fully functional and self-contained level-3 biosafety laboratory (BSL-3) overseen by a dedicated facility manager and a University Institutional Biosafety Committee, reporting to the USC Vice-President for Research. The BSL-3 has its own separate security system and operates under strict federal and state regulation, applying best practices and following procedural and experimental SOPs. The 2,000 sq ft space houses one shared equipment room, two in vitro procedure laboratories, two in vivo procedure labs, two animal holding areas as well as biosafety cabinets, HEPA-filtered cage racks, and a clean/dirty space for changing into and out of personal protective equipment. Use is by application only, and all researchers must undergo rigorous background checks and safety training. The space is monitored 24/7.
The Zilkha Neurogenetic Institute, has a fully-staffed Administrative Office with an experienced director of operations, facility manager, human resources manager, two full-time contracts & grants coordinators, purchasing agents, a budget/business technician, a program manager, executive assistant and receptionist. The institute acts as a hub for the neuroscience community across campuses, offering a weekly seminar series, hosting neuroscience graduate courses, journal clubs, special lectures, as well as grand rounds for the departments of Psychiatry, Neurology and Neurosurgery. The annual Zilkha Symposium on Alzheimer Disease and Related Disorders is held each spring, and the Zach Hall Lecture each fall. Throughout the year, the ZNI hosts conferences on a range of neuroscience topics from autism to retinal degeneration. The ZNI is a secure building, with security cameras throughout the facility and10 different levels of access controlled by key-card devices.