Thursday, May 27, 2010

How Microtubules Let Go of Their Attachments During Cell Division

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ScienceDaily (May 14, 2010) — Whitehead Institute researchers have determined a key part of how cells regulate the chromosome/microtubule interface, which is central to proper chromosomal distribution during cell division.

"This is the surveillance machinery that makes sure that the chromosomes are divided correctly between cells," says Whitehead Member Iain Cheeseman.

The findings are published in the journal Molecular Cell.

During cell division, the cell's DNA is consolidated into X-shaped chromosome pairs that align along the middle of the cell. Where the arms of the X cross, each chromosome has two kinetochores--protein complexes that facilitate microtubule attachment to the chromosome. As cell division progresses, these microtubules pull the right or left half of each chromosome towards the spindle poles to separate them to opposite ends of the cell.

Problems can frequently arise during this process. As a microtubule extends from a spindle pole, it may attach incorrectly to a kinetochore. When this happens, the cell needs a way to detect the mistake, detach the problematic microtubule, and reattach it correctly. If the issue is not addressed and cell division proceeds, the chromosomes typically fail to divide evenly, resulting in cells with the wrong number of chromosomes. This aberrant distribution of chromosomes can lead to cancer or premature cell death.

To correct attachment problems, cells rely on a system of phosphorylation -- the addition of a phosphate group to certain proteins -- to control whether or not microtubules stay bound to the kinetochore.

According to the Molecular Cell paper, the enzyme Aurora B resides within the inner kinetochore and adds phosphates to a key player in the kinetochore, called the KMN network, that attaches to the microtubule.

Aurora B's ability to phosphorylate a molecule wanes the farther that molecule is from the enzyme. In the case of a microtubule properly attached to the kinetochore, the microtubule's increased tension on the KMN network pulls the network taut and farther away from Aurora B, thereby reducing Aurora B's ability to phosphorylate the KMN network. If the microtubule is not correctly attached, the KMN network is not pulled away from Aurora B. The decreased distance lets Aurora B keep the KMN network phosphorylated, which destabilizes the microtubule's attachment to the kinetochore and allows the microtubule to detach and try again.

The KMN network is composed of several subunits arranged at different distances from Aurora B. Each subunit can be individually phosphorylated by Aurora B, which allows the attachment/detachment system to be controlled much like a dimmer rather than an on-off switch.

"This is a very sensitive system that allows the cell to dynamically respond to different attachment problems," says Julie Welburn, first author of the Molecular Cell paper and a postdoctoral researcher in the Cheeseman lab.

But for this system to function properly, phosphates also need to be removed from the KMN network to allow new microtubule attachments to form. In a recent Journal of Cell Biology article, the Cheeseman lab collaborated with researchers at the University of Pennsylvania to show that another enzyme, protein phosphatase 1 (PP1), counteracts Aurora B's activity. As tension increases at a properly attached microtubule, one KMN network subunit recruits PP1. PP1 then removes the phosphates from the molecules phosphorylated by Aurora B, thereby stabilizing the microtubule's attachment to the kinetochore. However, the recruitment of PP1 itself to kinetochores is controlled by Aurora B activity.

"I think it's really cool that this process is not a simple tug of war between adding a phosphate and taking it away," says Cheeseman, who is also an associate professor of biology at MIT. "But that PP1 itself is sensitive to the overall level of Aurora B activity. So, the higher the Aurora B activity, the lower the PP1 activity, and vice versa. It sets up this balance between them, so that you can switch between high phosphorylation and no phosphorylation very quickly."

Although the two papers clarify certain aspects of the microtubule interface, the picture is not yet complete.

"We're slowly finding the other targets in this process and understanding even better how this mechanism works to correct microtubule attachments," says Welburn.

This research was supported by the Smith Family Foundation, the Massachusetts Life Sciences Center, the Searle Scholars Program, and the National Institute Of General Medical Sciences.

Iain Cheeseman's primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at Massachusetts Institute of Technology.

Journal References:
1. Julie P.I. Welburn, Mathijs Vleugel, Dan Liu, John R. Yates, Michael A. Lampson, Tatsuo Fukagawa, Iain M. Cheeseman. Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochoremicrotubule interface. Molecular Cell, 2010; 38 (3): 383-392 DOI: 10.1016/j.molcel.2010.02.034
2. D. Liu, M. Vleugel, C. B. Backer, T. Hori, T. Fukagawa, I. M. Cheeseman, M. A. Lampson. Regulated targeting of protein phosphatase 1 to the outer kinetochore by KNL1 opposes Aurora B kinase. The Journal of Cell Biology, 2010; 188 (6): 809 DOI: 10.1083/jcb.201001006


Transcription Factor DksA Polices the Intersection of Replication and Transcription

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ScienceDaily (May 13, 2010) — DNA replication, the process by which a strand of DNA is copied during cell proliferation , and DNA transcription, the process by which the message in the DNA is translated into messenger RNA, involve the same "track" or DNA template. What happens when the two mechanisms are on the same track at the same time? Baylor College of Medicine researchers have identified the director -- the transcription factor DksA.

Dr. Jue D. (Jade) Wang, assistant professor of molecular and human genetics at Baylor College of Medicine, focuses her attention on replication -- the process by which a strand of DNA is copied during cell proliferation (growth and division).

Dr. Christophe Herman, also an assistant professor of molecular and human genetics at BCM, zeroes in on transcription -- the process by which the message in the DNA is translated into messenger RNA and ultimately the proteins that are workhorses of the cell.

Scientists in the two fields rarely communicate, but the two processes involve the same "track" or DNA template.

"What happens when two machines are on the same track but going in opposite directions?" said Wang. "These two processes are happening at the same time and use the same template."

Combining skills

The two laboratories combined their skills to answer that question and came up with a director -- the transcription factor DksA. A transcription factor is a protein that helps regulates expression (or the level) of gene activity.

A report on their work appears in the current issue of the journal Cell.

"We think this factor is one of the reason there are not more traffic jams," said Wang. "It is there to make sure that the traffic flows."

Director prevents conflict

Their experiments show that DksA acts on the process of transcription directly to prevent conflict between transcription and replication.

"The factor began our collaboration," said Herman. "We saw that it was regulating the process of transcription. It also tags along with RNA polymerase (the enzyme that prompts the process of making a strand of RNA from the DNA strand)."

When it sees the DNA polymerase (an enzyme critical to replication) come along, "it removes the RNA polymerase from the track," said Herman. That allows replication to take place and prevents the two "machines" from colliding.

The two did their work in a form of Escherichia coli (E. coli), a bacterium often used as a model organism in the laboratory. When DksA was not present in the bacteria, the cell was unstable, prompting a DNA damage response from halted replication.

"Stress can promote endogenous DNA damage," said Herman. Starvation is one method of such stress, he said. When DksA is present, it prevents disruption of replication and maintains the integrity of the DNA.

Findings raise questions

Previously, it was thought that the DNA polymerase simply knocked the RNA polymerase out of the way, said Herman.

"That is not the case. You need to have specific factors to remove the RNA polymerase," he said.

The findings raise as many questions as they answer, said Wang. Does the factor work before or after the enzymes collide?

"We don't know the mechanism yet," she said.

Others who took part in this work include Ashley K. Tehranchi, Matthew D. Blankschien, Yan Zhang, Jennifer Halliday, Anjana Srivatsan and Jia Peng, all of BCM.

Funding for this work came from a Human Frontier Young Investigator Grant, the Robert A. Welch Foundation and the National Institutes of Health.

Journal Reference:
Ashley K. Tehranchi, Matthew D. Blankschien, Yan Zhang, Jennifer A. Halliday, Anjana Srivatsan, Jia Peng, Christophe Herman, Jue D. Wang. The Transcription Factor DksA Prevents Conflicts between DNA Replication and Transcription Machinery. Cell, 2010; 141 (4): 595 DOI: 10.1016/j.cell.2010.03.036


Preventing Cells from Getting the Kinks out of DNA

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ScienceDaily (May 25, 2010) — Many standard antibiotics and anti-cancer drugs block the enzymes that snip the kinks and knots out of DNA -- DNA tangles are lethal to cells -- but the drugs are increasingly encountering resistant bacteria and tumors.

A new discovery by University of California, Berkeley, biochemists could pave the way for new research into how to re-design these drugs to make them more effective poisons for cancer cells and harmful bacteria.

"The development of the anti-bacterial and anti-tumor agents that target these enzymes thus far has been done entirely in the absence of any visualization of how these drugs actually interact with the protein itself. And they have done remarkably well," said James Berger, UC Berkeley professor of molecular and cell biology. "But we have increasing problems of resistance to these drugs. Being able to see how these drugs can interact with the enzyme and DNA is going to be critical to developing the next generation of therapeutics that can be used to overcome these resistance problems."

Berger and colleagues at Emerald BioStructues of Bainbridge Island, Wash., and Vanderbilt University in Nashville, Tenn., report their new findings in a paper appearing in the journal Nature.

The tangles in DNA, like those in a string of holiday lights, are a result of packing some six feet of DNA into a cell nucleus so small that it is invisible to the naked eye. Every time a cell divides, it has to unpack, duplicate and repack its DNA, generating about a million tangles among the newly-copied chromosomes in the process.

As Berger has shown in previous work, enzymes called topoisomerases home in on the sharp turns in a knot and then progressively snip the DNA, unloop it, and restitch it flawlessly. If, however, the enzyme slips up, that one snip can turn into a potentially mutagenic or cell-killing DNA break.

