Category: Biology

Power up your genome with chemistry

Post-genomic scienceResearchers have developed several tools to help them exploit the underlying chemistry of genomics, while novel chemistry has enabled faster, parallel sequencing methods that not only accelerate genomic research but also cut costs. The very same techniques allow sex chromosomes and complete genomes to be decoded faster and more cheaply than ever before.

Concomitantly, microfluidics technology is improving the way conventional fluorescence chemistry can be exploited in sequencing. Improved understanding of nanoscale channels – both synthetic and protein channels offers the possibility of studying individual biological macromolecules and microfabricated microarrays are opening up massively parallel opportunities. Novel chemical technologies are also opening up locked nucleic acids as well as non-DNA molecules such as microRNAs.

The so-called post-genomic era put the molecular smack in the middle of the biological quarter. Now, as cross-disciplinary communication matures, research at the intersection of chemistry and biology is working harder than ever to solve fundamental questions in science and medicine.

You can read the complete feature on the subject of chemistry in the post-genomic era from David Bradley in Science magazine today. It is the lead article on the Science Products page.

Anorexia and Kidney Disease

Anorexia nervosa is a serious and potentially fatal eating disorder usually characterized by a severely reduced appetite and often a total aversion to food. In the mainstream media, it is most commonly associated with teenage girls and the celebrity quest for a “size zero” figure. However, it is a serious and life-threatening disorder that goes far beyond the realm of body image and extreme dieting. Important clues as to the underlying causes of this disorder may be found in its association with chronic kidney disease.

According to Peter Stenvinkel of the Division of Renal Medicine, Karolinska University Hospital at Huddinge, Sweden, anorexia is observed frequently in kidney dialysis patients. The condition worsens as kidney disease progresses leading to severe muscle wasting and malnutrition, with all its associated health problems. Scientists had suggested a link to defective central nervous system control of appetite, so Stenvinkel and his colleagues have done an analysis of various biomolecules, including natural inflammatory compounds and sex hormones. Their results suggest that inflammation is closely linked to the development of anorexia in kidney patients and is more common in men than women.

Read the full story in today’s SpectroscopyNOW.

Frogs legs and AMPs

Antimicrobial peptidesSolid state NMR is unlocking the secrets of compounds found in natural membranes from frogs’ legs to human lungs that could lead to an entirely new class of antibiotic drugs. The compounds in question are antimicrobial peptides (AMPs) and they have been detected in every living creature studied so far. AMPs act as a first line chemical defence system in a huge range of organisms and could provide a novel approach to defeating drugs resistance in bacteria.

“Our overall mission is to use the kind of basic physical data we obtain from NMR to help interpret biological functions,” team leader Ayyalusamy Ramamoorthy of the University of Michigan explains. As with most discoveries of this nature, it will be several years before any clinical trials for specific health problems or diseases are complete. “How it works against viruses are under investigation in other labs,” Ramamoorthy told me.

You can find out more about AMPs as the front line defenders in the latest issue of SpectroscopyNOW.

Let’s Get Physical, Right Now

The latest issue of the monthly Spotlight column over on the physical sciences section of Intute is now online, this time featuring research from the earth sciences, the greening of chemistry in the developing world, and humans acquitted over Neanderthal extinction.

Cassava by David MonniauxChemists go veggie

Chemists working on tight budgets in developing countries may be able to swap flasks of laboratory reagents for extracts of celery and potatoes, or cassava and carrots and other inexpensive, …

Neanderthals more than severely put out by bad weather

Climate change saw off the last of the Neanderthals from their final stronghold on the Iberian peninsula thousands of years ago, according to …

Slumbering Yellowstone snores

Beneath the beautiful Yellowstone National Park in Wyoming lies a slumbering giant, a supervolcano who wakes every few hundred thousand years and wreaks havoc across hundreds of …

Viruses Do Not Eat Spaghetti

BacteriophagesThe faint glow from a single molecule combined with a stretch from “magnetic tweezers” could help scientists get a grip on how viruses that infect bacteria, so-called bacteriophages pack up their DNA. The research could lead to a resurgence of interest in the West for a potent treatment for infection that uses bacteriophages instead of antibiotics to attack disease-causing bacteria. The treatment side-steps the problem of bacteria evolving resistance to antibiotics because the agent of bacterial death can evolve just as quickly to cope with any defences put up by the bacteria.

