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What revelations caused the biggest buzz in chemistry labs around the globe during 2009? With the help of an expert panel of journal editors, Chemistry World reviews the ground-breaking research and important trends of the year's published chemical science papers. Life in 3D DNA origami, the folding of DNA into shapes on the nanoscale, moved from 2D into 3D during 2009. Hao Yan's team at Arizona State University kicked off this craze with a tetrahedron shaped 3D container made of DNA.1 A day later, Danish researchers led by Kurt Gothelf, from Aarhus University, published details of a nanosized 3D DNA...

<p>The blueprint of a small organism's cellular machinery has been unveiled, offering the most comprehensive view yet of the molecular essentials of life. But the research also shows just how far biologists have to go before they understand the complete biochemical basis of even the simplest of creatures.</p>

Scientists in the US have discovered a new class of biological antifreeze molecules - the first that do not contain proteins. The antifreeze, extracted from an Alaskan beetle capable of surviving at -60°C, consists of linked mannopyranose and xylopyranose sugars, termed xylomannan, associated with a lipid. Large molecules that cause thermal hysteresis - a difference between the melting and freezing points of a solution - have been identified in many organisms that survive in the cold, from Antarctic fish to plants and bacteria. In all cases identified so far, thermal hysteresis appears to be caused by proteins, known as antifreeze proteins or...

NASA scientists studying the origin of life have reproduced uracil, a key component of our hereditary material, in the laboratory. They discovered that an ice sample containing pyrimidine exposed to ultraviolet radiation under space-like conditions produces this essential ingredient of life. Pyrimidine is a ring-shaped molecule made up of carbon and nitrogen and is the basic structure for uracil, part of a genetic code found in ribonucleic acid (RNA). RNA is central to protein synthesis, but has many other roles. "We have demonstrated for the first time that we can make uracil, a component of RNA, non-biologically in a laboratory...

Darwin’s theory that species originate via the natural selection of natural variation is correct in principle but wrong in numerous aspects of application. Speciation is not the result of an unlimited naturalistic process but of an intelligently designed system of built-in variation that is limited in scope to switching ON and OFF permutations and combinations of the built-in components. Kirschner and Gerhart’s facilitated variation theory provides enormous potential for rearrangement of the built-in regulatory components but it cannot switch ON components that do not exist. When applied to the grass family, facilitated variation theory can account for the diversification of...

US scientists are targeting an enzyme essential to bacterial metabolism in the search for new antibiotics.Michael Burkart of the University of California, San Diego, and Anton Simeonov from the National Institutes of Health, Bethesda, and coworkers have developed a high-throughput kinetic assay to screen small molecules as inhibitors of surfactin-type phosphopantetheinyl transferase (Sfp-PPTase) enzymes.Transferases are among a group of enzymes that can add and remove groups from proteins after their polypeptide backbone has been built - a process known as posttranslational modification. The enzymes are of biological and pharmaceutical interest as their inhibitors have been suggested as avenues for antibacterial,...

In a Commentary essay, Carl Woese and Nigel Goldenfeld provide an analysis of biological thought that differs profoundly from that presented by those celebrating the Bicentenary of Darwin's birth and, incidentally, the recently published AP Biology Standards. "This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process. This problem [ . . ] became the private domain of a quasi-scientific movement, who secreted it away in a morass of petty scholasticism, effectively disguising the fact...

Enlarge ImagePre-RNA? Hybrids between proteins and nucleic acids may have helped genetic molecules evolve.Credit: Science/AAAS Researchers pondering the origin of life have long struggled to crack the ultimate chicken-and-egg paradox. How did nucleic acids like DNA and RNA--which encode proteins--first form, when proteins are needed for their synthesis? Now, scientists report that they've cooked up molecular hybrids of proteins and nucleic acids that skirt the dreaded paradox. Although it's unknown whether such molecules existed prior to the emergence of life, they offer insight into a chemical pathway that might have helped life arise. DNA and RNA sport a backbone...

