domenica 12 aprile 2009

Mass Spec Technique Analyzes Defensive Chemicals On Seaweed Surfaces For Potential Drugs

ScienceDaily (Apr. 13, 2009) — A new analytical technique is helping scientists learn how organisms as simple as seaweed can mount complex chemical defenses to protect themselves from microbial threats such as fungus. Known as desorption electrospray ionization mass spectrometry (DESI-MS), the technique for the first time allows researchers to study unique chemical activity taking place on the surfaces of these organisms.
Understanding this surface chemistry could one day allow scientists to borrow and adapt some of those defensive chemical compounds for use against cancer, HIV, malaria, drug-resistant bacteria and other diseases of humans. In a paper scheduled to be published online in the journal Proceedings of the National Academy of Sciences, researchers from the Georgia Institute of Technology describe a sophisticated chemical defense system that uses 28 different compounds to protect a species of seaweed against a single fungus.
"Plants and animals in the wild use chemistry as way to fight with one another," said Julia Kubanek, a professor in Georgia Tech's School of Biology. "Using this new technology, scientists can listen in on this fight to perhaps learn from what's going on and steal some of the strategies for human biomedical applications."
As part of a long-term project sponsored by the Natural Institutes of Health, Georgia Tech scientists have been cataloging and analyzing natural compounds from more than 800 species found in the waters surrounding the Fiji Islands. They have been particularly interested in Callophycus serratus, an abundant species of red seaweed that seems particularly successful – and adept at fighting off microbial infections.
Using the DESI-MS technique, the researchers analyzed recently-collected samples of the seaweed and found groups of potent anti-fungal compounds in light-colored microscopic surface patches covering what may be wounds on the surface of the seaweed. In laboratory testing, these bromophycolide compounds and callophycoic acids effectively inhibited the growth of Lindra thalassiae, a common marine fungus.
"It is possible that the alga is marshalling its defenses and displaying them in a way that blocks the entry points for microbes that might invade and cause disease," Kubanek said. "Seaweeds don't have B cells, T cells and immune responses like humans do. But instead they have some chemical compounds in their tissues to protect them."
Though all the seaweed they studied was from a single species, the researchers were surprised to find two distinct groups of anti-fungal chemicals. From one seaweed subpopulation, dubbed the "bushy" type for its appearance, 18 different anti-fungal compounds were identified. In a second group of seaweed, the researchers found 10 different anti-fungal compounds – all different from the ones seen in the first group.
"This species is producing some unique chemical compounds that other seaweeds don't produce, and it is producing a large number of compounds, each of which has a role to play in the overall defense against the fungus," Kubanek noted. "We think the compounds work together in an additive way."
Though chemically different, the compounds are structurally related and seem to arise from a similar metabolic pathway in the seaweed. Why one species of simple organism would produce 28 different anti-fungal compounds remains a mystery, though Kubanek believes the chemicals may also have other uses that are not yet understood.
The compounds have been tested for potential activity against drug-resistant bacteria, cancer, HIV, malaria and other human health threats. So far, preliminary testing suggests they have anti-malarial effects.
The DESI-MS technique allowed the researchers for the first time to analyze chemical activity occurring on the surface of the seaweed. Earlier techniques allowed identification of chemicals in the organism's tissue, but being able to confirm their location on the surface – the first line of defense against infection – confirms the role they play as defensive chemicals.
In DESI-MS, a charged stream of polar solvent is directed at the surface of a sample under study at ambient pressure and temperature. The spray desorbs molecules, which are then ionized and delivered to the mass spectrometer for analysis.
"This technique allows us to examine intact organisms and see how the chemical compounds are distributed," Kubanek explained. "For our research with seaweed, this is important because we'd like to understand how an organism distributes these compounds to protect itself from enemies."
In addition to Kubanek, others researchers contributing to the study included Leonard Nyadong, Asiri Galhena, Tonya Shearer, E. Paige Stout, R. Mitchell Parry, Mark Kwasnik, May Wang, Mark Hay, and Facundo Fernandez – all from Georgia Tech – and Amy Lane, now at Scripps Institution of Oceanography. Beyond the National Institutes of Health support, the research has also been sponsored by the National Science Foundation.
For the future, Kubanek and a graduate student are working to modify the most promising of the anti-malarial compounds, replacing some oxygen atoms for nitrogen atoms and bromine for chlorine and fluorine. The hope is to create a compound more potent against the malaria organism with less toxicity for humans.
"We are doing reaction chemistry using these 28 compounds as a starting point," she explained. "Learning about how other species avoid diseases may give us something we can use to avoid or treat our own diseases."
Adapted from materials provided by Georgia Institute of Technology, via EurekAlert!, a service of AAAS.

