News, Events and Workshops

The list of news and events is by no means a comprehensive one, so if you have anything you'd like to add email Sharon at

  • News from 2017

  • News from 2016:

    Paper of the Month

    Muhsin-Sharafaldine, M-R., Saunderson, S.C., Dunn, A.C., Faed, J.M., Kleffmann, T. and McLellan, A.D (2016) Procoagulant and immunogenic properties of melanoma exosomes, microvesicles and apoptotic vesicles. Oncotarget, 7(35):56279-56294. doi: 10.18632/oncotarget.10783.

    Muhsin POM

    Paper of the Month

    Kumar, S.V., Scottwell, S.Ų., Waugh, E., McAdam, C.J., Hanton, L.R., Brooks, H.J.L. and Crowley, J.D. (2016) Antimicrobial Properties of Tris(homoleptic) Ruthenium(II) 2-Pyridyl-1,2,3-triazole "Click" Complexes against Pathogenic Bacteria, Including Methicillin-Resistant Staphylococcus aureus (MRSA). Inorganic Chemistry, 55:9767-9777. DOI: 10.1021/acs.inorgchem.6b01574.

    Kumar POM

    Workshop: Structure Preservation by High-Pressure Freezing and Freeze Substitution

    On Thursday the 24th of November 2016 the OCEM will host a workshop on high pressure freezing and how it can be used to improve structural preservation. The morning will consist of talks from students and staff who are currently using high pressure freezing in their projects. The afternoon will feature a lab visit. The cost is $20 per lab group (to cover the cost of coffee and room booking). For enquiries contact

    HPF Workshop

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 20th of October, in the seminar room of the Benham (Zoology) building.

    Brian Tong, Department of Microbiology and Immunology
    Cryo-EM of a virus specific for bacterial phytopathogen

    Nadishka Jayawardena, Department of Microbiology and Immunology
    Nanomaterials from waste

    OCEM MMM Oct

    Paper of the Month

    Craw, D. and Lilly, K. (2016) Gold nugget morphology and geochemical environments of nugget formation, southern New Zealand. Ore Geology Reviews, 79:301-315.

    Craw POM

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 15th of September, in the seminar room of the Benham (Zoology) building.

    Professor Frank E. Brenker, Geoscience Institute, Goethe University, Frankfurt
    "The hunt for Stardust"

    OCEM MMM Sept

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 18th of August, in the seminar room of the Benham (Zoology) building.

    Megan Elder, Department of Anatomy
    "Illuminating sAPPa's effect on GluA1"

    Andrew McNaughton, Otago Centre for Confocal Microscopy
    "Does this confocal make my AFM look big?"

    OCEM MMM August

    Paper of the Month

    Raymond, M.R. and Wharton, D.A. (2016) The ability to survive intracellular freezing in nematodes is related to the pattern and distribution of ice formed. Journal of Experimental Biology, 219:2060-2065 doi:10.1242/jeb.137190.

    Raymond POM

    Paper of the Month

    Hampton, H.G., McNeil, M.B., Paterson, T.J., Ney, B., Williamson, N.R., Easingwood, R.A., Bostina, M., Salmond, G.P., Fineran, P.C. (2016) CRISPR-Cas gene-editing reveals RsmA and RsmC act through FlhDC to repress the SdhE flavinylation factor and control motility and prodigiosin production in Serratia. Microbiology, 162(6):1047-58. doi: 10.1099/mic.0.000283.

    Hampton POM

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 21st July, in the seminar room of the Benham (Zoology) building.

    Sally Kim, Department Of Zoology
    Does deformed wing virus affect Varroa sensitive hygiene in Honeybees?

    Dave Craw, Department Of Geology
    "Gold: nuggets and nanoparticles"

    OCEM MMM July

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 16th of June, in the seminar room of the Benham (Zoology) building.

    Monica Tromp, Department of Anatomy
    "SEM-EDS analysis of microfossils extracted from prehistoric human dental calculus in Oceania"

    Lien Sabrina Reichel, School of Pharmacy
    "Preservation methods to study nanoparticle uptake into human cerebral microvascular endothelial cells (hCMEC/D3) for electron microscopy"

    OCEM MMM June

    Paper of the Month

    Azhari, H., Strauss, M., Hook, S., Boyd, B.J. and Rizwan, S.B. (2016) Stabilising cubosomes with Tween 80 as a step towards targeting lipid nanocarriers to the blood-brain barrier. European Journal of Pharmaceutics and Biopharmaceutics, 104:148-155. doi: 10.1016/j.ejpb.2016.05.001

    azhari POM

    Submarine Volcano Project Wins EM Student Award

    Congratulations to Arran Murch who has received the April 2016 EM Student Award for his project "Implications of ash-particle characteristics for fragmentation during a big explosive submarine eruption". The award entitles the winner to 15 hours electron microscope time which Arran will use on the Zeiss SEM to image ash particles from submarine volcanic eruptions and measure the population, texture and size range of the bubbles. He will also use EBSD techniques on to quantify crystals of ash grains. Submarine eruptions account for around 85% of the total volcanic activity on earth but are underrepresented in the literature. Better understanding how magma evolves during ascent will lead to better predictions and mitigation of eruption hazards. Arran is a PhD student in the Geology Department and is supervised by Professor James White. The closing date for the next EM Student award is the 1st of September. For more information about the award and application forms visit the EM Student Award webpage.

    New Project Policy

    The Microscopy NZ annual general meeting will be held at 2PM on Wednesday the 8th of June. We will be using the videoconferencing service 'Zoom' which can receive video and audio from either computer or telephone (more information below). You can either call in, or if preferred the Dunedin group can call you if you let us know in advance the phone number you would like to receive the call on. There will be MNZ members in the following areas joining the AGM:
    Dunedin: AVC2, Information Services Building, University of Otago. Contact person is Allan Mitchell (
    Auckland: Contact person is Adrian Turner (
    Rotorua: Lloyd Donaldson (
    Christchurch: TBC
    If you are from Waikato or Wellington and would like to participate then please get in touch and as we are looking for contact people in these areas.

    New Project Policy

    OCEM: New projects policy involving PhD, MSc, Honours/PGDipSci students and postdoctoral fellows, assistant research fellows and research technicians:
    1. For PhD, MSc, Honours/PGDipSci students: To discuss the requirements of a new project with a staff member of the OCEM, it is expected that the lead supervisor(s), and supervisor(s) with EM expertise/experience, attend at least the first meeting along with the postgraduate student. A scheduled meeting may be postponed by an OCEM staff member if the supervisor(s) indicated above are absent from the meeting.
    2. For postdoctoral fellows, assistant research fellows and research technicians: To discuss the requirements of a new project with a staff member of the OCEM, it is expected that the lead Principal Investigator, and other Lead or Associate Investigators with EM expertise/experience, attend at least the first meeting along with the staff member. A scheduled meeting may be postponed by an OCEM staff member if the investigator(s) indicated above are absent from the meeting.
    3. At the first meeting, it is expected that an account code is provided for the new project to charge OCEM expenses to. The expiry date of this account code is also required. Authorization is also required from the lead supervisor or lead Principal Investigator that expenses accrued in the OCEM by the new project can be debited to the account code provided.
    4. This policy is effective from February 2016.

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 19th of May, in the seminar room of the Benham (Zoology) building.

    Abdullah Barazanchi, Department of Oral Rehabilitation
    "Evaluation of a novel 3-D printed cobalt chromium alloy for prosthodontic applications"

    Mihnea Bostina, Department of Microbiology and Immunology
    "Direct Electron Detectors and the race to high resolution"

    OCEM MMM April

    Paper of the Month

    Loch, C., Boessenecker, R.W., Churchill, M. and Kieser, J.(2016) Enamel ultrastructure of fossil and modern pinnipeds: evaluating hypotheses of feeding adaptations in the extinct walrus Pelagiarctos. Naturwissenschaften, 103(5-6):44. doi: 10.1007/s00114-016-1366-z.