In my previous post I mentioned work by Pablo Debenedetti on ‘toy models’ of water. The places to look are: Buldyrev et al., PNAS 104, 20177 (2007) (here) for the solvation thermodynamics of ‘spherical’ water; and Patel et al., Biophys. J. 93, 4116 (2007) (here) and J. Chem. Phys. 128, 175102 (2008) (here) for water-explicit lattice models of proteins. And in discussing recent work on the mechanism of urea-induced protein denaturation, I neglected to mention Bruce Berne’s PNAS paper from late last year with Ruhong Zhou, Dave Thirumalai and Lan Hua (105, 16928; paper here). That paper on MD simulations...

I have been meaning for some time to write about an interesting paper in JACS by Naoki Sugimoto’s group in Kobe. It found its way into an article that I wrote this week for Nature’s online news. So I’ve decided to simply post this article here – it’s not all strictly relevant to water in biology, but hopefully is interesting stuff anyway. This is the version before editing, which has more detail. Shape might be one of the key factors in the function of mysterious ‘non-coding’ DNA. Everyone knows what DNA looks like. Its double helix decorates countless articles on...

Nuclear magnetic resonance spies the atomic details of proteins in action. Scientists have used NMR to look at proteins including TTHA1718 (above) inside living cells.Nature The atomic structures of proteins at work inside cells can now be probed, thanks to researchers who have modified a technique that is already widely used in labs and for medical imaging.When a protein is inside a cell — rather than in a test tube — it behaves subtly differently because it may be interacting with other biological molecules that float around in the cellular space. Because proteins are hard to work with unless they...

Enlarge ImageNot guilty. Plants don't appear to produce methane, as had been previously reported.Credit: Srimathy Sriskantharajah Plants do not make the powerful greenhouse gas methane, according to new research that contradicts a controversial finding made in 2006. Instead, plants appear to merely be passing gas, so to speak, originally made by soil microbes. Methane comes from a variety of sources, including gas leaks, forest fires, and, of course, cow burps. Microbes in wetland soil can produce methane anaerobically (without using oxygen), but the idea that it can be produced aerobically (using oxygen) by plants, and on a large scale,...

Sole member of world's first single-species ecosystem depends on rocks and radioactivity for life. The rod-shaped D. audaxviator was recovered from thousands of litres of water collected deep in the Mponeng Mine in South Africa.Greg Wanger, J. Craig Venter Institute / Gordon Southam, University of Western Ontario Nestled kilometres down in the hot, dark vaults of Earth's crust, scientists have discovered a remarkably lonely bacterium species. The rod-shaped bacterium, Candidatus Desulforudis audaxviator, lives independently of any other organism in a part of the Mponeng gold mine near Johannesburg, South Africa, some 2.8 kilometres beneath Earth's surface. There, water flows from...

Green fluorescent protein bags the biggest gong in science. Aequorea victoria, source of the green fluorescent protein.G. OCHOCKI/SCIENCE PHOTO LIBRARY The molecule responsible for a jellyfish's glow has won its discoverer and developers this year's Nobel Prize in Chemistry. The green fluorescent protein (GFP) has revolutionized medical and biological science by providing a way to track the activity of individual proteins within a living cell, and thereby monitor how genes are expressed. The prize is shared equally between three scientists: Osamu Shimomura, now an emeritus professor at the Marine Biological Laboratory in Woods Hole, Massachusetts, Martin Chalfie of Columbia University...

Students stabbed and set alight Two French research students found stabbed to death following a flat fire had been tied up and suffered horrific, excessive injuries, police have said. The bodies of Laurent Bonomo and Gabriel Ferez, both 23, were found in a ground-floor flat in New Cross, south-east London, on Sunday night. They had suffered a total of 243 stab wounds to the head, neck and chest before being set alight. The biochemistry students had been studying at Imperial College, London. Det Ch Insp Mick Duthie said he had no idea why the students were killed. Fiancee's tribute Speaking...

IN one sense we know much less about Earth than we do about Mars. The vast majority of life forms on our planet are still undiscovered, and their significance for our own species remains unknown. This gap in knowledge is a serious matter: we will never completely understand and preserve the living world around us at our present level of ignorance. We are flying blind into our environmental future. Since the Swedish naturalist Carl Linnaeus inaugurated the modern system of classification two and a half centuries ago, biologists have found and given Latinized names to about 1.8 million species of...

