Monthly Archives: January 2013

Mass Spectrometry Method of the Year 2012

Mass spectrometry, mostly used in discovery-based proteomics, can also be applied to specifically analyze target proteins of interest. In the most mature technology for targeted analysis, known as selected (or multiple) reaction monitoring, a mass spectrometer called a triple quadrupole is programmed to detect specific peptides that uniquely represent proteins of interest, allowing researchers to quantitatively monitor these proteins with high sensitivity and reproducibility.


Mass spectrometry has an advantage over antibodies in that developing a new targeted assay is much faster than generating a new antibody, and issues of detection specificity (that is, antibody cross-reactivity) are greatly minimized. Antibodies still have the upper hand in terms of sensitivity of detection for low-abundance proteins. But a highly positive trait of mass spectrometry is its inherent ability to unambiguously detect multiple proteins in one experiment, allowing, for example, a systems biology researcher to look at what happens to protein levels upon perturbation of a protein network or a clinical researcher to measure how a panel of proposed biomarkers changes in a disease state.

An old technology made new

The triple quadrupole mass spectrometer (QQQ) was developed more than 30 years ago for small-molecule analysis. It operates as a dual mass filter that allows molecular ions of predetermined masses to be selected for fragmentation in the instrument. In recent years the use of the QQQ for targeted proteomics applications has escalated as methodological advances have made the technology more widespread.

Allison Doerr, Nature Methods, 10, 23, (2013)

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January 29, 2013 · 11:22 pm

CRP Protein Systemic Marker


The classical acute-phase protein, C-reactive protein (CRP), is an exquisitely sensitive systemic marker of disease with broad clinical utility for monitoring and differential diagnosis. Inflammation, the key regulator of CRP synthesis, plays a pivotal role in atherothrombotic cardiovascular disease. There is a powerful predictive association between raised serum CRP values and the outcome of acute coronary syndromes, and, remarkably, between even modestly increased CRP production and future atherothrombotic events in otherwise healthy individuals. Baseline CRP values also reflect metabolic states associated with atherothrombotic events. The presence of CRP within most atherosclerotic plaques and all acute myocardial infarction lesions, coupled with binding of CRP to lipoproteins and its capacity for pro-inflammatory complement activation, suggests that CRP may contribute to the pathogenesis and complications of cardiovascular disease.

C-reactive protein (CRP), named for its capacity to precipitate the somatic C-polysaccharide of Streptococcus pneumoniae,was the first acute-phase protein to be described, and is an exquisitely sensitive systemic marker of inflammation and tissue damage.

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January 28, 2013 · 12:16 pm

Ultrasonographic contrast enhanced images


Sunnybrook Health Sciences Centre, developed innovative method by using bubbles to find cancer. These are tiny microbubbles of gas, smaller than a red blood cell, that are injected in minute amounts into a patient’s veins. And when an ultrasound is used to track the bubbles, they ring like a bell, showing where they are! the bubbles essentially form a roadmap of the body’s small blood vessels. And the way those blood vessels form, will help indicate if cancer is present or not. In a healthy organ, blood vessels resemble a tree-like structure. But when cancer is present, those blood vessels look like a disorganized tangle of lines.

One study showed that Ultrasonographic US shows high concordance with CT or MR imaging, especially for the arterial phase. Discordance in the portal venous phase may reflect the tendency of CT and MR contrast agents, unlike microbubbles, to diffuse into interstitium.


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January 27, 2013 · 1:06 pm

Terahertz Spectroscopy for observing protein in natural environment

Observing the structural dynamics of proteins under conditions as close as possible to those in a living organism is essential for understanding the biological functions of proteins accurately. At Oxford we demonstrate that terahertz spectroscopy is a convenient probe of conformational changes in proteins suspended in physiological buffer solution. We have observed that the partial unfolding of photoactive yellow protein leads to a clear increase in absorption at terahertz frequencies. Using normal mode and molecular dynamics simulations we show that this increase in absorption is related to an increase in the density of delocalised vibrational modes in the more flexible partially unfolded state.