    Loch POM

    High Pressure Freezing Now Available in New Zealand

    The Leica EM PACT 2 High Pressure Freezer has arrived and we are now able to cryo-fix samples up to 200µm thick. Until now we had been limited to slam freezing, which produces only ~10µm of vitrified ice. The EM PACT 2 will freeze samples within milliseconds, ensuring simultaneous immobilisation of all macromolecular components and fantastic ultra-structural preservation. This will also facilitate the study of dynamic processes as cells can be live-imaged and then frozen using the Rapid Loader. This is the first High Pressure Freezer in New Zealand and was funded by Lottery Health Research, the Otago School of Medical Sciences and the Department of Anatomy. There are already 8 projects using the freezer, involving looking at bee antennae, blood vessels, and zebrafish. If you would like to discuss whether the High Pressure Freezer is suitable for your project contact Allan Mitchell.


    OCEM Autumn Newsletter

    The 2016 OCEM newsletter is now available for download. In this issue: arrival of the high pressure freezer; Avizo software installation; oscillating diamond knives; monthly microscopy meetings; funding successful for a direct detector; recent publication; EM student award; PhD projects; cryo-EM information; staff news.

    PDF Graphic

    OCEM 2016 Newsletter

    OSMS Photography Competition

    Entries are sought for the 2016 OSMS Photography Competition. The theme is Be Curious. This popular competition is once again being run in conjunction with the NZ International Science Festival (Be Curious) and all photographs will be on display in the Art Society Rooms, Dunedin Railway Station, during the Festival (8-16 July 2016). This photographic display is one of the most-visited events in the NZISF and has even inspired internet blogs in the past. This year we hope to make the photographs available in an on-line gallery. There are no restrictions on the type of photograph that is submitted - they could be of scientific work undertaken at Otago, but could equally be a photograph taken while out mountain biking. The only criteria are that the photograph should be taken by staff or students of the Otago School of Medical Sciences and the photograph should illustrate the "Be Curious" theme. If the photographs have previously been submitted to a journal (as part of a scientific paper) then it is the responsibility of the submitter to ensure that no copyright regulations are contravened.

    Prizes will be made in a number of categories:
    - the best entries from a member of the academic staff, general staff and students will each receive a framed version of their image and a $50 book voucher.
    - The best photo encapsulating Te Ao Maori (the Maori world) will receive a framed version of their image and a $50 book voucher. ( may provide some assistance with this).
    - Genetics Otago will provide a prize for the best photo with a 'gene theme'.
    - The Webster Centre will provide a prize on the general theme of 'infectious diseases research'.
    - The Brain Health Research Centre will provide a prize for the best photo with a neuroscience theme.
    - The overall winner will receive, in addition, book vouchers to the value of $100.

    Entries should be sent to Mrs Susan Butt ( The closing date for the competition is 17 June 2016.

    OCEM Calendar

    The OCEM calendar has been tremendously popular. Thank you to everyone who contributed. You can pick up a calendar from the unit or download a printable copy here:

    PDF Graphic

    2016 OCEM Calendar

    Paper of the Month

    Jing, Y., Liu, P. and Leitch, B. (2016) Region-specific changes in presynaptic agmatine and glutamate levels in the aged rat brain. Neuroscience, 312:10-18.

    Jing POM

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 21st of April, in the seminar room of the Benham (Zoology) building.

    Martina Kirilova, Department Of Geology
    "Introduction to 3D Visualization and Image Analysis with Avizo"

    Mike Jennings, Department Of Physiology
    "Tomography and Modelling of Primary Cilia"

    OCEM MMM April

    Paper of the Month

    Schleifenbaum, S., Prietzel, T., Aust, G., Boldt, A., Fritsch, S., Keil, I., Koch, H., Möbius, R., Scheidt, H.A., Wagner, M.F.X . and Hammer, N. (2016) Acellularization-Induced Changes in Tensile Properties Are Organ Specific - An In-Vitro Mechanical and Structural Analysis of Porcine Soft Tissues. PLoS ONE 11(3): e0151223. doi:10.1371/journal.pone.0151223.

    Schleifenbaum POM

    Monthly Microscopy Meeting

    The next meeting is at 9:00AM Thursday the 17th March in G05, 71 Fredrick Street.
    Ryan Murphy-Dawes, Department of Microbiology and Immunology
    "Electron Tomography of Cancer Cells Infected with Seneca Valley Virus"

    Bryce Peebles, Department of Marine Science
    "Determining Changes in Mollusc Shell Ultrastructure by using SEM"

    OCEM MMM March

    2017 New Zealand Conference on Microscopy

    The date of the 2017 New Zealand Conference on Microscopy has been announced. The conference will run from Tuesday the 31st of January - to Friday 3rd February 2017 at the Auckland University of Technology.

    MNZ 2017

    Paper of the Month

    D Craw, D MacKenzie & P Grieve (2015) Supergene gold mobility in orogenic gold deposits, Otago Schist, New Zealand, New Zealand Journal of Geology and Geophysics, 58:2, 123-136, DOI: 10.1080/00288306.2014.997746

    Craw et al 2015


    In early February 2016 the University will be receiving a visit from Helmut Gneagi (of Diatome). While he is visiting we will run a workshop on the 12th and 15-18th February "Visualisation of cellular structures at high resolution: sample preparation, data collection and image processing". The workshop will consist of morning lectures (sample preparation, image processing, image formation, fourier transformation, electron tomography) and afternoon practicals (high pressure freezing, sectioning, electron tomography, reconstruction, visualisation).

    Cryo-EM Declared Method of the Year 2015

    Nature Methods has devoted their most recent issue to cryo-EM. "The end of 'blob-ology': single-particle cryo-electron microscopy (cryo-EM) is now being used to solve macromolecular structures at high resolution." Read the full editorial.

    News from 2015:

    November Microscopy Meeting

    At this month's Microscopy Meeting (November 19th 9AM) we will hear from Virginia Toy and Joe White about their use of synchrotron CT, EDS, EBSD, FIB-SEM, TEM and just about every acronymised electron microscopy technique under the sun.

    Microscopy November Meeting

    Prosthodontics and Alzheimer's Treatment Research to Benefit from Free EM Time

    Congratulations to Megan Elder (Department of Anatomy) and Abdullah Barazanchi (Department of Oral Rehabilitation) on their successful applications to the EM Student Award.

    Abdullah's project "Evaluation of a novel 3D printed cobalt chromium alloy for clinical dental applications" hopes to advance alloys used in clinical dentistry as the bonding of porcelain to underlying metallic substructures is currently one of the most common procedures fixed in prosthodontics. He will use back-scatter imaging on the SEM to anaylse fracture models.

    Megan's project "Localizing sAPPa-induced GluA1 synthesis within the dendritic ultrastructure" will use correlative microscopy to test whether GluaA1 subunits are likely to contribute to altered neuronal plasticity and improve our understanding of Alzheimer's disease. First Megan will use fluorescent immunolabelling to mark newly synthesised GluA1 proteins before proceeding to use the TEM to visualise the signal in the dendritic ultrastructure.

    The EM Students Award covers up to 15 hours electron microscope usage and technical support time. Applications for the next round of awards closes on 1st April 2016.

    Looking at brains in a new way: Mapping its wiring diagram down to the level of single connections

    Jeff Lichtman

    The Promises (and Perils) of Connectomics

    Jeff Lichtman

    News from 2014:

    Allan Receives OSMS Research Support Award for Distinguished Contribution

    On the 17th December Allan Mitchell (OCEM Manager) received the 'OSMS Research Support - Distinguished Contribution' Award. This award rewards excellence and sustained contribution to a Department and the School over many years. Allan Mitchell's contribution over 40 years easily fulfils these criteria. Congratulations Allan!