Gary Lynch has spent decades trying to understand how the brain processes new information so that we can recall it later. The first time I spoke with the neuroscientist Gary Lynch, the conversation went something like this: Me: I'm interested in spending time in a laboratory like yours, where the principal focus is the study of memory. I'd like to explain how memory functions and fails, and why, and use the work in the lab as a means to illustrate how we know what we know. Lynch: You'd be welcome to come here. This would actually be a propitious time...

Mayo Clinic researchers have discovered a protein interaction that may explain how the deadly Huntington's disease affects the brain. The findings, published in and featured on the cover of the current issue of Human Molecular Genetics, show how the mutated Huntington's protein interacts with another protein to cause dramatic accumulation of cholesterol in the brain. "Cholesterol is essential for promoting the connection network among brain cells and in maintaining their membrane integrity. Both the level of cholesterol and its delivery to the proper locations in the cell are essential for the survival of neurons," explains Mayo Clinic molecular biologist Cynthia...

At the Institut Curie, CNRS and Inserm researchers have shown that cysteamine, which is already used to treat a rare disease called cystinosis, prevents the death of neurons in Huntington’s disease. Like Alzheimer’s and Parkinson’s, Huntington’s disease, is characterized by the abnormal death of neurons. Cysteamine raises neuronal levels of BDNF protein, a trophic factor which is depleted in Huntington’s disease, and by assaying BDNF in the blood it is possible to evaluate the effect of treatment. If other studies confirm these results, cysteamine could soon be used to treat Huntington’s disease, and BDNF could serve as a biomarker of...

Scientists at Harvard University have developed a computer model that, for the first time, can fully map and predict how small proteins fold into three-dimensional, biologically active shapes. The work could help researchers better understand the abnormal protein aggregation underlying some devastating diseases, as well as how natural proteins evolved and how proteins recognize correct biochemical partners within living cells. The technique, which can track protein folding for some 10 microseconds -- about as long as some proteins take to assume their biologically stable configuration, and at least a thousand times longer than previous methods -- is described this week...

Rename That Gene ?LUNATIC fringe,? ?head case? and ?one-eyed pinhead? might sound like insults from the schoolyard or talk radio. But these are actually examples of the kind of oddball names that scientists give to genes they discover. The idea is to make the names unique and memorable ? with so many genes being discovered and described, a little color helps scientists tell them apart. But the trouble comes when science is transmuted into medicine; what works in the lab may be jarring in the clinic. The names are causing problems for doctors who have to counsel patients about genetic...

A new class of drugs is looming on the horizon that could, if they live up to their promise, avert heart disease, diabetes, cancer and neurodegenerative disorders. By suppressing the common killers of age, the drugs, sirtuin activators, could significantly prolong both health and lifespan. But is the promise a mirage or a serious possibility? The drugs are designed to mimic the effects of caloric restriction, a low calorie but healthful diet known to make laboratory mice live longer and more healthily but is too hard for all but the most ascetic of humans to keep to. One such drug,...

The human body may seem to change little over the years, but beneath this deceptive calm, cells are in constant flux as old ones are discarded and new ones appear. How do the new recruits know where they are meant to go? Biologists at Stanford University say they have discovered a coordinate system in human cells that defines their position in the body. This seems to be the first time a cell-based positioning system has been reported for the adult body of any animal, though positioning systems that guide cells in embryogenesis are well known. The coordinate system, if confirmed,...

Georgia Tech invention captures cell properties and biochemical signals in action ATLANTA (July 24, 2006) — To create drugs capable of targeting some of the most devastating human diseases, scientists must first decode exactly how a cell or a group of cells communicates with other cells and reacts to a broad spectrum of complex biomolecules surrounding it. But even the most sophisticated tools currently used for studying cell communications suffer from significant deficiencies. Typically, these tools can detect only a narrowly selected group of small molecules or, for a more sophisticated analysis, the cells must be destroyed for sample preparation....