While the protein structure of these topoisomerases is known, the details of the chemical reactions that take place between the enzyme and DNA, and their reaction with the drugs that bind both, remain a mystery, Berger said. In fact, one of the main puzzles is why antibiotics like ciprofloxacin (Cipro) and anti-cancer drugs like etoposide, which vary widely in structure, have the same effect: jamming the enzyme and causing a break in the double-stranded DNA helix.

Berger and his colleagues found a way to obtain a picture that shows the interaction of the protein bound to DNA. The next step is to do the same for a drug bound to the protein/DNA complex, getting an image of exactly how these drugs interfere with the knot elimination machinery.

"The technique we used to trap this complex so that we could actually crystallize it and image it we think now gives us a handle on how to go after drug-bound complexes of human topoisomerases that have long eluded the field," said Berger, who also is a staff scientist at Lawrence Berkeley National Laboratory (LBNL).

The scientists' new picture of the enzyme bound to DNA also turned up something totally unexpected. Most enzymes that bind DNA to snip or stitch it together use two metal ions -- typically two magnesium ions -- to catalyze the reaction. Berger found that type II topoisomerases, which target double-stranded DNA, make use of only one of their two magnesium ions and instead use the amino acid arginine as their second catalytic center. The second magnesium merely provides structural integrity to the protein.

"We stumbled upon a new kind of cleavage mechanism for DNA, an example of a protein that uses a completely new approach for the same mechanism," Berger said. "It speaks to the evolutionary plasticity and adaptability of nature that continuously amazes us with finding new ways to carry out reactions that it needs to perform."

Berger now plans to use his trick to trap the enzyme on a short segment of DNA, allowing him to collect enough to crystallize and analyze in an X-ray beam from LBNL's Advanced Light Source, to trap both drug and enzyme on DNA. Once crystallized and imaged, he will have the first full picture of a topoisomerase interacting the way it does in a real cancer cell or microbe.

Berger's co-authors are UC Berkeley graduate student Bryan H. Schmidt; chemist Alex B. Burgin of Emerald BioStructures; and biochemists Joseph E. Deweese and Neil Osheroff of Vanderbilt University School of Medicine. The X-ray crystallography of the protein/DNA complex was conducted in Stanley Hall at the UC Berkeley branch of the California Institute for Quantitative Biosciences (QB3), with which Berger is affiliated.

The work was funded by grants from the National Cancer Institute of the National Institutes of Health, including some funds administered through the American Recovery and Reinvestment Act (ARRA) of 2009.

Journal Reference:
Bryan H. Schmidt, Alex B. Burgin, Joseph E. Deweese, Neil Osheroff, James M. Berger. A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature, 2010; DOI: 10.1038/nature08974


Gene Causes Blue Light to Have a Banana Odor in Fruit Flies

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ScienceDaily (May 26, 2010) — Scientists at Germany's Ruhr-Universitaet-Bochum have succeeded to genetically modify Drosophila (fruit fly) larvae allowing them to smell blue light.

The research team can activate single receptor neurons out of 28 olfactory neurons in the larvae for this sensory perception. Normally animals avoid light. However, blue light simulates in genetically modified larvae the smell of an odorant, e.g., banana, marzipan or glue -- odors which are all present in rotting fruit and attractive to fruit fly larvae. The team of scientists from Bochum and Gottingen, working under the auspices of Prof. Klemens Stortkuhl, hopes to gain insight into the processing of the neural network. They have published their findings in the journal Frontiers in Neuroscience Behavior.

Light has a “tasty” odor

The olfactory neurons of the only one millimeter sized genetically modified Drosophila larvae are all capable of producing the protein that is activated by light. The researchers can freely select which of the 28 cells will ultimately be light-sensitive using genetic markers. Prof. Stortkuhl explained that they were able to either activate cells which normally register repulsive odors and subsequently cause an aversion response, or cells that sense attractive odors such as banana, marzipan or glue. The activated neurons send an electrical signal if they are stimulated with blue light at a wavelength of 480 nm. The larva thus has the impression that it perceives odors. The experiment shows that it is possible by inserting photo activated proteins into neurons photo stimulation can produce an olfactory behavior in these larvae , whereas genetically unchanged larvae generally avoid light.

Animals are not hurt

Moreover, the researchers could measure the effect electrophysiologically. Thin electrodes can detect the signal of the light-activated neurons. The transmission of the nerve signal can be followed all the way into the brain, thus enabling non-invasive observation of neural networks. Prof. Stortkuhl pointed out that this method has the great advantage of enabling tests to be carried out on living animals without an injury. The research scientists hope to gain an insight into the network and mode of action of the brain. It must moreover be pointed out that the olfactory sense of the genetically modified fly larvae remains normal.

Same principle applies to other animals

The researchers now plan to use the same principle to undertake further studies on adult Drosophila, equipping them with photo-activated proteins to cause targeted isolated cerebral neurons to react. These successfully employed methods are now also being used in model systems i.e. mice in other laboratories including a work group at the RUB, to investigate similar issues using mice.

Journal Reference:
Bellmann D, Richardt A, Freyberger R, Nuwal N, Schwarzel M, Fiala A and Stortkuhl KF. Optogenetically induced olfactory stimulation in Drosophila larvae reveals the neuronal basis of odor-aversion behavior. Frontiers in Neuroscience Behavior, 2010; 4 (27) DOI: 10.3389/fnbeh.2010.00027


New Method for Producing 'Libraries' of Important Carbohydrate Molecules

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ScienceDaily (May 24, 2010) — Scientists some years back found ways to automate the production of DNA and proteins, making studies of these essential components of life far easier. With complex carbohydrates, it's been a different story.

Until now, the construction of so-called "libraries" of carbohydrate molecules for biological study has been slow and tedious. In what may change all that, a team of scientists from the University of Georgia has created a method for the rapid chemical synthesis of complex carbohydrates, and that method could dramatically change the availability of such molecules for research.

"In the past, it has simply taken too long to make these molecules, and it has held back progress in the field," said Geert-Jan Boons, Franklin Professor of Chemistry and director of the research. "Now, we have a new method of synthesis that will make well-defined molecules available for in-depth study."

The method was reported May 23 in the journal Nature Chemistry.

Other authors of the paper, all from UGA when the work was done, include doctoral students Thomas Boltje and Jin Park and postdoctoral associate Jin-Hwan Kim. The team is part of the Complex Carbohydrate Research Center at UGA, and Boons' appointment in chemistry is part of the Franklin College of Arts and Sciences.

The work was sponsored by the National Institute of General Medicine Sciences of the National Institutes of Health.

"The emerging field of glycomics has been severely hampered by a lack of robust, well-defined libraries of carbohydrate molecules, which are greatly needed to decipher the 'carbohydrate codes' used by cells for processes such as cell signaling, embryogenesis and neuronal development," said Pamela Marino, director of the glycobiology portfolio at the NIH's National Institute of General Medical Sciences. "Dr. Boons has established important new methodology for the rapid synthesis of complex oligosaccharides in a manner amenable to automation, moving the field a step closer to achieving automated synthesis of complex sugars."

Glycomics is the study of complete sets of complex carbohydrate structures expressed by specific cells, tissues or organisms. It examines the role of these molecules in areas such as physiology, genetics and disease pathology.

The stakes in being able to study and understand the function of oligosaccharides, chains of simple sugars found on the cell surface of all plant and animal cells, are immense. They are involved in such cellular processes as protein folding, the regulation of cell signaling, and fertilization. These complex carbohydrates also are being recognized by pathogens during infection, help control immune cell response and have a role in the development of cancer and autoimmune diseases.

The problem is that building carbohydrate chains for biological study has been difficult at best and slow. Unlike DNA, which can be induced to replicate itself millions of times in a laboratory for study, these compounds must be built a molecule at a time, and, even worse, they can be "linked" in different ways, making chemical bonding problematical at best. The problems associated with how to build carbohydrates in the lab go back more than a century.

Although there has been, according to the scientists, "tremendous progress" in chemical or enzymatic approaches used to build the compounds, it is "still very time-consuming, and it not uncommon that the preparation of a single, well-defined derivative can take as long as a year."

The new method offers the promise of cutting that time to hours because the procedures allow scientists to eliminate intermediate purification steps and will be amenable to automation.

"One of the ways to understand the problems we've had is that while DNA and proteins are linear molecules in which the nucleoside or amino acid building blocks are linked together one way, carbohydrates are branched, and they can be linked in two different ways," said Boons. "And it's very hard to control the configuration of these linkages in the laboratory. And that is essential if we are to find ways to build these new libraries of molecules for study."

The new method in the Nature Chemistry paper allows researchers to control the configuration of these linkages and install various branching points, making it much easier to synthesize these carbohydrate molecules without intermediate purifications.

To see how well the new method works, the team chose the important carbohydrates glucose and galactose to study, and the results for both showed that the method is sound, rapid and potentially important for the construction of complex carbohydrate molecules to study. Further research will confirm that the method will work on other complex carbohydrates, but all indications now are that it will.

Journal Reference:
Thomas J. Boltje, Jin-Hwan Kim, Jin Park & Geert-Jan Boons. Chiral-auxiliary-mediated 1,2-cis-glycosylations for the solid-supported synthesis of a biologically important branched α-glucan. Nature Chemistry, 2010; DOI: 10.1038/nchem.663


Bioengineers Say Cellular Workouts Strengthen Endothelial Cells' Grasp

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ScienceDaily (May 14, 2010) — University of Pennsylvania bioengineers have demonstrated that the cells that line blood vessels respond to mechanical forces -- the microscopic tugging and pulling on cellular structures -- by reinforcing and growing their connections, thus creating stronger adhesive interactions between neighboring cells.