    Sharon on Parental Leave

    OCEM technician Sharon Lequeux is on parental leave until mid-August 2015. If you need to discuss previous projects or work that Sharon has been involved with please contact OCEM Manager Allan Mitchell (

    EM Student Award Winners

    Congratulations to Gemma Cotton and Jenny McDowell who are recipients of the September 2014 EM Student Award which grants the students 15 hours electron microscope time. Gemma is being supervised by Dr. Carla Meladandri in the Department of Chemistry. Her project is titled 'Application of Antibacterial Silver Nanocomposite Materials for Treatment and Prevention of Periodontal Disease' and aims to incorporate these antimicrobial silver nanoparticles into a gel matrix for use preventing and arresting oral bacterial infections. Jenny is supervised by Prof. Richard Cannon in the Department of Oral Sciences. Her PhD project 'An evaluation of the chemical and morphological changes to juvenile bone, when exposed to a marine environment' will look at the effect water has on bone degradation after death.

    3D Electron Microscopy Workshop, 4th December 2014

    3d EM workshop

    The workshop will provide an introduction at theoretical and practical level covering the main aspects of electron microscopy techniques from sample preparation to data collection and image processing. There will be a focus on the practical aspects of image processing tools necessary for three-dimensional reconstruction.
    The course is aimed at 'innocent' beginners of transmission electron microscopes in biological sciences.
    Fourier Transform / Specimen preparation / Cryo-EM data collection / Intro Linux / Intro image processing (IMOD,SPARX,Chimera)
    To register email

    9:00 Introduction/cryo-EM
    9:30 The EM lab
    10:00 Fourier Transform
    10:30 Coffee break
    11:00 Specimen preparation
    11:30 Cryo data collection
    12:00 Intro Linux
    12:30 Lunch
    Demos in the afternoon:
    13:30 Intro Image processing
    14:00 2D alignments
    14:30 3D reconstruction
    15:00 Tea break
    15:30 IMOD & SPARX
    16:00 Visualization (Chimera)
    16:30 Q&A

    Seminar: High Pressure Freezing

    Allan Mitchell (Manager of the OCEM) will give a talk at the Anatomy Department's monthly seminar on Tuesday the 23rd of September at 1PM in the D'Ath lecture theatre. The talk will be about high pressure freezing techniques.

    Seminar: Changes in the Basement

    Allan Mitchell (Manager of the OCEM) has worked in support role for 35 year but within the constantly changing and evolving environment of the Electron Microscopy Unit. These changed have been driven by changes in technology, applications, expectations and by different funding models. He will talk about the need for continuity within change and the role of general staff members in providing that continuity. The talk is from 2.15-3PM on Thursday the 28th of August at the General Staff Conference.

    Seminar: The Matrix-Cilium-Golgi Continuum

    Mike Jennings

    Michael Jennings will present his PhD thesis "The Matrix-Cilium-Golgi Continuum" from 1-2PM on Friday the 22nd of August in the seminar room on the 9th floor of Dunedin Hospital. Michael was superivised by Professor Rob Walker and Associate Professor Tony Poole. There will be a light lunch available from 12.45PM.

    Beulah Leitch Louise Parr-Brownlie

    Neurological Foundation of New Zealand Funding For Anatomists

    Congratulations to Dr. Beulah Leitch and Dr Louise Parr-Brownlie on their recent success acquiring funding from the Neurological Foundation of New Zealand. Beulah's project "Ultrastructural identification of newly synthesised receptor proteins at activated synapses" and Louise's project "Characterising basal ganglia synapses onto motor thalamus neurons in health and Parkinson's disease" will both utilise transmission electron microscopy. To read more about the upcoming projects check out the Anatomy Department's news page.

    Alaa Bekhit

    Shock treatment makes waves

    Dr. Alaa Bekhit (Department of Food Science) has had his research featured in the Otago Daily Times. The research has been using short bursts of high-voltage electricity to improve the tenderness of red meat. Alaa and his team used the TEM to look at samples of beef.

    2014 Early Career Award winners named

    Dr. Khaled Greish

    Congratulations to TEM user Dr. Khaled Greish, a Senior Lecturer in the Department of Pharmacology and Toxicology, who was announced as one of the winners of an Early Career Award for Distinction in Research. His research focuses on designing novel anti-cancer nanomedicine and has resulted in two approved patents.

    Proof of Concept Competition

    Congratulations to TEM users Dr. Carla Meledandri and Dr. Don Schwass who won Otago Innovation's Proof of Concept Competition in 2011 and are on the brink of having their idea to eliminate bacteria around dental fillings being turned into a commercial product.

    Meledandri Schwass

    Quite an Effort!

    Allan Mitchell

    Today (4th June) marks 40 years that OCEM manager Allan Mitchell has been working for the Department of Anatomy at the University of Otago. The OCEM and OCCM unit went out for lunch to celebrate this milestone. There will also be recognised more formally at an event in a months time (details to be confirmed).

    Congratulations to Karen Reader

    Today (4th June) Karen Reader handed in her doctoral thesis "Quantitative ultrastructural differences in the cytoplasm of prepubertal lamb and adult ewe oocytes". Karen used the JEOL 6700F FE-SEM to take micrographs of semi-thin sections of resin embedded oocytes. She then used stereological methods to quantify mitochondria and other organelles in the oocytes. She now plans on completing a writing bursary and will then consider doing post-doctoral study.

    Seminar: FIB-TEM: Exploring Earth Materials with Ions and Electrons

    Dr. Richard Wirth will be presenting a seminar on Friday the 13th of June at 1100 in the Blue Lecture Theatre (located in the Dental School). He is visiting from the Helmholtz Centre Potsdam (GFZ German Research Centre for Geosciences) on a fellowship with the Mineralogical Society of America.

    Focused ion beam techniques have been applied in Geosciences since 10 -15 years. The basic principle of FIB is using accelerated Ga-ions to sputter material from a target. At the beginning of FIB application in Geosciences it was utilized as a tool to prepare site-specific samples for transmission electron microscopy (TEM). FIB enables sputtering electron transparent foils with typical dimensions 15 x 10 x 0.150 µm from precisely that location we are interested in. That capability increased the demand of TEM use in Geosciences substantially. Meanwhile, the availability of so called DualBeam devices, which are operating an ion column simultaneously with an electron column (FIB-SEM), has widened the application of FIB technique substantially. DualBeam machines are used not only for TEM sample preparation but also as micromachining tools, for orientation contrast imaging, 3D imaging, 3D cross sectioning, 3D EBSD and 3D EDS analysis. The combination of ion and electron techniques generated major progress in micro- and nano-structural analyses in Geosciences. Site-specific foils prepared from any material in Geosciences - from diamond to sedimentary rocks and to materials in Geobiology - cannot only be used for TEM investigations but also for Synchrotron FTIR, Brioullin spectroscopy, NanoSIMS and X-Ray microscopy investigations. Examples of different FIB-TEM applications in Geosciences are presented: nano-inclusions in diamond, EBSD on microcrystalline diamond (carbonado), 3D imaging of unusual grain boundaries in marble, nano-porosity in gas shale, distribution and behaviour of organic material in sediments, natural composite materials in a deep sea sponge (monorhaphis cuni) and Paleoproterozoic phosphogenesis in the 2 Ga years old Zaonega Formation.

    Richard Wirth

    OCEM 2014 Newsletter

    The 2014 OCEM newsletter is available as a PDF. The newsletter includes articles about the new JEM-2200FS Cryo-TEM, our new Academic Director, the 3D EM workshop, visiting research fellow Dr. Mike Strauss, recent publications, and workshops/keynotes speakers at the 2015 MNZ conference.
    PDF Graphic

    OCEM Electronic Newsletter

    Three Dimensional Electron Microscopy Workshop

    workshop workshop

    Three Dimensional Electron Microscopy Seminars Timetable

    Below is the timetable of seminar topics for Monday 31st March - Thursday the 3rd April. All morning seminars will be held in room 713 Pharmacy Building.

    Monday 31st March
    0900-0930 Introduction (Mihnea Bostina): Organisation, EM Software, Structural Biology and EM, Cryo-EM.
    0930-1000 Interaction of Waves and Particles with Matter (Sigurd Wilbanks): Electrons, X-rays and neutrons; absorption, scattering and diffraction; Resolution and data content.
    1000-1030 Principles of Image formation (Mike Strauss): Lenses, Deflectors, Detectors, Phase contrast, Projection Images, CTF.
    1100-1130 Conventional Specimen Preparation I (Allan Michell): Epoxy resin embedding, Cryosubstitution, Cryoultramicrotomy.
    1130-1200 Conventional Specimen Preparation II (Allan Michell): Cryosubstitution, Cryoultramicrotomy.
    1200-1230 Cryo Fixation (Jan Leunissen): Cryosubstitution, Vitrification, High and Low Density Ices, Hetero and Homonucleation, Water vs. Cell Freezing.

