#73: Life/Brain: Origin, Evolution, and Complexity. 08.6.9=1 - 6.20=5 11am.

#73: Life/Brain: Origin, Evolution, and Complexity: Design Principles. --------------------------- 'Race and intelligence' Wikipedia Jun19,08 http://tinyurl.com/chk5r --------------------------- ' How biological 'alchemy' can change a cell's destiny ' Peter Aldhous, "NewScientist" 2661: Jun18,08 http://tinyurl.com/4jpnen < src="file:///C:/DOCUME%7E1/TSAISH%7E1/LOCALS%7E1/Temp/moz-screenshot-1.jpg" alt="">

EDITOR'S CHOICE

Rowan Hooper, online news editor

: "" CALL it biological alchemy: specialist pancreatic cells that secrete digestive enzymes have been converted directly into insulin-producing beta cells. Meanwhile, epithelial cells from the back of the eye have been coaxed into becoming a versatile, new type of stem cell.

Both advances, reported last week in Philadelphia, Pennsylvania, at the annual meeting of the International Society for Stem Cell Research (ISSCR), may take us closer to a "regenerative" approach to repairing damaged tissue. And both are products of a wave of enthusiasm that has built since Shinya Yamanaka of Kyoto University in Japan showed that it is possible to "reprogram" adult cells back to an embryonic state. It's "Shinya-mania", jokes George Daley of the Children's Hospital Boston.

Yamanaka infected skin cells with retroviruses carrying the genes for four transcription factors - proteins that regulate the activity of other genes by binding to DNA. The viruses inserted themselves ... "

--------------------------- --------------------------- Asymmetrical 'Viral DNA imaged inside shell' KurzweilAI.net, Jun18,08 : "" UC San Diego researchers and colleagues used electron microscopy and 3D computer reconstruction to find and image the structure of an asymmetrical virus at 8 Angstroms (.8 nanometer) resolution. Tightly wound viral DNA in a bacteriophage (UCSD) Previously, only symmetrical spherical viruses had been imaged with this resolution. The image will help to unravel how the virus locks onto its host and infects the cells by injecting its DNA. University of California San Diego News Release "" --------------------------- --------------------------- 'Contact: Charlotte Webber charlotte.webber@biomedcentral.com 44-020-763-19980 BioMed Central Computer predicts anti-cancer molecules http://tinyurl.com/4usgty 'Change Lifestyle, Change Genes: 3 Months on Ornish Diet Changes 500 Genes, Many With Anticancer Effects' Daniel J. DeNoon; WebMD Health News; Reviewed by Louise Chang, MD June 16, 2008 http://tinyurl.com/6jdqgs : " The small molecules that are naturally produced in cells are called metabolites. Enzymes, the biological catalysts that produce and consume these metabolites are created according to a cell's genetic blueprints. Importantly, however, the metabolites can also affect the expression of genes. According to the authors "By comparing the gene expression levels of cancer cells relative to normal cells and converting that information into the enzymes that produce metabolites, CoMet predicts metabolites that have lower concentrations in cancer relative to normal cells". The research proves that by adding such putatively depleted metabolites to cancer cells, they exhibit anticancer properties. In this case, growth of leukemia cells was slowed by all nine of the metabolites suggested by CoMet. " - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'Magnetic Genes' Jun18,08 http://tinyurl.com/3gssej : "" Using a gene from a magnetically sensitive bacterium, scientists have genetically engineered mammalian cells to produce magnetic nanoparticles. The finding, by a team of Emory University researchers, ... The gene comes from a species of pond-dwelling bacteria that uses it to make tiny particles that function as a kind of biological compass needle. The researchers found that inserting the gene into the DNA of mouse cells caused the cells to produce their own magnetic nanoparticles. When the researchers then injected cells expressing the geneinto the brains of live mice, individual cells could be clearly seen with an MRI as a dark blob surrounded by paler normal tissue. " " the fact that a single bacterial gene could get a wide variety of cells to make their own magnets opens up a wide range of possibilities " ---------------------------------------------- 'Trio of super-Earths found around Milky Way star' Jun16,08: NewScientist.com news service: http://tinyurl.com/4znpa4 'Spacewalking microbes may reveal life's origins' Hazel muil NewScientist.com news service Apr15,08 http://tinyurl.com/4yfkgs : "" By sticking microbes to the outside of the International Space Station, Japanese researchers aim to test the "panspermia" theory that comets and asteroids can spread life between planets. The Japanese experiment is called Tanpopo, Japanese for "dandelion", after the plant's fluffy seeds, which travel long distances on the wind. The