instruments

True 3D fluorescence imaging at nanoscale resolution

jorgemata — Mon, 19 May 2008 02:56:49 -0700

Description

True 3D super-resolution fluorescence imaging is now possible, reports a study online this week in Nature Methods. The technique opens the door to previously unattainable detailed 3D fluorescence images of the inside of single cells.

Laser scanning microscopy is an invaluable tool for peering inside biological specimens. It can scan a focused imaging spot inside the sample to produce an image along a single thin internal plane, whose thickness is determined by the height of the imaging spot. A 3D image is created by assembling multiple image planes; thinner planes yield better vertical resolution. Unfortunately, the physical laws that govern light microscopy limit how small this imaging spot can be made, and this limits the 3D resolving power of the method, particularly in the vertical dimension.

Researchers from Max Max Planck Institute for Biophysical Chemistry & German Cancer Research Center designed a microscope that overcomes this limitation by producing a nearly perfectly spherical 40 nanometre diameter scanning spot. This allowed them to obtain the very first 3D fluorescence images capable of distinguishing the locations of different proteins in organelles as small as mitochondria.

The abstract says:

The resolution of any linear imaging system is given by its point spread function (PSF) that quantifies the blur of an object point in the image. The sharper the PSF, the better is the resolution. In standard fluorescence microscopy, however, diffraction dictates a PSF with a cigar-shaped main maximum, called the focal spot, which extends over at least half the wavelength of light (lambda = 400–700 nm) in the focal plane and > lambda along the optical axis (z). Although concepts have been developed to sharpen the focal spot both laterally and axially, none of them has reached their ultimate goal: a spherical spot that can be arbitrarily downscaled in size. Here we introduce a fluorescence microscope that creates nearly spherical focal spots of 40–45 nm (lambda/16) in diameter. Fully relying on focused light, this lens-based fluorescence nanoscope unravels the interior of cells noninvasively, uniquely dissecting their sub-lambda–sized organelles.

J M

Biomedical Sciences and Biotechnology

Source

Spherical nanosized focal spot unravels the interior of cells. Roman Schmidt1, Christian AWurm1, Stefan Jakobs1, Johann Engelhardt2, Alexander Egner1 & Stefan W Hell1,2. Nature Methods, May 18, 2008. DOI: 10.1038/nmeth.1214

1 Max Planck Institute for Biophysical Chemistry, Department of NanoBiophotonics, Goettingen
2 German Cancer Research Center (DKFZ), High-Resolution Optical Microscopy Division, Heidelberg

Microfluidics using a cheap 1980s-era desktop plotter

Alex Soojung-Kim Pang — Wed, 30 Apr 2008 20:38:58 -0700

Description

Via Attila Csordas, a Nature report on a project in which Harvard chemist Derek Bruzewicz and colleagued converted an old desktop plotter into "an impressively simple microfluidics device that can be produced without a clean room or photolithographic equipment."

The system works like this. By replica moulding, the pens of the plotter are replaced with PDMS [organic polymer poly(dimethylsiloxane)] versions that can deliver various types of 'ink'. The purpose of the ink, when cured, is to create channels in a filter-paper substrate, and after experimenting with the possibilities Bruzewicz et al. found that a syrupy mixture of 3:1 PDMS:hexane did just fine. Having chosen the appropriate paper, the trick then is to use the plotter to draw channel shapes, with the PDMS syrup penetrating the full depth of the paper to create water-tight chambers in various patterns....

The authors have tested different types of the device with well-tried colorimetric assays for identifying excess protein and glucose in urine, and found they performed well, with no cross-contamination between channels.

According to the HP Computer Museum (not actually part of HP), the particular plotter used in this project, a 7550

was the most advanced small plotter ever built. It had an incredible acceleration of 6g, making it one of the fastest plotters ever (and the most fun to watch). The 7550 had 8 pens and could plot on many types of media including paper, transparency film, vellum and polyester film.

It was introduced in 1984, and cost $3900 at the time; you can get them on eBay for $50.

