| Japan confirms its first case of new superbug gene By SHINO YUASA 2010-09-07T11:29:15ZTOKYO (AP) -- Japan has confirmed the nation's first case of a new gene in bacteria that allows the microorganisms to become drug-resistant superbugs, detected in a man who had medical treatment in India, a Health Ministry official said Tuesday.... hosted.ap.org |
Of men and chocolate biscuits It is a droll discovery that on a numerical basis, a human seems genetically less complex than a chocolate biscuitUS researchers have just completed the DNA sequence of Theobroma cacao, the fruit of which provides the world's chocolate and cocoa. The project – funded by Mars, the chocolate giant – is likely to benefit more than six million chocolate farmers in the tropics, by delivering disease-resistant trees, or tastier fruit, or higher yields per hectare, or all three. That the research was completed on a plant of interest to small farmers in the poorer nations is itself a measure of the progress of genomic science.Cacao joins more than 180 life forms for which scientists now have the complete genetic sequence. These include rice, wheat and poplar trees; yeast, grapes and the honeybee; chimpanzees, dogs, puffer fish and Norwegian rats; modern humans, the chicken and the laboratory mouse; and a host of microbes, including leprosy, bubonic plague and the malaria parasite. This is a gathering of knowledge that, even 20 years ago, could not have been imagined. Deoxyribonucleic acid, or DNA, was first isolated in a laboratory dish of pneumonia bacteria in 1944. Its story has been unfolded in one human lifetime, first by Francis Crick and James Watson, who described its structure in 1953; then by Frederick Sanger, who in 1975 first discovered a way to read the sequence of the genetic code; and lastly by Alec Jeffreys, who in 1985 identified a way of using repetitive patterns in inherited DNA to pinpoint a murder suspect. But even then, hardly anyone believed that it would be possible to "read" the entire sequence coiled up in the chromosomes of a living cell.The first living organism to be sequenced, in 1995, was a humble bacterium. The genetic recipes for yeast, a nematode worm and a fruit fly followed, and the human genome was completed in 2000. The heady mix of high-speed computing, sophisticated automation and research enthusiasm soon built up a momentum that proved unstoppable. Scientists are now matching genetic sequences to answer questions about plant and animal evolution, about the life cycles of disease, about human origins, about individual human responses to drug dosage, and about crop resistance to pests and mildews.The science has already delivered unexpected and humbling answers. Humans, who consider themselves the pinnacle of creation, have only about 30,000 genes. Cacao seems to have 35,000. Wheat DNA is believed to contain 40,000 genes. It is a droll discovery that on a numerical basis, a human seems genetically less complex than a chocolate biscuit. But it was the humans who sequenced wheat and cacao, and not the other way round. So clearly, size isn't everything.United StatesGeneticsPlantsguardian.co.uk © Guardian News & Media Limited 2010 | Use of this content is subject to our Terms & Conditions | More Feeds guardian.co.uk |
Nuclear receptors reveal glimpses into the evolution of complexity An international team of researchers charted the one billion year evolutionary course that a protein family followed, finding that today's novelty and complexity came about through many small changesDuring my lifetime, science and especially evolution, has been vigorously attacked by religious crackpots determined to inculcate humanity with their own unverifiable world view; that a supreme being specially created every living thing on earth. Yes, everything, even including mosquitoes, ticks, catholic priests and candirú -- those crazy Amazonian fish that swim into human penises and using their backward-facing spines, embed themselves into one's bladder. What sort of perverse supreme being would create such horrible creatures, anyway?But unlike kooks and wackaloons, who have an idiosyncratic sense of reality anyway, scientists rely upon solid, testable evidence to support their claims. To that end, proponents of "intelligent design" -- the modern incarnation of creationism -- have co-opted the use of words that sound scientific, hoping to deceive the public into accepting their beliefs as valid. For example, comparing proteins to intracellular "machines," IDists argue that there are so many complex molecular "machines" in cells that it boggles the mind to think they could have evolved de novo so many times. But did they?"[T]he fact is that most of these 'machines' are related to many other such 'machines' in the cell, and they are subtle variants on each other," said molecular archaeologist Joseph Thornton. Dr Thornton is an associate professor in the Center for Ecology and Evolutionary Biology at the University of Oregon in Eugene and an early career scientist for the Howard Hughes Medical Institute. "The complexity only had to evolve once, after which it was subtly altered by tinkering," said Dr Thornton. "But unless you really look under the hood of these proteins, the common template is obscured, and it appears that their complex functions had to evolve de novo in each one."Dr Thornton spearheaded an international team of researchers who "looked under the hood" at the template for a large and important family of proteins, the nuclear receptors (NRs). There are hundreds of different NRs and they regulate essential biological processes, such as development, metabolism and reproduction. They accomplish this by triggering the expression of specific genes in response to hormones, nutrients and other chemical signals. Many NRs are activated after binding to a specific hormone or other small molecule, known as a ligand, before they can bind DNA. However, some NRs function without the influence of a specific ligand, while others are incapable of activating gene expression, instead acting primarily as repressors by stopping the expression of particular genes. But which type of NR evolved first? The prevailing hypothesis is that the ancestral NR caused changes in the cell without having to bind