In the face of deadly emergent bacteria such as Escherichia coli O157, multiple-resistance Staphylococcus aureus (MRSA) and Clostridium difficile, there is renewed interest in this alternative to antibiotics. The same study might also lead to new insights into how to combat viruses that infect people too, including herpes and adenoma viruses.

Many viruses use a self-assembly stage in which a powerful molecular motor packs their genetic code into the viruses’ preformed protein shell, its capsid. Now, Carlos Bustamente and colleagues at the University of California, Berkeley, have demonstrated that the genetic code is not coiled up like so much spaghetti on a fork but is packed using a concertina type approach. You can find out more about the details of this work in the current news round-up on SpectroscopyNOW.com

People caught pubic lice from gorillas

GorillaNo, it’s not some kind of deviant gorillas in the mist story, apparently, millions of years ago our ancestors picked up pubic lice (crabs) either by sleeping in gorilla nests (without the gorilla) or through eating our silver-backed cousins. David Reed and colleagues at the University of Florida publish details of their findings today in BMC Biology journal.

Reed is quick to point out that there was no monkey business between gorillas and humans. Of course gorillas are apes not monkeys, but this would be a perfect story for Ricky Gervais podcast star Karl Pilkington. “It certainly wouldn’t have to be what many people are going to immediately assume it might have been, and that is sexual intercourse occurring between humans and gorillas,” Reed says, “Instead of something sordid, it could easily have stemmed from an activity that was considerably more tame.”

Reed suggests that 3.3 million years ago, gorilla lice took up residence in the pubic region in our ancestors, this was probably around the same time that evolution took us from a fully hirsute state to our current nakedness. With no hair on our bodies other than the head and pubic regions, the lice would have been hard pushed to linger anywhere else.

Mass debate on stem cell research

Embryonic stem cellsJust £300,000 (about $600k) is being plugged into a national public debate by the UK government on stem cell research. According to Science and Innovation Minister Malcolm Wicks the UK’s two major public funders of stem cell research will use the cash to run a national public discussion about this cutting-edge area of science.

The Biotechnology and Biological Sciences Research Council (BBSRC) and the Medical Research Council (MRC) will receive the funding as part of the government’s ScienceWise initiative. The aim will be to find out what are the public’s concerns, views and attitudes to this face-most moving area of science. It will also provide a forum for revealing the challenges that researchers face and the potential benefits of stem cell science.

At today’s launch Wicks said: “The Government believes that stem cell research offers enormous potential to deliver new treatments for many devastating diseases where there is currently no effective cure. Huge numbers of people are affected by these diseases and Britain is a world-leader in stem cell research. But there must be a proper dialogue with the wider public on the future of stem cell research. We need to raise public awareness about the potential opportunities
and challenges in this area.”

One key element of the initiative is to raise awareness of the world-class stem cell
research being carried out in the UK, at centres such as Newcastle University, and the progress being made towards practical treatments.

BBSRC’s Julia Goodfellow added, “It is essential that scientists working in areas such as stem cell research engage in a real dialogue with the public. The new programme will give scientists, funders and the government up-to-date information on what the public really think about stem cell research while giving people the chance to voice their views and concerns.” So, basically repeating what Wicks said. The MRC’s chief Colin Blakemore, had a slightly different slant. “Scientists who work
on stem cells want to ensure they maintain the trust and support of the public for their research,” he said. “But to achieve this, we need to explain what work is being carried out and why it’s being done.”

