Research & Research Facilities

Ongoing research projects in the Brain Dynamics group include the following:

1. Spatial orientation mechanisms (grid cells, place cells, head direction cells)
2. Offline reactivation of memory traces
3. The role of sleep and memory consolidation
   
4. The role of the hippocampus in information processing
5. Interactions between hippocampus and neocortex
6. The role of the prefrontal cortex in decision making
7. The role of neuromodulators for learning and information processing in cortex-basal ganglia circuits
8. Altered neural processing in psychiatric illnesses using pre-clinical (rodent) models
9. Addiction
10. Sound processing by cortical circuits in animal models of stroke, MS, and hippocampal lesions
11. Brain plasticity and motor control
12. Brain Aging
13. Brain/computer interface
14. Development of new mathematical tools for the analysis of brain dynamics, particularly for large-scale neural recordings
    
15. Neural network models of higher cognitive function

The animal facility at the Canadian Centre for Behavioural Neuroscience (CCBN) has six animal housing rooms, including one for mice. Polaris group researchers use a variety of strains of rats including Long-Evans, Brown Norway, and Fischer- Brown Norway hybrids. In addition to ordering rats and mice from companies, the CCBN has its own rat breeding colonies. Animals used for in vivo electrophysiology experiments are housed in a reverse light cycle room. This allows for studies to occur during the animals’ active period. The duties of the animal care staff include feeding and checking on all animals daily, ordering animals for researchers, maintaining breeding colonies, ensuring the availability of clean equipment, and coordinating special care animals may require such as post-operative care. The veterinarian approves and checks on all research protocols, helps train researchers in animal procedures, and works hard to ensure the health of all animals in the facility.

Animal Care Staff

Karen Dow-Cazal

Charlotte Holmes

Tyler Barrows

Jennifer Miller

Veterinarian

Isabelle Gauthier, DVM

The surgical suite in the Canadian Centre for Behavioural Neuroscience (CCBN) offers an aseptic environment for researchers to conduct various types of neurological surgeries such as the electrode array implanting (a.k.a. hyperdrives). The CCBN has three state of the art operating rooms: one large multi-purpose operation room and two small rooms. The large room has sufficient space where the researchers can bring their own peripheral equipment for the procedure. All operating rooms provide an advanced surgical environment under sterilized conditions and are equipped with a ventilation system, anaesthetic equipment, operating table, surgical microscope, surgical light, bench space, and a sink.

The CCBN also has a surgical preparation room in order to prepare for various surgical procedures. Sterilized surgical supplies such as drapes, solutions and various instruments are available in this room. An autoclave is available for sterilization of all surgical instruments. The room also serves as an animal recovery area; several medications, heating pad, and two types of animal bedding are available for post-operative treatment. After any surgery, animals are allowed to recover for several hours in this quiet room, and are carefully monitored and administered analgesics.

Hodgkin, our computing cluster, has 64 blade servers containing 48 GB of RAM and two 6-core Intel Xeon processors. When added up, Hodgkin has 768 available computing cores and 3 TB (3072 GB) of RAM for use. Each of the blade servers are running 64-bit Red Hat Enterprise Linux.

The scheduler used on Hodgkin is Platform LSF, which is officially supported by MATLAB. Hodgkin is currently configured to use the most current release of MATLAB (R2011a), and some older versions are available as well (R2010a and R2010b). MATLAB is the primary use of Hodgkin currently.

For our storage cluster, Huxley, we have 50 TB of hard drive space. This space is split up into two different 16TB volumes based on the type of project, with an extra 10 TB volume for general use. There is 5TB of scratch space for temporary files.

The contents of Huxley are backed up every night to an off-site location. The off-site location has 80TB of storage which allows us to have incremental backups. Data is backed up here for 6 months. Snapshots are kept for the most recent seven days, three weeks, and six months.