Adherens junctions, the structures that allow cohesion between cells in a tissue, appear to be modulated by endothelial cell-to-cell tugging forces. Both the size of junctions and the magnitude of tugging force between cells grow or decay in concert with activation or inhibition of the molecular motor protein myosin.

The findings extend the understanding of multi-cellular mechanics. The dynamic adaptation of cell-cell adhesions to forces may explain how cells can maintain multi-cellular integrity in the face of different mechanical environments. Understanding how forces affect cell-cell adhesion could provide new opportunities for therapies targeting acute and chronic dysfunction of blood vessels.

Because these adhesions between endothelial cells are what allow these cells to form a tight seal between the blood inside vessels and the surrounding tissues, the research also suggests that changes in mechanical forces might induce endothelial cells to modulate the "tightness" of adhesions with each other, which may then modify the permeability of blood vessels. In many disease states, such as septic shock, diabetes and in tumor vasculature, endothelial cells fail to form the type of tight adhesions with each other that are necessary to prevent the vessels from leaking into the surrounding tissue.

It is known that myosin activity is required for cell-generated contractile forces and that myosin affects cellular organization within tissues through the generation of mechanical forces against the actin cytoskeleton; however, whether forces drive changes in the size of cell-cell adhesions remained an open question. The team demonstrated that, when "exercised," the actomyosin cytoskeleton in a pair of cells can generate substantial tugging force on adherens junctions, and, in response, the junctions grow stronger. To prove a causal relationship, the group showed that exogenous forces, applied through a micromanipulator, also cause junction growth. This study marks the first time cell-generated forces at the adherens junction have been measured.

To investigate the responsiveness of adherens junctions to tugging force, bioengineer Chris Chen and his laboratory adapted a system of microfabricated force sensors to determine quantitative measurements of force and junction size. Researchers fabricated microneedles (3 microns wide, 9 microns tall, or one-fiftieth the size of a human hair) from a rubber polymer, polydimethylsiloxane, and coated them with an adhesive protein to allow cell attachment. This adhesive protein was transferred to the microneedle substrates in "bowtie patterns" which coaxed the cells to form pairs of cells with a single, cell-cell contact between them. Each cell in the pair attached to about 30 microneedles, and the researchers were able to measure the deflection of the needles as cells exerted traction (inward pulling) forces. The deflection of the needles was proportional to the amount of force generated by the structure.

"The role that physical forces play in cellular behavior has become better understood over the last ten years," said Chen, the Skirkanich Professor of Innovation in bioengineering in the School of Engineering and Applied Science at Penn. "Now we know that cell structures under mechanical stress don't necessarily break; they reinforce. Unlike passive adhesion such as with glue or tape, the cell-matrix and cell-cell adhesions that cells use as footholds to attach to surfaces and each-other are adaptive; when they experience force, they hold on tighter."

In prior research, Chen's team has demonstrated that the push and pull of cellular forces drives the buckling, extension and contraction of cells during tissue development. These processes ultimately shape the architecture of tissues and play an important role in coordinating cell signaling, gene expression and behavior, and they are essential for wound healing and tissue homeostasis in adult organisms.

This study was conducted by Chen, Zhijun Liu, Daniel M. Cohen, Michael T. Yang, Nathan J. Sniadecki and Sami Alom Ruiz of the Department of Bioengineering at Penn and John L. Tan and Celeste M. Nelson of the Johns Hopkins School of Medicine.

The research, published in the current issue of the journal Proceedings of the National Academy of Sciences, was funded by grants from the National Institutes of Health, Material Research Science and Engineering Center, Center for Engineering Cells and Regeneration of the University of Pennsylvania and Whitaker Foundation.

Journal Reference:
Z. Liu, J. L. Tan, D. M. Cohen, M. T. Yang, N. J. Sniadecki, S. A. Ruiz, C. M. Nelson, C. S. Chen. Mechanical tugging force regulates the size of cell-cell junctions. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0914547107


Development of Hands and Wings: Protein Pentagone Important

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ScienceDaily (May 14, 2010) — Whether we are talking about our own hand or something seemingly so distant from an evolutionary perspective as the wings of an insect: In order to make an organ out of a multitude of cells, the cells have to know where they are during the development of the still growing organ. Cells use this information to decide whether, for instance, they will later become a part of the thumb or the pinky finger. It has long been known that cells receive information on their position as well as growth stimuli from signaling molecules present in the cell tissue, so-called morphogens -- real jacks of all trades, which are put to work again and again in the course of development. They are only produced by a small group of cells and have the ability to spread across the cell tissue in the form of a concentration gradient.

As signaling molecules, morphogens can switch genes on or off, even in distant cells. The decisive factor is that morphogens can regulate the activity of different genes depending on their concentration. In this way, they help to produce different gene products which determine which part of an organ will develop in each region during development.

In order to do this, morphogens need to be able to move around in the tissue while at the same time fulfilling their role as signaling molecules. They achieve the latter by binding to receptors, where they switch genes on and off. Since morphogens cannot spread any further once bound to receptors, there must be regulatory mechanisms which counter the effect of the receptor binding but do not completely inhibit the signaling.

A research team led by Dr. Georgios Pyrowolakis from the Institute of Biology I has discovered a mechanism of this kind in a study conducted on the fruit fly drosophila melanogaster. The results of the study have now been published in an article entitled "Control of Dpp Morphogen signalling by a secreted feedback regulator" in the online version of the journal Nature Cell Biology. The contributors to the study are Dr. Robin Vuilleumier, Alexander Springhorn, Stefanie Koidl, and Dr. Giorgos Pyrowolakis from the Institute of Biology I of the University of Freiburg as well as Prof. Dr. Markus Affolter from the Biozentrum in Basel and Prof. Dr. Matthias Hammerschmidt and Dr. Lucy Patterson from the University of Cologne.

The scientists conducted experiments on the wing precursor of the fruit fly, in which a morphogen called „Dpp" is active. They discovered the extracellular protein pentagone, which helps Dpp to spread and maintain the balance between mobility and receptor binding. If pentagone is not available, Dpp remains close to where it was produced and is involved more intensively in the signaling process. This leads to defective growth and the loss of parts of organs.

Interestingly, Dpp switches off the gene coded for pentagone directly through signaling. Pentagone is thus only produced in cells which are distant enough from the region in which Dpp is produced. It then spreads out toward the Dpp source, helping Dpp to gain mobility by way of an interaction with the extracellular matrix. As the authors were able to demonstrate in their experiments, the negative regulation of the pentagone genes is essential for the correct formation of the Dpp gradients. Moving the pentagone synthesis to other regions of the wing precursor and thus separating it from the Dpp signaling will lead to disproportions in the wings.

So why does the Dpp switch off the genes which help it to be mobile and effective over long distances? This tactic could be the key to the robustness of a gradient which needs to be in the position to counteract any fluctuations that may occur in the morphogen production rate or mobility during organ development. Too much Dpp would lead to less pentagones and thus to decreased mobility of the morphogen. A shortage of Dpp, on the other hand, would result in increased pentagone production but would be compensated by the resulting increase in Dpp mobility. This would mean that cells are equipped with a system which allows them to monitor the form of the morphogen gradient continuously and correct irregularities. Initial evidence points to an evolutionary conservation of this system.

Journal Reference:
Vuilleumier et al. Control of Dpp morphogen signalling by a secreted feedback regulator. Nature Cell Biology, 2010; DOI: 10.1038/ncb2064


Stem Cells Use GPS to Generate Proper Nerve Cells

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ScienceDaily (May 12, 2010) — An unknown function that regulates how stem cells produce different types of cells in different parts of the nervous system has been discovered by Stefan Thor, professor of Developmental Biology, and graduate students Daniel Karlsson and Magnus Baumgardt, at Linkoping University in Sweden. The results improve our understanding of how stem cells work, which is crucial for our ability to use stem cells to treat and repair organs. The findings are publishing next week in the online, open-access journal PLoS Biology.

Stem cells are responsible for the creation of all cells in an organism during development. Previous research has shown that stem cells give rise to different types of cells in different parts of the nervous system. This process is partly regulated by the so-called Hox genes, which are active in various parts of the body and work to give each piece its unique regional identity -- a kind of GPS system of the body. But how does a stem cell know that it is in a certain region? How does it read the body's "GPS" signals? And how is this information used to control the creation of specific nerve cells?

In order to address these issues, the LiU researchers studied a specific stem cell in the nervous system of the fruit fly. It is present in all segments of the nervous system, but it is only in the thorax, or chest region, that it produces a certain type of nerve cell. To investigate why this cell type is not created in the stomach or head region they manipulated the Hox genes' activity in the fly embryo.

It turned out that the Hox genes in the stomach region stop stem cells from splitting before the specific cells are produced. In contrast, the specific nerve cells are actually produced in the head region, but the Hox genes turn them into another, unknown, type of cell. Hox genes can thus exert their influence both on the genes that control stem cell division behaviour and on the genes that control the type of nerve cells that are created.

"We constantly find new regulating mechanisms, and it is probably more difficult than previously thought to routinely use stem cells in treating diseases and repairing organs, especially in the nervous system," says Thor.