Pig Of The Future Might Be Free Of Diseases That Can Infect People

ScienceDaily (Apr. 13, 2009) — Pigs are known carriers of the bacterium Yersinia enterocolitica, and they can infect both other pigs and people. Human infection occurs through eating improperly-cooked pork. Professor Truls Nesbakken of the Norwegian School of Veterinary Science is trying to rid pigs of the bacterium.
The professor, who already has 2 Norwegian doctorates (Dr. scient and Dr. med. vet.), recently defended his thesis for the degree of Dr. philos., entitled "Control of human pathogenic Yersinia enterocolitica in the meat chain". It will make him the first scientist with 3 Norwegian doctorates. One of the scientific articles supporting the thesis shows that it is possible to keep swine herds in closed breeding pyramids free of Yersinia enterocolitica. This indicates that it is possible to keep Yersinia enterocolitica, which is presently extremely wide-spread in the pig population at large, under control. In man, the bacterium can cause serious arthritis, among other illnesses. The pig is the primary host of the bacterium, and the most common path of infection from pig to man is assumed to be direct infection from eating pork.
Norwegian abattoirs have already introduced several important measures to improve slaughter hygiene, which is also a subject of the doctorate. However, more remains to be done, indicated by the fact that 2 people who ate pickled pork for Christmas in 2006 died of yersiniosis. Only rarely does yersiniosis lead to such a tragic outcome, and most cases cause nothing more than intestinal infection or at worst a drawn-out arthritis.
Exciting research with consequences for public health
A pig herd free of infectious disease is referred to as SPF, meaning "specific pathogen-free". In a broader context, it is very likely that we can also produce pork free of Yersinia enterocolitica, Toxoplasma and Salmonella. In that case we are no longer talking of SPF-herds, but of a development towards HPF (human pathogen-free) herds. Such a development would depend, however, on its cost-effectiveness.
The development of SPF-herds, and ultimately HPF-herds, is part of a field of veterinary medicine called Veterinary Public Health (VPH), defined as the science and practice of veterinary medicine science concerned with the maintenance of human health. Central to VPH is the understanding, prevention and control of zoonoses, or diseases spread between animals and man. Adapted from materials provided by Norwegian School of Veterinary Science.

Epigenetics: DNA Isn’t Everything


ScienceDaily (Apr. 13, 2009) — Research into epigenetics has shown that environmental factors affect characteristics of organisms. These changes are sometimes passed on to the offspring. ETH professor Renato Paro does not believe that this opposes Darwin’s theory of evolution.
A certain laboratory strain of the fruit fly Drosophila melanogaster has white eyes. If the surrounding temperature of the embryos, which are normally nurtured at 25 degrees Celsius, is briefly raised to 37 degrees Celsius, the flies later hatch with red eyes. If these flies are again crossed, the following generations are partly red-eyed – without further temperature treatment – even though only white-eyed flies are expected according to the rules of genetics.
Environment affects inheritance
Researchers in a group led by Renato Paro, professor for Biosystems at the Department of Biosystems Science and Engineering (D-BSSE), crossed the flies for six generations. In this experiment, they were able to prove that the temperature treatment changes the eye colour of this specific strain of fly, and that the treated individual flies pass on the change to their offspring over several generations. However, the DNA sequence for the gene responsible for eye colour was proven to remain the same for white-eyed parents and red-eyed offspring.
The concept of epigenetics offers an explanation for this result. Epigenetics examines the inheritance of characteristics that are not set out in the DNA sequence. For Paro, epigenetic mechanisms form an additional, paramount level of information to the genetic information of DNA.
Such phenomena could only be examined in a descriptive manner in the past. Today, it has been scientifically proven, which molecular structures are involved: important factors are the histones, a kind of packaging material for the DNA, in order to store DNA in an ordered and space-saving way. It is now clear that these proteins have additional roles to play. Depending on the chemical group they carry, if they are acetylated or methylated, they permanently activate or deactivate genes. New methods now allow researchers to sometimes directly show which genes have been activated or deactivated by the histones.
Cells have a memory
Epigenetic marks, such as the modifications of the histones, are also important for the specialisation of the body’s cells. They are preserved during cell division and are passed on to the daughter cells. If skin cells divide, more skin cells are created; liver cells form liver cells. In both cell types, all genes are deactivated except the ones needed by a skin or liver cell to be a skin or liver cell, and to function appropriately. The genetic information of the DNA is passed on along with the relevant epigenetic information for the respective cell type.
Paro’s group is researching this cell memory. It is still unclear how the epigenetic markers are passed on to the daughter cells. During cell division, the DNA is doubled, which requires the histones – as the current picture suggests – to break apart. The question is therefore how cellular memory encoded by epigenetic mechanisms survives cell division.
Emerging area of research
A similar question remains for the inheritance of the epigenetic characteristics from parents to offspring. They now know that when the gametes are formed, certain epigenetic markers remain and are passed on to the offspring. The questions, which are currently being researched, are how much and which part of the epigenetic information is preserved and subsequently inherited.
The research is also looking at the influence of various substances from the environment on the epigenetic constitution of organisms, including humans. Diet and epigenetics appear to be closely linked. The most well known example is that of the Agouti mice: they are yellow, fat and are prone to diabetes and cancer. If Agouti females are fed with a cocktail of vitamin B12, folic acid and cholin, directly prior to and during pregnancy, they give birth to mainly brown, slim and healthy offspring. They in turn mainly have offspring similar to themselves.
Contradiction to Darwin?
Environmental factors, which change the characteristics of an individual and are then passed on to its offspring, do not really fit into Darwin’s theory of evolution. According to his theory, evolution is the result of the population and not the single individual. “Passing on the gained characteristics fits more to Lamarck’s theory of evolution”, says Paro.
However, he still does not believe Darwin’s theory of evolution is put into question by the evidence of epigenetics research. “Darwin was 100 percent right”, Paro emphasises. For him, epigenetics complement Darwin’s theory. In his view, new characteristics are generated and passed on via epigenetics, subject to the same mechanisms of evolution as those with a purely genetic origin.
Adapted from materials provided by ETH Zurich.