    Tuesday 1st April
    0900-0930 EM Lab (Richard Easingwood): SEM, Freeze Fracture, Carbon Evaporation, Glow Discharge, Vacuum Technology.
    0930-1000 2D alignment (Mike Strauss): Fourier Transform, Correlation (auto, cross), Euler Angles, SNR, Xrays (in ccd images).
    1000-1030 2D Classfication (Mihnea Bostina): Data reduction, Fourier Transform, Principal component analysis, Neural Network.
    1100-1130 Cryo-EM (Mazdak Radjainia): Advantages, radiation, contrast, SNR, sample size, organelles vs molecular complexes, limitations.
    1130-1200 EFTEM (Mike Strauss): Principles of filters, spectroscopy, ESI, elemental mapping.

    0900-0930 3D reconstruction (Mihnea Bostina): Mathematical Transforms, Projection, Fourier Slice Theorem, Resolution
    0930-1000 Single Particle Reconstruction (Mazdak Radjainia): Projection based alignment, initial model bias, back projection, Gradient based optimization.
    1000-1030 Single Particle Refinement (Mike Strauss) CTF correction, Parameters to vary, limitations in resolution (pixel size, SNR, beam damage, heterogeneity, number of images), processing time.
    1100-1130 Tomography experiments (Mihnea Bostina): Tilt series, Missing wedge, Anisotropic Resolution, eucentricity, thickness limits, energy filter
    1130-1200 Cryo-electron tomography (Mihnea Bostina): Low dose tomography, Advantages (molecular resolution, cryo-preservation, no stain) disadvantages (dose, sectioning very difficult).
    1200-1230 Tomography averaging (Mike Strauss): Applicability, process, missing wedge problem, need for validation, limitations.

    0900-0930 Light Microscope (Andrew McNaughton): Types (Confocal, epifluorescence, reflected, transmitted), possibilities, sample requirements, limitations.
    0930-1000 Correlative Light - Electron Microscope (Mike Strauss): Need for validation & verification, fluorescent probes vs e-dense probes, q dots, finding the area, imaging in EM.
    1000-1030 High Resolution Electron Microscopy (Mazdak Radjainia): High Resolution, how much data, minimize beam tilt, drift (mechanical, electronic, electrostatic effects), information limit.
    1100-1130 X-ray diffraction and Small Angle X-ray Scattering (Sigurd Wilbanks): Experimental requirements, X-ray sources, data quality.
    1130-1200 Mollecular Resolution Models (Sigurd Wilbanks): Model quality, use of databases, high resolution models with low resolution data.
    1200-1230 Fitting (Mazdak Radjainia): Resolution vs accuracy, parameterisation, SNR, pseudo-atomic interpretation.

    If you cannot register for 4 mornings of seminars but there are one or two that you would like to attend then you are welcome to come along without registering.

    Focus On Quake Origins Through Study Of Ice

    David Prior

    There is an article in the Otago Daily Times (Friday 21st February 2014) about the research Professor David Prior (Geology) and his group have been doing on the Zeiss Sigma VP FEG SEM. They have been using EBSD (electron back scatter diffraction) to image the microstructure of ice. To read the full article visit the ODT's website.

    Archaeal Virus-Host-Interactions

    Dr. Tessa E.F. Quax, The Laboratory of GENE Technology, Department of Biosystems, University of Leuven.

    1600h Monday 24th February, Room 208 Microbiology.

    Viruses that infect Archaea are particularly diverse and display unusually high genetic and morphologic diversity. Studies of archaeal viruses are important for understanding of viral diversity, origin and evolution. Sulfolobus islandicus Rod Shaped Virus 2 (SIRV2) is a model to study virus-host interactions in Archaea. The infection cycle of SIRV2 in its hyperthermophilic host S. islandicus was studied using a combination of RNA sequencing, genetic, biochemical and electron microscopic techniques.

    The virus is lytic and exploits a remarkable egress mechanism based on formation of pyramidal structures on the host cell envelope. They display sevenfold rotational symmetry and open during the last step of the infection cycle to allow release of newly assembled virions. These structures consists of multiple copies of a single virus encoded protein. This small and robust protein may be used as a universal membrane remodeling system for biotechnological applications.

    Novel Tools in Electron Microscopy: A contextual look a viral genome delivery, and a detailed look at chromatin organization

    Dr. Mike Strauss, visiting research fellow to the OCEM, will be presenting a seminar on Tuesday the 25th February at 1-2pm in the D'Ath lecture theatre (1st floor of the Hercus building).

    Three Dimensional Electron Microscopy Workshop

    OCEM has organised a three dimensional electron microscopy workshop that will run from March 31st to April 3rd. The course will cover subjects ranging from sample preparation techniques to advanced image processing techniques. The format will consist of a combination of lectures aimed at wider audience stressing the capabilities and limitations of various methods (in the mornings) and practical sessions focusing on more technical details involved in data collection and three dimensional reconstruction (in the afternoons). The course is aimed at students, postdocs, and principal investigators who intend to use electron tomography or single particle reconstruction in their research. The fees are $50 for the morning sessions. THE AFTERNOON WORKSHOPS ARE NOW FULL.

    Introduction to 3D electron microscopy
    Image formation, contrast transfer function, energy loss imaging
    Sample preparation: cryo fixation, chemical fixation, sectioning
    Data collection: electron tomography
    Data collection: frozen hydrated samples
    Image processing: 2D alignment, and classification of single particle images
    Single particles analysis: 3D reconstuction and refinement
    Electron tomography: reconstruction, segmentation, subtomogram averaging
    Hybrid methods: correlative microscopy, molecular modelling

    Please register using the form below. If you have any questions regarding the seminars or workshops contact Dr. Mihnea Bostina,

    Command Line Workshop

    Dr. Mike Strauss will be holding a workshop for those that wish to use Unix's command line. The workshop will cover...

    - Software installation: useful software for EM image analysis such as bsoft, IMOD, EMAN2 and others (5-10 min).
    - Intro to (Unix/linux/OSX) command line - this will cover the most basic and necessary elements of using the command line and navigating the computer with it (30-45 min).
    - Intro to Image processing: using the command line programs, we will process images, apply filters, and look at the basics of image processing (30-45 min).

    The workshop will be held in the OCEM's imaging suite on Thursday the 20th of February at 0900 and will run for 1-2 hours. Please bring along a lap top that runs on Linux or Mac.

    Please express your interest in attending by emailing

    OCEM Visited by Dr. Oikawa and Dr. Shimizu

    Tetsuo Oikawa

    On January 23rd the OCEM were visited by Dr. Tetsuo Oikawa (JEOL Senior Production Manager for TEM) and Dr. Yuko Shimizu (JADAS) software developer of JADAS) who were here to install JEOL Automatic Data Acquisition Software, which is used for collecting images for use in single particle reconstruction. While they were here they trained OCEM staff on the software. Earlier on in January Hiromitsu Furukawa and Miyoko Shimizu from System in Frontier Inc. visited the OCEM to install the software that will be used for tomography. The software will collect a tilt series and then reconstruct a 3D model of the sample. Photo: Dr. Oikawa on the TEM looking at a graphite sample.

    OCEM and OCCM to Host the 2015 MNZ Conference

    MNZ Conference

    We are pleased to announce that the OCEM and OCCM will host the 27th New Zealand Conference on Microscopy. The conference will take place over four days and will include workshops, seminars, displays from exhibitors, a poster presentation evening and Microscopy New Zealand's AGM. The conference will be held from Monday the 2nd of February to Thursday the 5th of February 2015. The first three days (2nd - 4th of February) will feature of a diverse programme of speakers and will be followed by a day of workshops on the 5th of February.