MB Johnston et al Chem. Phys. Lett., 455:289-292 (Apr 2008)

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January 26, 2013 · 12:20 am

Simple Method for Graphene Nanoribbon


A simple and highly efficient method is reported by NorthWestern University Scientists for creating graphene nanostructures with gaps that can be controlled on the sub-10 nm length scale by utilizing etch masks comprised of electrochemically synthesized multisegmented metal nanowires. This method involves depositing striped nanowires with Au and Ni segments on a graphene-coated substrate, chemically etching the Ni segments, and using a reactive ion etch to remove the graphene not protected by the remaining Au segments. Graphene nanoribbons with gaps as small as 6 nm are fabricated and characterized with atomic force microscopy, scanning electron microscopy, and Raman spectroscopy. The high level of control afforded by electrochemical synthesis of the nanowires allows us to specify the dimensions of the nanoribbon, as well as the number, location, and size of nanogaps within the nanoribbon. In addition, the generality of this technique is demonstrated by creating silicon nanostructures with nanogaps.

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January 26, 2013 · 12:12 am


Optical pumping is a process in which light is used to raise (or “pump”) electrons from a lower energy level in an atom or molecule to a higher one. It is commonly used in laser construction, to pump the active laser medium so as to achieve population inversion.


Figure : The time-resolved conductivity of isolated GaAs nanowires is investigated by optical-pump spectroscopy. Strong surface plasmon mode was observed due to charge trapping at the nanowire surface.

Reference: Oxford University TeraHertz group, Prof Johnston

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January 25, 2013 · 11:32 pm

Microprobe Imaging

bio_imageOxford scientists pioneered the use of microprobe ion sources for radiocarbon AMS.  This method had sub-micron resolution, and could be used to image radiocarbon labelled material in tissue or other biological samples at higher sensitivity and resolution than autoradiogr


Other area that they are working on is GC-AMS. With this method GC separation is used in conjunction with AMS measurement to detect the presence of radiocarbon in particular compounds. The method is highly sensitive with natural abundance radiocarbon measurable to a precision of about 10% for sample sizes of the order of 1ug.

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January 24, 2013 · 11:39 pm

Accelerator mass spectrometry dating and its application to archaeological and environmental problems

NewAMSAccelerator mass spectrometry (AMS) differs from other forms of mass spectrometry in that it accelerates ions to extraordinarily high kinetic energies before mass analysis. The special strength of AMS among the mass spectrometric methods is its power to separate a rare isotope from an abundant neighboring mass (“abundance sensitivity”, e.g. 14C from 12C). The method suppresses molecular isobars completely and in many cases can separate atomic isobars (e.g. 14N from 14C) also. This makes possible the detection of naturally occurring, long-lived radio-isotopes such as 10Be, 36Cl, 26Al and 14C. Their typical isotopic abundance ranges from 10−12 to 10−18. AMS can outperform the competing technique of decay counting for all isotopes where the half-life is long enough. source: wikipedia


Christopher Ramsey at Oxford University has been most concerned with the development of high precision techniques and their applications to archaeological and environmental problems. His area of research invovles the Accelerator Mass Spectrometry (AMS) techniques including the development of gas ion sources for AMS that allows the measurement of very small samples and a technique, GC-AMS with applications in the environmental and biological sciences.

Precision and accuracy in accelerator mass spectrometry (AMS) dating relies on the systematic reduction of errors at all stages of the dating process, from sampling to AMS measurement. With new AMS systems providing much better precision and accuracy for the final stage of the process, we need to review the process as a whole to test the accuracy of reported results. A new High Voltage Engineering Europa (HVEE) AMS system was accepted at Oxford in September 2002. Since then, the system has been in routine use for AMS dating and here we report on our experiences during the first year. The AMS system itself is known to be capable of making measurements on single targets to a precision of better than 0.2% for the (super 14) C/ (super 13) C ratio and better than 0.1% for the (super 13) C/ (super 12) C ratio. In routine operation, we measure known-age wood to a precision of just above 0.3%, including uncertainties in background and pretreatment. At these levels, the scatter in results is no higher than reported errors, suggesting that uncertainties of + or -25 to + or -30 (super 14) C yr can be reliably reported on single target measurements. This provides a test of all parts of the process for a particular material in a particular state of preservation. More generally, sample pretreatment should remove as much contamination as feasible from the sample while adding as little laboratory contamination as possible. For more complex materials, such as bone, there is clearly more work needed to prove good reproducibility and insignificant offsets in all circumstances. Strategies for testing accuracy and precision on unknown material are discussed here, as well as the possibilities of one day reaching precisions equivalent to errors of or -20 (super 14) C yr.
C B Ramsey et al, Towards high precision AMS: Progress and Limitations: RadioCarbon Journal, Vol 46, No 1, 2004



The 2007 Biblical Archaeology Society Publication Awards recognize the best books on archaeology and the Bible published in 2005 and 2006 and have been presented since 1985. The book comprises 27 chapters which stemmed from an invited meeting in Oxford organised by Levy and Higham in 2004.

