Saturday, March 27, 2010

CERN sets date for first attempt at 7 TeV collisions in the LHC

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Geneva, 23 March 2010. With beams routinely circulating in the Large Hadron Collider at 3.5 TeV, the highest energy yet achieved in a particle accelerator, CERN has set the date for the start of the LHC research programme. The first attempt for collisions at 7 TeV (3.5 TeV per beam) is scheduled for 30 March.

“With two beams at 3.5 TeV, we’re on the verge of launching the LHC physics programme,” explained CERN’s Director for Accelerators and Technology, Steve Myers. “But we’ve still got a lot of work to do before collisions. Just lining the beams up is a challenge in itself: it’s a bit like firing needles across the Atlantic and getting them to collide half way.”

Between now and 30 March, the LHC team will be working with 3.5 TeV beams to commission the beam control systems and the systems that protect the particle detectors from stray particles. All these systems must be fully commissioned before collisions can begin.

“The LHC is not a turnkey machine,” said CERN Director General Rolf Heuer.“The machine is working well, but we’re still very much in a commissioning phase and we have to recognize that the first attempt to collide is precisely that. It may take hours or even days to get collisions.”

The last time CERN switched on a major new research machine, the Large Electron Positron collider, LEP, in 1989 it took three days from the first attempt to collide to the first recorded collisions.

The current LHC run began on 20 November 2009, with the first circulating beam at 0.45 TeV. Milestones were quick to follow, with twin circulating beams established by 23 November and a world record beam energy of 1.18 TeV being set on 30 November. By the time the LHC switched off for 2009 on 16 December, another record had been set with collisions recorded at 2.36 TeV and significant quantities of data recorded. Over the 2009 part of the run, each of the LHC’s four major experiments, ALICE, ATLAS, CMS and LHCb recorded over a million particle collisions, which were distributed smoothly for analysis around the world on the LHC computing grid. The first physics papers were soon to follow. After a short technical stop, beams were again circulating on 28 February 2010, and the first acceleration to 3.5 TeV was on 19 March.

Once 7 TeV collisions have been established, the plan is to run continuously for a period of 18-24 months, with a short technical stop at the end of 2010. This will bring enough data across all the potential discovery areas to firmly establish the LHC as the world’s foremost facility for high-energy particle physics.

A webcast will be available on the day of the first attempt to collide protons at 7TeV. More details will be available at:


CERN Press Office,
+41 22 767 34 32
+41 22 767 21 41


Cancer genes silenced in humans

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Tiny particles carrying short strands of RNA can interfere with protein production in tumours.

Short sequences of RNA that can effectively turn off specific genes have for the first time been used to treat skin cancer in people.

The technique, called RNA interference (RNAi), gained its inventors a Nobel Prize in 2006, but researchers have struggled to get it to the clinic, partly because of problems in getting the molecules to their target.

Now, Mark Davis from the California Institute of Technology in Pasadena and his colleagues have found a way to deliver particles containing such sequences to patients with the skin cancer melanoma. When analysing biopsies of the tumours after treatment, they found that the particles had inhibited expression of a key gene, called RRM2, needed for the cancer cells to multiply. Their research is published today in Nature1.

The researchers created the particles from two polymers plus a protein that binds to receptors on the surface of cancer cells and pieces of RNA called small-interfering RNA, or siRNA, designed to stop the RRM2 gene from being translated into protein. The siRNA works by sticking to the messenger RNA (mRNA) that carries the gene's code to the cell's protein-making machinery and ensuring that enzymes cut the mRNA at a specific spot.

When the components are mixed together in water, they assemble into particles about 70 nanometres in diameter. The researchers can then administer the nanoparticles into the bloodstream of patients, where the particles circulate until they encounter 'leaky' blood vessels that supply the tumours with blood. The particles then pass through the vessels to the tumour, where they bind to the cell and are then absorbed.

Once inside the cell, the nanoparticles fall apart, releasing the siRNA. The other parts of the nanoparticle are so small, they pass out of the body in urine. "It sneaks in, evades the immune system, delivers the siRNA, and the disassembled components exit out", Davis says.

Fire at will

The study describes the science behind a phase I trial assessing the safety of the technique in 15 patients. When researchers analysed tumour samples from three of the patients who volunteered samples, they found fragments of the mRNA in exactly the length and sequence they would expect from the design of their siRNA. And in at least one patient, the levels of the protein were lower than they were in samples of the tumours taken before treatment. They also found that patients who were given higher doses had higher levels of siRNA in their tumours. "The more we put in, the more ends up where they are supposed to be, in tumour cells," Davis says.

Researchers will need more data from clinical trials to ensure that such therapies are safe to use in people. But Davis says that his study means there is now direct evidence that nanoparticles and RNAi can be used to attack harmful genes in humans — and not just in the test tube. "What's so exciting is that virtually any gene can be targeted now," he says. "Every protein now is druggable."

Davis says that by targeting specific genes he hopes these treatments will not have major side effects. "My hope is to make tumours melt away while maintaining a high quality of life for the patients," he says. "We're moving another step closer to being able to do that now."

But some researchers are concerned that the treatment has not been tested on more patients and that more samples were not taken from each patient. Molecular biologist Thomas Tuschl from Rockefeller University in New York says it is "exciting that such nanoparticles in multiple dosing schemes can reach the tissue and apparently have measurable effects". That is, he says, if one wants to believe the data from the single patient who had lower levels of the protein. "I hope these findings can be confirmed in the future," he adds.

Biomedical engineer Daniel Anderson from Massachusetts Institute of Technology in Cambridge has also been trying to develop RNAi delivery systems, and he thinks the data are a great start. "Generally, people who worry about making therapeutics understand that animals are not people," he says. "There are a lot of really exciting data with animals, but ultimately, the usefulness of these types of drug-delivery systems must be evaluated in humans, and that's why this is an important study. But it's not like we're done."

by Janet Fang

Davis, M. E. et al. Nature advance online publication DOI: 10.1038/nature08956 (2010).


See also:

New period of brain “plasticity” created with transplanted embryonic cells

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UCSF scientists report that they were able to prompt a new period of “plasticity,” or capacity for change, in the neural circuitry of the visual cortex of juvenile mice. The approach, they say, might some day be used to create new periods of plasticity in the human brain that would allow for the repair of neural circuits following injury or disease.

The strategy – which involved transplanting a specific type of immature neuron from embryonic mice into the visual cortex of young mice – could be used to treat neural circuits disrupted in abnormal fetal or postnatal development, stroke, traumatic brain injury, psychiatric illness and aging.

