May 2007 – David Bradley

Combined effort makes for glowing report

One of the most powerful techniques available to analytical scientists is Raman spectroscopy. Unfortunately, it is not easy to distinguish the low-intensity signals it produces when studying fluorescent species in cells because they are swamped by the much brighter glow from various cell components. Now, Dutch researchers have overcome this incompatibility to hybridize Raman with fluorescence microscopy by exploiting the optical properties of semiconductor fluorescent quantum dots (QDs). They have demonstrated hybrid Raman fluorescence spectral imaging in studies of single cells.

Biophysical engineers Henk-Jan van Manen and Cees Otto of the University of Twente, The Netherlands, have used fluorescent nanoparticles to broaden the scope of single-cell microscopy by combining it with intracellular chemical analysis based on Raman. The researchers explain that quantum dots allows weak Raman signals from DNA to shine through the ubiquitous glow from proteins and lipids.

You can read the full story in my SpectroscopyNOW column this week.

Udderly butterly

Cow Scientists in New Zealand hope to breed cows to produce low-fat, skimmed milk, not only that they are working on a new bovine breed that will produce milk that makes spreadable butter.

Apparently herd member Marge and her sisters and cousins, have the right genetic makeup required for producing skimmed milk straight from the udder and milk that makes and easily spreadable butter. The team hope to partner up with a friendly bull soon and have a commercial herd ready by 2011. Even more importantly from the human health perspective for those whole like the “white stuff” on their cereals in the morning, Marge’s milk is very low in saturated fats and so her offspring will hopefully produce high polyunsaturates and monounsaturated fat milk too.

Ed Komorowski, technical director at Dairy UK says that the New Zealand approach could be used to breed cows that still produce full-fat milk but with only the good fats, which could swing things back in favour of full-fat milk. In the UK, for example, only 25% of milk sold is full fat. “In future if whole milk can be made to contain unsaturated fats — which are good for you — then it might mean that people change back to whole milk products. The big thing about dairy products is taste, so this would be a way of giving the benefits of taste without the disadvantage of saturated fats,” he adds.

Milk from this new healthy breed of cattle could also overcome the problem of what to do with all the waste products of the dairy industry that are produced during the fat-reduction process. “If you can genetically produce milk without fat then that may turn out to be a very good solution to what might later be a big disposal issue,” says Komorowski.

The healthy cows were identified biotech company ViaLactia while screening milk compositions across the entire herd of 4 million New Zealand cattle. New Zealand dairy firm Fonterra has already made milk products from Marge’s milk and they maintain the positive taste.

The research is discussed in more detail in this week’s issue of Chemistry and Industry magazine from the UK’s Society of Chemical Industry.

Toxic hairdos, titanic smog, and paradoxical polymers

In my fortnightly Alchemist column over on ChemWeb, I take a fast and furious look at a few of the chemical happenings in the news. This week, geochemical biomarkers are rewarded for pioneering our historical understanding of climate change, while a seemingly paradoxical polymer emerges from mathematics to help compute future optical chips.

Also on the roster a Titanic effort has been undertaken to reveal the chemical nature of the smog that shrouds one of Saturn’s moons (Titan, in case you couldn’t guess) and we reveal the stickiest of sticky materials that can bond materials as disparate as copper and silica tighter than ever before.

At least one dyed in the wool media health scare story has been cut short this month with the discovery that chemical relaxers, used by African-American women to straighten their hair, do not cause breast cancer, after all.

And, finally, new forensic information can now be dabbed from fingerprints thanks to research carried out in the UK. Antibody assays carried out on fingerprints can now be used to tell if an unidentified suspect smokes, whether they use drugs, or even if they have an illness.

