new vitrobot™ at the emu • collaborative initiative of the...
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EMU Newsletter July/August 2006 | �
EMUNewsletter July/August 2006
www.emu.usyd.edu.au
New Vitrobot™ at the EMU • Collaborative Initiative of the
Department of Archaeology and EMU • Carbon Nanotube
Nanothermometers • Master of Applied Science
Automated, Robotic Preparation of Vitrified Samples for 2D and 3D Cryo-Electron Microscopy
We are proud to announce that the EMU has
purchased an automated vitrification robot,
or Vitrobot™, distributed by FEI/nanoSystems
Technology (Australia) in early July. Aquisition of
this high-end specimen preparation device was
a priority for A/Prof. Filip Braet since arrival in
the Key Centre.
For more than �0 years, Filip has closely collabo-
rated with the inventors of the Vitrobot™, Prof.
Peter Frederik (see figure) and Paul Bomans,
in assessing this guillotine-like device for the
automated preparation of intact whole-mounted
biological samples for subsequent cryo-electron
microscopy investigation.
Since the commercialisation of this instrument
by FEI in 2002, numerous papers have been
published in high-ranking journals (Science,
Nature, PNAS and much more) in which the
use of the Vitrobot™ was the key to success for
research outcomes.
It has allowed characterisation of samples
including cells, liposomes, new drug complexes,
chemical compounds, biomaterials, viruses,
single particles and metal particles at nanometre
resolution under native conditions.
Automated, robotic vitrification provides tight
control of temperature and humidity in the
sample preparation environment, as well as
precise control of timing for all steps in the
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Prof. Peter Frederik teaching the cryo-workshop participants
how to operate the Vitrobot™ during the ACMM19 Cryo-
Workshop held at the University of Sydney in February 2006.
More information:
A/Prof. Filip Braet
Acting Director
Tel. +6� 2 935� 76�9
process. Temperature and humidity in the
sample preparation environment determine the
rate of heat and mass transfer from the sample.
Operating at high relative humidity reduces
evaporation velocity and, when combined with
precise timing, improves the consistency of the
vitrified thin film specimens, and avoids osmotic
and thermal effects that may induce structural
changes in the sample.
Vitrification provides samples that are in a nearly
pristine natural state, and that lend themselves
well to the analysis of three-dimensional struc-
ture by single particle analysis and cryo-electron
transmission tomography. The ability of vitrifica-
tion to freeze samples in a moment of time holds
further promise in the development of time-
resolved cryo-electron transmission microscopy,
which would allow researchers to follow the
progress of molecular processes over time
courses as brief as a few milliseconds.
For further reading, see:
Frederik PM, Storms MH. Automated Robotic
Preparation of Vitrified Samples for 2D and 3D
Cryo-Electron Microscopy. Microscopy Today
2005;13:32-36.
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ARPH 2602: Scientific Analysis of Materials – A Collaborative Initiative of the Department of Archaeology and EMU
Archaeology was originally the preserve of those
who were interested mainly in the acquisition
of beautiful antiquities for private collectors and
museum display. There was little methodical or
scientific about the excavation and documenta-
tion, if any, of ancient material culture. The tech-
nology of manufacture and identification of raw
materials was of no interest to a predominantly
art historic following where identification, dating
and provenancing of objects was done tradition-
ally by physical, relative comparisons.
Over the last century, the development of
scientific analytical instruments and techniques
has dovetailed with our growing need to obtain
rigorous scientific information about the micro-
scopic world of ancient materials as a means of
answering increasingly complex archaeological
questions. Archaeology has slowly but surely
embraced science in its investigation of ancient
objects and materials, and the processes that
ultimately have led to the world we live in today.
It is a vast field, ranging from the manufacture or
modification of materials to environmental proc-
esses left to us in microscopic clues from bones,
seeds and pollens.
The discovery of X-rays was soon adapted to
the examination of Egyptian mummies and now
the refined technique of micro-CT scanning is
used for non-destructive examination of arte-
facts. The light microscope provides a tool for
enhanced physical examination, identification and
documentation, while the advent of scanning and
other electron microscopes has opened up the
world of chemical investigation and high resolu-
tion imaging. Now chemical typing or charac-
terisation complements the traditional physical
typologies providing a huge pool of data from
which so much more information can be gleaned
from our precious and finite material heritage.
The need to educate archaeologists in scientific
analysis and interpretation of data has become so
essential that we were inspired, if not driven, to
develop the unit of study Scientific Analysis of
Materials. It is a collaborative initiative between
the Department of Archaeology and the Australian
Key Centre for Microscopy and Microanalysis has
resulted in the evolution of a dynamic, cutting-
edge training experience. The couse introduces
the archaeology student, often a non-scientist, to
the basics of materials identification from atoms
up, to decay processes, to sampling strategies
and to techniques, to principles of X-ray spec-
troscopy and to a selection of analytical tech-
niques, all available here at the EMU.