Like all regions of the brain, the visual cortex undergoes a highly plastic period during early life. Cells respond strongly to visual signals, which they relay in a rapid, directed way from one appropriate cell to the next in a process known as synaptic transmission. The chemical connections created in this process produce neural circuitry that is crucial for the function of the visual system. In mice, this critical period of plasticity occurs around the end of the fourth week of life.

The catalyst for the so-called critical period plasticity in the visual cortex is the development of synaptic signaling by neurons that release the inhibitory neurotransmitter GABA. These neurons receive excitatory signals from other neurons, thus helping to maintain the balance of excitation and inhibition in the visual system.

In their study, published in the journal Science, (Vol. 327. no. 5969, 2010), the scientists wanted to see if the embryonic neurons, once they had matured into GABA-producing inhibitory neurons, could induce plasticity in mice after the normal critical period had closed.

The team first dissected the immature neurons from their origin in the embryonic medial ganglionic eminence (MGE) of the embryonic mice. Then they transplanted the MGE cells into the animals’ visual cortex at two different juvenile stages. The cells, targeted to the visual cortex, dispersed through the region, matured into GABAergic inhibitory neurons, and made widespread synaptic connections with excitatory neurons.

The scientists then carried out a process known as monocular visual deprivation, in which they blocked the visual signals to one eye in each of the animals for four days. When this process is carried out during the critical period, cells in the visual cortex quickly become less responsive to the eye deprived of sensory input, and become more responsive to the non-deprived eye, creating alterations in the neural circuitry. This phenomenon, known as ocular dominance plasticity, greatly diminishes as the brain matures past this critical postnatal developmental period.

The team wanted to see if the transplanted cells would affect the visual system’s response to the visual deprivation after the critical period. They studied the cells’ effects after allowing them to mature for varying lengths of time. When the cells were as young as 17 days old or as old as 43 days old, they had little impact on the neural circuitry of the region. However, when they were 33-39 days old, their impact was significant. During that time, monocular visual deprivation shifted the neural responses away from the deprived eye and toward the non-deprived eye, revealing the state of ocular dominance plasticity.

Naturally occurring, or endogenous, inhibitory neurons are also around 33-39 days old when the normal critical period for plasticity occurs. Thus, the transplanted cells’ impact occurred once they had reached the cellular age of inhibitory neurons during the normal critical period.

The finding, the team says, suggests that the normal critical period of plasticity in the visual cortex is regulated by a developmental program intrinsic to inhibitory neurons, and that embryonic inhibitory neuron precursors can retain and execute this program when transplanted into the postnatal cortex, thereby creating a new period of plasticity.

“The findings suggest it ultimately might be possible to use inhibitory neuron transplantation, or some factor that is produced by inhibitory neurons, to create a new period of plasticity of limited duration for repairing damaged brains,” says author Sunil P. Gandhi, PhD, a postdoctoral fellow in the lab of Michael Stryker, PhD, professor of physiology and a member of the Keck Center for Integrative Neurosciences at UCSF. “It will be important to determine whether transplantation is equally effective in older animals.”

Likewise, “the results raise a fundamental question: how do these cells, as they pass through a specific stage in their development, create these windows of plasticity?” says author Derek G. Southwell, PhD, a student in the lab of Arturo Alvarez-Buylla, PhD, Heather and Melanie Muss Professor of Neurological Surgery and a member of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF.

The findings could be relevant to understanding why learning certain behaviors, such as language, occurs with ease in young children but not in adults, says Alvarez-Buylla. “Grafted MGE cells may some day provide a way to induce cortical plasticity and learning later in life.”

The findings also complement two other recent UCSF studies using MGE cells to modify neural circuits. In a collaborative study among the laboratories of Scott Baraban, PhD, professor of neurological surgery; John Rubenstein, MD, PhD, professor of psychiatry, and Alvarez-Buylla, the cells were grafted into the neocortex of juvenile rodents, where they reduced the intensity and frequency of epileptic seizures. (Proceedings of the National Academy of Science, vol. 106, no. 36, 2009). Other teams are exploring this tactic, as well.

In the other study (Cell Stem Cell, vol. 6, issue 3, 2010), UCSF scientists reported the first use of MGEs to treat motor symptoms in mice with a condition designed to mimick Parkinson’s disease. The finding was reported by the lab of Arnold Kriegstein, MD, PhD, UCSF professor of neurology and director of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, in collaboration with Alvarez-Buylla and Krys Bankiewicz, MD, PhD, UCSF professor of neurological surgery.

The other co-author of the plasticity study was Robert C. Froemke, PhD, a postdoctoral fellow in the lab of Christoph Schreiner, MD, PhD, professor and vice chair of otolaryngology.

UCSF is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care.

Jennifer O’Brien

Related links:

UCSF News Release: “Novel Parkinson’s disease treatment strategy involves cell transplantation”

Science paper: “Cortical Plasticity Induced by Inhibitory Neuron Transplantation”

Alvarez-Buylla lab

Stryker lab

Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at UCSF


Scientists Uncover Cells That Mend a Broken Heart

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ScienceDaily (Mar. 25, 2010) — Humans have very limited ability to regenerate heart muscle cells, which is a key reason why heart attacks that kill cells and scar heart tissue are so dangerous.

But damaged heart muscles in the amazing, highly regenerative zebrafish have given Duke University Medical Center scientists a few ideas that may lead to new directions in clinical research and better therapy after heart attacks.

"Our hearts don't seem so complex that they shouldn't have the capacity to regenerate," said Kenneth Poss, Ph.D., senior author of the study in Nature and professor of cell biology at Duke. The data in this study showed that the major contributors to the regeneration of surgically removed heart muscle came from a subpopulation of heart muscle cells (cardiomyocytes) near the area where the removal occurred.

The study appears in the March 25 issue of Nature.

The team labeled cells in the heart and found that cells that activated the gata4 gene upon injury ultimately contributed to regenerating the heart muscle.

The team first used a labeled "fluorescent reporter" fish that shows the presence of gata4, a gene required for heart formation in the developing embryo. They found that fluorescence was undetectable in uninjured zebrafish ventricles, but when they clipped a small section of the heart, a subpopulation of cardiac muscle cells along the outer wall of the ventricles began to fluoresce. Some of these cells near the removal site ultimately proliferate and integrate into the wound, replacing the injury clot.

"We don't know the instructions or the mechanisms yet that mobilize these cells or cause them to proliferate, but we now know that they are the cells that are participating in new muscle growth," said Poss, who is also an investigator in the Howard Hughes Medical Institute.