Biomedical Sciences and Biotechnology

Source

http://pimm.wordpress.com/2008/03/28/low-budget-high-tech-microfluidics-device-out-of-a-50-plotter/
http://www.nature.com/nature/journal/v452/n7186/full/452421a.html

Viewing neurons in 3D

Alex Soojung-Kim Pang — Mon, 28 Apr 2008 15:17:24 -0700

Description

EurekAlert reports on a new technique for viewing neurons in 3D. Normal microscopes provide a two-dimensional view of neurons, but scientists at Baylor College of Medicine and Rice University have developed a technique that creates a 3D image in milliseconds:

they developed a “trick” to quickly move a laser beam in three dimensions and then adapted that laser beam to the multi-photon microscope they were using. That allowed them to “see” the neuron’s function in three dimensions, giving them a much better view of its activity.

A multiphoton microscope looks much like a conventional, upright microscope but it has an adaption that allows it to look at tissues in sections. A conventional multiphoton microscope does that very slowly, he said.

“With ours, you can do it very quickly. We are starting to see how a single neuron behaves in our laboratory,” [Dr. Gaddum Duemani Reddy] said. The next step, he said, will be to use to it to look a clusters or colonies of neurons. This will enable them to actually see the neuronal interactions.

Future of neuroscience

Source

http://www.eurekalert.org/pub_releases/2008-04/bcom-lan042508.php

Growing infrastructures for "citizen science" will help shape 21st century science

Hyungsub Choi — Sat, 26 Jan 2008 11:32:34 -0800

Description

We have thought a bit about the trend leading from the 20th century "science cities" to the 21st century "city science." This is the turn from the "Big" science and technology toward more distributed research activities. What would be the necessary infrastructure for this transition?

Jeff Johannes, medicinal chemist at a large pharmaceutical company, wrote an interesting posting on the blog Sceptical Chymist (http://blogs.nature.com/thescepticalchymist/features/10_miles_from_academia/):

Independence is a really good thing. Some amazing discoveries have come from qualified people or groups that were allowed to truly explore their own ideas, free of external bias or constraints. One clear example of the power of this concept exists in the context of popular music. During the 20th century there was an explosion of diverse musical genres that continues today. Many factors contributed to this process, but one of the most important was the fact that musical instruments and recording equipment gradually became cheaper while at the same time becoming more widely available. This made music accessible to anyone who had a desire to pick up an instrument and create music. Moreover, they could use their own recording equipment to communicate their ideas to interested parties. Today, with the advent of computers and digital recording, musicians can make home recordings of a rather high quality and easily share their songs on the internet. It is truly an exciting time to be a musician.

In terms of accessibility and expense, chemistry, and most modern sciences in general, are way behind music. A budding rock star can buy a $200 guitar at a local retailer and record songs at home, but when I think of chemistry, I think of $600,000 NMRs and $100,000 LCMS stacks installed in the hallowed halls of the worlds great schools. I consider myself extremely lucky to have access to such amazing equipment. But many scientists don’t.

While modern science is more technologically complex than music, I see no fundamental limitation to increasing the accessibility and reducing the cost of doing research. I think this is one of the great challenges facing science. Inexpensive scientific instruments would empower new scientists, give more independence to existing researchers, and lead to an increase in creativity in scientific research.

The indicator to watch to see whether scientific research is indeed following the trajectory of popular music is the availability of the scientific analogue of the "$200 guitar at a local retailer." Are there efforts to lower the cost of spectrometers, DNA analyzers, and NMR machines? Why don't scientific instruments follow the path of PCs, in a way that exponentially improves size and performance?

This has implications for the Brazilian case as well, about which Alex Pang has posted a few signals. In order to have a more diffuse model of scientific activity, one would need more readily available instruments. Perhaps science version of "One Laptop Per Child"?

Signals

The Amateur New York Subway Riding Committee - Collaborative Adventure Science

Citizens as sensors: the world of volunteered geography

Amateur cancer researcher (and patient) partners with academia and VC to prototype a cure