Molecular and cell biology
Tools and facilities to examine the structure and function of cells and biomacromolecules
Australian Proteome Analysis Facility (APAF)
The Australian Proteome Analysis Facility (APAF) has been providing mass spectrometry services for the analysis of proteins and proteome since 1995, with Q-tof, Orbitrap and Q-trap technologies coupled to nano-LC and UHPLC systems.
Services
APAF provides a range of proteomic services and expertise:
Contact
Australian Proteome Analysis Facility
Level 4, 4 Wally's Walk
Macquarie University NSW 2109
info.apaf@mq.edu.au
T: +61 2 9850 6201
Chromatography: FPLC: Akta Pure
Fast protein liquid chromatography system ideal for the purification and analysis of biomolecules. This system provides high performance, versatility and ease of use for low to medium pressure applications.
Used for: purification and analysis of biomolecules such as proteins using gel filtration, ion-exchange or affinity columns at analytical or preparative scale.
Specifications
- System pump: Piston pump, metering type
- Flow rate: up to 25 mL/min (0 to 20 MPa operating pressure)
- UV monitor: 190 - 700nm, up to 3 wavelengths (U9-M)
- Conductivity monitor
- Frac9-C fraction collector (Up to 576 fractions, 0.1 to 250 mL fraction volumes)
- Fraction vessel types:
- Deep well plates, 96, 48 or 24 wells
- Tubes 3, 5, 8, 15, 50 ml
- Bottle, 250 ml
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
4 Wally’s walk, room 311 (MUCAB)
Bookings – only after induction and training
Chromatography: FPLC: Akta Start
The Akta Start is a compact low pressure FPLC system suitable for the separation and analysis of biomolecules. This system provides is highly intuitive and can be operated using a touch screen.
Used for: quick purification of proteins or buffer exchange using 1-12mL columns eg HiTrap columns.
Specifications
- System pump: Peristaltic pump, single channel
- Flow rates: up to 5 mL/min (0 - 0.5 MPa operating pressure)
- Fixed wavelength UV monitor (280 nm)
- Conductivity monitor
- Frac30 fraction collector (Up to 30 fractions, 0.5 to 15 mL fraction volumes)
- Fraction vessel types:
- 1.5 ml/2 ml microcentrifuge tubes
- Tubes 5, 12, 15 mL
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
4 Wally’s walk, room 311 (MUCAB)
Bookings - only after induction and training
Chromatography: FPLC: Bio-Rad NGC Quest Plus system
The Bio-Rad NGC Quest Plus is a chromatography system for purifying all forms of biomolecules and optimising purification protocols.
Used for: purification and analysis of biomolecules such as proteins using gel filtration, ion-exchange or affinity columns at analytical or preparative scale.
Specifications
- F10 Pump: Flow rate up to 10 mL/min (0 to 25 MPa operating pressure)
- Simultaneous multi-wavelength detection of to four wavelengths
- Conductivity meter
- BioFrac fraction collector (up to 180 tubes, 0.02 - 250 mL fraction volumes)
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
4 Wally’s walk, room 311 (MUCAB)
Bookings - only after induction and training
Flow cytometer: BD Influx cell sorter
Flow cytometer is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles based on their optical properties. The BD influx cell sorter include a cell sorting option.
Used for:
- Cell counting
- Cell sorting
- Cell characteristics and function
- Microorganisms and biomarker detection
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
6 Wally’s walk, room 235
Bookings – only after induction and training
Flow cytometer: Beckman Coulter CytoFlex S
Flow cytometer is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles based on their optical properties.
Used for:
- Cell counting
- Cell characteristics and function
- Microorganisms and biomarker detection
Specifications
- 96-well plate sample loader
- Four laser options.
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Rates
Discounted rates apply for Macquarie university researchers.
Location
6 Wally’s walk, room 235
Bookings – only after induction and training
Spectrometer: Circular dichroism: Jasco J-1500
The J-1500 circular dichroism (CD) spectropolarimeter allows simultaneous measurement of 4 modes including CD, linear dichroism (LD), and absorbance. We have a range of accessories including long pass cut-off filters for excitation fluorescence spectroscopy, film stretchers for LD, Couette flow cells for LD, multiple -position thermostatted cuvette holder. Users are generally expected to provide their own quartz cuvettes
Circular dichroism (CD) measures the difference in absorbance of left- and right- handed polarized light of chiral molecules, which is commonly used to analyse the conformation of macromolecules, particularly protein secondary structure.
Linear dichroism (LD) measures the difference in absorption of light linearly polarised parallel and perpendicular to the orientation axis. LD can be used to give information about the conformation and orientation of structures with orientated molecules such as DNA complexes, fibrous proteins such as (e.g. cytoskeleton and amyloid
proteins) and membrane peptides/proteins in liposomes.
The J-1500 is a hybrid instrument consisting of a variable wavelength polarimeter for CD or LD and absorption spectrophotometer (~180-900 nm, Far-UV to Vis range). The J-1500 is fitted with a 6-position multi-cell changer
and Peltier temperature control unit. This set-up is ideally suited to:
- Determine protein secondary structure and analyse conformational changes
- Nucleic acid structure determination and changes upon binding or melting
- Other thermodynamic parameters and kinetics based measurements
Used for: routine solution state experiments on chiral molecules with a range of more sophisticated experiments possible including temperature controlled, kinetics, linear dichroism, fluorescence detected CD and LD.