This work was supported by the Swedish Research Council, by the Swedish Strategic Research Foundation, by the Knut and Alice Wallenberg foundation, by the Swedish Brain Foundation, by the Swedish Cancer Foundation, and by the Swedish Royal Academy of Sciences to ST.

Journal Reference:
Daniel Karlsson, Magnus Baumgardt, Stefan Thor. Segment-Specific Neuronal Subtype Specification by the Integration of Anteroposterior and Temporal Cues. PLoS Biology, 2010; 8 (5): e1000368 DOI: 10.1371/journal.pbio.1000368


How Botulism-Causing Toxin Can Enter Circulation

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ScienceDaily (May 11, 2010) — New research in the Journal of Cell Biology helps explain how the toxic protein responsible for botulism can enter circulation from the digestive system.

The study appears online May 10.

Botulism, a rare but serious paralytic illness, is caused by botulinum neurotoxin (BoNT), an extremely toxic protein that is produced by the bacterium Clostridium botulinum. In food-borne botulism, the nontoxic components of BoNT -- including hemagglutinin (HA) -- protect the toxin from the low pH and enzymes encountered in the digestive tract. BoNT then passes through the intestinal epithelial barrier to enter circulation from the gut.

Although studies have examined how BoNT crosses the intestinal epithelial barrier, the mechanism by which it accomplishes this feat has remained a mystery. In this study, a team of Japanese researchers led by Yukako Fujinaga shows that HA plays a role. HA binds epithelial cadherin (E-cadherin), disrupting E-cadherin-mediated cell-to-cell adhesion and thereby disrupting the epithelial barrier.

Interestingly, the research demonstrates a species-specific interaction between HA and E-cadherin. Although HA binds human, bovine, and mouse E-cadherin, for instance, it does not bind rat or chicken.

Journal Reference:
Yo Sugawara, Takuhiro Matsumura, Yuki Takegahara, Yingji Jin, Yoshikazu Tsukasaki, Masatoshi Takeichi, Yukako Fujinaga. Botulinum hemagglutinin disrupts the intercellular epithelial barrier by directly binding E-cadherin. Journal of Cell Biology, 2010; DOI: 10.1083/jcb.200910119


Friday, May 21, 2010

Scientists 'Boot Up' a Bacterial Cell With a Synthetic Genome

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ScienceDaily (May 20, 2010) — Scientists have developed the first cell controlled by a synthetic genome. They now hope to use this method to probe the basic machinery of life and to engineer bacteria specially designed to solve environmental or energy problems.

The study will be published online by the journal Science, at the Science Express website, on May 20.

The research team, led by Craig Venter of the J. Craig Venter Institute, has already chemically synthesized a bacterial genome, and it has transplanted the genome of one bacterium to another. Now, the scientists have put both methods together, to create what they call a "synthetic cell," although only its genome is synthetic.

"This is the first synthetic cell that's been made, and we call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer," said Venter.

"This becomes a very powerful tool for trying to design what we want biology to do. We have a wide range of applications [in mind]," he said.

For example, the researchers are planning to design algae that can capture carbon dioxide and make new hydrocarbons that could go into refineries. They are also working on ways to speed up vaccine production. Making new chemicals or food ingredients and cleaning up water are other possible benefits, according to Venter.

In the Science study, the researchers synthesized the genome of the bacterium M. mycoides and added DNA sequences that "watermark" the genome to distinguish it from a natural one.

Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.

The scientists then transplanted the synthetic M. mycoides genome into another type of bacteria, Mycoplasm capricolum. The new genome "booted up" the recipient cells. Although fourteen genes were deleted or disrupted in the transplant bacteria, they still looked like normal M. mycoides bacteria and produced only M. mycoides proteins, the authors report.

"This is an important step we think, both scientifically and philosophically. It's certainly changed my views of the definitions of life and how life works," Venter said.

Acknowledging the ethical discussion about synthetic biology research, Venter explained that his team asked for a bioethical review in the late 1990s and has participated in variety of discussions on the topic.

"I think this is the first incidence in science where the extensive bioethical review took place before the experiments were done. It's part of an ongoing process that we've been driving, trying to make sure that the science proceeds in an ethical fashion, that we're being thoughtful about what we do and looking forward to the implications to the future," he said.

This research was funded by Synthetic Genomics, Inc. Three of the authors and the J. Craig Venter Institute hold Synthetic Genomics, Inc. stock. The J. Craig Venter Institute has filed patent applications on some of the techniques described in this paper.

More information can be found on the J. Craig Venter Institute web site at:

Journal Reference:
Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science, May 20, 2010 DOI: 10.1126/science.1190719


Sunday, May 9, 2010

Understanding Proteins: Molecular Probe Tracks Changes in Chemical Bonds Using Spectroscopy

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ScienceDaily (Apr. 30, 2010) — Proteins are the molecular machines of our cells. In order to understand how they function, it is necessary to follow the changes they bring about at a molecular level. This may be done by way of infrared spectroscopy, or more specifically so-called Fourier transform (FTIR) spectroscopy, which can measure the vibrations of the individual chemical bonds in a protein and the changes that take place in them while the protein works. However, an FTIR spectrum of a typical protein consists of several thousand vibrations which overlap and interfere with one another, making it extremely difficult to isolate the series of vibrations responsible for effecting the changes.

An international team of biophysicists including PD Dr. Reiner Vogel and Dr. Ekaterina Zaitseva at the Institute of Molecular Medicine and Cell Research of the University of Freiburg as well as Shixin Ye and Thomas P. Sakmar in New York and Xavier Deupi in Barcelona has now succeeded in introducing a molecular probe into a protein and tracking the changes caused by it in detail using spectroscopy. Whereas the proteins in our cells are usually composed of a narrowly defined repertoire of building blocks, the amino acids, these cells were compelled to integrate a component introduced artificially by the scientists. This artificial building block, p-azido-phenylalanine, was tailored to the spectroscopic methods and carries a so-called azido group composed of three nitrogen atoms which is absorbed in an isolated spectral area and is thus not affected by other vibrations. The scientists applied this technique to the light receptor rhodopsin, a membrane protein in the sensory cells of the retina which is responsible for sight.

When rhodopsin absorbs a photon, it passes through a series of transitional stages, so-called intermediates, in which the changes induced by the light reaction within the receptor spread successively until the receptor is finally fully activated, after which it can activate subsequent elements in the signal transmission chain. With the help of the newly developed technique the scientists were able to analyze these structural changes within the individual intermediates more closely than ever before. In their article in the current issue of the journal Nature, they demonstrate among other things that the movements of complete structural elements appear much earlier after the absorption of light than previously assumed. The biophysicists are confident that their findings on rhodopsin will also impact our understanding of the activation of other receptors. Its sensitivity to electrostatic change will make this new technique an important new component in the repertoire of biophysics methods.

Journal Reference:
Shixin Ye, Ekaterina Zaitseva, Gianluigi Caltabiano, Gebhard F. X. Schertler, Thomas P. Sakmar, Xavier Deupi, Reiner Vogel. Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature, 2010; 464 (7293): 1386 DOI: 10.1038/nature08948


Our Genes Can Be Set on Pause: Embryonic Stem Cells Reveal Oncogene's Secret Growth Formula

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ScienceDaily (Apr. 29, 2010) — New evidence in embryonic stem cells shows that mammalian genes may all have a layer of control that acts essentially like the pause button on your DVR. The researchers say the results show that the pausing phenomenon, previously thought to be a peculiarity of particular genes, is actually a much more general feature of the genome.

The findings are reported in the April 30th issue of the journal Cell, a Cell Press publication.

"We're coming to the realization that we've been missing out on an entire second step in the control of gene expression," said Richard Young of the Whitehead Institute and Massachusetts Institute of Technology. "There's tremendous excitement," he said, and some healthy debate too.

Notably, Young's team has shown that the infamous cancer gene known as c-Myc plays a major role in the pause release of many genes throughout the genome. Their fundamentally important findings may therefore ultimately have practical application in the treatment of some of the nastiest cancers, according to the researchers.

For decades, scientists have known that transcription is controlled by the recruitment of DNA binding factors to promoters, where they act as a kind of molecular Velcro for the polymerase enzymes that copy DNA into the mRNA templates for proteins, Young explains. "We still believe that's true," he said. "The surprise is that's only the first step."

They've now shown that other players cause the recruited polymerases to freeze in their places -- in effect pausing gene activity. It is the job of still other transcription factors to act as a pause release.

As evidence for the importance of the pausing function, a genome-wide analysis of embryonic stem cells showed that the bulk of polymerases can be found adjacent to promoters at any given time, even when the genes in question are some of the most actively transcribed. Pause factors (known as DSIF and NELF) are usually there too, consistent with the notion that they bind the enzyme after it has only just gotten started transcribing the DNA. The interactions of still other players, including one that is recruited by the transcription factor c-Myc, must then release the pausing for the genes to come back 'on'.

Young said he initially thought the pausing process might be fairly unique to embryonic stem cells, but he doesn't think so any more. When they began the study, they also expected the embryonic cells would show this sort of pausing at select developmental genes only. Instead, they found that polymerase was paused at about 75 percent of all promoters.

"We found it was occurring everywhere -- at all genes," Young said. "The polymerases come for a visit and then they pile up downstream of the promoter." They make only a very small stretch of RNA before they stop, awaiting the signal to continue. Some of the paused polymerases appear to remain in their suspended state indefinitely, he says.