    We have already confirmed 4 international keynote speakers (Professor Werner Kühlbrandt; Dr. Paul Verkade; Professor Joanne Etheridge; Dr. Azdiar Gazder). Five workshops are on offer: single particle reconstruction, correlative light-electron microscropy, atomic force microscopy, electron backscatter diffraction (EBSD) and image analysis. To find out more about the programme please visit the conference website.

    2014 OCEM Calendar Available

    OCEM Calendar

    The first batch of 2014 OCEM calendars has been printed. If you would like a calendar (or extra copies) you can either pick one up from the unit or email to have one sent out. The calendar is also available online as a PDF for those that would like to print out their own copy. You can view selected calendar images from 2014-2012 on our gallery page.

    Thanks again to all who submitted images to be used in the 2014 calendar. The deadline for submissions of micrographs to be considered for the 2015 OCEM calendar is 30th November 2014. If you would like to submit an image please follow the instructions on the gallery page.

    Left: This years winning calendar cover "Gold nanorods synthesised in the Griesh laboratory. These nanorods are smaller than the wavelength of light and can be used for plasmonic photothermal therapy. This uses gold nanoparticles of a specific size that are made to vibrate and transfer heat energy to kill tumour cells. Gold nanorod synthesis is a very dynamic process, any minor changes can hugely effect the shape and size of these gold nanoparticles. This image depicts the ability to precisely control material geometries with nanoscale precision. There is great uniformity in the shape and size of these gold nanorods which is difficult to achieve. Credit: Neha Nitin Parayath (PhD candidate) and Dr. Sebastien Taurin, Department of Pharmacology and Toxicology."

    News from 2013:

    Ice Electron Backscatter Diffraction (EBSD) in Otago is operational

    Congratulations On Your Publication Richard

    Richard Easingwood (OCEM staff) has co-authored a publication that aims to improve the estimation of rotavirus size, surface charge and particle concentration in environmental samples.

    Citation: Farkas, K., Pang, L., Lin, S., Williamson, W., Easingwood, R., Fredericks, R., Jaffer, M.A., Varsani, A., (2013) A Gel Filtration-Based Method for the Purification of Infectious Rotavirus Particles for Environmental Research Applications. Food and Environmental Virology. 5:231-235.

    OCEM Featured on Front Page of ODT

    The OCEM unit's new JEOL 2200FS cryo-TEM was featured on the front page of the Otago Daily Times this morning (13th November 2013). To see the article and accompanying photo visit the ODT website.

    It's the really little things that count

    The new $2 million electron microscope at the University of Otago is causing a stir among researchers and could help pave the way for a new generation of anti-cancer therapies.

    The Otago Centre for Electron Microscopy, in the university anatomy department, has five electron microscopes but its latest, largely Japanese-made cryo-transmission electron microscope is capable of key tasks the others cannot perform.

    And it can magnify specimens at least one million-fold, much greater than the 300,000-fold magnification of the centre's earlier electron transmission microscope.

    The microscope is the only one of its configuration in the country, and has ''electron tomography'' capability.

    This means it can produce high resolution 3-D reconstructions of viruses and nanoparticles in a new way and is ''ideally suited for single particle reconstruction''.

    The machine has been installed and is expected to begin operating early next year.

    The high resolution images produced are likely to provide new insights into a host of scientific fields, including in human health, where much more detailed information about the way viruses interact with individual cells and about the subtleties of brain circuitry is likely to advance scientific understanding.

    A neuroscientist at the anatomy department, Associate Prof Dorothy Oorschot, who chairs the centre management committee, said the microscope, was a ''major development'' for the university.

    She will use the new equipment to study circuitry in part of the brain which controls movement. Another advantage is the microscope views frozen biological specimens at up to minus 180degC.

    Because the biological sections do not have to be preserved by using chemical fixatives, key microstructures can be viewed more clearly, and in closer to their natural state.

    Dr Mihnea Bostina, the recently appointed centre academic director, who is also a microbiology and immunology senior lecturer, wants to study the detailed surface structure of certain naturally occurring viruses which attack cancer cells in humans.

    Such viruses could be potentially useful as anti-cancer therapies but tended to be themselves attacked and destroyed by the body's immune system.

    Understanding the mechanical facts about the way such viruses and individual cancer cells ''locked'' together could help ultimately develop a new generation of smart drugs which could target cancer cells more precisely, he said.

    Project Viability to be Trialled Using OCEM's Zero Fee Scheme

    The project "Immobilisation of magnetically-interesting materials on appropriately functionalised surfaces" has had it's application approved under the Zero Fees Scheme. Dr. Humphrey Feltham and Professor Sally Brooker will be looking at Single-Molecule Magnets (SMMs) and Spin Cross Over compounds (SCO) that could potentially be used as molecule-sized storage units by covalently binding the compounds to a solid surface. The microscope time for this preliminary investigation has been gifted by the OCEM. If the results are promising it is hoped that the study will secure a larger EM-based grant and will be expanded to include the attachment of SMM and SCO to nanoparticles of various composition and sizes. To learn more about the OCEM's Zero Fee Scheme check out the webpage.

    Welcome Back Richard

    Cryos Titan TEM

    The EM is pleased to welcome back Richard Easingwood after his trip in September to Holland. While in Holland Richard attended an engineering course at Stirling Cryogenics. He is now able to perform maintenance on our liquid nitrogen generator which has almost reached 6000 operating hours and is scheduled for a major overhaul. He has also picked up a great number of tips and techniques to monitor and optimise the generator's performance.

    After the Stirling course Richard was able to catch up with Janice Griffith who took him to visit George Posthuma and the EM lab at the Cell Microscopy Centre at Utrecht University.

    He also had the chance to visit Ken Goldy at the Centre for Cellular Imaging and NanoAnalytics (C-CINA) at the University of Basel. This facility is a haven for cryo electronmicroscopists - the group around Henning Stahlburg is devoted to high resolution particle work. Richard was able to see the new FEI Titan Krios TEM, and used the unit's FEI Polara. He was taken through the process of preparing samples for cryo-TEM, including freezing specimens using a Vitrobot.

    Abstracts Due for Australian Conference on Microscopy

    A reminder that the deadline for abstract submission for the 23rd Australian Conference on Microscopy and Microanalysis combined with the 2014 International Conference on Nanoscience and Nanotechnology will close on 15th September. The early-bird registration deadline is 15th November.

    The conference will be held in Adelaide between 2nd and 6th February 2014. Website can be found at

    Presentation: High Pressure Freezing

    Professor David Prior and Jan Leunissen will be presenting a talk on High Pressure Freezing (HPF) on Tuesday the 10th of September at 0900 in the HOD office in the Geology Department. If you are interested in attending please contact David at as there are limited spaces.

    DNA Sequencing using an Electron Microscope?

    By labeling bases with heavy metals is it possible to produce long DNA sequences using a transmission electron microscope. This technique is able to produce long contiguous reads - thousands or even tens of thousands of bases long (compared to only hundreds with other approaches). This will be particularly useful for samples that are currently hard to sequence with short reads such as genomes that have many repeat elements. It's also perfect for virus identification or environmental samples, because it requires only small amounts of DNA and it is possible to sequence the entire strand in one shot. Already a 7249 base-pair viral genome has been sequenced.

    For more on the 'third generation of DNA sequencing' read through the interview with David Bell or his paper Bell, D. C., W. K. Thomas, K. M. Murtagh, C. A. Dionne, A. C. Graham, J. E. Anderson, and W. R. Glover. 2012. DNA base identification by electron microscopy. Microscopy and Microanalysis 18(05):1049-1053.

    The work from Bell et. al. (2012) was done using annular-dark field scanning transmission electron imaging on an aberration-corrected STEM. ADF-STEM imaging is just one of the exciting techniques that the OCEM's new JEOL 2200FS Cryo-TEM is capable of performing.

    ADF-STEM class=

    Image from Wikipedia.