a particular ligand first, suggesting that complexity -- the capacity to be regulated by chemical signals -- evolved independently in many lineages. But an alternative hypothesis suggests that the ancestral NR was a ligand-activated protein. This hypothesis, which has received scant attention, implies that minor evolutionary tinkering with the conserved ancestral type allowed NRs to respond to new molecular partners or, alternatively, to lose dependence on those partners after mutations that modified or degraded existing functions.To understand how the functional activity of NRs evolved, Dr Thornton's team searched GenBank and identified the DNA sequences, functions, and molecular structures of hundreds of NRs. Comparing these data, they used computers to extrapolate and reconstruct the biochemical characteristics of the ancestral NR, which first arose in the mists of time -- as long as a billion years ago, before all the different animal lineages evolved (figure):Contrary to the prevailing hypothesis, the team's computer analysis showed that the ancestral NR did require activation by a ligand. They also found that the underlying molecular mechanisms that allowed the ancestral protein to be activated by chemical signals were conserved in virtually all present-day NR descendants.The likely ancestor to all NRs arose before the earliest animal lineages, giving rise to two NRs in demosponges (see figure, above and also refer to photograph at top). Demosponges are simple, multicellular animals in the phylum porifera, which is the most basal of the animal groups and thus, is closest to the ancestral animal. The team tested the activity of the two demosponge NRs and found that they are activated by fatty acids, suggesting that the ancestral NR's ligand was probably also a fatty acid. Fatty acids are produced when fats are metabolised or broken down by the body. The researchers tinkered with the sponge NRs by making small changes that they predicted had followed the evolutionary changes to NR activity. They tested their predictions for how particular changes in the amino acids located in the ligand-binding pocket could change their mutant NR's binding character and function. As predicted, they found that some of their mutant NRs evolved partnerships with different hormones or other chemical signals after just a few changes that subtly affected the size and shape of the cavity where the signalling molecule binds. Other mutations made the NR structure more stable, removing the need for the protein to interact with a chemical signal before activating gene expression. These ligand-independent NRs are constitutive gene expression activators, like a light switch stuck in the "on" position. "Each body plan seems to be its own unrelated form, and how it might be possible to transform one form to another is mind-boggling," said Dr Thornton in an email message. "[But] when one identifies the underlying mechanisms for building these forms and reconstructs evolution vertically, tracing it through time from common ancestors, [then] the process of evolutionary transformation from a shared ancestral template becomes clear," said Dr Thornton. This idea also forms the core for research in developmental evolution, more commonly known as "evo-devo": the morphology of animals -- from jellyfish to fly to worm to fish to human -- are built using the same basic genetic toolkit, subtly reorganised and redeployed to build the wing of a fly or the limb of a human. "This is the protein version of this concept," explained Dr Thornton. "There is little true novelty in evolution, but remarkable creativity through the tinkering processes of mutation, selection and drift." "I find this issue interesting whether or not it's related to the controversy over intelligent design," added Dr Thornton. "It is about the nature of evolutionary creativity and the difficulty of seeing our own connections to our past." Sources:Bridgham, J., Eick, G., Larroux, C., Deshpande, K., Harms, M., Gauthier, M., Ortlund, E., Degnan, B., & Thornton, J. (2010). Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestor. PLoS Biology, 8 (10) DOI: 10.1371/journal.pbio.1000497Interview with Dr Joseph Thornton [email, 5 October 2010]GrrlScientistguardian.co.uk © Guardian News & Media Limited 2010 | Use of this content is subject to our Terms & Conditions | More Feeds guardian.co.uk |
My bright idea: Richard Miles Archaeologist and historian Richard Miles believes our quest for the perfect community is as relevant today as it was in 4500BCIf it is hard to talk of "civilisation" as an ideal to cherish because of the chauvinistic and elitist connotations it carries today, then no one has told Richard Miles. Or rather, it's a term that this 41-year-old archaeologist and historian wants to reclaim. Something of a throwback to another era himself, he has directed archaeological digs in Carthage and Rome, lectured at Cambridge University and now teaches classics at the University of Sydney.Next month he presents a six-part history series on BBC2 called Ancient Worlds in which he travels to Iraq and beyond in a "Search for the Origins of Western Civilisation", as the subtitle of an accompanying book puts it.Championing civilisation – it seems an old-fashioned, almost politically incorrect idea. What do you think about that?Civilisation is a word we only really see nowadays in inverted commas, but it's a useful concept when thinking about history. "Culture" has superseded it in many contexts, but that's such a bloated concept – we've given it so many meanings that it doesn't mean anything much anymore.So how do you define civilisation?Civilisation as a term suggests human agency. Things don't come together organically. There are winners and losers – and human will created the world we live in. It is the way in which people have articulated how and why they wanted to live in communities. It's about how we imagine the perfect community. And in terms of western civilisation, it can't be separated from the idea of the city. I think the most ambitious thing humans have ever done is deciding to live together with people whom they didn't know in cities. It's really difficult to build a community, to learn to celebrate difference and to live harmoniously