venerdì 10 aprile 2009

Biologists Discover How 'Silent' Mutations Influence Protein Production

ScienceDaily (Apr. 10, 2009) — Biologists at the University of Pennsylvania have revealed a hidden code that determines the expression level of a gene, providing a way to distinguish efficient genes from inefficient ones. The new research, which involved creating hundreds of synthetic green-glowing genes, provides an explanation for how a cell "knows" how much of each protein to make, providing just the right amount of protein to maintain homeostasis yet not too much to cause cell toxicity.
In the study, Penn biologists analyzed how protein levels are governed by synonymous, or silent, mutations within the protein-coding region.
Synonymous mutations do not change the amino-acid sequence of a protein, but they can nevertheless influence the amount of the protein that is produced. The researchers identified the mechanism underlying this regulation: synonymous mutations determine mRNA folding and thereby the eventual protein level. The researchers also identified a class of mutations that did not directly affect protein levels but slowed bacterial growth.
For biologists, these results fundamentally change the understanding of the role of synonymous mutations, which were previously considered evolutionarily neutral. The findings may also improve the design of therapeutic genes. Many drugs, such as insulin, are produced by transgenic cell lines. Using optimized genes will produce larger amounts of therapeutic proteins while keeping the transgenic, carrier cells healthy and fast-growing.
The human genome contains more than 20,000 genes that encode the proteins present in a human body. Some of these proteins are needed in bulk, while for others a tiny amount is sufficient and a large amount would be toxic. The question is how cells "know" how much of each protein to make.
To answer this question, Joshua B. Plotkin, senior author and the Martin Meyerson Assistant Professor in the Department of Biology in Penn's School of Arts and Sciences, and colleagues at Harvard University and the University of Edinburgh engineered a synthetic library of 154 genes that varied randomly at synonymous sites. All the genes encoded the same green fluorescent protein, enabling the researchers to easily study the effects of such mutations on protein levels when expressed in the bacterium Escherichia coli.
The silent mutations changed the amount of fluorescent protein by as much as 250-fold, without changing the properties of the protein. Codon bias, the probability that one codon of three adjacent nucleotides will code for one amino acid over another, was previously thought to be the cause for protein expression variance, but it did not correlate with gene expression in these experiments.
"At first we were stumped," Plotkin said. "How were the silent mutations influencing protein levels? Eventually, we looked at mRNA structure and discovered that this was the underlying mechanism."
The stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. To understand this observation, the researchers simulated the spatial arrangement of the messenger RNA molecule that carries the information from genes to proteins. They found that the inefficient genes produced tightly folded mRNA molecules that could not be accessed by the protein-making machinery. According to their analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.
The study, appearing in the current issue of the journal Science, was performed by Plotkin, as well as first author Grzegorz Kudla of the Department of Biology at Penn, Andrew W. Murray of the Department of Molecular and Cellular Biology at Harvard and David Tollervey of the Wellcome Trust Centre for Cell Biology at Edinburgh.
The study was funded by the Burroughs Wellcome Fund, James S. McDonnell Foundation, Penn Genome Frontiers Institute, Defense Advanced Research Projects Agency, Foundation for Polish Science and Wellcome Trust Centre.
Journal reference:
Grzegorz Kudla, Andrew W. Murray, David Tollervey, and Joshua B. Plotkin. Coding-Sequence Determinants of Gene Expression in Escherichia coli. Science, 2009; 324 (5924): 255 DOI: 10.1126/science.1170160
Adapted from materials provided by University of Pennsylvania, via EurekAlert!, a service of AAAS.

How Tumor Cells Move

ScienceDaily (Apr. 11, 2009) — Researchers in Heidelberg discover new protein that is suppressed in particularly aggressive cancer cell.
If cancer cells lack a certain protein, it could be much easier for them to penetrate healthy body tissue, the first step towards forming metastases. Scientists at the Pharmacology Institute of the University of Heidelberg have discovered the previously unknown cell signal factor SCAI (suppressor of cancer cell invasion), which inhibits the movement and spread of tumor cells in laboratory tests. When the factor’s functioning was disrupted, the cancer cells moved much more effectively in what are known as three-dimensional matrix systems, which imitate some of the tissue properties of the human body.
“The protein is apparently suppressed in many types of tumors, e.g. breast, lung, or thyroid,” explains Dr. Robert Grosse, head of the Emmy Noether Junior Research Group funded by the German Research Association (DFG) at the Pharmacology Institute. The new factor could be an interesting starting point for research into new mechanisms for fighting cancer. The research team’s results have now been published online in the prestigious international journal Nature Cell Biology.
Focus on particularly aggressive cancers
Tumor cells are extremely mobile and “adept” at penetrating healthy tissue to form metastases. They adapt to the consistency of the respective tissue by changing their shapes constantly and attach flexibly to surrounding tissues during movement with the help of special surface structures (receptors).
One of these receptors is what is known as b1-integrin, which is frequently formed in many tumors such as metastasizing breast cancer. “The cell signal factor SCAI controls the formation and function of b1-integrin,” says Dr. Robert Grosse. “If there is too little SCAI in tumor cells, then b1-integrin is overactive, so to speak. The cell can change more rapidly to a more aggressive form and penetrate surrounding tissue, a crucial step toward increased spreading of the tumor and the possible formation of metastases.”
In their recently published study, the Heidelberg researchers examined cells from skin cancer (melanoma) and breast cancer. In other projects, Dr. Robert Grosse’s team would like to study the function of the signal factor SCAI more closely in an animal model. “If the function of SCAI is confirmed to be decisive in the formation of especially aggressive tumor cells, this could be a promising starting point for developing new diagnostic methods or medication,” says the pharmacologist. It could also be possible to develop an agent that prevents the genetic suppression of the signal factor in cancer cells. But first the researchers need to better understand how the signal factor itself is regulated in the cell.
Journal reference:
Brandt et al. SCAI acts as a suppressor of cancer cell invasion through the transcriptional control of β1-integrin. Nature Cell Biology, 2009; DOI: 10.1038/ncb1862
Adapted from materials provided by University Hospital Heidelberg.