Chemrefer Chemspider Coupled

A mash up between Chemrefer, the search engine for open access chemistry papers, and molecular structure search engine Chemspider launched today. I have to confess to playing no small part in facilitating this collaboration having introduced the Chemspider team, virtually speaking, to the owner of Chemrefer, Will Griffiths, who was a Reactive Profilee in June 2006. You can access the chemical mash up here. Search for any term of interest and the new hybrid tool will return all the pertinent results that are available for instant free access from the journal publishers. There are something like 50000 papers accessible this way via a search of more than 14.5million+ chemical entities.

Ignore your internal critic and relax

Blogger in a hammock This item could have been called “How to out-psyche yourself”, it is not exactly rocket science, but then rocket science is not one of the common topics on Sciencebase, anyway. It’s a public holiday here, today. Yes, I know…again? Oh, and over there too? Anyway, I’ve pulled together some of the chillingest out posts from the last week or so and brought them together in an easy to catch, laid back post with few words, and a hammock on stand by in case the sun comes out. Incidentally, almost all these tips, or life-hacks as some people are wont to call them basically boil down to a simple phrase, that any analyst, physician, or psychiatrist could do well to hang on their surgery door, desk, and above their sphigmomanometer – Don’t Worry, Be Happy.

So, over on lifehack itself, they posted a top ten of simple ways to save yourself from messing up your life. Seems like heavy psychological stuff from the title, but it boils down to not worrying about your feelings, taking life in your stride, and avoiding dwelling on the ramblings of your internal critic. So far, so good.

Next, over on the American Lung Association site – heart I could understand, but lung? – they are touting, not ten, not twenty, not even fifty, but fifty-three (don’t ask), surefire ways to help you chill on any day of the week not just a public holiday. Among my favourites, is “Count to 1,000, not 10, before you say something that could make matters worse.” This goes for commenting on blog posts too: “Look, before you leap”, as my grandma used to say.

Some of the more “new-agey” stuff on the web often has a decent list of howtos for relaxation and such. I am not saying that WikiHow is new age, perish the thought, but they do have a how2relax section, with the classic: “Find a quiet place when you are feeling overwhelmed. Even the stall of a bathroom will work if you have no other place to go.” You can just picture all those overwhelmed office workers, “relaxing” in the bathroom, or maybe not, we do not want to revisit any kind of Ally McBeal moment on this site, thank you very much.

At this time of year, many poor unfortunates (PUs) will have to put aside worries about who is buying the next round, and concentrate on their exams. Thankfully, the venerable University of Cambridge offers those PUs, some useful advice on simple exam-time relaxation on their student counselling website. A classic tip offered there is: “don’t use your bed as a place to work during the day”. As if, have you ever heard anything so preposterous? Students using their beds to work on during the day? Of course not…

We now know how they do it in Cambridge, England, but what about across the Pond in that other townwise homonymous centre of excellence, Harvard University? Well, Harvard U, has a Relaxation Room, of course. “The body responds to stress with increased muscle tension,” so says the RR’s website and apparently in said room you can get a massage or give a massage. Now, I don’t know about you but I don’t recall any such offers while I was studying at university. How the times change.

Finally, an NYT article discusses how to deal with past bad experiences, not by ignoring them, but by retelling them in your internal narrative as if there happened to a third party rather than you.

Anyway, deciding the best way to relax is getting too stressful, I am going to fix that hammock and take that initial advice…the bit at the end of the first paragraph.

Toxic scaremongering

The Independent on Sunday today reports that a UK researcher is claiming that fizzy drinks which contain sodium benzoate preservative (E211) could be harmful to mitochondrial DNA in our cells. Apparently, Sheffield University molecular biologist Peter Piper tested the compound on yeast cells (one of the organisms the preservative is added to drinks to eliminate in the first place). More to the point, the levels at which he assaulted the yeast was the equivalent of a person drinking ten gallons of soda in one go.

This new scare story follows closely on the tail of the benzene in soda debacle Sciencebase reported last year and the almost historical tale of benzene contamination of mineral water scare of the early 1990s. Intriguingly, The Independent article does not seem to mention the words “dose” or “concentration” once.

