Wireless Probing, Shiny Bugs, Remote Scanning

brain-probeProbing the brain wirelessly – IR-absorbing lead selenide particles form the basis of a method for the study of neuronal activation in samples of brain tissues without the need for hard-wired electrodes. The technique instead utilises light-triggered nanostructured semiconductor photoelectrodes to probe activity.

Propagation improves MRI, allows remote scanning – Swiss researchers have succeeded in exciting and imaging nuclear magnetic resonance in the human body in a way that could represent a paradigm shift for imaging.

Plug and play molecular logic – A “plug and play” approach to building molecular logic units has been developed by chemists in the UK and Thailand. The team used various spectroscopic techniques, including fluorescence and NMR to monitor their logical constructions.

White light microscope – Silver nanoparticles that can generate white light could improve microscopy in research into cancer and bone diseases according to a paper in the March issue of Nano Letters.

Crystal structure not to be sneezed at – Researchers have obtained the X-ray crystal structure of a monoclonal antibody (mAb) bound to the lethal H5N1 strain of avian influenza virus A. The structure reveals that the heavy chain of the mAb inserts into a highly conserved pocket in the of the haemagglutinin protein stem.

Sperm assessment – Raman spectroscopy could enable fertility researchers and IVF clinicians to assess individual sperm. The process involves capturing an individual sperm cell between two highly focused beams of laser light with Raman pinning down features of the trapped wriggler’s DNA.

Stormwater Artwork

stormwater-artworkEarlier this year Laura Haddad of Haddad|Drugan emailed me with an unusual request regarding crystal structures. But, before I tell you about that, here’s a little background. Laura is working on an artistic installation called “Undercurrents”, that will be the basis of the public art component of a stormwater treatment facility on Seattle’s Elliott Bay.

The first phase has been in place since 2003 and includes a plaza and integrated sculpture, designed by Haddad. The concept reveals invisible site functions based around, in Laura’s words, “A poetically etched stainless steel swale in the paving channels surface drainage into Elliott Bay, mimicking the actions of the underground outfall pipes.”

The second phase of this project is now under construction and includes a new mechanical vault wrapped on three sides with a planted sculpted earth berm, conceptually conveying the message that a stormwater utility should be treated as green infrastructure. “The fourth side of this berm is a stainless steel retaining wall etched with a metaphoric pictogram depicting the processes of stormwater collection, transport, and treatment,” Laura told me. “Five gigantic mirrored stainless steel vent pipes extend out of the vault. Their reflections of the surrounding sky and landscape convey a concept of infrastructure merging with its environment.”

It all sounds quite wonderful, especially given the otherwise utilitarian nature of such a facility and their more common lack of aesthetics. Apparently Construction will be complete in August 2009, and so Laura was on a tight deadline when she emailed me.

Could I furnish her with molecular structures for two water treatment chemicals – sodium hypochlorite and sodium bisulfite? The idea would be to create a collage of chemicals showing how NaOCl is used to “treat” the water and the NaHSO4 used to “neutralize” the NaOCl. Seemed fair enough, I suggested I provide the “molecular” structures for both in various formats (space filling, van der Waals, ball and stick models etc and also generate nice three-dimensional crystal structure diagrams.

Obviously, neither of these compounds can be described as molecular in nature, but my first port of call was ChemSpider.com nevertheless, with it’s millions of chemical substances I assumed I’d find leads immediately. And, of course, I did. NaOCl and NaSO3 are both listed, but there were no CIF crystal structure files associated with their entries, which was odd. I double-checked with ChemSpiderMan (Tony Williams) who confirmed this, but then things started to get even more confusing.

I had imagined that the crystal structures of these two compounds would feature prominently in X-ray structure resources and so be widely available in a variety of downloadable formats from which Laura and I could work to create a suitable starting point for her steel etchings. But, after an hour or two of search I’d not found cif files or indeed anything related. I spoke to a contact, Noel O’Boyle, who suggested I check with CCDC. Unfortunately, their turnaround time would take me way past Laura’s (and so my) deadline. Noel also pointed out that there is no crystal structure for NaOCl because it does not exist as a solid, according to at least one resource. That would seem to scupper the idea of creating a 3D diagram of its crystal lattice, although another page on that same resource suggested that it does indeed exist as a white solid.

