Tag Archives: electron microscopy

It really is a nanoscale window into the biological world

The researchers at Virginia Tech Carilion Research Institute (VTC Research Institute) have sandwiched together a couple of chips, each with a hole (window) in the middle giving themselves a peek into biological processes as they occur, they hope. Here’s a more technical explanation from the Dec. 20, 2012 news release on EurekAlert,

Investigators at the Virginia Tech Carilion Research Institute have invented a way to directly image biological structures at their most fundamental level and in their natural habitats. The technique is a major advancement toward the ultimate goal of imaging biological processes in action at the atomic level.

The technique involves taking two silicon-nitride microchips with windows etched in their centers and pressing them together until only a 150-nanometer space between them remains. The researchers then fill this pocket with a liquid resembling the natural environment of the biological structure to be imaged, creating a microfluidic chamber.

Then, because free-floating structures yield images with poor resolution, the researchers coat the microchip’s interior surface with a layer of natural biological tethers, such as antibodies, which naturally grab onto a virus and hold it in place.

The lead researcher describes the difference between the usual imaging techniques and their newly developed technique (from the EurekAlert news release),

“It’s sort of like the difference between seeing Han Solo frozen in carbonite and watching him walk around blasting stormtroopers,” said Deborah Kelly, an assistant professor at the VTC Research Institute and a lead author on the paper describing the first successful test of the new technique. “Seeing viruses, for example, in action in their natural environment is invaluable.”

Ken Kingery’s Dec. ??, 2012 Virginia Tech Carilion Research Institute article, which originated the news release, describes the specific virus the researchers used the ‘window’ to spy on,

Rotavirus is the most common cause of severe diarrhea among infants and children. By the age of five, nearly every child in the world has been infected at least once. And although the disease tends to be easily managed in the developed world, in developing countries rotavirus kills more than 450,000 children a year.

At the second step in the pathogen’s life cycle, rotavirus sheds its outer layer, which allows it to enter a cell, and becomes what is called a double-layered particle. Once its second layer is exposed, the virus is ready to begin using the cell’s own infrastructure to produce more viruses. It was the viral structure at this stage that the researchers imaged in the new study.

Kelly and McDonald [Sarah McDonald, an assistant professor at the VTC Research Institute] coated the interior window of the microchip with antibodies to the virus. The antibodies, in turn, latched onto the rotaviruses that were injected into the microfluidic chamber and held them in place. The researchers then used a transmission electron microscope to image the prepared slide.

The technique worked perfectly.

The experiment gave results that resembled those achieved using traditional freezing methods to prepare rotavirus for electron microscopy, proving that the new technique can deliver accurate results. “It’s the first time scientists have imaged anything on this scale in liquid,” said Kelly.

There’s more to work to be done of course as the researchers refine the technique and try to ‘spy’ on more of the processes. In the meantime, the paper about this latest imaging research will be published in print in 2013 or it can be viewed online now (this is a open access article in a journal published by the Royal Society of Chemistry [RSC], you will need to sign up but this too is free),

Visualizing viral assemblies in a nanoscale biosphere
Brian L. Gilmore ,  Shannon P. Showalter ,  Madeline J. Dukes ,  Justin R. Tanner ,  Andrew C. Demmert ,  Sarah M. McDonald and Deborah F. Kelly

Lab Chip, 2013,13, 216-219

DOI: 10.1039/C2LC41008G Received 15 Jun 2012, Accepted 13 Nov 2012 First published on the web 19 Nov 201


Sick and tired of the ‘social media is changing how science is practiced’ narrative

The whole ‘social media is changing ______’ puzzles me. You can fill in the blank with science/government/social relationships/etc. It’s always the same notion. Somehow social media is engendering changes the like of which we’ve never seen before.

  • The February 2011 overthrow of Mubarak in Egypt was all due to social media, as is the current social unrest in many Middle Eastern Countries.
  • Social relationships are being negatively impacted (nobody talks to anybody else anymore or it’s opening new avenues for relationships)
  • The practice of science is being changed by the use of social media.
  • etc.

Mostly I’m concerned with the one about science since I recently ended up on a panel where the discussion turned on this topic. I think there are a lot of things having an impact on how science is practiced and trying to establish the role social media is playing, if any, is a little premature.