Tanpopo experiment should begin in 2011 after the bugs arrive at the Space Station. " 0-0-0) 'Genetic building blocks may have formed in space' Rachel Courtland; NewScientist.com news service: Jun13,08: Journal reference: Earth and Planetary Science Letters (vol 270, p 130) http://tinyurl.com/5vdk96 The Murchison meteorite contains the building blocks of DNA and RNA, which may have an extraterrestrial origin (Copyright: Chip Clark/Smithsonian Institution/www.si.edu) "" Some fundamental building blocks of our genetic code might have come from outer space, according to a controversial new meteorite study. The study suggests that some organic compounds associated with genetic material might have formed in a meteorite called Murchison before it landed in Australia in 1969. The chemicals are two kinds of nucleobases, ring-like carbon molecules that are essential for the creation of nucleic acids like DNA and RNA. The find might bolster claims that meteorites delivered some of the chemicals needed to create life. "It boosts the idea that the origin of life on Earth may have had an important contribution from an extraterrestrial object," says lead author Zita Martins, a chemist at Imperial College London in the UK. But it may be too early to conclude these nucleobases formed beyond the Earth, says Sandra Pizzarello, a chemist at Arizona State University in Tempe, US. The study "raises a very interesting question that was raised a very long time ago, but I don't think it solves it", she told New Scientist. No one knows how life got its start. Primitive Earth conditions might not have been favourable for the chemistry needed to create life's building blocks. Meteorite impacts Instead, researchers have argued that frequent bombardments by meteorites 3.8 billion years ago – when life is suspected to have first emerged – could have delivered the material to Earth, where it might have helped further the development of life. Studies of meteorites, as well as astronomical observations of interstellar dust and gas, have turned up a number of organic compounds, including sugars and phosphates. But nucleobases are also needed to make a nucleic acid like DNA or RNA. Such chemicals have been found in a number of meteorites, but no one was sure whether they were extraterrestrial in origin or the result of earthly contamination. Noisy signal To study the origins of these nucleobases, Martins and colleagues studied the mass of organic chemicals isolated from the meteorite. The team looked at two different isotopes of carbon in the chemicals, which included the nucleobases uracil and xanthine. The lighter version, carbon-12, is present on Earth in large amounts. Carbon-13 is more common in sweeping clouds of cold, interstellar gas. Large amounts of the stuff usually indicate the material did not form on Earth. The ratio of carbon-13 to carbon-12 was unusually high in the two nucleobases, leading the team to conclude the materials likely formed in the meteorite itself rather than on Earth. But Pizzarello says too many other chemicals were present in the samples to clearly distinguish the carbon ratio. "Analytically, it's not convincing," Pizzarello told New Scientist. Astrobiology - Learn more in our out-of-this-world special report. "" ------------------------------------------ ------------------------------------------ 0-0-1) 'Scientists Close to Reconstructing First Living Cell' Nikhil Swaminathan: Scietific American, Jun10,08 http://tinyurl.com/6f3gln "" Researchers get genetic material to copy itself in a recreation of a simple protocell that could have existed eons ago "" "" Modern cells are like microscopic cities: They have power plants (mitochondria), trash dumps (lysosomes), local government (the nucleus, with DNA serving as the legal charter), and many other activities going on inside their boundaries. They also have a border patrol in the form of a double-layered membrane that uses a series of protein-powered pumps, pores and channels to let nutrients in and keep other chemicals and substances out. But, cells were very different when life began 3.5 billion to four billion years ago. Rather than small metropolises, they were more like a purse that carried instructions—consisting of just a membrane with genetic information inside. They lacked the structures and proteins that now make them tick. The question is: How then were they able to take in the nutrients necessary to survive and reproduce? Harvard Medical School researchers report in Nature that they have built a model of what they believe the very first living cell may have looked like, which contains a strip of genetic material surrounded by a fatty membrane. The membranes of modern cells consist of a double layer of fatty acids known as phospholipids. But in designing a membrane for their cell, scientists worked with much simpler fatty acids that they believe existed on a primeval Earth, when