Currently, the In Situ Lab at the Canadian Center for Behavioural Neuroscience (CCBN) is far too small for the needs of the expanding Polaris Brain Dynamics Research Group. Funding has allowed the much needed expansion of the CCBN building to include a much larger and better equipped In Situ facility to support the work of the growing Polaris team as well as other research groups within the building.

Once completed the expanded In Situ Lab will primarily be used for Fluorescent In Situ Hybridization (FISH), a process that allows the detection and localization of mRNA on tissue sections. This lab will also be equipped to support other molecular biology processes including PCR, riboprobe synthesis and more. The larger facility will be capable of supporting multiple workstations simultaneously. Two Research Technicians will primarily be responsible for the In Situ Lab and will assist undergraduate students, graduate students, post-doctoral fellows and principal investigators in their research.

The new facility will have a vastly expanded workspace and will be furnished with two large fume hoods as well as a laminar flow hood for sensitive applications. The lab will include heating and cooling equipment such as 4oC fridges, a -20oC freezer, an ultralow -80oC freezer as well as two hybridization ovens and an economy oven. The room itself will be equipped with HEPA-filtered ventilation, washable ceiling tiles and positive pressure to reduce dust and contaminants. An adjoining reagent and specimen room will increase the storage capacity of the main In Situ room. The In Situ Lab will also be supplied with numerous amenities such as Reverse Osmosis (RO) water, a Nanopure Diamond filtration system, a Nanodrop 2000 spectrophotometer, a dishwasher, emergency safety equipment (emergency shower, eye wash station and first aid kit) and two large double sinks.

The new in situ lab is in its final stages of construction. It is expected to be fully operational by September 2011.

The Polaris Imaging Facility features two state-of-the-art NanoZoomer Digital Pathology (NDP) systems (Olympus & Hamamatsu), which serve as powerful tools in neuroscientific research in brain circuitry and neural networks. The NanoZoomer systems are capable of rapid and automated scanning of whole-brain images in fluorescence and/or bright field. In addition, each system can scan up to six individual slides in manual or automated batch mode. The option of fully automated batch processing maintains consistent focus information. Depending on section thickness or quantification parameters, researchers may choose to scan tissue samples in multiple layers up to 21 z- focal planes, a feature which enables detailed 3D reconstruction. NanoZoomer systems are capable of visualizing samples labeled with multiple fluorescent immediate-early gene markers. Utilizing the different transcription durations of immediate-early genes, researchers can capture snapshots of brain activity within different behavioural epochs with high spatial and temporal resolution. These snapshots can also provide details regarding change in brain activity as a result of various manipulations or behavioural conditions. The high resolution and large-scale visualization features allow researchers to focus on whole-brain sections or to zoom into specific regions such as hippocampal subregions. These images are stored in a compressed digital format that permits mass storage without sacrificing image integrity or resolution by employing millions of pixel resolution. This also allows for a diverse array of zoom and magnification scales during review processes. These NanoZoomer systems are complemented with a diverse suite of practical software for image analysis and quantification. The NDPView application enables simultaneous viewing of multiple images for easy cross-regional and cross-sectional comparison. Capitalizing on Hamamatsu's advanced sensor technology, scans are fast, reliable, and consistent. These features culminate to provide high data throughput abilities for the tracking of neuronal network activity and brain circuitry dynamics.

Voltage sensitive dye imaging (VSDI) allows direct recording of cortical activity within large neuronal populations (>10mm) with high spatial (down to 20-50 µm) and temporal (down to the millisecond) resolution. This technique is based on the use of a dye (e.g. RH1691 - Optical Imaging) that binds to cell membranes and acts as a local probe indicating the level of depolarization by an emission of fluorescent photons. This fluorescent signal mainly reflects dendritic activity of excitatory neurons in superficial layers.

Voltage-sensitive dye signals are small and require a high sensitivity and high speed imaging system. The lab is equipped with a MiCAM ULTIMA CMOS camera (SciMedia) which can achieve a high-speed image acquisition rate of up to 10,000 frames per second. The camera was mounted at the top of an Olympus MVX10 Macro Zoom System microscope equipped with epifluorescence, and a 100W halogen lamp gated by a shutter (Uniblitz) provides excitation light.