Perhaps there are individuals who drink large volumes of soda every day without realising there are other harmful effects of such drinks, like the concentrated sugar intake, or the relatively high levels of caffeine stimulant. But, even high-speed Digger users only claim to drink a couple of litres of Mountain Dew each day, not the ten gallons equivalent of the experiments. Perhaps experiments will push the safety threshold well below 10 gallons (please excuse the mixed units), maybe even to 1 gallon, but that’s still an awful lot of soda for anyone, even for a hardened Digger, to be drinking every day, surely?

There are many reasons to not drink soda, so instead choose tap water, choose life…

No, wait a minute, fish do their four essential biological “F’s” in water – Feeding, Fighting, Fleeing…Fu Mating. Best stick to beer.

Credit where credit is due

A fellow blogger, who regularly comments on this site, once asked me about the re-use of images on his blog. He’d published a logo or something similar from an organisation that does not grant re-use permission for such materials. So I advised him to remove it from his blog before they sent in the suits.

In the world of journalism, as opposed to the blogosphere, minor copyright infringement, such as the mistaken re-use of an image accompanying an article often results in a standard copyright infringement notice, removal of the offending image, and a notice of apology. Obviously, in print it is slightly different, but yesterday’s news is today’s fish and chips wrapper anyway (at least it was until they banned the use of old newspapers in chip shops).

Blogs fall into a slightly different camp. Not quite amateur, if they are getting big numbers of visitors and running ads, for instance, but certainly not in the same journalistic league as the NYT or the BBC news sites.

Anyway, a quick legal refresher: Unless it states somewhere that you can use an image without limitations, you must assume that the publisher and/or the authors reserve all rights, this means you usually cannot re-publish an image without express permission of the copyright holder, regardless of the benefits wider dissemination of the image and its associated context might bring.

The exception is a press release, unless it says you must seek permission. Usually the whole of a press release is intended for free publication with or without editorial attention at the discretion of the editor. Of course, press releases do not always include images, so an intrepid journalist or blogger must look elsewhere for illustrations.

There are exceptions to the copyright rules that might be used in this regard. Images produced by the US government or its employees are copyright free. So anything from NASA, for instance. Other public domain images, and images with a creative commons or other openaccess or copyleft statement are essentially free for use with credit and conditions as outlined in their respective terms and licensing document.

To search flickr for creative commons images you can use this link – http://www.flickr.com/search/?l=commderiv&w=all&q=photo&m=text – substitute the word “photo” in the link for an appropriate keyword, but be sure to check the CC license of the flickr’er in question.

Indeed, don’t take my word for any of this. You need to check each specific image and if in doubt, request permission for re-use, whether you are a blogger, journalist or publisher. There are other exceptions, but usually those who create images or other intellectual property want, at the very least, credit for their efforts. That, of course, includes images from other publications that have added value to an author’s image.

The current interpretation of copyright law is aimed at protecting those who produce creative works, but this often seems to be to the detriment of the individual when publishers have adopted the copyright. Publishers, however, it can be argued, do add significant value to the material they publish. I have seen it from the inside. They do so, not only from the point of view of validating the information to be published, but also to the point of rendering the words and pictures in a form that is intelligible to the target readership. Whether or not the author or reader should pay for that added value is a different matter. Publishing is currently in a state of flux in that regard with new experimental business models in place that seek to invert the traditional approach of reader pays.

Regardless, with the copyright law as it currently stands: assume you cannot, unless you know you can, and if you are unsure, seek permission, add a credit, and carry on blogging.

Youtube for science

Athenaweb moving picture science On June 27, AthenaWeb, the science and science communication portal funded by the European Commission, will morph into an online TV channel for European science.

The development of AthenaWeb V2 is headed by Lab To Media’s Kathleen Van Damme who says that this is “Europe’s big chance to take a leading position in science film streaming, reconciling scientific programmes on TV with content accessible at any time.” It all sounds very interesting, but will it cut the PUS* and become a major PEST** site?