We had Rosie Redfield on the panel. Rosie is a professor at the University of British Columbia who was part of the ‘arsenic life’ story that took the internet by a storm in late November/early December 2010. (Confession: I got caught up in the excitement in my Dec. 6, 2010 posting and recanted in my Dec. 8, 2010 posting.) Recently, there’s been a story about ‘arsenic life’ by Carl Zimmer for Slate magazine titled, How #arseniclife changed science. Here’s Zimmer’s set up (from the Slate article),

On November 29, NASA announced that it would soon hold a press conference to “discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.” Wild speculation ran amok—perhaps scientists had found living things on one of Saturn’s moons. At the press conference, the scientists did not unveil an actual extraterrestrial, but they did have big news. A new paper had just been published in the journal Science, they said, which described bacteria that seemed able to build their own DNA from arsenic. If that were true, it would be an historic discovery, because no such ability has ever been found among Earth’s life-forms.

The paper was published online in late November and attracted a great deal of discussion and criticism almost immediately on blogs (Rosie Redfield’s RRResearch amongst them) and on twitter via the hash tag topic, #arseniclife. The print version of the paper, along with critical letters, will appear in the June 3, 2011 issue of Science.

Here’s Zimmer’s take on what makes this particular scientific dust-up different,

For those of us who have been tracking #arseniclife since last Thanksgiving, however, today comes as an anticlimax. There’s not much in the letters to Science that we haven’t read before. In the past, scientists might have kept their thoughts to themselves, waiting for journals to decide when and how they could debate the merits of a study. But this time, they started talking right away, airing their criticisms on the Internet. In fact, the true significance of the aliens-that-weren’t will be how it helped change the way scientists do science.

Zimmer goes on to describe this new practice,

Redfield and her colleagues are starting to carry out a new way of doing science, known as post-publication peer review. Rather than leaving the evaluation of new studies to a few anonymous scientists, researchers now debate the merit of papers after they have been published. The collective decision they come to stays open to revision.

Post-publication peer review—and open science in general—is attracting a growing number of followers in the scientific community. But some critics have argued that it’s been more successful in theory than in practice. The #arseniclife affair is one of the first cases in which the scientific community openly vetted a high-profile paper, and influenced how the public at large thought about it.

Post-publication peer review existed before social media as per ‘cold fusion’ (Wikipedia essay). I remember it because I wasn’t particularly interested in science at the time but this was everywhere and it went on for months. There was the initial excitement and enthusiasm (the ‘cold fusion’ scientists were featured on the cover of Times or Newsweek or maybe both in the days when those magazines were powerhouse publications). Then, as the initial enthusiasm died down, the storm of scientific criticism started (those other scientists may not have had social media but they made themselves felt). The story took place over eight to 10 months and achieved public awareness in a way that scientists can only fantasize about these days.  By comparison, the arsenic story blew up and disappeared from public consciousness within roughly two weeks, if that.

Social media may yet change how science is practiced but I wouldn’t use Zimmer’s story about #arsencilife to support that belief, in fact, I think it could support another idea altogether.

The ‘arsenic’ story was, by comparison, with ‘cold fusion’ greatly truncated and most members of the public never really heard about it and, as a consequence, were not exposed to the furious debate and discussion as they were with  ‘cold fusion’.  They did not get exposed to how science ‘really works and therein lies a problem because they did not see the uncertainties, the mistakes, and revised ideas.

As for what factors may be having an impact on scientific practice, I’d suggest reading Identifying good scientists and keeping them honest on The Black Hole blog by David Kent. Here’s an excerpt,

In a February 2011 interview with Lab Times, Cambridge scientist Peter Lawrence1 reflects on his own career and complains that “the heart of research is sick” as he charts the changes in the way in which science is pursued.  Briefly, he cites impact factors and the increased need to assign metrics to scientists (# of publications, H-index, etc) as main drivers of producing low quality research and unfairly squeezing out some good scientists who do not publish simply for the sake of publishing.  Impact factor fever runs deep throughout laboratories but, most damagingly, exists at the funding agency and university administrative level as well.