Young said he thinks this second layer of control likely offers cells some added flexibility. In some cases, he notes, this sort of pausing seems to allow a rapid response to particular cues. The pause function might also be necessary, he says, because polymerases can be surprisingly sloppy in doing their jobs. The enzymes will often transcribe in two directions, one of them clearly backwards.

"It's a little clueless," Young said. "Pause control may be a way of ensuring that transcription continues only in the correct direction, and at real genes instead of willy-nilly."

Although Young is not an expert in cancer, he says that the connection of this pausing process to c-Myc could make some waves.

"Myc is so important in cancer," he says, noting that Myc is implicated in at least 15 percent of human cancers including some of those that are the toughest to get rid of and that tend to come back. There is some evidence in mice that shutting Myc down can lead cancer cells to shrivel up and die, but Myc itself isn't an ideal drug target.

"Now we know what Myc does and we know the kinase it recruits," Young said. That's key because kinases often do make good drug targets.

The new findings therefore offer new insight into how Myc works and a new rationale and strategy for trying to shut it down as a way to treat cancer. Young said there is surely a lot more to learn about pause control and its release too, with potentially other implications for human disease.

The researchers include Peter B. Rahl, Whitehead Institute for Biomedical Research, Cambridge, MA; Charles Y. Lin, Whitehead Institute for Biomedical Research, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA; Amy C. Seila, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA; Ryan A. Flynn, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA; Scott McCuine, Whitehead Institute for Biomedical Research, Cambridge, MA; Christopher B. Burge, Massachusetts Institute of Technology, Cambridge, MA; Phillip A. Sharp, Massachusetts Institute of Technology, Cambridge, MA, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA; and Richard A. Young, Whitehead Institute for Biomedical Research, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA.

Journal Reference:
Peter B. Rahl, Charles Y. Lin, Amy C. Seila, Ryan A. Flynn, Scott McCuine, Christopher B. Burge, Phillip A. Sharp, Richard A. Young. c-Myc regulates transcriptional pause release. Cell, 2010; 141 (3): 432-445 DOI: 10.1016/j.cell.2010.03.030


Saturday, May 8, 2010

Chromosome 'Glue' Surprises Scientists

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ScienceDaily (May 7, 2010) — Proteins called cohesins ensure that newly copied chromosomes bind together, separate correctly during cell division, and are repaired efficiently after DNA damage. Scientists at the Carnegie Institution have found for the first time that cohesins are needed in different concentrations for their different functions. This discovery helps to explain how certain developmental disorders, such as Cornelia de Lange and Roberts Syndrome arise without affecting cell division essential to development. The research was made possible by a new technique developed by the scientists for membrane-bound cells (called eukaryotes), which enables scientists to gradually reduce the concentration of a protein in living cells.

The paper, published on line May 6, and in the May 25, 2010, print edition of Current Biology, opens the door to a better understanding of developmental disorders and to the study of other proteins with multiple functions.

"One of the biggest surprises is that only a small amount of cohesin, the protein 'glue' that keeps replicated chromosomes bound together, is needed for the cell division process and that's what we think cohesin's primary role is," said lead author Jill Heidinger-Pauli at Carnegie's Department of Embryology.

A cell has a four-phase life cycle: growth, synthesis, growth, and mitosis. During the synthesis phase, DNA inside the cell's nucleus is duplicated and two identical daughter chromosomes called sister chromatids result. These twins must remain connected until the cell is ready to divide. This moment occurs in the last step of the cell cycle, the mitosis phase, where chromosomes condense, and fibrous structures called spindles form. Cohesin keeps the sisters properly glued until it is time for the spindles to pull the sisters to opposite sides of the cell. The cell then separates into two, resulting in two genetically identical cells. Cohesin is also important for other processes outside of cell division. Cohesin plays a critical role in DNA condensation and the repair of DNA damage. Cohesin facilitates efficient DNA repair by gluing sister chromatids together so that if the DNA of one sister is damaged, the other sister can be used as a template for repair. This is critical for preventing the loss of genetic information.

To monitor how much cohesin is needed for these different processes, the researchers exploited a genetic trick which lets a stop codon occasionally code for an amino acid. A codon is a set of three DNA bases that codes either for a particular amino acid or stops the translation (the reading) of the DNA sequence. If the translation process is halted prematurely due to the insertion of a stop codon, a fully functional protein can't be formed. The researchers inserted one or more stop codons early into a DNA sequence that codes for a cohesin protein. Normally this would result in the death of the cell, but the researchers had inserted another mutation, called SUP53, into the cell which resulted in the occasional production of full length cohesin protein. This method resulted in reduced production of cohesin, but did not change the timing of when cohesin was made, or its amino acid sequence.

"We found that DNA repair, chromosome condensation, and the stability of repeat sequences of DNA were all compromised by decreasing cohesion to 30% of normal levels," remarked Heidinger-Pauli. Interestingly, sister-chromatid cohesion and chromosome segregation were not affected even with levels at only 13% of normal. We also looked at how reducing the amount of cohesin changes how it interacts with chromosomes. Normally cohesin binds to regions throughout chromosomes, but we found that when cells only had a small amount of cohesin, cohesin preferentially binds to the center of chromosomes. We didn't know that this hierarchy existed before, and it helps explain why some cohesin functions might be more affected than others."

Journal Reference:
Jill M. Heidinger-Pauli, Ozlem Mert, Carol Davenport, Vincent Guacci, and Douglas Koshland. Systematic Reduction of Cohesin Differentially Affects Chromosome Segregation, Condensation, and DNA Repair. Current Biology, May 6, 2010 DOI: 10.1016/j.cub.2010.04.018


New Nerve Cells -- Even in Old Age: Researchers Find Different Types of Stem Cells in the Brains of Mature and Old Mice

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ScienceDaily (May 9, 2010) — After birth the brain loses many nerve cells and this continues throughout life -- most neurons are formed before birth, after which many excess neurons degenerate. However, there are some cells that are still capable of division in old age -- in the brains of mice, at least. According to scientists from the Max Planck Institute of Immunobiology in Freiburg, different types of neuronal stem cells exist that can create new neurons. While they divide continuously and create new neurons in young animals, a large proportion of the cells in older animals persist in a state of dormancy. However, the production of new cells can be reactivated, for example, through physical activity or epileptic seizures. What happens in mice could also be applicable to humans as neurons that are capable of dividing also occur in the human brain into adulthood.

The research is published in the journal Cell Stem Cell.

You can't teach an old dog new tricks. The corresponding view that the brain loses learning and memory capacity with advancing age prevailed for a long time. However, neuronal stem cells exist in the hippocampus -- a region of the brain that plays a central role in learning and memory functions -- that can produce new nerve cells throughout life. It is known from tests on mice that the newly formed cells are integrated into the existing networks and play an important role in the learning capacity of animals. Nonetheless, the formation of new cells declines with age and the reasons for this were unknown up to now.

Together with colleagues from Dresden and Munich, the Freiburg researchers have now succeeded in explaining for the first time why fewer new neurons are formed in the adult mouse brain. They managed to identify different populations of neuronal stem cells, thereby demonstrating that the hippocampus has active and dormant or inactive neuronal stem cells. "In young mice, the stem cells divide four times more frequently than in older animals. However, the number of cells in older animals is only slightly lower. Therefore, neuronal stem cells do not disappear with age but are kept in reserve," explains Verdon Taylor from the Max Planck Institute of Immunobiology.

The precise factors that influence the reactivation of dormant stem cells are not yet clear. The cells can, however, be stimulated to divide again. The scientists observed more newborn hippocampal neurons in physically active mice than in their inactive counterparts. "Consequently, running promotes the formation of new neurons," says Verdon Taylor. Pathological brain activity, for example that which occurs during epileptic seizures, also triggers the division of the neuronal stem cells.

Horizontal and radial stem cells

The different stem cell populations are easy to distinguish under the microscope. The first group comprises cells which lie perpendicular to the surface of the hippocampus. Most of these radial stem cells are dormant. As opposed to this, over 80% of the cells in the group of horizontal stem cells -- cells whose orientation runs parallel to the hippocampus surface -- continuously form new cells; the remaining 20% are dormant but sporadically become activated. The activity of genes such as Notch, RBP-J and Sox2 is common to all of the cells.

Radial and horizontal stem cells differ not only in their arrangement, apparently they also react to different stimuli. When the animals are physically active, some radial stem cells abandon their dormant state and begin to divide, while this has little influence on the horizontal stem cells. The result is that more radial stem cells divide in active mice. The horizontal stem cells, in contrast, are also influenced by epileptic seizures.

It would appear that neuronal stem cells are not only found in the brains of mice. The presence of neurons that are formed over the course of life has also been demonstrated in the human hippocamus. Therefore, scientists suspect that different types of active and inactive stem cells also arise in the human brain. It is possible that inactive stem cells in humans can also be activated in a similar way to inactive stem cells in mice. "There are indicators that the excessive formation of new neurons plays a role in epilepsy. The use of neuronal brain stem cells in the treatment of brain injuries or degenerative diseases like Alzheimers may also be possible one day," hopes Verdon Taylor.