Light micrograph of copper-red glass from ancient Mesopotamia
(modern Iraq) showing compositional streaking, a cooling
crack and gas bubbles (seeds).
The scanning electron microscope (SEM) is a valuable
tool for archaeological sciences.
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EMU Archaeology Course Contents
The learning experience involves a combination
of lectures and practical sessions with plenty of
opportunity for student interaction. The three-
hour sessions are taught by a team of highly
qualified experts derived largely from the EMU
staff. We distil complicated scientific information,
principles and concepts with the aim of provid-
ing the student with a basic understanding, while
stimulating and guiding scientific inquiry. The
science is made comprehensible by carefully re-
lating its applications to archaeological problems
through case studies and examples. The student
is equipped with an understanding of the scope
and variety of analytical techniques and the data
they provide, and how to apply them to archaeo-
logical research.
Wendy ReadeAssociate Lecturer, Microscopy and ArchaeometryTel. +6� 2 935� [email protected]
More information:
Macro View: Introduction to the Scientific Study of Archaeological Objects and Materials
Forensic Approaches to Archaeology: An Introduction to Analytical Methods and Scientific Studies in Archaeological Inquiry
Archaeological Materials: Their Nature and Interaction with the Burial Environment
Strategies for Sampling for Analysis: Considerations of Requirements, Ethics and Practicalities
Documentation for Analysis: Sound Scientific Inquiry Requires Careful and Accurate Recording
Examination and Identification of Objects and Materials
Sample Preparation Practical
The Micro World: Principles and Techniques for Investigating Archaeological Materials
The Structure of Archaeological Materials: Atoms, Molecules and Isotopes
Light Microscopes: Magnification Enhances Observation
Light Microscopy Practical Session: Archaeological Applications
X-Ray Spectroscopy: How Chemical Data from Archaeological Objects are Collected, Presented, and Interpreted
Vibrational Spectroscopy: Applications in Fibre and Pigment Studies and Principles of Two Techniques
Vibrational Spectroscopy Practical Session: Ancient and Historical Textile Fibre and Pigment Identification
Faunal Remains: The Identification and Analysis of Ancient Animal Bone - an Introduction to Archaeozoology
Digital Image Analysis and Micro-CT: Applications to Archaeology
Scanning Electron Microscopy (SEM): Principles and Applications to Studies of Manufacture, Structure and Composition of Artefacts
SEM Tour: What does an SEM look like?
SEM Practical Session: Structure and Composition of Textile Fibres and Ceramics (by Telepresence)
Micro-Fossils in the Archaeological Record: Further Applications of Microscopy
Human Environmental Interactions through the Fossil Record: Landscape Use and Impacts in the Prehistoric Past
Investigating Residues on Artefacts: An Introduction to the Range of Residues that may be Preserved and the Methods for Identification and Recovery
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Dr Zongwen Liu’s Successful Research on Carbon Nanotube Nanothermometers
Since it was reported (Nature ��5 (2002) 599)
that carbon nanotubes containing liquid gallium
(Ga) can be used as nanothermometers, scien-
tists have been seeking practical ways to read
these nanothermometers and measure temper-
ature at the nanometre scale. Researchers in the
EMU (Zongwen Liu, Kyle Ratinac, and Simon
Ringer) and their collaborators from the National
Institute for Materials Science (NIMS) in Japan
recently proposed a method for temperature
measurement with nanothermometers. They
demonstrated that a thin layer of solid gallium
oxide can be formed at moderate temperatures
due to partial oxidation of the gallium, and that
this can serve as a temperature marker. Thus,
the original temperature can be retrieved by
reheating the carbon nanotube in a transmission
or scanning electron microscope to let the liquid
gallium to expand to the marker (see the figure
at right).
The present oxidation-assisted technique
improves upon the previous method proposed
by Zongwen and his former colleagues (Appl.
Phys. Lett. 83 (2003) 29�3). This new approach
is much simpler because it avoids the need for
preliminary calibration of a single nanothermom-
eter. It is also far more reliable because it does
not focus on a single nanothermometer, thereby
avoiding the risk of damage or loss of that par-
ticular nanothermometer. Finally, this technique
demonstrated improved accuracy (better than
5%) over the original method. While it has been
proven (Zongwen Liu et al. Phys. Rev. Lett. 93
(200�) 09550�) that gallium remains liquid down
to –70 °C or –80 °C when encapsulated within
nanotubes, depending on the phase formed
during solidification, the oxidation-assisted
temperature measurement is only suitable
for temperatures that are well above room
temperature.
The manuscript describing this new method,
which was published in Nanotechnology (�7
(2006) 368�), was downloaded 250 times in
the first four weeks after it appeared online on
27 June. Other media stories on this method
can be found through the web links below.