WINSTON-SALEM, N.C. — Inside the Wake Forest Institute for Regenerative Medicine’s spacious new headquarters here, when asked how many siblings he has, Anthony Atala gives a long gentle laugh instead of a reply. Just to have shared that he was born in Peru and comes from a large family is more than he normally divulges about his personal life to journalists. But asked about his work with urothelial cells — the cells that line the bladder, ureter and urethra — Dr. Atala bends forward and talks a blue streak. Which might be expected of a urologist and tissue engineer who...

Biologists say they have gained a new insight into the basic cause of Parkinson's disease that, if confirmed, could lead to a novel class of drugs. The cause of the disease appears to lie in the nerve cell's internal delivery system for shuttling packets of chemicals around, a team of researchers led by Susan Lindquist of the Whitehead Institute in Cambridge, Mass., report in today's issue of Science. Tremors and other symptoms of Parkinson's result from the death of certain neurons. Another sign of the disease is the appearance inside these neurons of clumps of protein known as Lewy bodies....

A large number of mice died unexpectedly in a test of a new technique for inactivating genes that has been widely proclaimed a breakthrough, scientists are reporting today. The finding could give rise to new caution about the technique, called RNA interference, which is already widely used in laboratory experiments and is starting to be tested in people as a means of treating diseases by silencing the genes that cause them. But Dr. Mark A. Kay and colleagues at the Stanford University School of Medicine report today in the journal Nature that the technique, also called RNAi for short, caused...

For three billion years, life on earth consisted of single-celled organisms like bacteria or algae. Only 600 million years ago did evolution hit on a system for making multicellular organisms like animals and plants. The key to the system is to give the cells that make up an organism a variety of different identities so that they can perform many different roles. So even though all the cells carry the same genome, each type of cell must be granted access to only a few of the genes in the genome, with all the others permanently denied to it. People, for...

PASADENA -- Norman Horowitz, a geneticist best known for his work on the "one-gene, one-enzyme' hypothesis and the experiments aboard the Viking lander to search for life on Mars in 1976, died Wednesday at his home in Pasadena. He was 90. A pioneer of the study of evolution through biochemical synthesis, Horowitz was a professor of biology at Caltech for many years. After a distinguished career studying the genetics of the red bread-mold Neurospora crassa, he began collaborating with the Jet Propulsion Laboratory in 1965 after becoming interested in the biochemical evolution of life and its possible applications to the...

They live in the forests and limestone outcrops of Laos. With long whiskers, stubby legs and a long, furry tail, they are rodents but unlike any seen before by wildlife scientists. They are definitely not rats or squirrels, and are only vaguely like a guinea pig or a chinchilla. And they often show up in Laotian outdoor markets being sold as food. It was in such markets that visiting scientists came upon the animals, and after long study, determined that they represented a rare find: an entire new family of wildlife. The discovery was announced yesterday by the Wildlife Conservation...

PASADENA, Calif. - A close flyby of Saturn's big moon Titan by the international Cassini spacecraft revealed an upper atmosphere brimming with complex organic material, a finding that could hold clues to how life arose on Earth, scientists said Monday. Cassini flew within 638 miles of Titan's frozen surface on April 16 and discovered a hydrocarbon-laced upper atmosphere. Titan's atmosphere is mainly made up of nitrogen and methane, the simplest type of hydrocarbon. But scientists were surprised to find complex organic material in the latest flyby. Because Titan is extremely cold — about minus 290 degrees — scientists expected the...

DUNKESWELL, England - Dr. Jim Tanner pored over two children's growth charts spread out on the table before him, observing the annual dots, casting an expert eye on where they landed amid the centiles and curves, lingering over the meager data about the 8-year-old girl, but venturing a tentative - and, to her father, namely me, an unnerving - conclusion. "We're already seeing that she is going into early adolescence," Dr. Tanner mused, peering over his glasses. "Eight and a half, hmmm. Well, probably, probably, it's the beginning. That would be slightly early, but for a takeoff for a girl...