together, and we fail all the time.The first cities appeared in Mesopotamia in Iraq around 4500BC. Why there?If you look at Mesopotamia, you've got two big rivers, the Euphrates and the Tigris, running through it, and the surrounding land isn't particularly fertile, but it could be. You've got to harness the power of the river by building irrigation canals, for instance – but you can't do that on an ad hoc basis, so it made sense for people to work together for mutual gain.People there were very aware of the precariousness of life. There's an idea that as organised religion develops, outside of civilisation and order is nothing but watery chaos.What is the role of religion here?In some respects, cities are bottom-up processes, but they are also top-down initiatives – and elites soon develop. Religion is older than the city, but the elites quickly build temples and turn themselves into priests. As they become more powerful the temples they build also have huge storehouses. What you see is that the man who has a surplus of material is the powerful man. This is because everyone is living hand-to-mouth, and if you have a bad harvest one year, well, you're stuffed.Do we also see the emergence of bureaucracy here?Writing certainly develops as an elite initiative at this time. It helps them to harness the workforce – it's a way of communicating with the gods; and it's a way for the elites to list what you have, and what they have. As well as liberating you from the everyday worries of being on your own and working your patch of land, the city also subjugates and imprisons you. This is the pay-off, the paradox.How well can you get inside the mindset of someone from that period? If you are looking at fine buildings or the literature of the period, you have to be aware that you are only dealing with the mindset of the elite. But archaeology is going to give you some answers. It often acts as a parallel narrative to history: if you start digging with a textbook in your hand, you are soon going to get confused. You have to be comfortable with the idea that there are many different versions of history.For example, when you're excavating in Carthage, as I have done, you suddenly come across this black tide mark – and that is the destruction layer of the city: 146BC. But inside it has lots of bits of broken pottery. What can that tell you? It can tell you what sort of crockery was in vogue in Carthage in 146BC, and if you know where it comes from, it also tells you who's trading with whom.Do I know what a peasant on a farm or temple-owned property was thinking in Mesopotamia 4000BC? In Iraq, I've excavated these bevel- rimmed bowls, which archaeologists have found in their thousands. The fact there are so many, and that they appear at the same time, and that they look a bit like ration bowls – that suggests a uniformity, that there's a central authority coming into play, and that people are being forced into particular ways of thinking and doing things.But in terms of their world view? No. I don't think you can ever get to that.When we think of western civilisation we think of the ancient Greeks and Romans, but was their contribution so clear-cut? One of the problems with the concept is that it is pegged as a very imperialistic view of the world in which the Greeks and the Romans were the engines of civilisation. Well, they were important, but these ideas didn't just develop from them. There's a more interesting story involving the Mediterranean and the near east.You can see the connections between different civilisations formed from trade. The Babylonians were around at the same time as the Greeks, and when they traded, they didn't just take cargo with them, but people and ideas. Boat technology; interest-bearing loans; and, most importantly, the alphabet. The Greek alphabet is derived from the Phoenician alphabet, which comes from the near east.But why are the Greeks so amazing? Because they took other people's ideas and made them better, as with the alphabet. The Phoenician alphabet was a bit like text language – all consonants. So the Greeks take the alphabet, add vowel sounds and make it expressive, and within 100 years you get the Iliad.Between the heyday of cities such as Uruk and the rise of the Greeks and Romans, isn't there what you can call a dark age? The bronze age is a connected world. But it can't sustain itself; it's too rigid, elitist and top-heavy – and civilisation is a bit like a flickering flame. It almost goes out, but in certain places it keeps going and it will spread out again.In the concept of civilisation, there is an inherent notion that things are always going to get better. I quite clearly break with that; I think of it being more like a heart monitor, zig-zagging up and down. The interesting thing about civilisation is our need to try to develop the perfect community for ourselves, and how we fail, but also how we come back to try again.Civilisation is like a leap of faith, it's not a godlike exercise in improvement. But there is something in that old-fashioned concept. We shouldn't kid ourselves that we don't think certain advancements are better than others. Within reason, and without being racist or imperialist, as a historian you should make those value judgments, but you need to then back them up.Can we see in the hordes who travelled to Uruk the same pattern of migration to urban areas in search of a better life that we see in the developing world today? And by that token, do the teeming slums of Mumbai or Lagos represent civilisation?Yes, they do; and they are imagining the best ways to live together as much as a group of people in Manhattan. And this is something we should celebrate rather than shy away from.ArchaeologyAnthropologyCaspar Llewellyn Smithguardian.co.uk © Guardian News & Media Limited 2010 | Use of this content is subject to our Terms & Conditions | More Feeds guardian.co.uk |
Asian carp create nagging fear in Lake Erie towns WHEATLEY, Ontario (AP) -- Well before dawn, Todd Loop takes his fishing tug onto Lake Erie in pursuit of yellow perch, walleye and other delicacies - a livelihood that has sustained his family for three generations but faces a future as murky as the freshwater sea on a moonless night.... hosted.ap.org |