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January 21, 2013 · 7:08 pm

Spinning nanotubes fiber

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January 18, 2013 · 7:21 am

Photo Conductive Atomic Force Microscopy: pcAFM


The performance of organic solar cells is highly dependent on film morphology. However, directly correlating local film structures with device performance remains challenging. Photoconductive atomic force microscopy (pcAFM) can be used to map local photocurrents with 20 nm resolution in donor/acceptor blend solar cells of the conjugated polymer poly[2-methoxy-5-(3‘,7‘-dimethyloctyl-oxy)-1,4-phenylene vinylene] (MDMO-PPV) with the fullerene (6,6)-phenyl-C61-butyric acid methyl ester (PCBM) spin-coated from various solvents. Photocurrent maps under short-circuit conditions (zero applied bias) are presented here as well as under various applied voltages. Significant variation is found in the short-circuit current between regions that appear identical in AFM topography. These variations occur from one domain to another as well as on larger length scales incorporating multiple domains. These results suggest that the performance of polymer−fullerene blends can still be improved through better control of morphology.

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David S. Ginger et al, University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, Nano Lett., 2007, 7 (3), pp 738–744


Fig1cNew Scanning Probe Techniques: pcAFM

A relative of conductive AFM (cAFM), pcAFM records local photocurrents directly in contact mode, essentially by using a metalized AFM probe as the top contact to form a nanoscale solar cell. In pcAFM, we typically use focused laser illumination to photoexcite the sample. The small collection area leads to a small photocurrent, and even high-quality devices with external quantum efficiencies over 50%, we find it beneficial to use high-intensity illumination to improve signal to noise. For instance, a green laser (Crystal Laser GCL-005L, 5mW, 532nm, see Figure 1c) is focused to a diffraction-limited spot on the sample and aligned with the tip; after attenuation, the laser intensity, and therefore the expected sample damage, is often comparable to that in confocal microscopy experiments on biological samples. We also use blue and red lasers as required to match the absorption spectrum of the material being studied. Contact AFM tips with metal overall coating, usually Au (Budget Sensors, ContE-GB, k ~ 0.2N/m), are used for measurement. A small setpoint value is used to minimize destruction of the polymer layer whilst also to keep the conductive coating free from surface contamination. Perhaps one of the most significant practical challenges to using pcAFM is obtaining a good electrical image without causing significant damage to the sample. Patience, and a willingness to sacrifice many AFM cantilevers in the name of science are often necessary.


Figure 1. (A) Schematic of a typical bulk heterojunction organic photovoltaic device. Schematic diagrams of the (B) trEFM and (C) pcAFM experimental setups based on Asylum Research’s MFP-3D-BIO™ AFM System.

Read More…Asylum Research



January 15, 2013 · 10:08 am

Imaging is key to advance our understanding of development biology


Do we even understand the key principles let alone the specific details that orchestrate development biology? We believe that the answer to this question is still no.

……..we believe imaging will play a key role in advancing our understanding of developmental mechanisms across the scales….. imaging can be used to watch, measure, and even perturb developmental processes at all the relevant scales: molecular, cellular, tissue, and organismal. Importantly, we wish to challenge the simplistic notion that imaging is inherently ‘descriptive’ while molecular approaches are inherently ‘mechanistic’…………..key mechanisms and principles are found at many scales. Imaging can assay all of these scales, while molecular approaches are often irrelevant. Observing that tissue Y does not form when gene X is missing does not constitute an explanation of how tissue Y forms, nor what key principles are important in controlling its formation; it is important information, but it is an observation that should begin a mechanistic investigation, not end one. On the other hand, careful time-lapse microscopy has the potential to reveal the dynamics of gene regulatory networks, collective behaviors of cells, and tissue mechanics that underlie the formation of tissue Y.


The molecular paradigm of development has several limitations. One is that mechanism can often not be reduced to a single gene. As developmental biologists, we know that you cannot really draw a straight line between genes and phenotypes. Rather, the mechanisms that control development happen through the often nonlinear interactions of many genes in a dynamic network. Another limitation is that currently, much of development uses only a static readout such as looking at the terminal phenotype of a mutant. Understanding function often results from seeing the dynamics of a process occurring over time such as protein levels in a molecular circuit going up and down as a cell fate decision is computed.