the first cell likely formed. The key, says study co-author Jack Szostak, a Harvard geneticist, was to develop one porous enough to let in needed nutrients (such as nucleotides, the units that make up genetic material, or DNA) but strong enough to protect the genetic material inside and keep it from slipping out after replicating. In an attempt to duplicate an early cell, scientists put fatty acids (that were likely membrane candidates) and a strip of DNA into a test tube of water. While in there, the fatty acids formed into a ring, or membrane, around the genetic segment. The researchers then added nucleotides—units of genetic material—to the test tube to determine whether they would penetrate the membrane and copy the DNA inside it. Their findings: the nucleotides did enter the cell, latch onto and replicate the DNA over 24 hours. What scientists now must figure out, Szostak says, is how the original and copycat DNA strands separated and this early cell divided or reproduced. "We're trying to solve a whole series of problems, step by step," he says, "and build up to replicating an evolving system." David Deamer, a biomolecular engineer at the University of California, Santa Cruz, says he believes the team is on its way to making a prototype of a primitive cell that has "essentially all the basic properties of life." "" --------------------------------------- 0-1) 'Bacteria make major evolutionary shift in the lab' NewScientist.com news service; Bob Holmes: Jun9,08 http://tinyurl.com/3r6jr2 : "" A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait. " " ...have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events. Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations. The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens. Profound change Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities. But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity. " " Rare mutation? By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over. That meant the "citrate-plus" trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence. To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again. " " Evidence of evolution The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve. Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later. In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories. " " ...it says you can get these complex traits evolving by a combination of unlikely events... " " Journal reference: Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0803151105) Read our Evolution: 24 myths and misconceptions special report. Evolution - Learn more about the struggle to survive in our comprehensive special report. "" --------------------------------------- 0-2) 'Bacterial Chemical Sensors on the Horizon?' medGadget Jun13,08 http://tinyurl.com/3mtoy5 "" New research out of MIT has deciphered part of the bacterial communication network that has long frustrated scientists. The multitude of communication pathways in bacteria share common enzymes, yet they are still able to communicate without any interference or "crosstalk." The MIT scientists were able solve this problem, and even program their own bacterial communication pathways, by finding pairs of amino acid co-evolution. " " "If an organism has tons of this class of signaling pathway, why do we not get a lot of crosstalk?" said Laub. "How does the kinase pick out the right target?" Based on earlier studies, the MIT researchers theorized that the specificity of the interaction is determined by a subset of amino acids on the histidine kinase and a corresponding subset of amino acids on the response regulator. To confirm their theory, they looked for patterns of amino acid co-evolution in pairs of histidine kinases and their target response regulators. Co-evolution occurs when a mutation in one of the two proteins is followed by a secondary mutation in the corresponding amino acid on the other protein, allowing the protein pair to maintain their interaction. After searching a vast database of nearly 1,300 protein pairs, they identified a small set of co-evolved amino acids. They then confirmed that these amino acids govern signaling specificity by successfully rewiring five of the pathways by mutating the target amino acids. " --------------------------------------- 0-3) 'Thinking ahead: Bacteria anticipate coming changes in their environment' Jun9,08 http://tinyurl.com/6qpgkn A new study by Princeton University researchers shows for the first time that bacteria don't just react to changes in their surroundings -- they anticipate and prepare for them. The findings, reported in the June 6 issue of Science, challenge the prevailing notion that only organisms with complex nervous systems have this ability. "" "What we have found is the first evidence that bacteria can use sensed cues from their environment to infer future events," said Saeed Tavazoie, an associate