Journal Reference:
Sebastian Lugert, Onur Basak, Philip Knuckles, Ute Haussler, Klaus Fabel, Magdalena Götz, Carola A. Haas, Gerd Kempermann, Verdon Taylor, Claudio Giachino. Quiescent and Active Hippocampal Neural Stem Cells with Distinct Morphologies Respond Selectively to Physiological and Pathological Stimuli and Aging. Cell Stem Cell, 2010; 6 (5): 445 DOI: 10.1016/j.stem.2010.03.017


Clues to Neuronal Health Found in Tree-Like Nerve Cell Structures

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ScienceDaily (May 6, 2010) — A breakthrough about the formation and maintenance of tree -like nerve cell structures could have future applications in the treatment of neurodegenerative diseases and the repair of injuries in which neurons are damaged.

The findings by the international team led by Prof. Benjamin Podbilewicz of the Technion-Israel Institute of Technology Faculty of Biology are published in the May 6th issue of Science Express.

While biologists have known for years that many neurons form complicated tree-like structures, it was not known HOW the neurons form and maintain them. To unravel this mystery, the team first studied the dynamic development of two neurons (called PVDs) required for reception of strong mechanical stimuli in the round worm Caenorhabditis elegans (C. elegans). [Prof. Podbilewicz cites Martin Chalfie, the Nobel laureate from Columbia University, as having previously shown that when a worm is hit on the body, it responds by moving away, demonstrating that the PVDs are necessary for C. elegans to sense pain.]

"The PVDs also elaborate neuronal trees comprising structural units we call 'menorahs,' because they look like multi-branched candelabra," said Prof. Podbilewicz, adding that each of these tiny branches is just one-millionth of an inch in diameter.

Using light and electron microscopy in live and fixed C. elegans, the team also studied how the number, structure and function of these menorahs were maintained. In doing so, they discovered that a membrane protein called EFF-1 (which is also essential for the mediation of fusion between cells to form giant, multi-nucleate cells) has important roles in menorah formation and maintenance.

According to Prof. Podbilewicz, EFF-1 also acts in the PVDs to trim the branches of neuronal tree menorahs. When the gene encoding for EFF-1 was deleted, the C. elegans displayed disorganized menorahs with many more branches. And too much EFF-1 in the PVD reduced branching. By cutting, retracting and fusing branches, EFF-1 prunes excess or abnormal branches, serving as part of a quality control process that is important for sculpting and maintenance of complicated menorahs.

The scientists arrived at their findings during studies of the small (one millimeter long) C. elegans, which is considered to be an ideal animal for studying neuronal biology. Since humans are believed to have more than 100 billion neurons, understanding how they develop, connect and function is nearly impossible. But since C. elegans has just 302 neurons, the animal has been a veritable gold mine in the study of neurons, as well as many other fields of biology (including how organs form, how embryos develop, aging, and the programmed death of cells).

Also contributing to this research were Dr. Gidi Shemer and Meital Oren-Sussa of the Technion Department of Biology; David Hall from the Albert Einstein College of Medicine; and Millet Treinin from the Hebrew University-Hadassah Medical School.

Journal Reference:
Meital Oren-Suissa, David H. Hall, Millet Treinin, Gidi Shemer, and Benjamin Podbilewicz. The Fusogen EFF-1 Controls Sculpting of Mechanosensory Dendrites. Science, 2010; DOI: 10.1126/science.1189095


Pluripotent and Differentiated Human Cells Reside in Decidedly Different Epigenomic Landscapes

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ScienceDaily (May 6, 2010) — Human embryonic stem cells (hESCs) possess remarkable properties of self-renewal and pluripotency, the ability to become almost any kind of cell within the body. And yet they share the same genome or set of genes with lineage-committed cells, cells fated to be or do one thing.

Scientists have long suspected that the distinct properties of different cells were attributable to their particular epigenomes -- the collection of attendant molecules, compounds and chemicals that direct and influence the behaviors and functions of genes. The question has been: how much do the epigenomes of hESCs and lineage-committed cells differ? The answer was not clear.

In a paper published in the May 7 issue of Cell Stem Cell, Bing Ren, PhD, a professor of cellular and molecular medicine at the University of California, San Diego and a member of the Ludwig Institute for Cancer Research, reports with colleagues that the epigenomic landscapes of hESCs and lineage-committed cells are, in fact, drastically different.

"You can think of it this way," said Ren. "Neurons and skin cells share the identical set of genetic material -- DNA -- yet their structure and function are very different. The difference can be attributed to differences in their epigenome. This is analogous to computer hardware and software. You can load the same computer with distinct operating systems, such as Linux or Windows, or with different programs and the computer will run very different types of operations.

"Similarly, the unique epigenome in each cell directs the cell to interpret its genetic information differently in response to common environmental factors. Understanding the differences of epigenomic landscapes in different cell types, especially between pluripotent and lineage-committed cells, is essential for us to study human development and mechanisms of human diseases."

To compare these epigenomic landscapes, Ren and colleagues looked at chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, the latter a type of cell commonly found in animal connective tissues. Chromatin is a complex combination of DNA and proteins that makes up chromosomes. The basic component of the chromatin is a complex of proteins called histones. Histone proteins can be chemically modified depending upon the contexts of the underlying gene sequences and can influence gene activities locally.

The scientists found that nearly one-third of the genome differs in chromatin structure. Most of the changes arise from dramatic redistributions of repressive chromatin modifications that involve the addition of methyl-groups to particular lysine residues on the histone protein.

"A fundamental question is how the identical genome sequence gives rise to a diversity of cell types with different gene expression profiles and cellular functions," said David Hawkins of the Ludwig Institute and co-first author of the study. "We've found evidence that lineage-committed cells are characterized by significantly expanded domains of repressive chromatin that selectively affect genes involved in pluripotency and development. In other words, these epigenetic mechanisms play a critical role in deciding a cell's fate and function, and in maintaining it."

The findings are likely to push forward the emerging science of epigenetics, which seeks to identify the processes that impact gene regulation and help determine human development and disease. Ren is director of The San Diego Epigenome Center at the Ludwig Institute. San Diego is one of four centers in the United States participating in the National Institutes of Health's Roadmap Epigenomics Program, a five-year, $190 million effort.

Co-authoring the paper with Ren are R. David Hawkins, Gary C. Hon, Leonard K. Lee and QueMinh Ngo, E. Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Zhen Ye, Celso Espinoza and Saurabh Agarwahl, all of the Ludwig Institute for Cancer Research in La Jolla, CA; Li Shen and Wei Wang, department of chemistry and biochemistry at the University of California, San Diego; Ryan Lister, Mattia Pelizzola and Joseph R. Ecker at the Genomic Analysis Laboratory, The Salk Institute for Biological Studies in La Jolla, CA; and Jessica Antosiewicz-Bourget, Victor Ruotti, Ron Stewart and James A. Thomson at the Morgridge Institute for Research in Madison, WI.

Journal Reference:
R. David Hawkins, Gary C. Hon, Leonard K. Lee, QueMinh Ngo, Ryan Lister, Mattia Pelizzola, Lee E. Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Jessica Antosiewicz-Bourget, Zhen Ye, Celso Espinoza, Saurabh Agarwahl, Li Shen, Victor Ruotti, Wei Wang, Ron Stewart, James A. Thomson, Joseph R. Ecker, Bing Ren. Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells. Cell Stem Cell, Volume 6, Issue 5, 479-491, 7 May 2010 DOI: 10.1016/j.stem.2010.03.018


O Rly?

Stem Cells: In Search of a Master Controller

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ScienceDaily (May 6, 2010) — With thousands of scientists across the globe searching for ways to use adult stem cells to fight disease, there's a growing emphasis on finding the "master regulators" that guide the differentiation of stem cells. New research from Rice University and the University of Cambridge suggests that a closely connected trio of regulatory proteins fulfills that role in hematopoietic stem cells (HSCs), the self-renewing cells the body uses to make new blood cells.

The results appear in the online journal PLoS Computational Biology. Working with experimentalists at Cambridge, Rice bioengineers Oleg Igoshin and Jatin Narula created a computer model that accurately describes the observed behavior of the three regulatory proteins that are collectively known as the "Scl-Gata2-Fli1 triad."

"We don't yet have the experimental verification that this is the master-level regulator for HSCs, but based on our model, we can say that it has all the properties that we would expect to find in a master-level regulator," said Igoshin, an assistant professor in bioengineering at Rice.

All plants and animals have stem cells, a constantly replenished feedstock of unspecialized progenitor cells that have the ability to become any of several specialized types of cell. An HSC is a type of adult stem cell that forms new blood cells. In a healthy human adult, HSCs are used to form about 100 billion new white and red blood cells each day.

But HSCs also need to be able to self-renew, or make the additional stem cells needed to replenish the body's supply. Self-renewal becomes particularly important after significant blood loss through injury or when patients receive bone marrow transplants.

Igoshin and Narula, a graduate student, worked with experimentalists Aileen Smith and Berthold Gottgens at the Cambridge Institute for Medical Research to create a mathematical model that accurately describes the complex interplay among the three HSC regulatory proteins in the Scl-Gata2-Fli1 triad. Based on previous studies at Cambridge, it was obvious that the triad plays an essential role in HSC development. In creating their computer model, Igoshin and Narula were able to quantify the way the three interact and thus shed light on their combined role in regulating HSCs.

To qualify as a master regulator, the triad needed to meet two criteria. It had to act as a "bistable" switch, a one-way button that toggled from the "replenish HSC" state to the "differentiate" state. Second, it needed to ignore extraneous signals and throw the switch only when a signal persisted.

