Cores and Centers

The Zilkha Neurogenetic Institute has a fully staffed Administrative Office with a director of operations, facilities manager, human resources manager, one senior research administrator, one research administrator, one associate research administrator, one project manager, one budget/business analyst, and an executive assistant. The institute acts as a hub for the neuroscience community across campuses, offering a seminar series, hosting neuroscience graduate courses, journal clubs, special lectures, as well as grand rounds for the Departments of 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. It houses investigators from ZNI/PHNS, Otolaryngology, Molecular Microbiology and Immunology, and Surgery.

The Biomarker Core facility is located in Dr. Zlokovic’s laboratory space in ZNI room 301 at the University of Southern California (USC), Keck School of Medicine. The Core has established collaborations with several clinical investigators, including 1) USC ADRC (Chui, Zlokovic, Toga, Schneider, Ringman, Yassine); 2) Washington University Knight ADRC (Morris, Fagan, Benzinger); 3) Banner Alzheimer’s Institute and Mayo Clinic Arizona; (Ryman, Casseli); 4) MarkVCID (Wang, Ringman); and 5) Dominantly Inherited Alzheimer’s Network (DIAN) including Washington University site (Bateman, Morris, Fagan) and USC site (Ringman).

The Biomarker Core has been using the state-of-the-art, ultrasensitive electrochemiluminescent Meso Scale Discovery (MSD) multiplex platform technology since 2013 to conduct simultaneous measurements of ~40 different neurovascular unit (NVU) biomarker categories in cerebrospinal fluid (CSF). The Core is working closely with MSD scientific staff members to develop custom MSD assays, including converting existing enzyme-linked immunosorbent assays (ELISAs) to MSD assays and the original development of MSD assays for novel analytes of interest. These assay developments are being conducted for analyte measurement in human and mouse samples. MSD’s V-PLEX product line is validated for state-of-the-art performance and quality. Surpassing FDA’s analytical standards, V-PLEX assays guarantee lot-to-lot consistency to ensure reproducible and reliable results to advance scientific research. MSD continues developing additional assays compatible with mouse biofluid and tissue samples. The Biomarkers Core: 1) coordinates biofluid collection, processing, and delivery, 2) assays CSF and plasma for NVU and AD biomarkers, 3) provides further technological developments, and 4) facilitates data management, requests, and distribution. The Core will continue to develop and improve MSD assays for the few biomarkers currently assayed with ELISA to provide a larger dynamic range of detection. The Core also performs S-PLEX multiplex MSD assays for Aβ and tau biomarkers in human plasma and pTau231 and pTau 181 biomarkers in mouse CSF and plasma. In summary, the Core is well-equipped to provide the services, resources, and expertise needed for NIH-funded projects.

Access-restricted -80°C freezers (NUAIRE) are available to store human and animal CSF biofluids. Samples are diligently tracked in a password-protected database. The Core has MSD MESO QuickPlex SQ120 multiplex platform (Meso Scale Diagnostics, LLC. Rockville, Maryland) for ultrasensitive electrochemiluminescent immunoassay detection and SpectraMax M2 Multimode Microplate Reader (Molecular Devices, LLC. Sunnyvale, California) for reading ELISA plates. MSD and microplate readers are each connected to Dell laptops with the MSD Discovery Workbench software and SoftMax Pro software, respectively. The Core uses a centralized data system to manage the data and requests in collaboration with other Cores: Administrative, Clinical, Imaging, and Data management and Statistics.

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 Cell Engineering and Regeneration Core at ZNI is now openly serving the research community at USC. The main goal of the core is to develop unique cell-based research tools for tackling key questions of the nervous system. The core is directed be Dr. Zhen Zhao, with assistance from Ms. Tenghuan Ge. The core provides effective support in cell culture and assays with multiple brain cell types for the studies of neurological and neurodegenerative diseases, including engineering genetic mutations and rare variants that are associated with human CNS diseases, and developing sophistic assays that can mimic injury and disease conditions. They are currently serving nearly 20 research labs, and facilitate the multidisciplinary collaborations between genetics, biochemical cellular, system and physiological levels at ZNI and beyond.

The center aims at bringing together a group of systems neuroscientists in ZNI, with their research focused on deciphering the structure and function of neural circuits in the mammalian brain with cutting-edge techniques. The general long-term research goals are to understand 1) how sensory perception is achieved and how sensory-evoked behaviors and emotions are generated and regulated, 2) how brain circuits adapt to dynamic changes of the external environment, and 3) how specific changes in brain circuits result in neurological and psychiatric disorders, especially the related sensory processing disorders (SPD). The center will promote interactions and collaborations among investigators in ZNI and will support the exploration of translational potentials of discoveries and developed approaches in clinical treatments of SPDs. It will also serve as a platform to foster the career development of junior scientists.

Resources available to the center

As the focus of the research center is on neural circuitry and brain functions, the center has the state-of-the-art research platforms with cutting-edge techniques on circuit tracing, optogenetics, chemogenetics, imaging, electrophysiology, and sensory behavioral assays: a) For imaging, the laboratories of the center are equipped with most advanced platforms for imaging brain circuits, including laser confocal microscopy, two-photon confocal microscopy, light-sheet microscopy, slide scanner, and tissue clearing such as CLARITY; b) For circuit tracing, all the labs are capable of handling and stereotactically injecting different types of viral and chemical tracers; c) For electrophysiology, the laboratories are equipped with full sets of electrophysiological recording setups for both in vivo and in vitro recordings, including the pioneering in vivo whole-cell and two-photon imaging guided patch clamp recordings, in vivo multichannel recordings for chronic implantation and acute head-fixed preparations, as well as slice whole-cell recording; d) For functional imaging, the center is now equipped with optic fiber photometry, two-photon calcium imaging, miniature endomicroscope imaging for in vivo studies; e) Optogenetics and chemogenetics have been integrated into all electrophysiological and imaging systems; f) For sensory behavioral assays, we have developed different apparatuses for quantitative behavioral monitoring and measuring for different types of behaviors such as motor, emotional and social behaviors. The center will have full sets unique systems and behavioral level resources in USC for neural circuit and sensory processing studies

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.

(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 Functional Biological Imaging Center is a newly formed pre-clinical imaging resource at the Zilkha Neurogenetic Institute takes advantage of state-of-the-art preclinical MRI/PET instrumentation provided by MR Solutions (Guildford UK). Simultaneous acquisition of PET and MR images is a newly emerging technology that marries the exquisite sensitivity of PET with the high spatial resolution and soft tissue contrast of MRI.

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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.