Finding a key origin of heart muscle provides a target for studies that will help scientists understand cardiac muscle regeneration, said lead author Kazu Kikuchi, a postdoctoral fellow in the Poss lab. "By studying this important cell population, we expect results that could help in the repair of diseased human hearts."

The team uncovered other interesting findings.

They still needed to know whether the new cardiomyocytes were connecting in a useful way to the muscle that was spared by injury. They found that within two weeks of the injury, the new heart cells started to show normal electrical coupling needed to keep the heart beating in rhythm. A month later, the electric coupling was the same as in the uninjured heart, Poss said. "This is the first evidence that I know of that the new cardiomyocytes do become electrically coupled. It's exciting because the new muscle has to approach the functional level of the existing muscle to be of use." This experiment was done in collaboration with colleagues at Brigham and Women's Hospital in Boston.

Another finding was that the fish heart muscle found a way to work around scar tissue, a finding with interesting implications for the human heart, which stubbornly scars after heart muscle dies during a heart attack. Poss and the team found a genetic way to manipulate the zebrafish to slow down the regenerative process and form cardiac scars after tissue removal, which they normally don't do.

The scientists were able to make the tissue form a scar by blocking a certain genetic signaling pathway. Then they returned the activity of the pathway to the animal to learn whether regeneration could occur after scar tissue formed.

The manipulation worked, and the researchers saw the gata4 label expressed in cells near the scar. They could also see a wall of new muscle forming around the scarred tissue removal site.

"I think this experiment is relevant to a lot of heart attack victims who have established scars," Poss said. "We would like to know ultimately to what extent regenerative therapy of the heart could help people who have lived with scars for a long time. When we allowed the regenerative signaling pathway to remain active after the scar was formed, we didn't see removal of scar tissue, but we did see improvements in the tissue near those injuries."

Poss said there is more to learn from the zebrafish. "We want to know the sources of all of the different cell types in the regenerated heart tissue, and the molecular events responsible for activating those sources," he said. "There is a lot left to learn about the mysterious regenerative abilities of animals like zebrafish and salamanders."

Other authors include Jennifer E. Holdway, Yi Fang and Gregory F. Egnaczyk of the Duke Departments of Cell Biology and the Howard Hughes Medical Institute (Gregory Egnacyzk is also in the Duke Dept. of Medicine); Andreas A. Werdich and Calum A. MacRae of the Cardiovascular Division, Brigham and Women's Hospital in Boston; Ryan M. Anderson and Didier Y. R. Stainier of the Department of Biochemistry and Biophysics, University of California -- San Francisco; and Todd Evans of the Department of Surgery, Weill Cornell Medical College, Cornell University in New York, NY.

The study was funded by postdoctoral fellowships from American Heart Association, the Juvenile Diabetes Research Foundation, the Japan Society for the Promotion of Science (JSPS), NIH training grants, NHLBI grants, the National Institute for General Medical Sciences, the March of Dimes, and grants from the AHA, Pew Charitable Trusts and the Whitehead Foundation.

Journal Reference:
Kikuchi et al. Primary contribution to zebrafish heart regeneration by gata4 cardiomyocytes. Nature, 2010; 464 (7288): 601 DOI: 10.1038/nature08804


Wednesday, March 24, 2010

Newly Discovered Gene Explains Mouse Embryonic Stem Cell Immortality

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ScienceDaily (Mar. 24, 2010) — Researchers at the National Institute on Aging (NIA), part of the National Institutes of Health, have discovered a key to embryonic stem (ES) cell rejuvenation in a gene -- Zscan4 -- as reported in the March 24, 2010, online issue of Nature. This breakthrough finding could have major implications for aging research, stem cell biology, regenerative medicine and cancer biology.

ES cells are unique because, along with the ability to develop into nearly any type of cell in the body, they can produce infinite generations of new, fully operational ES cells (daughter cells). ES cells are essentially immortal, meaning that they can divide indefinitely to produce additional generations of functional ES daughter cells. Other cells can only produce a certain number of generations of daughter cells before they no longer function properly. This is partially because the telomere, the protective end of the chromosome which carries the cell's genetic information, shortens each time a cell divides. When a telomere becomes too short, it can no longer protect the cell. At that time, the cell dies, turns itself off, known as cell senescence, or produces abnormal and possibly dysfunctional cells.

Until now, the mechanism for the ES cell's immortality had been a mystery. The prevailing theory was that ES cells practiced "self-renewal," meaning that when they divided, they produced daughter cells that were completely unaltered (including telomere length) from the parent. NIA researchers discovered that the process occurring in ES cells can be more appropriately described as "rejuvenation" than the "self-renewal." As in other cells, when ES cells replicate, the daughter cells are not identical to the parent and the telomeres are shorter. However, ES cells express a unique Zscan4 gene that, when activated (or turned on), rejuvenates the ES cell, restoring it to its original vigor.

This rejuvenation includes telomere lengthening through recombination, when a shorter telomere combines with a longer telomere to elongate itself. Zscan4 then turns off. The gene is not turned on every time that the cell replicates -- approximately 5 percent of the cells will have an activated gene at any one point. The process is a cycle of cell replication (with telomere shortening) and intermittent activation of Zscan4 (cell rejuvenation).

Researchers are currently investigating whether a similar mechanism also operates in human cells.

Journal Reference:
Zalzman et al. Zscan4 regulates telomere elongation and genomic stability in ES cells. Nature, 2010; DOI: 10.1038/nature08882


Secret to Healing Chronic Wounds Might Lie in Tiny Pieces of Silent RNA

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ScienceDaily (Mar. 22, 2010) — Scientists have determined that chronic wounds might have trouble healing because of the actions of a tiny piece of a molecular structure in cells known as RNA.

The Ohio State University researchers discovered in a new animal study that this RNA segment in wounds with limited blood flow lowers the production of a protein that is needed to encourage skin cells to grow and close over the sore.

In a parallel experiment using human skin cells, the researchers silenced the RNA segment with an experimental drug and saw those protein levels rise. The skin cells multiplied as a result.

The combination of findings suggests that targeting this RNA segment with a drug that could be used topically on skin might offer new strategies for treating chronic wounds, which are sometimes fatal and cost the U.S. health-care system an estimated $25 billion annually.

The research appears this week in the online early edition of the Proceedings of the National Academy of Sciences.

RNA in cells is responsible for using instructions from DNA to make proteins, but the piece of RNA identified in this study has a completely different role. It is a microRNA, a small segment of RNA that blocks an important protein-building process. The RNA segment in question is known as miR-210.