In the hip science of ultrasmall nanotechnology, fantastical future possibilities like rampaging nanorobots capture the most attention, but the first fruits of the field have been more mundane: tiny bits of mostly ordinary stuff that just sit there. Yet these bits - nanoparticles - gain wondrous new capabilities simply because they are so small. Nanoparticles of various sorts are already found in products like sunscreen, paint and inkjet paper. More exotic varieties offer promise in medicine for sensitive diagnostic tests and novel treatments: the detection of Alzheimer's disease by finding a protein in spinal fluid, for instance, or nanoparticles that...

CAMBRIDGE, Mass. PARENTS and doctors have long talked up the powerful properties of spinach. Now an unlikely group has joined the chorus: researchers seeking to put more oomph in batteries. Scientists at the Massachusetts Institute of Technology, the University of Tennessee, the United States Naval Research Laboratory and the Defense Advanced Research Projects Agency have found a way to harness the energy that plants use during photosynthesis to convert light to energy. They are using the process to extend the life of batteries in cellular phones, laptop computers and other portable electronic devices. While the research is still at an...

Like most fields, modern biology focuses most of its attention on how things are built and created: how a cell reads the blueprints encoded in DNA and how it takes that information to manufacture proteins in molecular factories. Two Israelis and one American won this year's Nobel Prize in Chemistry yesterday for their work on the opposite, less glamorous function of a cell: how it breaks down proteins that are damaged or have outlived their usefulness. The winners are Dr. Aaron Ciechanover, 57, and Dr. Avram Hershko, 67, both professors of biochemistry at the Technion-Israel Institute of Technology in Haifa,...

Two American scientists who solved the enigma of how people can smell 10,000 different odors and recall them later were awarded the 2004 Nobel Prize in Physiology or Medicine yesterday. The winners, who will share the $1.3 million award, were Dr. Richard Axel, 58, a professor at Columbia University, and Dr. Linda B. Buck, 57, of the Fred Hutchinson Cancer Research Center and a professor at the University of Washington in Seattle. Until publication of their fundamental paper in 1991, the sense of smell had been "the most enigmatic of our senses," the Nobel Assembly of the Karolinska Institute in...

New Haven — What people think about many of the big issues that will be discussed in the next two months - like gay marriage, stem-cell research and the role of religion in public life - is intimately related to their views on human nature. And while there may be differences between Republicans and Democrats, one fundamental assumption is accepted by almost everyone. This would be reassuring - if science didn't tell us that this assumption is mistaken. People see bodies and souls as separate; we are common-sense dualists. The President's Council on Bioethics expressed this belief system with considerable...

IN THE MAYA MOUNTAINS, Belize - Timothy J. Baroni stepped out of his tent and checked his gear: hunting knife, heavy boots, tackle box, sharp machete and two fine cigars. "All set," he said. "Let's go find some fungi." With that, Dr. Baroni and two colleagues, Dr. D. Jean Lodge and Dr. Dan Czederpiltz, plunged into the Central American jungle. The three are mycologists - mushroom experts - who spent 10 days in August searching for new species in the mountains of southern Belize. The ridge they were exploring, Doyle's Delight, is nine miles east of the Guatemalan border and...

DURHAM, N.C. -- Biochemists at Duke University Medical Center have discovered key components that enable the cell's DNA repair machinery to adeptly launch its action in either direction along a DNA strand to strip out faulty DNA. Such flexibility exemplifies the power of the repair machinery, which guards cells against mutations by editing out errors that occur during the process of chromosome replication. Malfunction of the "mismatch repair" machinery is the cause of several types of cancer, including relatively common forms of colon cancer. The researchers, led by Howard Hughes Medical Institute investigator Paul Modrich, Ph.D., at Duke, reported their...

New word in life's lexiconResearchers find 22nd amino acid in a microbe.24 May 2002JOHN WHITFIELDThere's a new word to life's vocabulary. DNA letters can be rearranged to spell out a 22nd amino acid, researchers have discovered. DNA: the letters of life have more permutations than we thought. © Getty Images The scientists who cracked life's genetic code in the 1950s said that it writes a mere 20 'words' - the amino acids from which the myriad proteins in all life are built. But in 1986 another amino acid was discovered in bacteria. "We thought the 21st was an aberration,...