So, is £300,000 enough to do the job? Compare this with the ludicrous amounts of money available to anti-science type lobby groups which amount to millions and it really does look like a pittance. Half of that amount could easily be eaten up by an independent designer putting together a corporate logo for the project and the other half will have gone on snacks and wine for the launch party buffet, or am I being far, far too cynical? You tell me.

Natural Family Planning

Natural family planningCould the contraceptive pill be replaced by a “natural” approach to family planning? It could if a study by Petra Frank-Herrmann of the Department of Gynaecological Endocrinology at the University of Heidelberg, Germany, proves reproducible (pardon the pun).

She and her colleagues have demonstrated that using two indicators for the fertile period in a woman’s menstrual cycle and avoiding unprotected sex during that time is just as effective as the contraceptive pill for avoiding unplanned pregnancies. The study was published in Human Reproduction this week.

The symptothermal method (STM) uses temperature and cervical secretion to pinpoint a woman’s fertile time. The German team carried out the largest prospective study of the method yet and found that if couples abstained from unprotected sex during this time the rate of unplanned pregnancies per year was 0.4% and 0.6% respectively. Out of all the 900 women who took part in the study, including those who had unprotected sex during their fertile period, 1.8 per 100 became unintentionally pregnant.

“For a contraceptive method to be rated as highly efficient as the hormonal pill, there should be less than one pregnancy per 100 women per year when the method is used correctly,” Frank-Herrman explains, “The pregnancy rate for women who used the STM method correctly in our study was 0.4%, which can be interpreted as one pregnancy occurring per 250 women per year.”

The authors were also surprised by the relatively low rate of unintended pregnancies (7.5%) among women who had unprotected sex during their fertile period. ‘If people are trying for pregnancy you expect a pregnancy rate of 28% per cycle,’ said Frank-Herrmann. ‘Therefore, we think that some of the couples were practicing conscious, intelligent risk-taking, and were having no unprotected sex during the few highly fertile days, but had unprotected intercourse on the days at the margins of the fertile time when the risk of pregnancy was lower.’

Antioxidant buzz

Honey beeBees making honey from honeydew rather than nectar produce a sweet material that has greater anti oxidant properties than nectar honey, according to a study of 36 honey samples from Spain with different floral origins. The study published this month in the Journal of the Science of Food and Agriculture could point to a way to improve the health benefits of this natural sweetener.

The composition of honey depends greatly on where honeybees collect their raw materials. There are two key sources. Honeybees can collect nectar from flowers, and this generates nectar honeys or they can collect fluids exuded by plants, honeydew.

‘Honey is a natural source of antioxidants, and among honeys, honeydew honey is the best,’ says researcher Rosa Ana Pérez, who works at the Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario, in Madrid, Spain.

Each of the 36 honeys was exposed to a range of physical and chemical tests. Honeys with high antioxidant properties also had high total polyphenol content, net absorbance, pH and electrical conductivity.

‘These laboratory results show some aspects that people could use to get an idea about which honeys are likely to have the most potent antioxidant properties,’ says Pérez.

Oxidation is a chemical process in which electrons are transferred from from one substance to an oxidizing agent. Antioxidants are basically compounds that slow the rate of oxidation and are as important the chemistry laboratory as they are in the human body. Antioxidants work either by reacting with intermediates and inhibiting the oxidation reaction directly, or themselves reacting with the oxidizing agent and acting as a molecular decoy to prevent the oxidation reaction from occurring.

All living things try to sustain a reducing (the opposite of oxidizing) environment within their cells to prevent damage by oxidation of their biomolecules. Compounds such as glutathione and ascorbic acid (vitamin C) as well as enzymes (peroxidases and oxidoreductases) act as antioxidants. If you do not have adequate levels of antioxidants in your body then oxidative stress and cell damage can occur. More controversial is the notion that supplementing with antioxidants a balanced diet of fruit and vegetables has any additional benefits, claims of anticancer effects and reduced risk of cardiovascular disease have yet to be proved. Indeed, excess of certain antioxidants can do more harm than good.