ETA June 17, 2011: For anyone who’d like to read some updated and contrasting discussion about the #arseniclife aftermath for scientific practice and science education there are two June 16, 2011 guest posts for Scientific American, one from Rosie Redfield and the other from Marie-Claire Shanahan. Plus, if you are interested in more details about the cold fusion story and the role electronic communication played, check out Marie-Claire Shanahan’s post,  Arsenic, cold fusion and the legitimacy of online critique, on the Boundary Vision blog.

Scientific research, failure, and the scanning tunneling microscope

“99% of all you do is failure and that’s maybe the most difficult part of basic research,” said Gerd Binnig in a snippet I’ve culled from an interview with Dexter Johnson (Nanoclast blog on the IEEE [Institute of Electrical and Electronics Engineers] website) posted May 23, 2011 where Binnig discussed why he continued with a project that had failed time and time again. (The snippet is from the 2nd audio file from the top of the posting)

Binnig along with Heinrich Rohrer is a Nobel Laureate. Both men won their award for work on the scanning tunneling microscope (STM), which was the project that had failed countless times and that went on to play an important part in the nanotechnology narrative. Earlier this month, both men were honoured when IBM and ETH Zurich opened the Binnig and Rohrer Nanotechnology Center in Zurich. From the May 17, 2011 news item on Nanowerk,

IBM and ETH Zurich, a premiere European science and engineering university, hosted more than 600 guests from industry, academia and government, to open the Binnig and Rohrer Nanotechnology Center located on the campus of IBM Research – Zurich. The facility is the centerpiece of a 10-year strategic partnership in nanoscience between IBM and ETH Zurich where scientists will research novel nanoscale structures and devices to advance energy and information technologies.

The new Center is named for Gerd Binnig and Heinrich Rohrer, the two IBM scientists and Nobel Laureates who invented the scanning tunneling microscope at the Zurich Research Lab in 1981, thus enabling researchers to see atoms on a surface for the first time. The two scientists attended today’s opening ceremony, at which the new lab was unveiled to the public.

Here’s an excerpt from Dexter’s posting where he gives some context for the audio files,

As promised last week, I would like to share some audio recordings I made of Gerd Binnig and Heinrich Rohrer taking questions from the press during the opening of the new IBM and ETH Zurich nanotechnology laboratory named in their honor.

This first audio file features both Binnig’s and Rohrer’s response to my question of why they were interested in looking at inhomogenities on surfaces in the first place, which led them eventually to creating an instrument for doing it. A more complete history of the STM’s genesis can be found in their joint Nobel lecture here.

The sound quality isn’t the best but these snippets are definitely worth listening to if you find the process of scientific inquiry interesting.

For anyone who’s not familiar with the scanning tunneling microscope, I found this description in the book, Soft Machines; Nanotechnology and Life, by Richard Jones.

Scanning probe microscopes rely on an entirely different principle to both light microscopes and electron microscopes, or indeed our own eyes. Rather than detecting waves that have been scattered from the object we are looking at, on feels the surface of that object with a physical probe. This probe is moved across the surface with high precision. As it tracks the contours of the surface, it s moved up or down in a way that is controlled by some interaction between the tip of the probe and the surface. This interaction could be the flow of electrical current, in the case of a scanning tunneling microscope, or simple the force between the tip and the surface in the case of an atomic force microscope. pp. 17-18

New $15M electron microscope lands at McMaster University, Ontario

McMaster University (at their Canadian Centre for Electron Microscopy) is the first post secondary institution in the world to get a new electron microscope which offers scientists the ability to see atoms in sharper detail than possible with other microscopes. The Titan 80-300 Cubed microscope was shipped from the Netherlands and received at the university in June 2008 and is available to researchers across the country. There are currently plans for projects such as developing more efficient batteries, looking at how air pollution particles damage lungs, and creating higher density memory storage. For more details you can see an Oct. 15, 2008 article in the Globe & Mail here (note: they put their articles behind a paywall shortly after they make them public) or you can try here (note: scroll down). I had no luck finding information on the McMaster site or on the Canadian Centre for Electron Microscopy. Finally, the most powerful electron microscope is owned by the US Department of Energy but unlike the one at McMaster it is not commercially available.