professor of molecular biology, who conducted the study along with graduate student Ilias Tagkopoulos and postdoctoral researcher Yir-Chung Liu. The research team, which included biologists and engineers, used lab experiments to demonstrate this phenomenon in common bacteria. They also turned to computer simulations to explain how a microbe species' internal network of genes and proteins could evolve over time to produce such complex behavior. "The two lines of investigation came together nicely to show how simple biochemical networks can perform sophisticated computational tasks," said Tavazoie. In addition to shedding light on deep questions in biology, the findings could have many practical implications. They could help scientists understand how bacteria mutate to develop resistance to antibiotics. They also may help in developing specialized bacteria to perform useful tasks such as cleaning up environmental contamination. In one part of the study, the researchers studied the behavior of E. coli, the ubiquitous bacterium that travels back and forth between the environment and the gut of warm-blooded vertebrates. They wanted to explain a long-standing question about the bug: How do its genes respond to the temperature and oxygen changes that occur when the bacterium enters the gut? " " ...aerobic (oxygen) to anaerobic (oxygen-less) respiration... " " ...An increase in temperature had nearly the same effect on the bacterium's genes as a decrease in oxygen level. Indeed, upon transition to a higher temperature, many of the genes essential for aerobic respiration were practically turned off. " " ...grew the bacteria in a biologically flipped environment where oxygen levels rose following an increase in temperature. Remarkably, within a few hundred generations the bugs partially adapted to this new regime, and no longer turned off the genes for aerobic respiration when the temperature rose. "This reprogramming clearly indicates that shutting down aerobic respiration following a temperature increase is not essential to E. coli's survival," said Tavazoie. "On the contrary, it appears that the bacterium has "learned" this response by associating specific temperatures with specific oxygen levels over the course of its evolution." " " ..."Their biochemical networks were filled with seemingly unnecessary components," said Tagkopoulos. "That is not how an engineer would design logic-solving networks." Pared down to their essential elements, however, the networks revealed a simple and elegant structure. The researchers could now trace the different sequences of gene and protein interactions organisms used in order to respond to cues and anticipate mealtimes. "It gave us insights into how simple organisms such as bacteria can process information from the environment to anticipate future events," said Tagkopoulos. The researchers said that their findings open up many exciting avenues of research. They are planning to use similar methods to study how bacteria exchange genes with one another (horizontal gene transfer), how tissues and organs develop (morphogenesis), how viral infections spread and other core problems in biology. "What is really exciting about our discovery is that it brings together and establishes deep connections between the traditionally separate fields of microbial ecology, network evolution and behavior," said Tavazoie. Source: Princeton University "" --------------------------------------- 1) 'Origins of the brain: Complex synapses drove brain evolution' Jun8,08 http://tinyurl.com/6ghmwn One of the great scientific challenges is to understand the design principles and origins of the human brain. New research has shed light on the evolutionary origins of the brain and how it evolved into the remarkably complex structure found in humans. "" The research suggests that it is not size alone that gives more brain power, but that, during evolution, increasingly sophisticated molecular processing of nerve impulses allowed development of animals with more complex behaviours. The study shows that two waves of increased sophistication in the structure of nerve junctions could have been the force that allowed complex brains - including our own - to evolve. The big building blocks evolved before big brains. " " the protein components of nerve connections - called synapses " " Professor Seth Grant, Head of the Genes to Cognition Programme at the Wellcome Trust Sanger Institute and leader of the project. "... We found dramatic differences in the numbers of proteins in the neuron connections between different species". "We studied around 600 proteins that are found in mammalian synapses and were surprised to find that only 50 percent of these are also found in invertebrate synapses, and about 25 percent are in single-cell animals, which obviously don't have a brain." Synapses are the junctions between nerves where electrical signals from one cell