Specifications
- Operates from 950 – 163 nm
- Light source : 150 W air-cooled Xenon lamp or 450 W water-cooled Xenon lamp (factory-installed option)
- Detector : Head-on photomultiplier tube PMT
- Optional photomultiplier tube PMT
- Optional InGaAs
- Modulator : Piezoelastic modulator
- Measurement wavelength range : 163 to 950 nm
- Wavelength accuracy : 0.1 nm from 163 to 250 nm
- 0.2 nm from 250 to 500 nm
- 0.5 nm from 500 to 800 nm
- Spectral bandwidth: 0.01 to 16 nm
- Slit width : 1 to 4000 μm
- Digital Integration Time (D.I.T.) : 0.1 msec to 30 sec.
- Scanning mode : Continuous scan
- Step scan
- Auto response(D.I.T) scan
- Scanning speed : up to 10000 nm/min
Contact
Alison Rodger or Sophie Goodchild
4 Wally’s walk, laboratory 302
Department of Molecular Sciences
Macquarie University
sophie.goodchild@mq.edu.au
T: 02 9850 8235
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 302 (restricted access)
Spectrometer: Circular dichroism: Jasco J-810
Circular dichroism (CD) measures the difference in absorbance of left- and right-handed polarized light, which can be a powerful tool for identification and characterisation of chiral molecules. The J-810 is a hybrid instrument consisting of a variable wavelength polarimeter and absorption spectrophotometer (~180-900 nm, Far-UV to Vis range). Our J-810 is also fitted with an Optical Rotation Dispersion (ORD) module and Peltier temperature control unit making it ideally suited to measure optical purity/identification of small molecules and natural products chemistry.
Specifications
- Light source: 150 W Xenon arc lamp (air cooled)
- Wavelength range: ~180 to ~900 nm (standard)
- Four Channel Simultaneous Data Acquisition: Input channels: 2 internal plus 2 external signals can be acquired simultaneously
- ORDM-401 unit fitted
Contact
Alison Rodger or Sophie Goodchild
4 Wally’s walk, laboratory 302
Department of Molecular Sciences
Macquarie University
sophie.goodchild@mq.edu.au
T: 02 9850 8235
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 302 (restricted access)
Spectrometer: Light Scattering: Malvern Zeta Sizer Nano SP
The Malvern Zetasizer Nano is a light scattering system suitable for characterisation of colloid dispersions, nanoparticles and macromolecules such as polymer and protein solutions (3.8 nm to 100 μm, concentration ~0.1ppm to 40%w/v, pH 1-13, sample dependent). Three different light scattering measurements can be performed:
- Dynamic Light Scattering (DLS) – is used to measure the diffusion of particles under Brownian motion, and convert this to a size distribution using the Stokes-Einstein relationship. Non-invasive back-scatter (NIBS) technology is incorporated to give better sensitivity and the ability
to measure particles at high concentration. - Electrophoretic Light scattering (ELS) – is used to measure zeta potential. An electric field is applied to the sample and mixed mode measurement, phase analysis light scattering (M3-PALS) is used to measure electrophoretic mobility and determine a zeta potential distribution.
- Static Light Scattering (SLS) – is used to determine the molecular weight (> ~1KDa) of proteins and polymers. The scattering intensity at a range of concentrations is measured to construct a Debye plot. From this the weight-average molecular weight and second virial coefficient can
be calculated to provide a measure of protein solubility.
Specifications
- Measurement range: 3.8nm – 100 microns diameter (sample dependent)
- Measurement principle: Electrophoretic Light Scattering
- Minimum sample volume: 150µL (20µL using diffusion barrier method)
- Accuracy: 0.12µm.cm/V.s for aqueous systems using NIST SRM1980 standard reference material
- Sensitivity: ~0.1-10mg/mL (BSA/Lysozyme)
- Temperature control range: 0°C - 90°C +/-0.1
- Light source: He-Ne laser 633nm, Max 4mW
Contact
Alison Rodger or Sophie Goodchild
4 Wally’s walk, laboratory 302
Department of Molecular Sciences
Macquarie University
sophie.goodchild@mq.edu.au
T: 02 9850 8235
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 302 (restricted access)
Spectrometer: UV-visible : Jasco V-760
The V-760 is a double-beam UV-Visible spectrometer that measures light absorption, reflectance or transmittance in the visible to ultraviolet region (187-900 nm). The extended photometric linearity of the V-760 (up to 6 AU) enables measurement of highly absorbing samples which is particularly useful for materials with low transmission properties such as solid films. The V-760 is also fitted with a 6-position multi-cell changer and Peltier temperature control unit making it an ideal UV-vis instrument for kinetic and thermodynamic experiments.