DNA From Old Insects: No Need To Destroy The Specimen

ScienceDaily (Apr. 9, 2009) — Ancient DNA can now be retrieved from various insect remains without destruction of the specimens.
Together with eight other authors, Philip Francis Thomsen and Eske Willerslev, from the Centre for Ancient Genetics and Environments, Natural History Museum, University of Copenhagen, use a previously published non-destructive DNA extraction method (Gilbert et al. 2007) to retrieve DNA from ancient macrofossils from permafrost sediments and historical museum beetle specimen.
DNA is successfully retrieved from Siberian macrofossils up to 26,000 years old and dried museum beetle specimens up to 188 years old. This reveals that the method has great potential for aDNA research.
Despite the massive diversity of the group, insects are almost neglected in aDNA studies, which have focused mainly on vertebrates, plants and—to a lesser extent—microbes, revealing aDNA research as a powerful tool for testing hypotheses in biology.
A major constraint on the use of historical, and particularly ancient, insect specimens in aDNA research, is the destructive nature of the sampling procedure. Obviously, this is a problem related to many aDNA sources, but is of particular concern with small specimens, such as insects, where even limited sampling may destroy important morphological characters. So far, most ancient genetic studies on insects have suffered from such destructive sampling procedures.
The results obtained with the non-destructive sampling method in this study, suggests that destruction of specimens is no longer necessary to include insects in aDNA studies.
The use of historical museum specimens has important applications in population genetic studies, where historical specimens could reveal former genetic structures, undetectable with modern material only. Ancient insect macrofossils hold potentials in studies on former ecosystems and climates.
Finally the study applies a classic DNA extraction method for sediments, to look for insect DNA in temperate soil from New Zealand around 1,800-3,000 years ago. DNA from a beetle and a moth or butterfly is obtained from the soil, which includes no visible insect remains. Hence, the DNA is extracted directly from the soil. Retrieval of insect DNA from sediments, have applications for reconstruction of ancient biodiversity, unobtainable in any other way.
Journal reference:
Thomsen PF, Elias S, Gilbert MTP, Haile J, Munch K, et al. Non-Destructive Sampling of Ancient Insect DNA. PLoS ONE, 2009; 4 (4): e5048 DOI: 10.1371/journal.pone.0005048
Adapted from materials provided by Public Library of Science, via EurekAlert!, a service of AAAS.

Gene Linked To Deadly Disorder In Newborns Identified

ScienceDaily (Apr. 10, 2009) — After 12 years of searching, UCLA scientists have tracked down the first known gene mutation responsible for a heartbreaking disorder that kills newborn babies. Published in the April 1 online edition of the American Journal of Human Genetics, their findings will allow for earlier testing of embryos at risk for the disease.

Many things go awry in short-rib polydactyly syndrome. The fetus develops extra fingers and toes and its skeleton doesn't grow, resulting in stunted ribs that prevent the lungs from maturing in the womb. Unable to breathe on its own, the child dies shortly after birth.
Parents currently must wait until the second trimester of pregnancy for a diagnosis – a long time to wait for potentially agonizing news about one's unborn child.
"Now that we've identified the genetic basis of the disease, families will be able to obtain a prenatal diagnosis within about 12 weeks," explained Dr. Deborah Krakow, associate professor of orthopedic surgery and human genetics at the David Geffen School of Medicine at UCLA. "Parents will also be able to screen embryos conceived in vitro to help select those free of the genetic mutation before uterine implantation."
Roughly one in 300 people are carriers of short-rib polydactyly syndrome. Both parents must carry the mutated gene in order for their child to inherit the disease.
In the hope of finding a common genetic link to the disease, the UCLA team studied DNA samples from three families whose children died of short-rib polydactyly syndrome. Dr. Stan Nelson, UCLA professor of human genetics, and his laboratory employed powerful genomic technology to rapidly test hundreds of thousands of gene variations in each fetus.
"It took scientists 10 years to map the human genome," Nelson said. "New technology enables us to search a child's entire genome in two weeks without testing the parents or other family members. It's a highly efficient way to quickly sample DNA and identify shared gene variations among people."
In the UCLA study, the research team identified a DNA sequence shared by all three infants from a single family. Like a signpost, it directed the scientists to a chromosomal location they suspected of housing the disease-causing gene.
"Each of us inherits different chromosomes from our mothers and fathers," explained Nelson. "If the child's genome contains the same DNA from both parents, we know that the mother and father are related in some way. They share a piece of ancestral DNA -- a common red flag for people known to have or carry a genetic disease."
After narrowing her search to three identical regions on the genome, Krakow zeroed in on one as the likely culprit. Her hunch proved correct. Not only did she identify the mutation in the initial family that lost three children, but she confirmed its presence in two other families whose infants also died of the disease.
Krakow and Nelson's next step will be to seek out other genes that contribute to short-rib polydactyly syndrome and uncover how these factors interact to cause the disorder.
"One of the reasons this disease is hard to crack is that it is caused by multiple genes, not just one," said Krakow. "We are searching for other gene variants in other families affected by the syndrome."
The DNA-scanning techniques developed by Nelson and his colleagues can be used to identify any hereditary disease-causing gene. The findings will enhance doctors' abilities to determine individual genes' specific roles and provide a more complete picture for healthy and abnormal human development.
Roughly 3 percent of all infants are born with birth defects. Some 5 percent of these children suffer from genetic defects affecting the skeleton. In this group, about 5 percent are short-rib polydactyly syndrome patients.
The National Institute of Child Health and Human Development funded the study.
Coauthors include Amy Merrill, Barry Merriman, Clare Farrington-Rock, Natalia Camacho, Eiman Sebald, Vicente Funari, Matthew Schibler, Marc Firestein, Zachary Cohen, Maryann Priore, Alicia Thompson, David Rimoin and Daniel Cohn, all affiliated with UCLA and Cedars-Sinai Medical Center.
Adapted from materials provided by University of California - Los Angeles, via EurekAlert!, a service of AAAS.