    Entries Sought For 2014 Calendar

    OCEM Calendar

    If you have a EM image that is visually interesting, scientifically significant or has a story behind it - please submit it so that we can use it in the 2014 calendar. Email

    Brain Mapping At The Level Of Synapses: Combining Viral Vector Technology With Immunohistochemistry And Transmission Electron Microscopy

    NRG Seminar

    This month's Neuroscience Research Group seminar will feature 3 speakers:

    Associate Professor Dorothy Oorschot, Department of Anatomy
    Dr. Stephanie Hughes, Department of Biochemistry
    Dr. Mihnea Bostina, Academic Director of the Otago Centre for Electron Microscopy

    The talk is titled "Brain mapping at the level of synapses: Combining viral vector technology with immunohistochemistry and transmission electron microscopy". Stephanie will explain how the the virus markers are made, Dorothy will talk about her EM technique of using virus to identify particular neurons in the brain for her TEM studies then Mihnea will introduce tomography and how it can be applied to projects such as this.

    The talk will be on Wednesday 14th August at 12pm in G10, opposite the hospital (the old Bowler, large seminar room). Entry is from the car park on the opposite side to Frederick St.

    Pizza will be supplied.

    Why Vaccines Are Good And How We Can Make Them Better

    Congratulations to Sarah Hook on her recent promotion to Professor in the School of Pharmacy. Sarah is a member of the OCEM User Group committee. She will be giving her Professorial lecture "Why vaccines are good and how we can make them better" on Tuesday the 13th of August at 1730 in the Archway 1 lecture theatre.

    Sarah Hook Lecture

    Hot Topic Lecture: Spectrum of animal brain and behavioral deficits closely resembling human extreme prematurity

    The 2013 Hot Topic Lecture will be presented by Associate Professor Dorothy Oorschot from the Department of Anatomy. Assoc Prof Oorschot will speak about her recent Journal of Neuroscience paper 'Spectrum of animal brain and behavioral deficits closely resembling human extreme prematurity'. The lecture will be held on Wednesday 31 July at noon in Hunter Centre Room 122, and a light lunch will be provided.

    Hot topic lecture

    Congratulations to Anatomy Researchers

    oorschot publication

    Congratulation to Dorothy Oorschot, Logan Voss, Matthew Covey, Liping Goddard, William Huang, Penny Birchall and Sarah Kohe from the Department of Anatomy and David Bilkey from the Department of Psychology for their recent publication "Spectrum of Short- and Long-Term Brain Pathology and Long-Term Behavioral Deficits in Male Repeated Hypoxic Rats Closely Resembling Human Extreme Prematurity" in the The Journal of Neuroscience. This paper used stereology of rat cerebrum TEM micrographs to measure the g-ratio and the number and diameter of myelinated axons in the callosal periventricular white matter (P14/15).

    Welcome to Dr. Mihnea Bostina

    The new Academic Director of the OCEM, Dr. Mihnea Bostina, arrived in Dunedin on Thursday last week. Despite having been on a very long flight from Montreal and probably feeling very jet-lagged, Mihnea came down to the unit on Friday to meet the OCEM team. The OCEM has not had an Academic Director before but it was decided that in order for the new 200kv cryo-TEM to be utilised to its maximum capability we would need someone to provide academic leadership and expertise in cryo-transmission electron microscopy and electron tomography. Dr. Bostina completed his PhD in Biophysics and Structural Biology at the Max Planck Institute of Biophysics in Frankfurt, Germany and a research fellowship at Harvard University in Boston, USA. His research interest is using single particle reconstruction to study the structural biology of viruses. Dr. Bostina will hold a 0.5 FTE appointment as Academic Director of the OCEM and a 0.5 FTE appointment as a Senior Lecturer in the Department of Microbiology and Immunology where he will be involved in teaching and graduate supervision.

    Unloading Cryo-TEM

    Dr. Bostina gets stuck in - opening up the cryo-TEM crate.

    Arrival of the JEOL 2200FS Cryo-TEM

    Unloading Cryo-TEM Unloading Cryo-TEM

    Many hands make light work... Crates were disassembled within minutes.

    Unloading Cryo-TEM Unloading Cryo-TEM

    Unloading Cryo-TEM Unloading Cryo-TEM

    Hold your breath... A 1.5 tonne crate is suspended in air with a forklift (left). Some impressive forklift reversing skills were demonstrated by Fliways (right).

    Unloading Cryo-TEM Unloading Cryo-TEM

    Sharon helps to demo the crate (left). Fliways, OCEM and property services work together to navigate the 1.4 tonne microscope down an awkwardly angled slope (right).

    Unloading Cryo-TEM Unloading Cryo-TEM

    More wrapping than Christmas Day (left). We don't have a plan B, so it HAS to fit (right).

    Unloading Cryo-TEM Unloading Cryo-TEM

    Clearing doorway no. 1 (left). Clearing doorway no. 2 (with 2mm to spare). Let the celebrations begin (right).

    OCEM Preparation Laboratory is PC2 Compliant

    Samples and materials requiring PC2 containment may now be worked with and stored in the B14 preparation laboratory. Anyone wanting to work (unsupervised) in the laboratory must have completed PC2 training within the last 12 months and have supplied Sharon Lequeux ( with a record of their training BEFORE entering the lab. Even if you do not intend to work with PC2 material (e.g. filling up a bottle with distilled water) we still require your training record. Presently all training records (for users other than OCEM staff) that were collected last year have expired and we require your new record. All users that have not received PC2 training within the last 12 months can contact Mark Gould ( for an induction.

    Labelling Cryosections with FluoroNanogold

    Ever considered using correlative microscopy to find difficult-to-locate structures in experimental tissue? Here are a couple of images taken recently of cryosections from liver tissue labelled for catalase with Alexa Fluor® 488 FluoroNanogold Fab' Fragment of Goat Anti-Rabbit IgG. The label is a fluorophore conjugated to a gold particle so it can be seen under both a fluorescence microscope and an electron microscope. The small pinpoints of light are the peroxisomes (which contain a lot of catalase) and the larger spheres are the cell nuclei. Taken at 20x and 100x magnification on a fluorescence microscope.

    Liver tissue 20x Liver tissue 100x

    Ionic Regulation in Nematodes Studied by Energy-dispersive X-ray Spectroscopy

    In this seminar Professor David Wharton (Department of Zoology) will discuss a novel method he is developing to undertake EDS measurements on fluid samples. "In it I describe the measurement of the elemental composition of nematode pseudocoelomic fluid by EDS/SEM (x-ray microanalysis) achieved by absorbing the fluid into Sephadex beads - a technique first used to sample the surface fluids of human airways. I have used this to get the first measurements of the composition of pseudocoelomic fluid from single nematodes and how that composition changes in response to changes of specific ions in the external medium."

    Friday 12th July, Zoology Benham Seminar Room, 12.00PM.

    Renovations Complete

    A montage of the completed renovations in B09. The Microscope will be installed on July the 16th.

    Cryo-TEM Room Alterations Finished

    Cryo-TEM Update

    A montage of the renovations being undertaken for the new Cryo-TEM. Renovations are due to be finished by mid-July.

    Cryo-TEM Room Alterations

    Early Career Awards for Distinction in Research

    Congratulations to Dr. Carla Meledandri (Chemistry) and Dr. Virginia Toy (Geology) who were both recipients of the five Early Career Awards for Distinction in Research awarded this year.

    A lecturer in chemistry, Dr. Meledandri gained a PhD from Dublin City University in 2008, and her research focuses on the design and preparation of nanoscale materials, particularly for use in nanomedicine. She has been using the CM100 for transmission electron microscopic analysis of silica nanoparticles to determine the size and size distribution of the particles.

    An Otago graduate, Dr. Virginia Toy is a senior lecturer in geology who is extensively involved, both as a researcher and as a co-ordinator, in scientific drilling into active structures such as New Zealand's Alpine Fault. She co-ordinates the Deep Fault Drilling Project. She has been using the Zeiss Sigma VP FEG-SEM to take images of clay gouge sections adjacent to the principle slip surface of the Alpine Fault on the Australasian plate and examine the microstructures to understand the deformation mechanisms involved in their creation. She is also using EDS to look at the element signatures in quartz fragments within the gouge.