The research involves wounds that are ischemic, that is, they heal very slowly or are in danger of never healing because they lack blood flow and oxygen at the wound site. These types of wounds affect about 6.5 million patients each year, and are common complications of diabetes, high blood pressure, obesity and other conditions characterized by poor vascular health.

"When blood supply is inadequate, many things are deficient at the wound site, including oxygen. That leads to a condition called hypoxia," said Chandan Sen, professor and vice chair for research in Ohio State's Department of Surgery and senior author of the study. "We have shown that hypoxia induces miR-210, which actually blocks the ability of the cells to proliferate, a step necessary for the wound-closure process."

Sen's lab has studied the effects of low oxygen on wound healing for years, but just now has been able to identify the sequence of events connecting low oxygen and the inability of skin cells to grow. Sen, who is also executive director of the Comprehensive Wound Center at Ohio State, said this is the first publication to suggest microRNAs regulate the healing process in chronic wounds.

Sen and colleagues created ischemic and non-ischemic wounds on mouse skin for comparison. To create the ischemic wounds, they established a flap of skin with limited blood flow and placed the wound in the middle of the flap.

The scientists used a number of technologies -- including laser Doppler imaging and hyperspectral scanning -- to demonstrate that the wounds received differing levels of blood flow. Additionally, they used a specialized probe to measure actual oxygen levels in the wounds and showed that oxygen in the ischemic wounds on the mice closely matched oxygen levels measured in chronic human wounds in clinical settings.

In these ischemic mouse wounds, the researchers observed that the hypoxic, or low- oxygen, conditions led to the presence of a specific type of protein called hypoxia inducible factor-1a, or HIF-1a. This protein can turn genes on and off and, in this case, appears to influence the behavior of at least one microRNA as well.

By placing markers in the wounds for these substances, the scientists could observe their relationships in the wound. The presence of HIF-1a in low-oxygen conditions led to the activation of the miR-210, and that microRNA in turn lowered levels of the protein needed to kick skin cells into action. This protein is called E2F3.

In contrast, the non-ischemic wounds on the mice showed abundant levels of the E2F3 protein and healed normally within about seven days.

To test these relationships further, the researchers set up experiments using a line of human skin cells most responsible for closing over a wound.

Under normal oxygen levels, the scientists manipulated the cells to activate the HIF-1a protein that normally is induced by hypoxia. When the HIF-1a was present, the cells contained high levels of the miR-210, which in turn lowered levels of the E2F3 protein.

The researchers further manipulated these conditions by inserting an experimental drug into the cells called an antagomir, a synthetic molecule that renders microRNAs inactive and which was designed to act specifically on miR-210. When the miR-210 levels were lowered with the antagomir, the E2F3 protein levels rose and the skin-cell growth increased significantly. When the miR-210 levels were artificially raised using a molecule that mimics its behavior, the skin cells' growth was compromised.

"MicroRNAs are induced only by certain conditions. They have specific profiles in the daily biology of a given organ, but under conditions of an injury, certain microRNAs wake up," Sen said. "Once it sees hypoxia, miR-210 wakes up, and then it governs what happens with the E2F3 protein after that."

Antagomirs are a burgeoning area of drug development research. They are considered potent agents that can interfere with microRNA behavior throughout the body. Their use in wound healing, on the other hand, might benefit from the need to use them only topically on the skin, Sen said. He plans to investigate their effects on wounds in further animal studies.

The National Institutes of Health supported this research.

Co-authors on the paper are Sabyasachi Biswas, Sashwati Roy, Jaideep Banerjee, Syed- Rehan Hussain and Savita Khanna of the Department of Surgery; Gurugahan Meenakshisundaram and Periannan Kuppusamy of the Department of Internal Medicine; and Avner Friedman of the Mathematical Biosciences Institute, all at Ohio State.

Journal Reference:
Sabyasachi Biswas, Sashwati Roy, Jaideep Banerjee, Syed-Rehan A. Hussain, Savita Khanna, Guruguhan Meenakshisundaram, Periannan Kuppusamy, Avner Friedman, and Chandan K. Sen. Hypoxia inducible microRNA 210 attenuates keratinocyte proliferation and impairs closure in a murine model of ischemic wounds. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.1001653107


Cracking the Plant-Cell Membrane Code

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ScienceDaily (Mar. 23, 2010) — To engineer better, more productive crops and develop new drugs to combat disease, scientists look at how the sensor-laden membranes surrounding cells control nutrient and water uptake, secrete toxins, and interact with the environment and neighboring cells to affect growth and development. Remarkably little is known about how proteins interact with these protective structures. With National Science Foundation funding, researchers at the Carnegie Institution's Department of Plant Biology are using the first high-throughput screen for any multicellular organism to pinpoint these interactions using the experimental plant Arabidopsis.

They have analyzed some 3.4 million potential protein/membrane interactions and have found 65,000 unique relationships. They made the preliminary data available to the biological community by way of the website Since proteins are similar in all organisms, the work is relevant to fields from farming to medicine.

"This is just the beginning," remarked Wolf Frommer director of Carnegie's Department of Plant Biology. "Arabidopsis shares many of its genes with other organisms including humans. As the library of interacting proteins grows, scientists around the world will be able to study the details of protein interactions to understand how they are affected by forces such as climate change and disease and how they can be harnessed to produce better crops and medicines more effectively."

All of a cell's internal machinery relies on the binding of proteins. Complementary shaped proteins dock with one another to start processes, such as turning on a gene or letting in the proper nutrient. These membrane proteins make up some 20-30% of the proteins in Arabidopsis, a relative of the mustard plant.

The team uses a screen called the mating-based protein complementation assay, or split ubiquitin system. Ubiquitin is a small protein. The scientists fuse candidate proteins onto a version of ubiquitin that is split in half. When the two candidates interact, the two halves of the ubiquitin reassemble, triggering a process that liberates a transcription factor -- a protein that switches a gene on -- which then goes to the nucleus. When genes are turned on in the nucleus, the researchers are alerted to the successful interaction. The ultimate goal is to test the 36 million potential interactions as well as the sensitivity of the interactions to small molecules with a high-throughput robotics system.

The group plans to start a second round of screening at the end of this month to test another 3.4 million interactions.

This work was made possible by grants from NSF 2010 : Towards a comprehensive Arabidopsis protein interactome map: Systems biology of the membrane proteins and signalosomes (grant MCB-0618402) in addition to support from Carnegie. Other participants on the 2010 project include UCSD, Penn State and the University of Maryland. The group previously donated 2010 clones to the Arabidopsis Biological Resource Center (ABRC is at Ohio State University), and more recently another 1010 for other scientists to use to help advance fields from medicine to farming.