DNA Origami Seeds Control Complex Nucleation Processes

ScienceDaily (Apr. 9, 2009) — The construction of complex man-made objects--a car, for example, or even a pizza--almost invariably entails what are known as "top-down" processes, in which the structure and order of the thing being built is imposed from the outside (say, by an automobile assembly line, or the hands of the pizza maker).
"Top-down approaches have been extremely successful," says Erik Winfree of the California Institute of Technology (Caltech). "But as the object being manufactured requires higher and higher precision--such as silicon chips with smaller and smaller transistors--they require enormously expensive factories to be built."
The alternative to top-down manufacturing is a "bottom-up" approach, in which the order is imposed from within the object being made, so that it "grows" according to some built-in design.
"Flowers, dogs, and just about all biological objects are created from the bottom up," says Winfree, an associate professor of computer science, computation and neural systems, and bioengineering at Caltech. Along with his coworkers, Winfree is seeking to integrate bottom-up construction approaches with molecular fabrication processes to construct objects from parts that are just a few billionths of a meter in size that essentially assemble themselves.
In a recent paper in the Proceedings of the National Academy of Sciences (PNAS), Winfree and his colleagues describe the development of an information-containing DNA "seed" that can direct the self-assembled bottom-up growth of tiles of DNA in a precisely controlled fashion. In some ways, the process is similar to how the fertilized seeds of plants or animals contain information that directs the growth and development of those organisms.
"The big potential advantage of bottom-up construction is that it can be cheap"--just as the mold that grows in your kitchen does so for free--"and can be massively parallel, because the objects construct themselves," says Winfree.
But, he adds, while bottom-up approaches have been extremely useful in biology, they haven't played as significant a role in technology, "because we don't have a great grasp on how to design systems that build themselves. Most examples of bottom-up technologies are specific chemical processes that work great for a particular task, but don't easily generalize for constructing more complex structures."
To understand how complexity can be programmed into bottom-up molecular fabrication processes, Winfree and his colleagues study and understand the processes--or algorithms--that generate organization not just in computers but also in the natural world.
"Tasks can be solved by carrying out well-defined rules, and these rules can be carried out by a mindless mechanism such as a computer," he says. "The same set of rules can perform different tasks when given different inputs, and there exist 'universal programs' that can perform any task required of it, as specified in its input. Your laptop is such a universal computer; it can run any software that you download, and in principle, any feasible task could be programmed."
These principles also have been exploited by natural evolution, Winfree says: "Every cell, it appears, is a kind of universal computer that can be instructed in seemingly limitless ways by a DNA genome that specifies what chemical processes to execute, thus building an active organism. The aim of my lab has been to understand algorithms and information within molecular systems."
Winfree's investigations into algorithmic self-assembly earned him a MacArthur "genius" prize in 2000; his collaborator, Paul W. K. Rothemund, a senior research associate at Caltech and a coauthor of the PNAS paper, was awarded the same no-strings-attached grant in 2007 for his work designing scaffolded "DNA origami" structures that self-assemble into nearly arbitrary shapes (such as a smiley face and a map of the Western Hemisphere).
The structures designed by Rothemund, which could eventually be used in smaller, faster computers, were used as the seeds for the programmed self-assembly of DNA tiles described in the current paper.
In the work, the researchers designed several different versions of a DNA origami rectangle, 95 by 75 nanometers, which served as the seeds for the growth of different types of ribbon-like crystals of DNA. The seeds were combined in a test tube with other bits of DNA, called "tiles," heated, and then cooled slowly.
"As it cools, the first origami seed and the individual tiles form, as their component DNA molecules begin sticking to each other and folding into shape--but the tiles and origami don't stick to each other yet," Winfree explains.
"Then, at a lower temperature, the tiles start to stick to each other and to the origami. The critical concept here is that the DNA tiles will only form crystals if the process gets started by a seed, upon which they can grow," he says.
In this way, the DNA ribbons self-assemble themselves, but only into forms such as ribbons with particular widths and ribbons with stripe patterns prescribed by the original seed.
The work, Winfree says, "exhibits a degree of control over information-directed molecular self-assembly that is unprecedented in accuracy and complexity, which makes me feel that we are finally beginning to understand how to program information into molecules and have that information direct algorithmic processes."
The other authors of the paper are undergraduate Robert D. Barish and visiting scholar Rebecca Schulman. The work was supported by grants from the National Aeronautics and Space Administration's astrobiology program, the National Science Foundation, and the Focus Center Research Program, and a gift from Microsoft Research.
Journal reference:
Barish et al. An information-bearing seed for nucleating algorithmic self-assembly. Proceedings of the National Academy of Sciences, March 24, 2009; DOI: 10.1073/pnas.0808736106
Adapted from materials provided by California Institute of Technology, via EurekAlert!, a service of AAAS.