"In examining the results from the model, we found the triad did have the characteristics of a master regulator," Narula said. "The first time it's switched on, all the cells stay on. It also handles deactivation in a controlled manner, so that some cells differentiate and get deactivated and others don't. Finally, it has the ability to discern whether or not the level of signal is present only for a short burst or for a significantly long time."

Igoshin said additional experimental research is needed to verify the computer model's prediction that the Scl-Gata2-Fli1 triad is the master-level controller for HSCs. However, he said the prediction is particularly intriguing in light of previous studies that suggest other similarly wired regulatory triads are key players in other types of stem cells, including embryonic stem cells.

"It's possible that this triad motif is reused elsewhere," Igoshin said. "The proteins could be different in each case, but the motif structure of their interconnections is common and may be repeated elsewhere in nature. That's one of the most intriguing aspects of this research."

The research was supported by Rice University, the National Science Foundation, and Leukemia and Lymphoma Research UK.

Journal Reference:
Jatin Narula, Aileen M. Smith, Berthold Gottgens, Oleg A. Igoshin. Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate. PLoS Computational Biology, 2010; DOI: 10.1371/journal.pcbi.1000771


Manufacturing Antibodies

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ScienceDaily (May 5, 2010) — Scientists have developed a range of unique and highly specific monoclonal and polyclonal antibodies -- the proteins produced in the blood which counteract bacteria, viruses or cancerous cells. This was achieved by first producing a number of recombinant proteins which are important components of cellular signalling pathways. These proteins themselves have direct uses in immunisation and experimental studies. A further key advance is the incorporation of novel fluorochrome dyes with specific monoclonal antibodies, which can then be used in diagnosis of leukaemia and rheumatic diseases; also in oncology and haematology research.

The human immune system protects the body from disease by identifying and destroying the agents of disease -- bacteria, viruses and also its own cells if they become transformed into a potentially cancerous tumour. The immune system depends on the activity of antibodies, which are naturally produced within its white blood cells. The structure of antibodies has many millions of variations; each capable of recognising and marking a specific antigen, for example from a specific bacterium, so that the bacterium of that strain can be identified and destroyed by other types of white blood cells. If a molecule from a specific bacterium binds to a receptor protein on the surface of the white blood cell, the protein, which is an important component of the signalling pathway, triggers a response within the cell. In addition, antibodies can serve as an extremely useful research and diagnostic tool, as they can bind with great specificity and sensitivity to their target structures and then can be visualised by staining with specific dyes.

The project is EUREKA project E! 3424 RECAN.

The Antibodies fabric

Modern molecular techniques now enable in vitro production of some of the receptor proteins. The RECAN project used recombinant techniques to produce them -- combining defined DNA sequences with the DNA of bacteria to alter the coding for specific traits, and then harvesting the altered protein derived from that recombinant DNA.

The recombinant protein was then used to immunise test subjects using standard hybridoma technology. This involves fusion of specific antibody-producing cells with cancer cells to form hybrid cell lines, growing them in tissue culture, and retaining and purifying the antibodies produced. In this project, a first test group was used to produce antibodies derived from monoclonal antibodies, and another to produce antibodies derived from polyclonal antibodies.

"We used a standard technology" says Professor Vaclav Horejší of the Institute of Molecular Genetics in Prague (IMG). "But what's unique about our project is the products -- especially the monoclonal antibodies, which are of unique specificity, with great commercial potential and in some cases also useful for diagnostics."

Fluorescent labelling

The RECAN project has also made important advances in cytofluorometry, which is the use of specific fluorescent markers to distinguish between types of cells. The project partners developed methods to prepare monoclonal antibodies bound to several types of a new range of fluorochrome dyes. Antibodies bound to these dyes can readily be distinguished from those labelled with more conventional dyes.

One particular focus of this part of the project was to develop methodology for the immunophenotyping of leukaemia, and Exbio aims to be one of the first European companies to offer use of these novel fluorochrome dyes to screen leukaemia patients and those with rheumatoid arthritis. One of the monoclonal antibodies recognizes an important signalling protein called ZAP70, which is a characteristic marker of certain types of leukaemia and therefore can be used for diagnostic purposes. Although this method is already established, new monoclonal antibodies are still necessary to develop a standard protocol for routine diagnosis of this type of leukaemia, using the best reagents.

A ready market; a fruitful collaboration

The products generated as a result of the RECAN project are already commercially available worldwide through Exbio. The recombinant protein products can be used for immunisation in the production of antibodies, and also as specific internal standards for their production and determination. Production of the specific monoclonal and polyclonal antibodies makes it possible to target new antigens, which will contribute to the development of new immunochemical assays. Finally the fluorescently-labelled antibodies will find numerous applications in both diagnosis of conditions, and also in research studies in aspects of haematology, oncology, immunology and other areas of biomedical research.

The RECAN project made optimum use of existing techniques by applying them to a new area. In doing so, it produced a new range of products which make significant improvements over existing possibilities. Professor Horejší comments that collaboration was important -- the project partners were in touch before RECAN began, but they were each able to contribute different skills. The IMG laboratory developed most of the recombinant proteins and used them for immunisation and the production of the hybridoma cell lines delivering the monoclonal antibodies. The Magdeburg immunology laboratory was responsible for independent testing of several of the monoclonal antibodies and evaluating their qualities in specialised immunochemical techniques. Exbio applied its unique expertise in fluorescent labelling of monoclonal antibodies. The company also prepared several batches of polyclonal antibodies and prepared them for commercialisation, including the optimisation of large scale production, purification and stabilisation.


Tags On, Tags Off: Scientists Identify New Regulatory Protein Complex With Unexpected Behaviour

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ScienceDaily (May 5, 2010) — During embryonic development, proteins called Polycomb group complexes turn genes off when and where their activity must not be present, preventing specialised tissues and organs from forming in the wrong places. They also play an important role in processes like stem cell differentiation and cancer.

In a study published online in Nature, scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, identified a new Polycomb group complex, and were surprised by how it acts.

Another Polycomb group complex was already known to silence genes by placing a chemical tag near them. Juerg Mueller and his group at EMBL found that the new Polycomb complex they discovered, PR-DUB, removes that same tag.

"Surprisingly, this new complex which takes the tag off seems to act in the same tissues and at the same developmental stages as the one that puts the tag on," says Mueller, "and both opposing activities must occur to keep the gene silenced in our model organism, the fruit fly Drosophila."

The reason for this unexpected behaviour is yet to be experimentally confirmed, but it may be a case of fine-tuning, with the newly-found complex ensuring that the chemical tagging is kept at its optimal level.

The human equivalent of PR-DUB is known to be a tumour-suppressor, and Mueller and colleagues discovered that, in test-tubes at least, it behaves the same way as the fruit fly complex, removing that same gene-silencing tag. Knowing how the complex acts in the fruit fly could help scientists uncover its function in the cells of mammals such as ourselves, and thus begin to shed light on its relation to cancer.

Journal Reference:
Johanna C. Scheuermann, Andrés Gaytán de Ayala Alonso, Katarzyna Oktaba, Nga Ly-Hartig, Robert K. McGinty, Sven Fraterman, Matthias Wilm, Tom W. Muir, Jürg Müller. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature, 2010;
DOI: 10.1038/nature08966


Key Step for Regulating Embryonic Development Discovered

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ScienceDaily (Apr. 23, 2010) — Deleting a gene in mouse embryos caused cardiac defects and early death, leading researchers to identify a mechanism that turns developmental genes off and on as an embryo matures, a team led by a scientist at The University of Texas M. D. Anderson Cancer Center reported April 24 in Molecular Cell.

"Our study focused on regulation of two genes that are critical to the healthy development of the heart, but many other genes are regulated in this way," said senior author Edward T.H. Yeh, M.D., professor and chair of M. D. Anderson's Department of Cardiology. "This novel pathway marks an advance in our understanding of how developmental genes are turned on and off."

All cells in an embryo contain the same DNA. Different genes are turned off and on in different cells at different times to form specific tissues and organs as the embryo develops. This gene regulation is accomplished by epigenetic processes that control gene expression without altering DNA. Instead, epigenetic processes attach chemical groups to genes or to histones, proteins that are intertwined with DNA to form chromosomes, to activate genes or to shut them down.

"Our findings provide a new window through which to look at epigenetic control," Yeh said, "and how epigenetics and development are unexpectedly tied together by the SUMO/SENP2 system."

The key actors are members of two tightly associated families of proteins that Yeh and colleagues discovered and continue to study. The first, Small Ubiquitin-related Modifier, or SUMO, attaches to other proteins to modify their function or physically move them within the cell (SUMOylation). The second, Sentrin/SUMO-specific protease 2, or SENP2, snips SUMO off of proteins (de-SUMOylation).

This line of research started when Yeh and colleagues knocked SENP2 out of mouse DNA and found that the embryos died at about day 10. Their hearts had smaller chambers and thinner walls. Through a series of experiments, the team worked backward from this observation to show:

1. A group of proteins called the polycomb repressive complex 1 (PRC1) that silences genes must first bind to a particular methylated address on a histone and,
2. A key component of the complex must be SUMOylated to make this connection, which results in
3. the silencing of Gata4 and Gata6, genes that are essential for cardiac development.
4. In early development, SENP2 works as a switch to turn on Gata4 and Gata6

"When SENP2 is turned on, it peels SUMO off of PRC1, which then falls off the histone, and when that happens, the lock is removed and genes are transcribed," Yeh said. Gata4 and Gata6 are free to properly develop the heart.