Specifications
- Optical System: Czerny-Turner mount, double monochromator, fully symmetrical double beam
- Light Source: Halogen lamp, deuterium lamp
- Wavelength range: 187 to 900 nm (+/-0.1 nm at 656.1 nm)
- Photometric Range: -4-6 AU +/-0.3 %T
- Scanning Speed: 10-400 nm/min
Contact
Alison Rodger or Sophie Goodchild
4 Wally’s walk, laboratory 302
Department of Molecular Sciences
Macquarie University
sophie.goodchild@mq.edu.au
T: 02 9850 8235
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 302 (restricted access)
Spectrometer: Nuclear Magnetic Resonance: Bruker AVIIIHD 400 MHz NMR Spectrometer
The Avance 400 MHz NMR spectrometer, with the SampleXpress 60 Holder Autosampler and Iconnmr automation software, is the workhorse of the NMR facility. Samples are conveniently submitted and queued for analysis.
Used for: routine solution state 1D and 2D experiments on small molecules
Specifications
- 5mm BBFO SmartProbe™ (19F/31P-109Ag)
- Actively-shielded high performance Z-gradient
- 19F{1H} and 2D 1H/19F correlation spectroscopy
- Operating temperature range: -150°C to +150°C
- Ascend 400 MHz (9.4 T) Magnet
- Drift rate < 4.0 Hz/hr
- BCUII (Bruker Chiller Unit)
- Accessible temperatures ≥ 200 K
- SampleXpress 60 Holder Autosampler
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 014 (highly restricted access)
Spectrometer: Nuclear Magnetic Resonance: Bruker AVIIIHD 500 MHz NMR Spectrometer
The Avance 500 MHz NMR spectrometer is set up to run variable temperature experiments (-70°C to 100°C) routinely. Very low temperature experiments (-70°C to -150°C) can also be run with use of the liquid nitrogen evaporator and staff assistance. It is highly sensitive for carbon detection, thus it is
often utilized to acquire data for the complete characterization of small to medium sized organic molecules.
Used for: variable temperature solution state experiments, characterization experiments
Specifications
- 5mm BBFO SmartProbe™ (19F/31P-109Ag)
- Actively-shielded high performance Z-gradient
- 19F{1H} and 2D 1H/19F correlation spectroscopy
- Operating temperature range: -150°C to +150°C
- Ascend 500 MHz (11.7 T) Magnet
- Drift rate < 5.0 Hz/hr
- Magnet leg upgrade to damp vibrations above 3.8 Hz
- BCUII (Bruker Chiller Unit)
- Accessible temperatures ≥ 200 K
- SampleCase 24 Holder Autosampler
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 014 (highly restricted access)
Spectrometer: Nuclear Magnetic Resonance: Bruker AVII 600 MHz NMR Spectrometer
The AVII 600 MHz NMR spectrometer is equipped with cryoprobe and is utilized for experiments where the upmost of sensitivity is required, such as protein studies and natural product characterisations.
Used for: characterisation of natural products, protein NMR structure determination. Variable temperature work is not permitted.
Specifications
- 5 mm TXI Cryoprobe with Z-gradient (1H/13C/15N/2H observe)
- 3 high power channel operation
- SampleXpress Lite 16 Holder Autosampler
- BCU05 (Bruker Chiller Unit)
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Rates
Discounted rates apply for Macquarie university researchers.
Location
4 Wally’s walk, room 014 (highly restricted access)
Surface Plasmon Resonance (SPR): Biacore X100 biosensor
Protein-protein and protein-ligand interactions can be studied using surface plasmon resonance. A protein or a ligand is bound to the surface of a sensor chip (purchased by the user from Biacore) using one of several standard chemical methods, e.g. a biotinylated ligand may be bound to a streptavidin chip. Buffer containing the analyte is then allowed to flow over the surface of the chip, with binding and release monitored in real time.
Used for: studying protein-ligand interaction
Specifications
- Automatic sampling loading
- Size limit: > 100 Da
- Typical concentrations (proteins): pM - μM range
- Sample volume50-120 μl
- Flow rate: 1-100 μl/min
- Temperature: 4 - 45°C
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
4 Wally’s walk, room 311 (MUCAB)
Bookings - This instrument will be available for booking in January 2020
Thermal analysis: Isothermal Titration Calorimetry: Microcal Auto iTC200
The MicroCal Auto-iTC200 is a fully automated, low volume, highly sensitive isothermal titration calorimeter. Binding affinity, stoichiometry, enthalpy and entropy are measured in solution in a single experiment, without labeling.
Used for: characterising molecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids and other biomolecules. Can be used to confirm binding, determine stoichiometry, detect protein-protein or protein-ligand interactions.
Specifications
- Measures Affinity (Kd), enthalpy (ΔH), entropy (ΔS) and stoichiometry
- Sample capacity: 4x 96 well plates
- Sample volume: 370 μL
- Cell volume: 200 μL
- Injection syringe volume: 40 μL
- Temperature range: 2 - 80˚C
Contact
Dr Aleksei Marianov
4 Wally’s Walk, room 221
Macquarie University
aleksei.marianov@mq.edu.au
T: 02 9850 4219
Location
4 Wally’s walk, room 311 (MUCAB)
Bookings - only after induction and training