Towards A Natural Pacemaker

ScienceDaily (Apr. 10, 2009) — Artificial heart pacemakers have saved and extended the lives of thousands of people, but they have their shortcomings – such as a fixed pulse rate and a limited life. Could a permanent biological solution be possible?
Richard Robinson and colleagues at New York's Columbia and Stony Brook Universities certainly think so, and their work published in The Journal of Physiology brings the dream a step closer to reality.
The body's own natural pacemaker, called the sinoatrial (SA) node, is extremely vulnerable to damage during a heart attack, often leaving the patient with a weak, slow or unreliable heartbeat. The heart has limited ability to recover from the damage, so the conventional approach is to fit an electronic device to monitor and control the beat directly.
Therapies to help raise the heart rate biologically could be a much better solution, but there are some major hurdles. The way electrical signals are generated in the SA node – and hence the heart rate – are far from simple. There are three separate electrical pathways between cells, called HCN or 'funny' channels (because of their complex behaviour), that could be involved.
Dr Robinson's work helps to shed light on the secrets of the HCN channels, but more importantly describes a cell culture they have developed that accurately mimics HCN function in whole mammalian hearts, making future research in the area far quicker and easier.
The researchers used their new cellular model to genetically 'rewire' two of the HCN channels. The resulting heart rate was very rapid with irregular pauses, just as has already been observed in dogs and mice.
It is early days – but the valuable new computer and cellular models are ideal for testing potential new drugs to influence heart rate and pave the way for new genetic biological pacemakers to be developed.
Dr Robinson commented that the new developments “will facilitate the development of practical biological pacemakers by allowing more complete and rapid assessment of individual channel mutations through combined culture and simulation studies prior to full testing in animal models.”
Journal reference:
Zhao Xin, Annalisa Bucchi, Ronit V. Oren, Yelena Kryukova, Wen Dun, Colleen E. Clancy, and Richard B. Robinson. In vitro characterization of HCN channel kinetics and frequency dependence in myocytes predicts biological pacemaker functionality. The Journal of Physiology, 2009; 587 (7): 1513 DOI: 10.1113/jphysiol.2008.163444
Adapted from materials provided by Wiley - Blackwell, via AlphaGalileo.

Research Could Lead To New Non-antibiotic Drugs To Counter Hospital Infections

ScienceDaily (Apr. 9, 2009) — Lack of an adequate amount of the mineral phosphate can turn a common bacterium into a killer, according to research to be published in the April 14, 2009, issue of the Proceedings of the National Academies of Science. The findings could lead to new drugs that would disarm the increasingly antibiotic-resistant pathogen rather than attempting to kill it.
Pseudomonas aeruginosa is one of the most serious hospital-acquired pathogens. A common cause of lung infections, it is also found in the intestinal tract of 20 percent of all Americans and 50 percent of hospitalized patients in the United States.
It is one of the hundreds of bacteria that colonize the human intestinal tract, usually causing no apparent harm. It might even be beneficial to its host. Once the host is weakened by an illness, surgical procedure or immunosuppressive drugs, however, P. aeruginosa can cause infection, inflammation, sepsis and death.
Why P. aeruginosa can suddenly turn on its host has eluded researchers—until now. Scientists have long known that after an operation or organ surgery, levels of inorganic phosphate fall. The authors of the PNAS paper, led by scientists at the University of Chicago, hypothesized that phosphate depletion in the stressed intestinal tract signals P. aeruginosa to become lethal.
To test this theory, they let worms (Caenorhabditis elegans) feed on "lawns" of P. aeruginosa and Escherichia coli grown in both low-phosphate and high-phosphate media. Only the worms that ate P. aeruginosa with low levels of phosphate died. The researchers dubbed the phenomenon "Red Death" since unexpected large red spots appeared on the worms before they died.
"These findings provide novel insight into the mechanisms by which P. aeruginosa is able to shift from indolent colonizer to a lethal pathogen when present in the intestinal tract of a stressed host," said Alexander Zaborin, lead author of the study and a research professional at the University of Chicago’s Department of Surgery.
"It's almost as if the bacterium sense when to strike," said John Alverdy, corresponding author of the study and professor of surgery at the University of Chicago Medical Center. "That should come as no surprise since the bacteria are smart, having been around for 2 billion years."
Bacteria seek phosphate as an important nutrient, Alverdy explained. And rather than try to look for it in the blood steam of critically ill patients, where they would encounter armies of antibiotics and disease-fighting white blood cells, they find it inside organ tissues. This process damages and sometimes even kills their host.
Experiments with mice showed that the harm caused when P. aeruginosa becomes activated to express lethal toxins inside the intestinal tract can be mitigated by providing excess phosphate.
The research findings could lead to a pharmaceutical product that would restore healthy phosphate levels in the intestines of such stressed and compromised patients, Alverdy said.
"Antibiotics attempt to kill harmful bacteria, but in the process they often kill beneficial bacteria," said Olga Zaborina, an associate professor at the University of Chicago’s Department of Surgery and another key researcher in this study. "A more sensible approach to fighting infectious diseases may be to try to understand the circumstances that provoke a microbe to cause harm in the first place and then find ways to pacify them without destroying them."
Containment on a case-by-case basis might be a more effective and longer-lasting strategy than a scorched earth policy, Alverdy said. Midway Pharmaceuticals, which Alverdy founded in 2005, is developing a pipeline of non-antibiotic compounds that contain or disarm specific bacteria.
Appreciation of the subtle mechanisms in pathogens that colonize the intestinal tract of critically ill patients has important implications for the design of phosphate-based compounds that might prevent P. aeruginosa and other pathogens from turning lethal, the researchers concluded.
Despite the use of powerful antibiotics, P. aeruginosa remains a leading cause of sickness and death among hospitalized patients who have undergone surgery or have reduced immunity. If the bacterium attacks critical body organs such as the lungs, urinary tract and kidneys, it is likely to be fatal. P. aeruginosa thrives on moist surfaces, so it is often found on catheters, causing cross-hospital infections. It is also implicated in a common form of dermatitis associated with poor hygiene and inadequate maintenance of hot tubs.
The PNAS paper is called "Red Death in Caenorhabditis elegans caused by Pseudomonas aeruginosa PA01." Other institutions contributing to this research are INRS-Institut Armand-Frappier; Centre for Biomolecular Sciences at the University of Nottingham; and the Computation Institute at the University of Chicago. The research was supported by grants from the National Institutes of Health, Charles B. Huggins, and the Royal Society.
CAPTION: When worms (Caenorhabditis elegans) ate the bacteria Pseudomonas aeruginosa that were raised on low levels of phosphates, unexpected large red spots appeared in their intestinal tracts. The worms then died, so researchers dubbed the condition "Red Death." They theorized that providing P. aeruginosa with phosphate would protect weakened or immunosuppressed hospital patients from this lethal pathogen.
Image courtesy of John Alverdy, University of Chicago Medical Center
Journal reference:
Zaborin et al. Red death in Caenorhabditis elegans caused by Pseudomonas aeruginosa PAO1. Proceedings of the National Academy of Sciences, 2009; DOI: 10.1073/pnas.0813199106
Adapted from materials provided by University of Chicago Medical Center, via EurekAlert!, a service of AAAS.