In short, SUMO helps the PRC1 complex repress genes, and SENP2 reverses this repression, allowing gene transcription and expression.

"By understanding how development unfolds, we can better control this process, which includes cell proliferation and organ development," Yeh said. "This will help us to better understand cancer.

"SUMO and SENP are important in cancer development, neurological diseases and heart development. Everything under the sun can be regulated by this system," Yeh said. "Here we've established a new role for SUMOylation, mediating the interaction between protein and protein methylation in epigenetic regulation."

Funding for this research was provided by from the National Natural Science Foundation of China, National Basic Research Program of China and grants from the U.S. National Cancer Institute. Yeh also is the McNair Scholar of the Texas Heart Institute/St. Luke's Episcopal Hospital.

Co-authors with Yeh are co-first author Yitao Qi, Ph.D., and Robert Schwartz, Ph.D., both of the Texas Heart Institute/St. Luke's Episcopal Hospital, and co-first author Xunlei Kang, M.D., Ph.D., Yong Zuo, Ph.D., Qi Wang, Yanqiong Zou and Jinke Cheng, D.V.M., all of the Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine in Shanghai.

Journal Reference:
Xunlei Kang, Yitao Qi, Yong Zuo, Qi Wang, Yanqiong Zou, Robert J. Schwartz, Jinke Chengsend, Edward T.H. Yeh. SUMO-Specific Protease 2 Is Essential for Suppression of Polycomb Group Protein-Mediated Gene Silencing during Embryonic Development. Molecular Cell, Volume 38, Issue 2, 191-201, 23 April 2010 DOI: 10.1016/j.molcel.2010.03.005


Key Protein Controls T-Cell Proliferation

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ScienceDaily (May 4, 2010) — New research has identified that a key protein called PEA-15 stops T-cell proliferation by blocking the cell's ability to reproduce. The control of T-cell proliferation is essential in preventing certain blood cancers and autoimmune diseases, as well as the orchestration of the immune response to infection.

Findings of the study are reported in a recent online issue of The FASEB Journal, a publication of The Federation of American Societies for Experimental Biology.

A team of researchers from the University of Hawai'i Cancer Research Center, Rutgers University and Washington University in St. Louis examined the normal function of PEA-15, which acts as a tumor suppressor in some cancers including brain, ovarian and breast cancers. They found that PEA-15 normally controls lymphocyte (white blood cell) proliferation.

To determine the normal role of this protein, investigators examined mice lacking PEA-15. They found that those without the protein had both spatial learning disabilities and a pronounced increase in lymphocyte (white blood cell) proliferation. Upon closer inspection, they further found that loss of PEA-15 particularly affected a group of lymphocytes called T-cells. T-cells are involved in killing invading pathogens as well as stimulating more long-term immunity. The PEA-15 protein works by acting as a brake on a group of proteins that activate cell cycling and proliferation when they recognize a signal from an invading organism. Lymphocytes without PEA-15 continue proliferating beyond normal response levels as if they lack the "brakes" to stop.

"Understanding how T-cell expansion is controlled at the molecular level should lead to new methods to control the immune response during infection as well as perhaps helping the development of novel ways to utilize these cells to attack tumors," said Joe Ramos, Ph.D. principal investigator and assistant professor in natural products and cancer biology at the University of Hawaii. "Dysregulation of PEA-15 function might also play a role in the development or progression of lymphomas or leukemias," he added. "Finding ways to regain normal function of PEA-15 might contribute to identification of new approaches to treat these cancers. "

The study was funded by grants from the National Institutes of Health (NCI) to Joe W. Ramos at the University of Hawai'i Cancer Research Center and Andrey Shaw from Washington University in St. Louis. Support for Guy Werlen at Rutgers University came from the New Jersey Commission on Cancer Research.

Journal Reference:
Pastorino et al. The death effector domain protein PEA-15 negatively regulates T-cell receptor signaling. The FASEB Journal, 2010; DOI: 10.1096/fj.09-144295


Gene flaw found in induced stem cells

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Key difference between reprogrammed adult mouse cells and embryonic stem cells discovered.

Stem-cell researchers have puzzled over why reprogrammed cells taken from adult tissues are often slower to divide and much less robust than their embryo-derived counterparts.

Now, a team has discovered the key genetic difference between embryonic and adult-derived stem cells in mice. If confirmed in humans, the finding could help clinicians to select only the heartiest stem cells for therapeutic applications and disease modelling.

Induced pluripotent stem (iPS) cells are created by reprogramming adult cells, and outwardly seem indistinguishable from embryonic stem (ES) cells. Both cell types are pluripotent — they can form any tissue in the body.

Yet subtle distinctions abound. Last month, for example, Su-Chun Zhang and his colleagues at the University of Wisconsin–Madison compared the ability of both types of pluripotent cell to form human neurons in a laboratory setting, and found that iPS cells did so with markedly lower efficiency than ES cells (B.-Y. Hu et al. Proc. Natl Acad. Sci. USA 107, 4335–4340; 2010).

Last year, researchers also reported consistent differences in gene expression between the two cell types (M. H. Chin et al. Cell Stem Cell 5, 111–123; 2009). However, because scientists have always obtained iPS and ES cells from different sources — in general, iPS cells are derived from skin samples taken during biopsies and ES cells from excess embryos from fertility clinics — it was impossible to tell whether the discrepancies could be chalked up to the unique biology of the cells or the genetics of the underlying tissue.

Silence please

A team led by Konrad Hochedlinger at Massachusetts General Hospital in Boston has now derived iPS and ES cells with identical DNA. The iPS cells were less efficient than the ES cells at incorporating into chimeric mice — a standard test of pluripotency, or 'stemness'. The team added the stem cells into embryos from mice of a different colour; once each mouse matures, the colouring of its coat reveals how much the stem cells contributed to forming its tissue.

When the scientists compared genome-wide expression patterns between the two cell types, they discovered that a small stretch of DNA on the long arm of chromosome 12 displayed significantly different gene activity. In this region, two genes and a slew of tiny regulatory sequences called microRNAs were consistently activated in the ES cells and silenced in the iPS cells, regardless of whether the reprogrammed cells came originally from skin, brain, blood or other tissue. Although the function of the key genes is unknown, this region is usually silenced in mouse sperm cells and activated in other types of cell, so reprogramming might somehow mimic the silencing process, the authors speculate.

"This is an important step towards identifying the differences that may exist in those imperfectly reprogrammed cells," says Sheng Ding, a stem-cell researcher at the Scripps Research Institute in La Jolla, California.

The discovery raises the possibility that human iPS cells carry similar silenced sequences that make them less effective than ES cells, according to team member Matthias Stadtfeld, also from the Massachusetts General Hospital, who presented the work at a meeting of the New York Academy of Sciences on 23 March. "It points towards the possibility that hot spots for epigenetic abnormalities exist also in human iPS cells," he says. "A profound abnormality like that could confound results obtained with patient-specific iPS cells."

John Hambor, director of stem-cell-based drug discovery at Cell Therapy Group, a consultancy based in Madison, Connecticut, cautions that although the iPS cells in the experiment did not meet the strictest criteria of stemness — they did not introduce significant colouring into chimeric mice — they may still have been able to form many types of tissue, something the researchers did not explicitly test. Stadtfeld agrees, noting that the silenced genes "might not matter for tissues in which [such] genes have no role".

Although findings in mice don't always apply to humans, if a similar gene signature is found in human cells, it could help researchers to identify which iPS cells to avoid using, and which stand the best chance of producing the desired tissue. Hochedlinger's team has therefore begun to look at human ES and iPS cells in search of similar gene-activity patterns to those they found in mice.

by Elie Dolgin


Friday, May 7, 2010

New Computational Method to Uncover Gene Regulation

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ScienceDaily (Apr. 27, 2010) — Scientists have developed a new computational model to uncover gene regulation, the key to how our body develops -- and how it can go wrong.

The researchers, from The University of Manchester (UK), Aalto University (Finland) and the European Molecular Biology Laboratory Heidelberg (Germany), say the new method identifies targets of regulator genes.

The human genome contains instructions for making all the cells in our body. An individual cell's make up (e.g. muscle or blood) depends on how these instructions are read. This is controlled by gene regulatory mechanisms. Uncovering these mechanisms holds a key to greatly improving our understanding of biological systems.

One important regulatory mechanism is based on genes that actively promote or repress the activity of other genes. The new research addresses the problem of identifying the targets these regulator genes affect.

The new method, presented in the latest edition of Proceedings of the National Academy of Sciences (PNAS), is based on careful modelling of time series measurements of gene activity. It combines a simple biochemical model of the cell with probabilistic modelling to deal with incomplete and uncertain measurements.

Dr Magnus Rattray, a senior researcher at Manchester's Faculty of Engineering and Physical Sciences, said: "Combining biochemical and probabilistic modelling techniques as done here holds great promise for the future. Many systems we are looking at now are too complex for purely physical models and connecting to experimental data in a principled manner is essential."

Dr Antti Honkela, his colleague at Aalto University School of Science and Technology, added: "A major contribution of our work is to show how data-driven machine learning techniques can be used to uncover physical models of cell regulation. This demonstrates how data-driven modelling can clearly benefit from the incorporation of physical modelling ideas."

Journal Reference:

A. Honkela, C. Girardot, E. H. Gustafson, Y. H. Liu, E. E. M. Furlong, N. D. Lawrence, M. Rattray. Model-based method for transcription factor target identification with limited data. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0914285107