Van Damme is not revealing too much at this stage, you will have to wait till launch day to find out what the new vortal will be offering. But, in a very unvegetarian press release it is stated that the revedelopment “will beef up its services to current communities and extend its scope to provide direct on-line placement of ‘non-broadcast’ videos made by researchers, teachers and professors.”

Inevitably, the new site will have a new look and feel, you would be rather disappointed if they had not updated and refreshed the site. It will also have a special domain for broadcasters, podcasts, blog spots, and high-quality full-screen viewing. Critically, and perhaps allowing the site to stake a claim on the Web 2.0 ethic, it will also present a greater emphasis on community shaping and hopes to become the leading site for sharing scientific imagery, films, and news. Most importantly of all though, AthenaWeb V2, will, the press release claims remain free of charge.

On a much smaller scale Sciencebase readers are invited to join our science TV channel on Searchles, which currently has a mere handful of videos, including a tribute to DNA pioneer Rosalind Franklyn, mentioned in my philosophy of science essay and how to demonstrate Newton’s laws of motion with Lego models. Those probably amount to about 30 minutes of footage, compared with AthenaWeb’s more than 750 science videos, stacking up to 100 hours.

*PUS – public understanding of science
**PEST – public engagement with science and technology

Balancing your gut bugs

Mouse Could those so-called “bio” yogurts and milk-type drinks with Scandinavian sounding names actually do you any good? Possibly.

According to a study published in the journal Molecular Systems Biology this week, microbial flora in the gut can profoundly affect how you absorb nutritients from your food and your overall health. Jeremy Nicholson and colleagues at Imperial College London suggest that keeping a balanced gut flora may prove important to prevent some human metabolic diseases. Those active yogurts and one-day milk substitutes containing live microbes could play a role in helping you maintain the balance.

Our guts are an internal ecosystem all their own. Quite bizarrely, the microbial community living in our intestines has 100 times as many genes as the whole of the human genome. It is almost as if those living inside you outrank you yourself. However, we rely on these microbes for the normal processes of digestion and waste disposal just as much as the microbes themselves need the lining of our intestine as their stamping ground. We, and all other mammals, are not so much individuals as “superorganisms”, a collective, a symbiotic biological system.

Nicholson and his team used metabolic profiling techniques to monitor changes in bile acid composition and lipid (fatty molecule) metabolism in mice whose gut flora had been replaced by human bacterial flora. Perhaps not surprisingly, the mice showed alteration in the composition of their bile acids and circulating lipoprotein levels, and displayed symptoms such as lipid accumulation in the liver that would eventually lead to disease. Closer inspection of the mouse gut, revealed that the human gut microbes could not form a strong and stable ecosystem.

Nicholson’s findings demonstrate that gut microbes control the absorption and storage of nutrients from our food and help us harvest its energy. They also show that the wrong type of microbes can lead to disease by affecting the chemical and metabolic balance of the gut and liver.

So, should you drink those liquid bio yogurts? If you can pronounce them easily then there is probably no harm in asking for them at your healthfood store, but the message is clear: steer well away from mice.

Chemists Pull Rank

The RSC recently published a league table showing the top-ranking, living chemists. The league is based on the so-called h-index. This parameter was devised by Jorge Hirsch in 2005 in order to measure the impact of an individual chemist’s research. Put simply, the h-index is equal to the highest number of papers that chemist has published which have gained at least that number of citations from other authors. According to the Chemistry World Blog today, thirty more chemists have been added to the league. Hirsch argued that the h-index avoids bias by combining total published papers with a citation parameter it does not reward the prolific but mediocre. The original league was created by Henry Schaefer and colleagues manually by trawling ISI citation data, but I am sure an intrepid chemical web student could create a suitable script to do the job automatically.