Genes From Tiny Algae Shed Light On Big Role Managing Carbon In World's Oceans

ScienceDaily (Apr. 10, 2009) — Scientists from two-dozen research organizations led by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Monterey Bay Aquarium Research Institute (MBARI) have decoded genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain its delicate balance in the oceans. These findings, from a team led by Alexandra Z. Worden of MBARI and published in the April 10 edition of the journal Science, will illuminate cellular processes related to algae-derived biofuels being pursued by DOE scientists.
The study sampled two geographically diverse isolates of the photosynthetic algal genus Micromonas—one from the South Pacific, the other from the English Channel. The analysis identified approximately 10,000 genes in each, compressed into genomes totaling about 22 million nucleotides. "Yet, surprisingly, they are far more diverse than we originally thought," said Worden. "These two picoeukaryotes, often considered to be the same species, only share about 90 percent of their genes."
To put this in perspective, humans and some primates have about 98 percent genes in common. Worden said that the algae's divergent gene complement may cause them to access and respond to the environment differently. "This also means that as the environment changes, these different populations will be subject to different effects, and we don't know whether they will respond in a similar fashion." She said that their apparently broad physiological range (exemplified by their expansive geographical range) may result in increased resilience as compared to closely related species, enabling them to survive environmental change better than organisms with a narrower geographic range. Testing the hypotheses developed through cataloging their respective inventory of genes, Worden said, will go a long way towards understanding their biology and ecology.
Algae were blazing the pathway of photosynthesis long before plants colonized land—so the results bear significantly on terrestrial plant research as well.
"Genome sequencing of Micromonas and the subsequent comparative analysis with other algae previously sequenced by DOE JGI and Genoscope [France], have proven immensely powerful for elucidating the basic 'toolkit' of genes integral not only to the effective carbon cycling capabilities of green algae, but to those they have in common with land plants," said Eddy Rubin, DOE JGI Director.
Tiny Micromonas, less than two microns in diameter, or roughly a 50th of the width of a human hair, are one of the few globally distributed marine algal species, thriving throughout the world's oceans from the tropics to the poles. They capture CO2, sunlight, water, and nutrients and produce carbohydrates and oxygen. Their productivity—which provides food resources within marine food webs—as well as their knack for capturing carbon, and influencing the carbon flux that may have bearing on climate change, make these algae keen target of study.
"Micromonas is a representative of a well-sampled group of green algae with the largest number of sequenced genomes. With these four genomes in hand--two Micromonas and two Ostreococcus--we can observe patterns of genome organization as well as the diversity between different organisms in this group," said JGI's Igor Grigoriev, one of the senior authors of the paper.
Embedded in the genetic code are clues about how photosynthesis transformed from a barren orb into the earth we know today.
"The Micromonas genomes encapsulate features that now appear to have been common to the ancestral algae that initiated the billion-year trajectory that led to the 'greening'—the rise of land plants—of the planet," said Worden. As highlighted in the Science article, comparing the strains to each other and in turn to the other characterized algal and plant genomes, will help to illustrate the dynamic nature of evolutionary processes and provide a springboard for unraveling the functional aspects of these and other phytoplankton populations.
Motility is another distinguishing aspect of the ecology of Micromonas. In the relatively viscous saltwater of the ocean, the flagellated Micromonas could give Michael Phelps a run for his money. Unlike other algae genera sequenced to date, these swift swimmers can cut through the water column at a rate of 50 body lengths per second, and are phototactic, meaning that they can swim towards the sunlight from which they derive their energy.
In previous studies, Worden and her colleagues showed that picoeukaryotes such as Micromonas comprised, on average, only a quarter of the picophytoplankton cells in a Pacific Ocean sampling, but were responsible for three-quarters of the net carbon production. They were also shown to be subject to heavy grazing pressure; their lack of a cell wall may make them more digestible as prey. In this case carbon may be efficiently sequestered by the "biological pump," the suite of processes that enable the algae to capture atmospheric carbon and transport it from the ocean surface zones to the depths below.
This research serves as a complement to field studies seeking to confirm emerging key players in global carbon fixation. "By understanding which genes a specific strain employs under certain conditions, we gain a view into the factors that influence the success of one group over another," Worden said. "We may then be able to develop models that could more effectively predict a range of possible future scenarios, that will result from current climate change." Micromonas may well serve as a bellwether for current and future ocean conditions, helping to guide appropriate decision making, which given the prevailing CO2 trends, is urgently needed.
The genome sequencing of Micromonas was conducted under the auspices of the DOE JGI Community Sequencing Program (CSP), supported by the DOE Office of Science.
Journal reference:
Worden et al. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science, 2009; 324 (5924): 268-272 DOI: 10.1126/science.1167222
Adapted from materials provided by DOE/Joint Genome Institute.