Website links:
http://www.nanowerk.com/spotlight/spotid=667.
php
http://www.physorg.com/news73��0605.html
TEM micrographs showing a nanothermometer with a marker
(a) and the subsequent temperature retrieving by reheating
the nanotube in TEM (b-d). Scale bar = 100 nm.
Dr Zongwen Liu
Senior Research Associate
Tel. +6� 2 935� 7535
More information:
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Master of Applied Science (Microscopy and Microanalysis)
Biomolecular imaging
and analysis comprise
highly developed
techniques that are
applicable across a spectrum of biomedical disci-
plines from pathology to bioengineering. Similarly,
nanomaterials characterisation using atomic
scale imaging lies at the forefront of technological
development and research in subdisciplines of
the material, physical and engineering sciences.
These are the two streams of the Master of
Applied Science, Microscopy and Microanalysis.
Overview
Modern microscopy encompasses light-, laser-,
and electron-based imaging techniques per-
formed with high-end, sophisticated instruments.
Complimentary to the imaging is the analysis
conducted with software capable of generating
multidimensional and multichannelled (coloured)
reconstructions of micro- and nano-scaled
structures. The importance of the imaging field
is reflected in studies involving intravital visu-
alisation of tumours, which have advanced our
understanding of how cancer cells interact with
normal, host cells to drive cancer progression. In
addition, advanced nanomaterials characterisa-
tion has explained the mechanical behaviour and
other properties of many important engineering
materials.
Graduates of this program have a great future in
PhD research and access to a number of career
options in forensic, biomedical, biotechnological,
chemical, geological, archaeological, metallurgi-
cal, physical, engineering and nanotechnological
fields that require imaging expertise. This course
is highly suitable for undergraduates as well as
professionals who would like to acquire new skills
or obtain professional qualification in an area
related to their current employment.
Dr Lilian SoonTel. +6� 2 935� 5322Lecturer, Structural Biology &Postgraduate Coursework [email protected]
More information:
Units of Study
MCAN 5005 Introductory Microscopy & Microanalysis; Core. The course provides an introduction to the fundamental principles of optics and the related principles of spectroscopy that are commonly used in microscopy and microanalysis.
MCAN 5006 Electron Microscopy; Core.Trains participants, with no prior knowledge of electron microscopy, to become operators of scanning and transmission electron microscopes.
MCAN 5101 Confocal & Fluorescence Microscopy; Option. Training in the use of the confocal microscope and specimen preparation in immunochemistry, cell loading and GFP for applications in cell biology and medicine.
MCAN 5102 Biological Specimen Preparation; Option. Participants will develop knowledge and skills in specimen preparation for light and electron microscopy including fixing, embedding, sectioning, coating, staining and cryo-techniques.
MCAN 5103 Materials Preparation and Microscopy; Option. Practical training in the preparation of specimens for electron microscopy from a wide range of materials using electropolishing, ion milling, ultramicrotomy, and focused ion beam (FIB).
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A/Prof. Filip Braet
Tel. +6� 2 935� 76�9
Editors
Ms Ellie Kable
Tel. +6� 2 935� 7566
Ms Uli Eichhorn
Tel. +6� 2 935� ��93
The Electron Microscope UnitNanostructural Analysis Network Organisation
Major National Research Facility
The University of Sydney
NSW, 2006, Australia
Tel. + 6� 2 935� 235�
Fax + 6� 2 935� 7682
www.emu.usyd.edu.au
MCAN 5104 Image Analysis; Option.Teaches the processing and the extraction of quantitative data from images. Participants will develop knowledge of both traditional stereology techniques and modern digital image processing and analysis.
MCAN 5110 Nanostructural Analysis of Materials; Option. Explores the relationships between the structure and properties of materials using techniques for the quantitative determination of the nanoscale structure and chemistry of materials.
MCAN 5111 Microscopy of Biomolecular Processes; Option. Teaches advanced techniques to study molecular cellular processes including signalling, uptake and metabolism of drugs/carcinogens and immunogold labelling using cryo-procedures for EM.
MCAN 5112 Advances in Modern Microscopy; Option. This unit provides students with knowledge of and training in the application of the very latest advances in microscopy techniques and technologies.
MCAN 5201 Project and Report A; Core for Masters. Gives students the opportunity to extend the practical work encountered in other modules, and gain skills in carrying out and writing up a research project.
MCAN 5202 Project and Report B; Core for Masters. See MCAN 520�.
MCAN 5203 Project and Report C; Core for Masters/Research Path. This unit of study is an extension of Project and Report A and B and is only for those students approved for the research path to further extend their research.
MCAN 5210 Research Methodology; Optional for Masters, Core for Masters/Research Path. This unit covers the principles and practice of research methodology including literature review,experimental design, statistics and data analysis, intellectual property and commercialisation, and written and oral communication.