How Plants Put Down Roots: Geneticists Research Organ Development in the Plant Embryo

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ScienceDaily (Mar. 16, 2010) — In the beginning is the fertilized egg cell. Following numerous cell divisions, it then develops into a complex organism with different organs and tissues. The largely unexplained process whereby the cells simply "know" the organs into which they should later develop is an astonishing phenomenon.

Scientists from the Center for Plant Molecular Biology (ZMBP) of the University of Tübingen and the University of Wageningen, in cooperation with colleagues from the Max Planck Institute for Developmental Biology, have investigated how this process is controlled. Based on their studies of the thale cress, Arabidopsis thaliana, they have succeeded in demonstrating how the plant forms its first roots: the root founder cell in the tiny group of cells contained in the seed is activated by a combination of a plant hormone and a transcription factor. These insights could contribute to the breeding of plants with a particularly effective root system in the future.

The research appears in Nature, advance online publication on March 10, 2010.

In the seed of the thale cress, the embryo forms from the fertilised egg cell that initially divides into two daughter cells. One of these two cells later goes on to form almost the entire embryo, while the other generates connective tissue that anchors the embryo in the endosperm or nutritive tissue. When the embryo has grown into a small cluster of cells, the connective tissue cell that borders the embryo is stimulated by activating signals to become part of the embryo and form the root tissue.

The scientists studied these processes in detail under the supervision of Gerd Jürgens and Dolf Weijers and succeeded in identifying several of the players involved in this complex regulatory network.The formation of the root tissue depends firstly on the accumulation of the plant hormone auxin, which is channelled to the root founder cell by the embryo. This process is reinforced by the transcription factor MONOPTEROS. However, this is not sufficient on its own.

The researchers concluded that MONOPTEROS must deliberately activate other genes. In a comprehensive survey of all of the genes activated by MONOPTEROS, they identified two genes that already play a role in embryonic development: TMO5 and TMO7 (TMO = Target of MONOPTEROS). Both of these genes are required for the formation of the root tissue. For this purpose, the protein formed by the TMO7 gene must migrate from the location of its emergence in the embryo to the root founder cell.

"With TM07 we have identified a hitherto unknown intercellular signal for root formation in the embryo," says Gerd Jürgens. The detective work in the plant researchers' genetics laboratory does not end here, however. "Because the transcription factor TM07 is involved in other regulatory network of plant development, there can be no doubt that it holds further insights in store for us," says Jürgens.

Journal Reference:
Alexandra Schlereth, Barbara Möller, Weilin Liu, Marika Kientz, Jacky Flipse, Eike H. Rademacher, Markus Schmid, Gerd Jürgens und Dolf Weijers. MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature, 2010;
DOI: 10.1038/nature08836


Mouse Work: New Insights on a Fundamental DNA Repair Mechanism

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ScienceDaily (Mar. 23, 2010) — Adding a new link to our understanding of the complex chain of chemistry that keeps living cells alive, a team of researchers from the University of Vermont (UVM), the University of Utah, Vanderbilt University and the National Institute of Standards and Technology (NIST) has demonstrated for the first time the specific activity of the protein NEIL3, one of a group responsible for maintaining the integrity of DNA in humans and other mammals.

Their work, published in the Proceedings of the National Academy of Sciences, sheds new light on a potentially important source of harmful DNA mutations.

Since it first was identified about eight years ago, NEIL3 has been believed to be a basic DNA-maintenance enzyme of a type called a glycosylase. These proteins patrol the long, twisted strands of DNA looking for lesions -- places where one of the four DNA bases has been damaged by radiation or chemical activity. They cut the damaged bases free from the DNA backbone, kicking off follow-on mechanisms that link in the proper undamaged base. The process is critical to cell health, says NIST biochemist and Senior Research Fellow Miral Dizdaroglu, "DNA is damaged all the time. About one to two percent of oxygen in the body becomes toxic in cells, for example, creating free radicals that damage DNA. Without these DNA repair mechanisms there wouldn't be any life on this planet, really."

The glycosylases seem to be highly specific; each responds to only a few unique cases of the many potential DNA base lesions. Figuring out exactly which ones can be challenging. NEIL3 and its kin NEIL1 and NEIL2 are mammalian versions of an enzyme found in the bacterium E. coli, which first was identified in work at UVM. The lesion targets of NEIL1 and NEIL2 have been known for some time, but NEIL3, a much more complicated protein twice the size of the others, had resisted several attempts to purify it and determine just what it does. In a significant advance, a research team at UVM managed to clone the house mouse version of NEIL3 (99 percent identical to the human variant), and then prepare a truncated version of it that was small enough to dissolve in solution for analysis but large enough to retain the portion of the protein that recognizes and excises DNA lesions.

Using a technique they developed for rapidly analyzing such enzymes, NIST researchers Dizdaroglu and Pawel Jaruga mixed the modified protein with sample DNA that had been irradiated to produce large numbers of random base lesions. Because glycosylases work by snipping off damaged bases, a highly sensitive analysis of the solution after the DNA has been removed can reveal just which lesions are attacked by the enzyme, and with what efficiency. The NIST results closely matched independent tests by others in the team that match the enzyme against short lengths of DNA-like strands with a single specific target lesion.

In addition to finally confirming the glycosylase nature of NEIL3, says UVM team leader Susan Wallace, tests of the enzyme in a living organism -- a tailored form of E. coli designed to have a very high mutation rate -- had an unexpected bonus. Measurements at NIST showed that NEIL3 is extremely effective at snipping out a particular type of lesion called FapyGua (2,6-diamino-4-hydroxy-5-formamidopyrimidine) and seems to dramatically reduce mutations in the bacterium, a result that points both to the effectiveness of NEIL3 and the potentially important role of FapyGua in causing dangerous mutations in DNA.

Journal Reference:
M. Liu, V. Bandaru, J.P. Bond, P. Jaruga, X. Zhao, P.P. Christov, C.J. Burrows, C.J. Rizzo, M. Dizdaroglu and S.S. Wallace. The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo. Proceedings of the National Academy of Sciences, 2010;
DOI: 10.1073/pnas.0908307107


Monday, March 22, 2010

Biology May Not Be So Complex After All, Physicist Finds

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ScienceDaily (Mar. 19, 2010) — Centuries ago, scientists began reducing the physics of the universe into a few, key laws described by a handful of parameters. Such simple descriptions have remained elusive for complex biological systems -- until now.