    "Announcing the awards, the deputy vice-chancellor, research and enterprise, Prof. Richard Blaikie said the five scholars were ''shining examples'' of the depth and breadth of talent among the university's up-and-coming researchers. Their work was already creating ''new knowledge that underpins improvements in health, technology, social wellbeing and our understanding of environmental processes''. The five academics were well-placed to be among Otago's future research leaders, Prof Blaikie said. Each award winner receives a $5000 grant to use for research and scholarly development, and becomes a member of the university's O-Zone group of early-to-mid career researchers."

    You can read the full article in the Otago Daily Times.

    Cryo-TEM Update

    LFB Alterations

    The new JEM-2200FS Cryo-TEM arrived in Dunedin in early May. However due to delays with the room alterations in B09 the microscope is being kept in storage until the room is complete. Engineers from JEOL are anticipated to arrive in the second half of July to install the microscope.

    We are looking forward to a visit from the new Academic Director Dr. Mihnea Bostina, who will arrive in mid-July to supervise the installation of the cryo-TEM.

    Zeiss FEG-SEM Operational Again

    The Zeiss FEG-SEM is now operational again (9th June). If you would like to use the microscope please make a booking on the Zeiss SEM Calendar.

    "This Is Just Getting Ridiculous,"

    A third flood has struck the Lower Floor Basement this morning (4th June). The cause was a broken radiator that had been turned on. As with the last flood, the water poured from the ceiling showering the Zeiss FEG-SEM. The Zeiss is still out of action until further notice.

    Flood in LFB
    Flood in LFB

    MORE Flooding in Lower Floor Basement

    The Zeiss FEG-SEM is currently out of action due to a flood in the Lower Floor Basement. A second old radiator burst on Thursday night (the 23rd of May) above the SEM and was not discovered until Friday morning. The Zeiss will not be available for use until further notice.

    Congratulations to EM Student Award Winners Yuanyuan Feng and Monica Tromp

    Congratulations to Yuanyuan Feng (Botany) and Monica Tromp (Anatomy) who have each won an EM Student Award in the most recent round of applications (April). The EM Student Award grants the students 15 hours electron microscope time.

    Coccolithophores contribute about 50% of CaCO3 production in the ocean and are sensitive to changes in the seawater carbonate system and ocean acidification. Yuanyuan Feng's PhD project 'Global change controls on the morphology of a NZ strain coccolithophore Emiliana huxleyi' will use the JEOL 6700F FE-SEM to determine the morphotype and take biometric measurements (size and diameter) of coccoliths that have been grown in different environmental conditions to look at the effect of pCO2, phosphate, nitrate, irradiance and temperature. Feng is supervised by Dr. Catriona Hurd, Dr. Michael Roleda and Dr. Philip Boyd. You can read more about Feng's research here

    Microfossil and bacterial residues from the teeth of prehistoric people and pigs can be used to learn more about the diet, health and environment that existed at that time. Monica Tromp's project 'Microscopic analysis of microfossils extracted from anceint human and pig dental calculus from prehistoric western Polynesia' will use SEM electron dispersive spectroscopy (EDS) and backscatter to identify siliceous microfossils and bacteria from human and pig dental calculus from Lapita sites to examine changes in plant resource use through time and across different islands. Monica is supervised by Dr. Hallie Buckley.

    Applications for the next round of awards closes on the 1st of September. For more information please visit the EM student award page.

    Flooding in Lower Floor Basement

    Flood in LFB
    Flood in LFB1
    Flood in LFB2

    Over the weekend of 18th/19th of May an old radiator in room B21 burst causing a small flood in the Lower Floor Basement. The flood was not discovered until Monday morning. Luckily no equipment was damaged. Tom Czertowicz and Markham Phillips, proactive Geology post-graduate students, proved handy with a mop until we were able to source a wet-vac. The radiator has been turned off and the Zeiss FEG-SEM is able to be used again.

    Download the 2013 OCEM Calendar

    The 2013 OCEM Calendar is available to download and print off. It is designed to be printed double sided on A3 paper. You are able to print it off on a normal printer - it will be half the regular size once folded.

    Word Graphic

    2013 OCEM Calendar

    OCEM and OCCEM to Host the 2015 NZ Conference on Microscopy

    Microscopy New Zealand Inc.

    The Otago Centre for Electron Microscopy (OCEM) and the Otago Centre for Confocal Microscopy (OCCM) will host the 27th New Zealand Conference on Microscopy in early February 2015.

    The conference will take place over four days and will include workshops, seminars, displays from exhibitors, a poster presentation evening and Microscopy New Zealand's AGM.

    Microscopy New Zealand Inc. is New Zealand's professional society for users of microscopes. The principal aims of the Society is to promote microscopy in New Zealand, facilitate opportunities for the training of New Zealand microscopists and to provide a support network for members. MNZ actively promotes participation of young researchers and members by providing funding opportunities to attend conferences on microscopy. MNZ is a member of the International Federation of Societies for Microscopy.

    Seminar: Atomic Force Microscopy of Polymer and Biological Samples

    The OCEM will be hosting a special seminar about the Atomic Microscopy of Polymers and Biological Samples. The seminar will be held on Tuesday 30th April from 10.30am to 11.30am in the Red Lecture Theatre, Ground Floor, Scott Building, Great King Street (Medical School complex). Please note the time. This is not a lunchtime seminar.

    We will review the basic concepts of the Atomic Force Microscope, distinguishing the differences between contact and intermittent contact mode. A brief history of the AFM will be provided, including recent advances. We will focus on the use of intermittent contact modes such as "tapping mode" or "peak force tapping" for the analysis of soft samples such as polymers and biological materials. We will focus on three major advantages of the AFM: 1) quantitative topographic nano-analysis 2) phase imaging to determine qualitative nano-mechanical information such as loss tangent and stiffness and 3) the ability for in-situ dynamic imaging.

    Extensive Renovations Being Undertaken in the Lower Floor Basement

    On Monday the 11th of March the Phillips EM410LS TEM was decommissioned. A wake was held for the microscope, which was dismantled by the Model Engineering Club for use in model steam engines. Other parts have been taken to be used in steam punk creations. Rooms B09 and B09B are currently undergoing extensive renovations to prepare for the arrival of the new JEM2200FS Cryo-TEM. Gillian, Richard and Sharon still have their desks in B08, but access is now through a side door South of the original entry point. The CM100 can no longer be accessed through the B09 entrance, but can be accessed by walking through the Preparation Laboratory (B14). The liquid nitrogen is temporarily being housed in B21 (opposite the new entrance to the staff office).

    Allan Mitchell 410TEM Dunedin Model Engineering Club

    Winston Churchill Memorial Trust Fellow Featured in 'Materials World' Magazine for Electron Microscopy Work

    An article featuring work completed by Dr. Debra Carr (Cranfield University) during her Winston Churchill Memorial Fellowship visit to the University of Otago will be featured in the April 2013 issue of the Institute of Materials, Minerals and Mining's 'Materials World' magazine. Debra worked with Professor Jules Kieser at the Sir John Walsh Research Institute, and Liz Grivan at the Otago Centre for Electron Microscopy on two projects that investigated (i) damage to apparel and debris in bony wounds due to gunshot and (ii) characterising damage to underwear during alleged sexual assault incidents. You can read more about Debra's fellowship on our 2012 news page or on her blog.

    IOM3 April 2013

    Material Evidence Feature

    First Round of EM Student Award Closes April 1st 2013

    Undergraduate and postgraduate students enrolled at the University of Otago are welcome to apply for the Electron Microscopy Student Research Award. The award provides 15 hours of electron microscopy time and aims to advance the initiation of new research projects that utilise electron microscopy. The deadline for applications is the 1st of April 2013. For more details visit the EM Student Award Webpage.

    Cryoultramicrotomy and Immunocytochemistry Expert to Visit OCEM

    Janice Griffith

    The OCEM is honoured to host Janice Griffith in April and May 2013. Janice is a Senior Electron Microscopy Research Technician at the Cell Microscopy Centre, University Medical Centre Utrecht (Netherlands), which is world renowned for their technical developments in electron microscopy.