The final limitation of the current paradigm is that mechanism does not occur only at the molecular level; mechanism happens at all scales…………….

Microscopy to mechanism across the scales of development, Harvard and Oxford Universities

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January 14, 2013 · 5:57 pm

fMUS functional micro ultra sound imaging

A recent adaptation of high-frequency ultrasound imaging (Foster et al., 2002) allows quantitative measurement of changes in CBV and CBF.

stuart foster

Functional micro-ultrasound imaging (fMUS) is a new modality for hemodynamic imaging. ► fMUS enables quantification of relative CBV and CBF throughout the rat brain. ► Color Doppler ultrasound imaging identifies cortical arterioles and venules. ► rCBV is lower and flow rate is higher in cortical arterioles than in cortical venules. ► The CBF-CBV relationship is different in cortical vs. subcortical gray matter.

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“Dr Stuart Foster, PhD (Scientist Profile), Sunnybrook Research Institute, Toronto,Canada”. Retrieved 2012-05-01.

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January 10, 2013 · 6:06 pm

Photoacoustic Tomography


A novel scanning technique that combines optics with ultrasound could provide detailed images at greater depths

A new technique called photoacoustic (or optoacoustic) tomography, which marries optics with ultrasonic imaging, should in theory be able to provide detailed scans comparable to those produced by magnetic-resonance imaging (MRI) or X-ray computerised tomography (CT), but with the cost and convenience of a hand-held scanner. Since the technology can operate at depths of several centimetres, its champions hope that within a few years it will be able to help guide biopsy needles deep within tissue, assist with gastrointestinal endoscopies and measure oxygen levels in vascular and lymph nodes, thereby helping to determine whether tumours are malignant or not. There is even scope to use photoacoustic imaging to monitor brain activity and gene expression within cells.

The field of contrast agents is central to future developments in microultrasound. In particular, researchers at the University of Toronto are studying the use of microbubble (< 3 micron dia.) and sub-micron particle contrast agents at high frequencies and applying these to models of cardiovascular disease and cancer[5]. They have recently demonstrated Molecular Imaging approaches based on targeted microbubble contrast agents and believe these approaches will also make an important contribution to bioresearch.

To create a photoacoustic image, pulses of laser light are shone onto the tissue being scanned. This heats the tissue by a tiny amount—just a few thousandths of a degree—that is perfectly safe, but is enough to cause the cells to expand and contract in response. As they do so, they emit sound waves in the ultrasonic range. An array of sensors placed on the skin picks up these waves, and a computer then uses a process of triangulation to turn the ultrasonic signals into a two- or three-dimensional image of what lies beneath.

The technique works at far greater depths (up to seven centimetres) than other optical-imaging techniques such as confocal microscopy or optical-coherence tomography, which penetrate to depths of only about a millimetre. And because the degree to which a particular wavelength of light is absorbed depends on the type of tissue and, in the case of blood, on whether it is oxygenated or deoxygenated, there is, in effect, a natural contrast agent. This makes the technique superior to ultrasound alone when it comes to picking out detailed features such as veins.

MRI and CT scans are also capable of delivering this kind of detail. But they usually require contrast dyes to be injected into the bloodstream, says Lihong Wang, a photoacoustic researcher at Washington University in St Louis, Missouri. CT scans also involve potentially harmful ionising radiation. And MRI and CT scans are very expensive, using machines that cost millions of dollars and require dedicated staff to operate them.

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January 10, 2013 · 6:00 pm

Diffuse Reflectance Spectroscopy distinguishes signs of malignancy


Minute deposits of calcium in breast tissue act as a marker for breast cancer. Diffuse reflectance spectroscopy has now been used to show how deposits in benign conditions can be distinguished from those present in the early stages of the disease.

Microcalcification in breast tissue can be a sign of malignancy, but more often than not they are simply a residue of a benign condition. Now, researchers at Massachusetts Institute of Technology and Case Western Reserve University have turned to diffuse reflectance spectroscopy to help them develop a clinical approach that might help doctors distinguish between cancerous and noncancerous incidence of such deposits.

Mammography often reveals microcalcification causing concern for patients and requiring an invasive biopsy to test the tissue for malignancy. However obtaining tissue from the specific region containing the deposit is difficult and in 15 to 25 percent of cases impossible. This means an inconclusive test and requires follow-up with more invasive surgery.

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January 8, 2013 · 1:37 pm


Educreations Teach what you know, Learn what you don’t.

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January 4, 2013 · 4:30 pm