VSDI combined with electrophysiological techniques (e.g. EEG or high density electrode arrays) is a powerful tool for studying large neuronal ensemble dynamics with the highest spatiotemporal resolution nowadays available.

Currently, we are simultaneously performing VSDI and electrophysiological recordings in vivo in adult and developing rats.

The Olympus FV1000 MPE 2-photon microscope was purchased through a Canadian Foundation for Innovation (CFI) grant and installed in November, 2011. The scope is an Olympus BX61WI upright with two water-immersion lenses, a X10, N.A. 0.6 and a X25, N.A. 1.05, both equipped for DIC imaging. Both lenses were specially designed for 2-photon microscopy. Four high-efficiency non-descanned detectors provide efficient capture of the back-scattered fluorescent signal. For compatibility with the other facilities microscopy equipment the fluorescent filters are DAPI, FITC, Tx-red and Cy5. The stage is a Siskiyou 25mm XY translation platform and is large enough to hold electrophysiology equipment. Since this is a dedicated 2-photon instrument, only a single IR laser, a Spectra-Physics Mai Tai DeepSee, is included. The laser is tunable from 690nm - 1040nm. Group Velocity Dispersion (GVD) and laser beam auto-expander provide beam dispersion compensation and back aperture illumination optimization.

The advantage of a 2-photon system over a confocal microscope is the enhanced ability to image deeply into a specimen with a minimum of radiation damage and fluorescence quenching. The instrument accomplishes this by projecting a femtosecond pulsed infared beam into the specimen to excite fluorescent dyes.

The 2-Photon scope will be used in a number of ways, including serial section block face imaging and categorizing neuronal cells into classes. Block face imaging will be accomplished through the use of a specially designed vibratome that will reside on the mechanical stage. Neurons will be classified using "Brainbow" mice in conjunction with immediate-early gene product imaging.

The Olympus FV1000 spectral confocal system was purchased through a Canadian Foundation for Innovation (CFI) grant and installed in August, 2011. It includes a BX81 upright microscope with 4X, X10, X40 oil, and X60 oil lenses. All lenses are high N.A. plan apochromats with DIC optics. The lasers are all diodes with lines at 405nm, 473nm, 559nm and 635nm. Fluorescent filters include DAPI, FITC, Tx-Red and Cy5 mounted on a motorized turret. Four PMT detectors, including two spectral and two filter-based, enable high-precision (1nm steps up to 100nm), high-resolution (2nm bandwidth), high-speed (100nm/ms) spectroscopy. The spectral scan unit is capable of capturing 16 frames per second at a resolution of 256 X 256 pixels or 4 frames per second at 512 X 512 pixels. This instrument is the only confocal to date that offers two means of spectral un-mixing through “normal” and “blind” deconvolution. A Prior X,Y,Z movement stage enables the automatic capture of tiled images for the production of large area composites.

The advantage of a confocal microscope over a conventional microscope is the ability to optically section samples by virtue of the confocal pinhole. This aperture is located in the light path in close proximity to the detectors and serves to remove out-of-focus illumination and thus capture thin (10 nm) optical slices in an image stack that can be rendered into 3-D movies (see associated videos).

The spectral confocal is a facility workhorse and is used for a multitude of functions mostly related to imaging immediate-early gene products.

The Hitachi H-7500 TEM was purchased in 2000 through a Natural Sciences and Engineering Research Council of Canada grant. It is a standard research TEM capable of 2nm resolution (theoretical = 0.2nm) and has a maximum accelerating voltage of 125K. The scope is equipped with a SIA-L11C digital camera with 16 megapixel resolution and the operating system has been upgraded to Windows XP. The stage is a goniometer enabling the production of 3-D images.

Because an electron microscope uses electrons rather than photons for imaging, the resolution limit is approximately 1000 times lower than what can be achieved with a light microscope. In addition, due to the small apertures employed, the depth of focus and depth of field are significantly greater than that of a light microscope.