are transferred through a series of biochemical switches to the next. However, synapses are not simply soldered joints, but mini-processors that give the nervous systems the property of learning and memory. Remarkably, the study shows that some of the proteins involved in synapse signalling and learning and memory are found in yeast, where they act to respond to signals from their environment, such as stress due to limited food or temperature change. "The set of proteins found in single-cell animals represents the ancient or 'protosynapse' involved with simple behaviours," continues Professor Grant. "This set of proteins was embellished by addition of new proteins with the evolution of invertebrates and vertebrates and this has contributed to the more complex behaviours of these animals. "The number and complexity of proteins in the synapse first exploded when muticellular animals emerged, some billion years ago. A second wave occurred with the appearance of vertebrates, perhaps 500 million years ago" " " Most important for understanding of human thought, they found the expansion in proteins that occurred in vertebrates provided a pool of proteins that were used for making different parts of the brain into the specialised regions such as cortex, cerebellum and spinal cord. Since the evolution of molecularly complex, 'big' synapses occurred before the emergence of large brains, it may be that these molecular evolutionary events were necessary to allow evolution of big brains found in humans, primates and other vertebrates. Behavioural studies in animals in which mutations have disrupted synapse genes support the conclusion that the synapse proteins that evolved in vertebrates give rise to a wider range of behaviours including those involved with the highest mental functions. For example, one of the 'vertebrate innovation' genes called SAP102 is necessary for a mouse to use the correct learning strategy when solving mazes, and when this gene is defective in human it results in a form of mental disability. "The molecular evolution of the synapse is like the evolution of computer chips - the increasing complexity has given them more power and those animals with the most powerful chips can do the most," continues Professor Grant. Simple invertebrate species have a set of simple forms of learning powered by molecularly simple synapses, and the complex mammalian species show a wider range of types of learning powered by molecularly very complex synapses. "It is amazing how a process of Darwinian evolution by tinkering and improvement has generated, from a collection of sensory proteins in yeast, the complex synapse of mammals associated with learning and cognition," said Dr Richard Emes, Lecturer in Bioinformatics at Keele University, and joint first author on the paper. " " Professor Grant's team have identified recently evolved genes involved in impaired human cognition and modelled those deficits in the mouse. "This work leads to a new and simple model for understanding the origins and diversity of brains and behaviour in all species" says Professor Grant, adding that "we are one step closer to understanding the logic behind the complexity of human brains" Citation: Emes RD, Pocklington AJ, Anderson CNG, Bayes A, Collins MO, Vickers CA, Croning MDR, Malik BR, Choudhary JS, Armstrong JD and Grant SGN (2008), Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nature Neuroscience published online Sunday 8 June 2008 ; http://dx.doi.org/10.1038/nn.2135 Source: Wellcome Trust Sanger Institute "" --------------------------------------- 2) 'Researchers show how the brain can protect against cancer' Jun9,08 http://tinyurl.com/4k5flj Scientists have been aware for many years that if cancer patients are not able to deal with the stress associated with being sick, the cancer will progress faster than in calmer patients. To counteract this phenomenon, physicians encourage treatments that help cancer patients handle their stress. Scientists theorized that the stress relief may have come as a result of increased beta-endorphin peptide (BEP), the "feel good" hormones in the brain that are released during exercise, a good conversation, and many other aspects of life that give humans pleasure. "" Researchers at Rutgers hypothesized that BEP producing neurons do not just make us feel good, but also play roles in regulating the stress response and immune functions to control tumor growth and progression. In a paper published today in the Proceedings of the National Academy of Science, Dr. Dipak K. Sarkar and his colleagues demonstrate the physical mechanisms that support their hypothesis. " " Previous research has shown that too few, or inactive, BEP neurons are associated with various diseases. ...depression and schizophrenia. ...obese patients. In both these cases ...higher levels of infection and more incidence of cancer. " " Source: Rutgers University ""