Emory biophysicist Ilya Nemenman has identified parameters for several biochemical networks that distill the entire behavior of these systems into simple equivalent dynamics. The discovery may hold the potential to streamline the development of drugs and diagnostic tools, by simplifying the research models.

The resulting paper, now available online, will be published in the March issue of Physical Biology.

"It appears that the details of the complexity of these biological systems don't matter, as long as some aggregate property, which we've calculated, remains the same," says Nemenman, associate professor of physics and biology. He conducted the analysis with Golan Bel and Brian Munsky of the Los Alamos National Laboratory.

The simplicity of the discovery makes it "a beautiful result," Nemenman says. "We hope that this theoretical finding will also have practical applications."

He cites the air molecules moving about his office: "All of the crazy interactions of these molecules hitting each other boils down to a simple behavior: An ideal gas law. You could take the painstaking route of studying the dynamics of every molecule, or you could simply measure the temperature, volume and pressure of the air in the room. The second method is clearly easier, and it gives you just as much information."

Nemenman wanted to find similar parameters for the incredibly complex dynamics of cellular networks, involving hundreds, or even thousands, of variables among different interacting molecules. Among the key questions: What determines which features in these networks are relevant? And if they have simple equivalent dynamics, did nature choose to make them so complex in order to fulfill a specific biological function? Or is the unnecessary complexity a "fossil record" of the evolutionary heritage?

For the Physical Biology paper, Nemenman and co-authors investigated these questions in the context of a kinetic proofreading (KPR) scheme.

KPR is the mechanism a cell uses for optimal quality control as it makes protein. KPR was predicted during the 1970s and it applies to most cellular assembly processes. It involves hundreds of steps, and each step may have different parameters.

Nemenman and his colleagues wondered if the KPR scheme could be described more simply. "Our calculations confirmed that there is, in fact, a key aggregate rate," he says. "The whole behavior of the system boils down to just one parameter."

That means that, instead of painstakingly testing or measuring every rate in the process, you can predict the error and completion rate of a system by looking at a single aggregate parameter.

Charted on a graph, the aggregate behavior appears as a straight line amid a tangle of curving ones. "The larger and more complex the system gets, the more the aggregate behavior is visible," Nemenman says. "The completion time gets simpler and simpler as the system size goes up."

Nemenman is now collaborating with Emory theoretical biologist Rustom Antia, to see if the discovery can shed light on the processes of immune cells. In particular, they are interested in the malfunction of certain immune receptors involved in most allergic reactions.

"We may be able to simplify the model for these immune receptors from about 3,000 steps to three steps," Nemenman says. "You wouldn't need a supercomputer to test different chemical compounds on the receptors, because you don't need to simulate every single step -- just the aggregate."

Just as the discovery of an ideal gas law led to the creation of engines and automobiles, Nemenman believes that such simple biochemical aggregates could drive advancements in health.

Journal Reference:
Golan Bel, Brian Munsky, Ilya Nemenman. The simplicity of completion time distributions for common complex biochemical processes. Physical Biology, 2009; 7 (1): 016003
DOI: 10.1088/1478-3975/7/1/016003


How Cells Protect Themselves from Cancer

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ScienceDaily (Mar. 18, 2010) — Cells have two different protection programs to safeguard them from getting out of control under stress and from dividing without stopping and developing cancer. Until now, researchers assumed that these protective systems were prompted separately from each other. Now for the first time, using an animal model for lymphoma, cancer researchers of the Max Delbrück Center (MDC) Berlin-Buch and the Charité -- University Hospital Berlin in Germany have shown that these two protection programs work together through an interaction with normal immune cells to prevent tumors.

The findings of Dr. Maurice Reimann and his colleagues in the research group led by Professor Clemens Schmitt may be of fundamental importance in the fight against cancer. The research appears in the journal Cancer Cell.

Researchers have known for some time that -- paradoxically -- oncogenes themselves can activate these cell protection programs in an early developmental stage of the disease. This may explain why some tumors take decades to develop until the outbreak of the disease. The Myc oncogene triggers apoptosis (programmed cell death), inducing damaged cells to commit suicide in order to protect the organism as a whole. By means of chemotherapy, physicians activate this protection program to treat cancer.

The second protection program -- not as well understood as apoptosis -- is senescence (biological aging). This program is triggered by another oncogene, the ras gene. Senescence stops the cell cycle, and the cell can no longer divide. But in contrast to apoptosis the cell continues to live and is still metabolically active. Professor Schmitt, physician at Charité University Hospital and research group leader at the MDC, was able to show on an animal model for lymphoma that senescence can block the development of early-stage malignant tumors.

Myc oncogene triggers cascade to activate both protection programs

Now, for the first time, Dr. Reimann, Dr. Soyoung Lee, Dr. Christoph Loddenkemper, Dr. Jan R. Dörr, Dr. Vedrana Tabor and Professor Schmitt have provided evidence that the Myc oncogene plays a key role in the activation of both protection programs -- without the presence of the ras oncogene. "What is remarkable about this finding is that an oncogene can first trigger apoptosis and interact with the tumor stroma -- the tissue that surrounds the tumor which also contains healthy cells -- and with the immune system and then is able to switch on signals which lead to tumor senescence," Professor Schmitt said, summarizing how the interaction works.

"Fundamental significance"

According to the researchers' findings, the cascade occurs as follows: First the Myc oncogene triggers apoptosis in the lymphoma cells. The dying, apoptotic cells attract macrophages of the immune system, which devour and dispose of the dead lymphoma cells. The thus activated macrophages in turn secrete messenger molecules (cytokines), including the cytokine TGF-beta. It can block the growth of cancer cells in the early stage of a tumor disease. The MDC and Charité researchers discovered that the cytokines in the tumor cells that had escaped apoptosis switch on the senescence program and suppress the cancer cells.

"Our findings promise to have fundamental significance for elucidating the pathogenesis not only of lymphoma cancers, but of cancer in general. Our results indicate that senescence triggered by the immune system's messenger molecules may be a further important active principle, apart from apoptosis induced by chemotherapy."

At present the researchers in Professor Schmitt's group are focusing intensively on chemotherapy-mediated senescence. "If by inducing senescence we could obtain a sustained suppression of the cancer cells we can no longer destroy, this would mean exciting new possibilities for therapy," Professor Schmitt said.