The primary use of the scope is to image thin sections of rat neural tissue but it has also been used for several other procedures including colloidal gold labeling and negative staining.

Our in vitro electrophysiology lab contains a full suite of equipment for preparing live sections of brain tissue and performing intracellular recordings using patch-clamp techniques under visual guidance. The recording rig is based on an Olympus BX51-WI microscope with IR-DIC components and an IR-capable camera. Electrodes are fabricated on-site with a Sutter P-97 Flaming/Brown micropipette puller, and are positioned in the work area with two Sutter MP-225 micromanipulators. An Axon 700B amplifier and Digidata 1440A data acquisition system are used for data collection. For stimulus presentation, we have built a custom real-time control system based on a real-time linux workstation running RTXI. This allows real-time feedback to recorded neurons, permitting a full complement of 'dynamic clamp' techniques. For instance, with this rig we are able to simulate and insert fictive conductances into real neurons to assess how biophysical properties of the neural membrane contribute to excitability. We also use this rig to record the response of neurons in slice preparations to complex inputs that mimic time-varying features of neurons recorded in intact brains.

Our acute electrophysiology lab contains a fully equipped electrophysiology suite and a surgery preparation suite for recording neuronal activity in anesthetised rats. The recording studio contains a Kopf stereotaxic frame with multiple manipulators, a surgery microscope and a complete anaesthetizing unit. The recording studio contains a digital recording system consisting of amplifiers, analog to digital converters so that data can be recorded to a computer, and recording software through which amplifier parameters can be controlled. Currently, our systems allow simultaneous recordings from 128 channels; however, all systems are expandable to 256 channels. Each of these channels can be used both for recording local field potentials as well as the spiking activity of individual neurons. For our recordings, we use the high-end technology of silicon probes (Neuronexus). The silicon probes allow us to monitor activity of more than 100 neurons simultaneously. The recording sites can be arranged over a distance of millimeters, thus allowing the simultaneous recordings of neuronal activity in the various cortical layers and/or in multiple cortical columns. Importantly, the geometrically precise distribution of the recording sites also allows for the determination of the spatial relationship of the isolated single neurons. Using those technologies we are currently studying: 1) neuronal reorganization after stroke, 2) coding of sensory stimuli in the cortex, 3) role of spontaneous activity, and 4) effects of various drugs on cortical plasticity.

The Polaris group is equipped with extensive facilities for recording brain activity in behaving rodents. These facilities consist of five neural ensemble recording studios, each of which are made up of a control room housing the amplifiers and computers required for acquisition of the electrophysiological signals, and an experimental room housing the apparatuses on which the animals are tested. In each experimental room, the chronically implanted electrodes of the experimental subject are plugged into cables connected to a ceiling-mounted automatically rotating commutator, allowing the animal to rotate freely without twisting the cables; the commutator is in turn connected to the amplifiers by way of cables running through the ceiling into the adjoining control room. Video of the animal is simultaneously recorded in order to track behaviour. Additionally, one of the five studios is equipped for simultaneous drug delivery.

Each recording studio contains a digital recording system consisting of amplifiers, analog to digital converters so that data can be recorded to computer, and recording software through which amplifier parameters can be controlled. Currently, each of our systems allow for simultaneous recording from 128 electrode channels, which represents a practical limit imposed by current electrode technology; however, all systems are expandable to 256 channels. Each of these channels can be used both for recording local field potentials as well as the spiking activity of individual neurons. Typically, groups of four electrodes are twisted together to make what is called a tetrode, which can record spikes from up to 10-15 neurons simultaneously. Using a process akin to the triangulation used by radar systems to locate objects, we can determine how many cells a given tetrode is recording from and, more importantly, we can determine which of those cells any given spike is emanating from. Thus, using all 128 electrode channels, we are able to record from hundreds of individual neurons in a single animal.

