New Vitrobot™ at the EMU • Collaborative Initiative of the ...sydney.edu.au/acmm/pdf_doc/news/EMU_News_0806.pdfNew Vitrobot™ at the EMU • Collaborative Initiative of the Department

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

[email protected]

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

[email protected]

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

[email protected]

Editors

Ms Ellie Kable

Tel. +6� 2 935� 7566

[email protected]

Ms Uli Eichhorn

Tel. +6� 2 935� ��93

[email protected]

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.