    While at Otago Janice will help the OCEM to develop cryoultramicrotomy, immunocytochemistry, and correlative microscopy expertise so that we can provide cutting edge biomedical imaging research support to the University of Otago. She will also be collaborating with Professor Richard Cannon (Director, Molecular Microbiology Laboratory, Department of Oral Sciences) on a project "Subcellular localisation of efflux pumps heterologously expressed in yeast" as Janice has significant experience working with yeast systems.

    Model of Primary Cilia Wins First Place in Nanotechnology Exhibition

    Primary Cilia

    Congratulations to PhD candidate Mike Jennings and Research Associate Professor Tony Poole who won first place in the 'Art of the Invisible' nanotechnology exhibition in Auckland recently, which presents images from the work of New Zealand graduate students who research in the field of nanotechnology.

    The exhibition was held in conjunction with AMN6: the Sixth International Conference on Advanced Materials and Nanotechnology in February. Mike created a model of a primary cilia using electron tomography. To create this model he took thick 330nm sections from embedded tissue and spent many hours on the 410 TEM locating primary cilia. Once he had located cilia he took the sections to AgResearch and took a series of tilted images with their 300kv TEM. He then brought the dataset back to Otago and reconstructed a model cilia. You can read the full article on the ODT's website.

    'New Technologies' OCEM and OCCM Seminar

    On Thursday the 4th of April at 0900-1100 the Otago Centre for Electron Microscopy and Otago Centre for Confocal Microscopy will present a combined seminar consisting of the talks that were presented by staff and post-graduate students at the Microscopy New Zealand 2013 Conference.

    0900 'Correlative Light Electron Microscopy - What? Why? How?' presented by Allan Mitchell (technical manager of the OCEM).
    Abstract: Correlative Light Electron Microscopy (CLEM) enables researchers to confirm conclusions drawn from the fluorescence data improving the quality of their publication. The 3 main features that define CLEM are: 1. Locating the structure of interest in the light microscope. 2. Placing the structure into the context of the larger region by using stains and labels. 3. Examining at higher resolution in the TEM to obtain more specific data. Fluorescence microscopy is an increasingly important tool for analysing cell function. Genetic markers such as GFP and its variants, have resulted in a wide range of new applications. New data is being produced ranging from the whole organism down to cellular machinery including single molecules. However, fluorescence microscopy cannot reveal the full story. Its low spatial resolution and the lack of reference space can be a problem. To resolve these problems the transmission electron microscope is required. CLEM seeks to develop techniques that combine the capabilities of each imaging system. However, in the past specimen preparation techniques have been considered almost mutually exclusive. The continuing refinement of preparation methods, probes, software and hardware are allowing the full potential of correlative microscopy to be realised. This talk will highlight efforts at the Otago Centre for Electron Microscopy to introduce CLEM as a routine technique for biological investigations.

    0930 'Using Correlative Microscopy to Map YB-1 Protein in Aggressive Cancer Cells' presented by Sharon Lequeux (technician at the OCEM).
    Abstract: Correlative light-electron microscopy (CLEM) allows high-resolution imaging by electron microscopy of the same structures seen using light microscopy. Cell function is shown using fluorescent labelling and is correlated to cellular structures using electron microscopy. The ability to locate proteins in their context within cells has seen CLEM become increasingly in demand. We used a fluorescent dye conjugated to a gold label to understand the role of Y-box binding protein 1 (YB-1) in aggressive breast cancer epithelial cells (line MCF-7). YB-1 is a nucleic acid binding factor involved in multiple biological processes including cell proliferation, DNA repair, translation and transcription. As a transcription factor it binds to DNA within the nucleus; however it is also involved in the post-translational modification of proteins. YB-1 is upregulated in aggressive cancers and previous work suggests that YB-1 translocates to the nucleus after cell stress (Woolley et al. 2011). CLEM allows us to determine the precise subcellular localisation of YB-1. By labelling YB-1 together with other proteins that it interacts with in specific regions of the cell, we can gain insight as to which cellular processes are altered in response to stress. To test the effects of stress on the cancer cells the cells were dosed with cisplatin (a drug used in the treatment of cancer), fixed and flat embedded in LR White acrylic resin. Ultrathin sections were labelled with Alexa Fluor® 488 goat anti-rabbit IgG, 5 nm colloidal gold conjugate. They were visualised with a laser confocal microscope and then a 100kv transmission electron microscope. This talk will focus on our methods and future plans.

    0950 'SEM Imaging and Stereology of Oocyte Organelles in Semi-Thin Sections' presented by Karen Reader (Scientist at AgResearch and PhD candidate).
    Abstract: Oocytes require the correct quantity and distribution of organelles in order to complete maturation, fertilisation and embryo development. It is also known that oocytes from prepubertal animals are less able to undergo normal embryo development than their adult counterparts. The aim of this research was to develop a more rapid method of imaging and quantifying organelles in oocytes from prepubertal and adult ewes. Oocytes were fixed and processed for TEM. Serial 2micron thick sections were cut through the whole oocyte and mounted on slides. The section with the maximum oocyte diameter was re-embedded, ultrathin sectioned for TEM, and the section next to it imaged directly in a SEM using a back-scattered electron detector. Stereology techniques were used to measure the density and volumes of organelles in SEM and TEM images. There were no differences in the volume fractions of vesicles and mitochondria in the oocytes between the SEM and TEM images; however, the volume of individual mitochondria was greater when measured in the SEM images. Lipid droplet volume density was difficult to estimate in the TEM images due to their uneven distribution and large size. However, SEM imaging and grey-scale thresholding allowed quick measurement of lipid density in the whole oocyte section. In conclusion, the SEM method enabled more rapid quantification of organelles than the TEM method and therefore enabled more oocytes to be measured to identify differences in the volumes and distribution of organelles between adult and lamb oocytes.

    1020 'Microstructural Analysis of the Porcelain-Fused-to-CoCr-Metal Interface Using Electron Backscatter Diffraction' presented by Kai Chun (PhD candidate).
    Abstract: Ceramic fractures and chipping in porcelain-fused-to-metal (PFM) restorations are generally associated with metal-ceramic incompatibility which influences the residual stress state within the porcelain. This has led to a substantial amount of research concentrated on the porcelain while very little focus is directed towards the metal substructures itself. Therefore, the objective of the present study was to use a relatively novel technique (especially within the dentistry field) known as electron backscatter diffraction to analyse and determine the phase and grain distribution at the metal-porcelain interface. The study focused on identifying the microstructural characteristics of the alloy from the metal-porcelain interface and into bulk of the metal as well as the effects of typical heat treatments (~900ÅćC) undergone during the manufacturing stage. The findings in this study observed significant difference in grain size at the metal-porcelain interface (~2micron) compared to the bulk of the metal (>200micron). Phase identification indicated that the finer grains at the metal-porcelain interface were predominantly hexagonal phase while the bulk of the metal had a dendritic-like structure made up of both cubic and hexagonal phases. These results have not been observed or reported in previous literature and the implications of the significant grain size reduction at the metal-porcelain interface as a result of heat treatment are unknown.

    1040 'A Void: Holey Places' presented by Andrew McNaughton (technical manager of the OCCM).
    Abstract: Biologists and material scientists often view each other as different species, especially when it comes to the types of samples they deal with. Consequently, it's easy to miss useful software and analytical methods because the label appears wrong for the proposed purpose. When it comes to quantifying holes / voids / spaces, it doesn't matter if they are in rocks, metal, cheese or bone. They're all the same as far as most software is concerned. A useful plugin to ImageJ / Fiji is BoneJ, a title which would cause many material scientists to click "next page" if it appeared in their search results. But are you sure trabecular thickness, volume fraction and bone surface aren't of use to you - really sure? A talk about some common features of a variety of specimens, mostly derived from micro-CT data, and how some analytical methods may be more applicable to apparently unsuitable samples than they first appear.

    The seminar will be held in the Blue Lecture Theatre (Walsh Building/School of Dentistry). Morning tea will be provided at 1100 in the Academic Staff Room (Dental School).

    Blue Lecture Theatre Location