Rats are implanted with electrode arrays called hyperdrives which permit fine tuning of electrode position, allowing targeted isolation of the neurons of interest. We custom design our hyperdrives using 3D-computer aided design (CAD) software, which are then produced using stereolighography (3D plastic printing) technology. These custom designed drives allow flexible targeting of multiple brain regions simultaneously, greatly increasing the sophistication of our studies.

Each recording studio has a separate system for controlling and delivering precisely timed rewards and stimuli, including brain stimulation reinforcement which permits the use of complex behavioural paradigms that would not be possible with conventional food reinforcement. These control systems can be programmed to either respond to keyboard input from the experimenter or to be triggered by specific behavioural or electrophysiological events recorded by the acquisition hardware, providing us a tremendous amount of flexibility in designing our experiments.

Planned workshop for room EP1271.
Expected Completion Date September 2011.
The workshop will be supervised by Geoff Minors, Senior Research Technologist. The workshop will be used for the fabrication and manufacturing of projects required and storage of materials.

Equipment:

• Small metal lathe 7" x 12" Capacity
• Bench top Milling Machine bed dimension 15-3/8" x 3-5/8"
• CNC Sherline Milling Machine 4 axis control
• Table Saw. Wood cutting
• Miter chop saw
• Soldering station with fume extraction
• Tools as required to manufacture parts
• Bench top space
• Tool cabinet with selection of hand tools
• SolidWorks Cad software. Used in design and development of parts
• Future items needed include:
  • Band Saw
  • Bench grinder
  • Bench vice
  • Hand tools
  • Sheet metal forming equipment
  • Jig saw
  • Electric sander
  • Shop vac

The Polaris group develops its own electronic circuits to adapt its data recording system to get reliability and good quality. These electronics (tetrode probe, silicon probe, single electrode) are composed to process data from the brain and manage stimuli, reward delivery and several controls (visual, auditory and electrical stimuli).

The Polaris group also develops Printed Circuit Boards (PCB) such as:

• Electrode Interface Boards (EIB) which adapt different kinds of probes to the Head Stage.
• Electronic circuits which convert high amplitude signals to the Transistor–transistor logic (TTL), triggering events, and amplification.

For some developments, Polaris researchers are using an open-source electronic prototyping platform based on flexible, easy-to-use hardware and software (http://www.arduino.cc). For other needs, the group is using a Field-Programmable Gate Array (FPGA). These systems allow researchers to manage data with good accuracy and a lot of flexibility.

Prototyping circuits are done with spice modeling (http://www.5spice.com). All the PCB are developed on Eaglecad (http://www.cadsoftusa.com) and are ordered from several PCB companies (ExpressPCB, http://www.expresspcb.com ; JetPCB , http://www.jetpcbassembly.com ; Silvercircuits, http://www.custompcb.com). All designs are imported into Computer-Aided Design (CAD) software (http://www.solidworks.com) to avoid mechanical conflicts with other parts. All the electronic parts come from electronic providers such as DigiKey (http://www.digikey.com), Mouser Electronics (http://www.mouser.com), or Robotshop (http://www.robotshop.com).

Lethbridge Brain Dynamics provides a variety of behavioral testing facilities to study neurophysiological and molecular mechanisms of spatial navigation, learning and memory in rats and mice. Behavioral paradigms/tasks are designed to investigate brain functioning during development, normal and pathological aging, and in various neurodegenerative diseases (e.g., Alzheimer's disease) and in animal models for neurological disorders (e.g., stroke, schizophrenia, drug addiction, epilepsy). The rodent's behavior can be tracked and/or filmed using both commercially available and custom designed tracking systems, and high-speed and conventional video systems, respectively. Most of the tasks are computer-controlled (commercial and home-written special algorithms) that enable both on-line and off-line analysis of the animal’s behavior and/or task modification. The behavioural tasks are ideally suited for electrophysiological (large-scale parallel neural recording), pharmacological (permanent or temporal inactivation of brain regions) and/or molecular imaging (large scale mapping of behavior-associated immediate early genes) studies in freely behaving animals. Available paradigms and tasks are outlined in the following table.