I turned to several other contacts. Sheffield University’s Mark Winter, famous for, among other things his WebElements.com site, pointed me to a clutch of research papers from the 1970s showing various polymorphs of the bisulfite, but no NaOCl, maybe Noel was right. Another good friend, science photographer Dana Lipp suggested I contact the tech services department of Phillips Analytical or some other manufacture of XRD equipment. In the meantime, chemist Venkat Thalladi of Worcester Polytechnic Institute, Massachusetts, by way of Richard Wobbe, sent me a message with an attachment – the CIF file for sodium bisulfite! Unfortunately, he also confirmed that he didn’t think the crystal structure for NaOCl had been confirmed.

At this point, I gave Laura an update on the structure situation. By her own admission, her “brain does not wrap around molecules and chemistry” so she was at my chemical mercy, although she also pointed out that given that it’s art, there is room for artistic licence.

In the end, I provided NaOCl in the various molecular model formats discussed and Laura was very happy to work with those. I also fired up Thalladi’s CIF in Crystal Diamond, tweaking it somewhat to get the most aesthetic layout and then rendering with Pov-ray to produce a shadowed, 3D perspective on the crystal lattice at high resolution, a thumbnail crop from which is shown here.

So, if you’re ever in Seattle’s Elliott Bay and visiting the stormwater treatment facility on a site-seeing tour, do check out Laura’s steely artwork and rest assured that the chemistry is accurate. If you have similar artistic requirements please get in touch. But, more pressingly if you know of a crystal structure for NaOCl do leave a comment

Nervous scoop

An action shot of the protein Scp1, which plays a crucial role in the development of the nervous system has been obtained using crystallography by researchers in the US. Their structure could provide drug designers with a template for creating small molecule inhibitors of this protein that would be useful in neurological research.

Joseph Noel and Samuel Pfaff of the Salk Institute for Biological Studies and colleagues there and at the University of California, San Diego (UCSD) and The Scripps Research Institute, La Jolla explain that a network of signalling molecules controls embryonic stem cell differentiation. Controlling the controllers might allow scientists to nudge embryonic stem cells into becoming specific cell types, which would be useful in basic research and for potential therapies.

Read on…

Expanding proteins

Expanding proteinsA new study reveals that the static snapshots recorded in protein crystallography may be missing the bigger picture. Investigations of a bacterial protein using cryomicroscopy shows the protein in a balloon-like mode previously hidden from sold state studies. The discovery suggests that techniques complementary to X-ray crystallography are essential if molecular biology is to gain a complete understanding of protein structure.

Steven Ludtke, assistant professor of biochemistry and molecular biology and co-director of the National Center for Macromolecular Imaging at Baylor College of Medicine and colleagues Dong-Hua Chen and Wah Chiu there and Jiu-Li Song and David Chuang at The University of Texas Southwestern Medical Center in Dallas, studied a mutant protein and came to this perhaps not so startling conclusion. The protein GroEL chaperones misfolded proteins and nudges them into their active folded state in the cell. Protein misfolding is implicated in a number of neurodegenerative diseases, such as Alzheimer’s disease and the prion diseases including Creutzfeldt-Jakob disease.

The full story is now available at SpectroscopyNOW

Geekish girls

The Cnet newsite has a rather politically incorrect item this week listing the Top Ten girl geeks. I’m not entirely sure how they’re defining geek but among those listed are Marie Curie, Ada Byron (Lovelace), Rosalind Franklin (after whom my wife wanted to name our daughter), and…Paris Hilton (don’t ask).

So, where’s crystallography pioneer Dorothy Crowfoot Hodgkin? And, what about Judith Howard, first female Professor of Chemistry in the UK? Then there’s Helen Sharman first British woman in space (also a chemist), finally what about Margaret Thatcher (she trained as a chemist too and then spent her time in office effectively dismantling UK science, can’t get more geekish than that!

Spectral Lines

The latest news round-up science news at spectroscopyNOW from David Bradley is now available online. Read about how Crystallography finds missing piece of haem puzzle, Computing enzymes, The inside story of rocks and fossils, Portable IR lays David’s surface bare, Swell idea for medicine, Electronic speed camera; all the latest spectroscopy news and more.

While you’re there you can grab a free subscription to spectroscopy magazine too.

Political scientists

Who says science isn’t political? One of my oldest contacts in the world of crystallography recently contacted me about the Petition for Open Data in Crystallography. The initiative, like similar efforts in the realm of genomics, hopes to persuade the curators of crystal structure information (the CSD, ICSD, CRYSMET and ICDD) to provide an open access, “lite” version of their content, crystal data and powder patterns. I’d urge you to take a look and vote on this important issue before the next meeting of the IUCr in August 2005.