Journal Reference:
Maurice Reimann, Soyoung Lee, Christoph Loddenkemper, Jan R. Dörr, Vedrana Tabor, Peter Aichele, Harald Stein, Bernd Dörken, Thomas Jenuwein, and Clemens A. Schmitt. Tumor Stroma-Derived TGF-β Limits Myc-Driven Lymphomagenesis via Suv39h1-Dependent Senescence. Cancer Cell, 2010; 17 (3); 262-272 DOI: 10.1016/j.ccr.2009.12.043


Omega 3 Curbs Precancerous Growths in Those Prone to Bowel Cancer, Study Suggests

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ScienceDaily (Mar. 21, 2010) — A purified form of an omega 3 cuts the number and size of precancerous bowel growths (polyps) in people whose genetic make-up predisposes them to bowel cancer, finds research published ahead of print in the journal Gut. Furthermore, this particular omega 3 (eicosapentaenoic acid or EPA) seems to be as effective as the prescription medicine used to treat familial bowel polyps, but without the associated cardiovascular side effects.

The researchers base their findings on 55 patients, all of whom had the inherited genetic mutation that prompts the development of precancerous polyps in the bowel -- known as familial adenomatous polyposis, or FAP for short.

People with FAP are at significantly increased risk of developing bowel cancer and require surgery to remove large sections of their bowel. Subsequently, some also need regular monitoring. All 55 patients had previously undergone surgery and were being monitored by endoscopy -- a procedure involving a camera on the end of a flexible tube passed through the rectum.

Twenty eight of the patients were randomly assigned to six months of treatment with 2 g daily of a new highly purified form of the omega 3 polyunsaturated fatty acid (PUFA) EPA. The other 27 were given the same amount of a dummy treatment (placebo).

The EPA capsules were enteric coated to prevent the indigestion that can sometimes be associated with omega 3 supplements. Dietary omega 3 PUFA mainly comes from oily fish, such as salmon, mackerel, and herring.

An assessment of the number and size of polyps at the beginning and end of the six month study period revealed significant differences between the two groups of patients. The number of polyps increased by almost 10% among those treated with the placebo, but fell by more than 12% among those treated with the EPA capsules, representing a difference of almost 22.5%.

This was still clinically significant, even after taking account of influential factors, such as age and sex.

Similarly, polyp size increased by more than 17% among those in the placebo group but fell by more than 12.5% in those taking the EPA capsules, representing a difference of just under 30%.

The authors note that the effects of EPA were similar to those produced by celecoxib, which is used to help curb the growth of new and existing polyps in patients with FAP.

The use of celecoxib has been associated with harmful cardiovascular side effects in older patients. In this study, EPA produced few side effects and these were no more common than those produced by the placebo. This formulation of omega 3 might also help to prevent bowel cancer in people with the common non-familial form of bowel polyps, suggest the authors. As omega 3 PUFAs in general are safe and even good for cardiovascular health, EPA could be especially suitable for older patients at risk of both bowel cancer and heart disease, they say.


Read also:
Wikipedia - Eicosapentaenoic acid
University of Maryland Medical Center - Eicosapentaenoic acid (EPA)

Fruit Flies and Test Tubes Open New Window on Alzheimer's Disease

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ScienceDaily (Mar. 16, 2010) — A team of scientists from Cambridge and Sweden have discovered a molecule that can prevent a toxic protein involved Alzheimer's disease from building up in the brain. They found that in test tube studies the molecule not only prevents the protein from forming clumps but can also reverse this process. Then, using fruit flies with Alzheimer's disease, they showed that the same molecule effectively "cures" the insects of the disease.

Alzheimer's disease is the most common neurodegenerative disorder and is linked to the misfolding and aggregation of a small protein known as the amyloid β (Aβ) peptide. Previous studies in animal models have shown that aggregation of Aβ damages neurones (brain cells) causing memory impairment and cognitive deficits similar to those seen in patients with Alzheimer's disease. The mechanisms underlying this damage are, however, still not understood.

The new molecule -- designed by scientists in Sweden -- is a small protein known as an Affibody (an engineered binding protein). In this new study, researchers at the University of Cambridge and the Swedish University of Agricultural Sciences found that in test-tube experiments this protein binds to the Aβ peptide, preventing it from forming clumps and breaking up any clumps already present.

In a second experiment, they studied the effect of this Affibody in a Drosophila (fruit fly) model of Alzheimer's disease previously developed at Cambridge.

Working with fruit flies that develop the fly equivalent of Alzheimer's because they have been genetically engineered to produce the Aβ protein, they crossed these flies with a second line of flies genetically engineered to produce the Affibody.

They found that offspring -- despite producing the Aβ protein -- did not develop the symptoms of Alzheimer's disease.

According to lead author Dr Leila Luheshi of the Department of Genetics at University of Cambridge: "When we examined these flies we found that the Affibody not only prevented and reversed the formation of Aβ clumps, it also promoted clearance of the toxic Aβ clumps from the flies' brains."

"Finding a way of preventing these clumps from forming in the brain, and being able to get rid of them, is a promising strategy for preventing Alzheimer's disease. Affibody proteins give us a window into the Alzheimer's brain: by helping us understand how these clumps damage brain cells, they should help us unravel the Alzheimer's disease process."

According to Professor Torleif Härd of the Swedish University of Agricultural Sciences and one of the senior authors of the study: "Our work shows that protein engineering could open up new possibilities in Alzheimer's therapy development."

The study was supported by grants from the Swedish Research Council, the MIVAC Swedish Foundation for Strategic Research Centre, the German Academic Exchange Service, and in the UK by the MRC, the Engineering and Physical Sciences Research Council and the Wellcome Trust.

Journal Reference:
Luheshi et al. Sequestration of the Aβ peptide prevents toxicity and promotes degradation in vivo. PLoS Biology, 2010; 8 (3): e1000334
DOI: 10.1371/journal.pbio.1000334


Chemists Influence Stem-Cell Development With Geometry

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ScienceDaily (Mar. 18, 2010) — University of Chicago scientists have successfully used geometrically patterned surfaces to influence the development of stem cells. The new approach is a departure from that of many stem-cell biologists, who focus instead on uncovering the role of proteins in controlling the fate of stem cells.

"The cells are seeing the same soluble proteins. In both cases it's the shape alone that's dictating whether they turn into fat or bone, and that hasn't been appreciated before," said Milan Mrksich, Professor in Chemistry and a Howard Hughes Medical Institute Investigator, who led the study. "That's exciting because stem-cell therapies are of enormous interest right now, and a significant effort is ongoing to identify the laboratory conditions that can take a stem cell and push it into a specific lineage."