Life Sticks: Bioengineers' Sticky Insights Illuminate Biological Processes

ScienceDaily (Apr. 10, 2009) — Sticky is good. A University of California, San Diego bioengineer is the first author on an article in the journal Science that provides insights on the "stickiness of life." The big idea is that cells, tissues and organisms hailing from all limbs of the tree of life respond to stimuli using basic biological "modules."
For example, the researchers outlined similar strategies across biology for fulfilling the tasks of "sticking together" (cell-cell interactions), "sticking to their surroundings" (cell-extracellular matrix [ECM] interactions), and responding to forces.
Adam Engler, a bioengineering assistant professor from UC San Diego's Jacobs School of Engineering, is the first author of the Review article entitled "Multiscale Modeling of Form and Function" published in the 10 April issue of the journal Science. According to Engler, there is something inherent in the nature of the ever-present tasks of sticking together and responding to forces that causes common form and function to emerge. For example, even though the cells within bacteria, fungi, sponges, nematodes and humans do not use exactly the same proteins to stick together, all of these organisms rely on fundamental components of cell-cell adhesions for survival. For this reason, the capacity to form complex multilayer organisms through cell-cell interactions is likely based on the evolutionary advantage to adhere to new environments and survive in potentially hostile environments, the authors say.
The team also described a universal need for cells, tissues, organs and organisms to respond to forces. Two examples of very different biological structures that nevertheless rely on responsiveness to forces for proper function are leg bones and breast acini. Breast acini are hollow spherical objects at the ends of breast ducts that are made of a layer of cells that secrete milk proteins. Breast acini form hollow spheres, according to Engler, because this form maximizes the surface to volume ratio. When pressure builds up, acini can hold more and more volume until they need to push the milk proteins down the duct.
"This kind of structure is conserved in a variety of dissimilar systems that respond to forces in a manner similar," said Engler. The long bones of the human skeleton are another example, where their elongated and cylindrical form optimizes the distribution of body weight while remaining very light.

Thinking Wide

Engler hopes that the observations and connections he and his coauthors make regarding the ubiquitous need for vastly different cells, tissues, organs and organisms to use common biological modules will encourage other scientists and engineers to think beyond their specific areas of specialization.
"In our Science paper, I think we have arrived at an interesting way to describe known biological processes and bring concepts together that are traditionally not considered," said Engler. "I hope this paper will encourage researchers to interact with disciplines previously assumed to be dissimilar and foster new interdisciplinary interactions like we have here at UCSD with the Institute for Engineering in Medicine."
Engler's primary appointment is in the Department of Bioengineering at UC San Diego's Jacobs School of Engineering. The Department of Bioengineering ranks 2nd in the nation for biomedical engineering, according to the latest US News rankings. The bioengineering department has ranked among the top five programs in the nation every year for the past decade.
Engler has secondary appointments in Material Science and Biomedical Sciences. He is a member of the UCSD Stem Cell Institute and the UCSD Institute for Engineering in Medicine.
Engler is a bioengineer and mechanical engineer by training. He earned a Ph.D. in mechanical engineering from the University of Pennsylvania, and went on to a post doctoral fellowship in molecular biology at Princeton University before coming to UC San Diego in 2008. He is already involved in a number of interdisciplinary collaborations at UC San Diego.
One collaboration involves Engler, Shu Chien, who is University Professor of Bioengineering and Medicine, and Director of UC San Diego's Institute of Engineering in Medicine (IEM), and materials science professor Sungho Jin from the Jacobs School of Engineering's Mechanical and Aerospace Engineering (MAE) and NanoEngineering departments. In a January 2009 paper in the journal PNAS, researchers led by this team unveiled a new way to help accelerate bone growth through the use of nanotubes and stem cells. This new finding could lead to quicker and better recovery, for example, for patients who undergo orthopedic surgery.
Engler's lab recently began a collaboration with Rick Lieber, Ph.D., Professor and Vice Chair of UC San Diego's Department of Orthopedic Surgery and Director of the National Center for Skeletal Muscle Rehabilitation Research, based at UC San Diego. Lieber is also Senior Research Career Scientist at the Veterans Affairs San Diego Health System. The team is trying to uncover the cause of unexplained lower back pain in patients with no obvious disk degeneration, pinched nerves or other known causes of lower back pain.
"No matter what your area of expertise, there is someone that has a complementary area of expertise that can really help you ask new and interesting questions," said Engler.

Interdisciplinary Research

Mathematicians, engineers and stem cell biologists have not traditionally worked together, but these kinds of interdisciplinary collaborations have been the key to developing new techniques and new disciplines, explained Engler, who told a story of how his own dabbling into interdisciplinary research led to fruitful results.
As a graduate student, Engler helped put an experimental stem-cell-based surgical technique into a more appropriate mechanical context. The project began when he was approached by a surgeon puzzled by the results he was getting after injecting stem cells into damaged rat heart tissue in hopes of regenerating healthy heart tissue.
"As a matrix biologist and a mechanical engineer I said, 'Perhaps we need to look at what the host tissue is actually doing. What is being damaged and what is changing within the tissue due to the lack of oxygen?'" Engler and his collaborators found the cells in the damaged heart tissue were excreting collagen and making stiff scar tissue. "The engineer in me then analyzed the mechanical properties of the tissue and found out it was three to four times more rigid than the background healthy muscle. The biologist in me then characterized the cells in vitro and was able to show that these cells do respond to the mechanical properties of their environment."
Engler published his findings in 2006 in the high profile journal Cell and in the American Journal of Physiology. (Read New Scientist's description of Engler's findings.) One idea for improving such cell-based therapies, according to Engler, could involve injecting "smarter stem cells" that have been programmed to respond to some environmental stimuli but ignore other stimuli.

Journal reference:

Adam J. Engler, Patrick O. Humbert, Bernhard Wehrle-Haller, and Valerie M. Weaver. Multiscale Modeling of Form and Function. Science, 2009; 324 (5924): 208-212 DOI: 10.1126/science.1170107
Adapted from materials provided by University of California - San Diego, via EurekAlert!, a service of AAAS.