The UChicago team found that making cells assume a star shape promotes a tense cytoskeleton, which provides structural support for cells, while a flower shape promotes a looser cytoskeleton. "On a flower shape you get the majority of cells turning to fat, and on a star shape you've got the majority of cells turning into bone," said Kris Kilian, a National Institutes of Health Fellow in Mrksich's research group. The UChicago team published its findings in the March 1 Early Edition of the Proceedings of the National Academy of Sciences.

Mrksich cautioned that the method is far from ready for use in the harvest of stem cells for therapeutic use, but it does signal a potentially promising direction for further study.

Mrksich's research group has a long history of developing methods for patterning surfaces with chemistry to control the positions, sizes and shapes of cells in culture, and applying those patterned cells to drug-discovery assays, and studies of cell migration and cell adhesion.

Funding was provided by the National Cancer Institute and the National Institute of General Medical Sciences.

Journal Reference:
Kristopher A. Kilian, Branimir Bugarija, Bruce T. Lahn, and Milan Mrksich. Geometric cues for directing the differentiation of mesenchymal stem cells. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0903269107


Notch Protein: Opposing Functions of Key Molecule in Development of Organisms

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ScienceDaily (Mar. 12, 2010) — Scientists headed by ICREA researcher Marco Milán, at the Institute for Research in Biomedicine (IRB Barcelona), reveal a surprising new function of Notch protein that contrasts with the one known to date. Found in the cell membrane, this protein activates a signalling pathway that regulates the expression of genes that make the cell divide, grow, migrate, specialise or die. Notch activity is required for the correct development of organisms and for the maintenance of tissues in adults.

When Notch acts at an incorrect time or in an incorrect context, it can give rise to the generation of tumours, among these leukaemia, breast cancer, colon cancer, skin cancer, lung cancer and renal carcinomas.

"The same pathways responsible for the development and growth of organisms are involved in the transformation of healthy cells into cancerous ones," says Marco Milán, so "all new data on the modulation of Notch activity, the first step in the chain, may be relevant for the design of effective therapies." Marco Milán's group has now discovered that the presence of Notch proteins in the cell membrane is also required to inactivate the pathway. The description of the new role of Notch, found in the fly Drosophila melanogaster, and the mechanism that regulates this function have been published in the journal Current Biology, which belongs to the Cell group.

Stop! Notch is a double agent

In order for the Notch pathway to be activated, ligand-type proteins from neighbouring cells bind to the Notch receptor. When the ligand and receptor come into contact, the Notch receptor is processed and the intracellular part moves to the nucleus to activate gene expression. This is the basic and "extremely simple activation system" of the Notch signalling pathway, which is based on short distance contact between cells through a ligand and a receptor.

In a developing wing and through a technique called Clonal Analysis, the researchers manipulated groups of cells, among groups of normal cells, to remove Notch receptor expression. The scientists used the Drosophila wing because it is an excellent model to describe how cells behave when a certain gene is mutated and to determine and test how this mutation affects adjacent cells. This was the objective of the study designed by Isabelle Becam, post-doctoral researcher in Milán's Group and first author of the article. "As expected, the cells lacking Notch did not activate the pathway, but what was surprising was the observation that neighbouring cells did." Becam then questioned whether the absence of Notch in a group of mutated cells could cause activation.

Indeed, the analyses demonstrated that the Notch receptor sequesters the ligands and prevents these from connecting to the Notch receptors of adjoining cells. The experiments showed that the absence of the receptor in the mutated cells leaves many ligands free, ready to enter into contact with Notch receptors of the non-manipulated cells. "It is strange, but in the cell emitting the signal, Notch receptor captures the ligands by acting as a silencer while in the cell receiving the signal the binding of ligands with Notch allows activation of the pathway." "In fact," says Milán, "it is all to do with a fine balance between ligands and receptors of the emitting and receiving cell." In other words, Notch is a kind of double agent and exerts opposing functions: repressing or activating the pathway depending on whether it is located in cells emitting or receiving the signal. It must be noted that such a simple activation system involves multiple repression mechanisms, "because this is a crucial but also dangerous signalling pathway," explains Milán.

The researchers have discovered the self-repression mechanism of Notch in Drosophila and it should be checked now whether this also operates in mice and humans. They speculate that it does because the ligand-receptor system of Notch activation has been conserved in all organisms. "If this new mechanism is also present in vertebrates, it should be taken into consideration when designing effective therapies against certain kinds of cancer, such as T-cell acute lymphoblastic leukaemia (T-ALL)," concludes Milán.

It is well established that the Notch pathway controls the development of T lymphocytes, cells of the immune response system found in blood. The cells destined to become lymphocytes receive the appropriate signalling through Notch receptors. In more than half T-ALL patients the Notch receptor is permanently activated in the T-cell precursors. Thus the continuous proliferation of cells is stimulated until tumours form. "A priori, blocking the Notch receptor could appear to be a good strategy to combat this kind of leukaemia. However, the results of our work suggest that blocking the receptor only in some cells would cause undesirable effects in adjacent cells," warns Milán.

Journal Reference:
Isabelle Becam, Ulla-Maj Fiuzza, Alfonso Martínez-Arias and Marco Milán. A role of Notch in ligand cis-inhibition in Drosophila. Current Biology, DOI: 10.1016/j.cub.2010.01.058


Computational Feat Speeds Finding of Genes to Milliseconds Instead of Years

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ScienceDaily (Mar. 16, 2010) — Like a magician who says, "Pick a card, any card," Stanford University computer scientist Debashis Sahoo, PhD, seemed to be offering some kind of trick when he asked researchers at the Stanford Institute for Stem Cell Biology and Regenerative Medicine to pick any two genes already known to be involved in stem cell development. Finding such genes can take years and hundreds of thousands of dollars, but Sahoo was promising the skeptical stem cell scientists that, in a fraction of a second and for practically zero cost, he could find new genes involved in the same developmental pathway as the two genes provided.

Sahoo went on to show that this amazing feat could actually be performed. The proof-of- principle for his idea, to be published online March 15 in the Proceedings of the National Academy of Sciences, opens a powerful, mathematical route for conducting stem cell research and shows the power of interdisciplinary collaborations in science. It also demonstrates that using computers to mine existing databases can radically accelerate research in the laboratory. Ultimately, it may lead to advances in diverse areas of medicine such as disease diagnosis or cancer therapy.

Biologists have long used math and statistics in their work. In the simplest case, when looking for genes involved in a certain biological process, they look for genes that have a symmetrical correlation. For instance, if they know gene A is involved in a certain process, they try to determine if gene C is correlated with gene A during the same process.

Four years ago, while studying for his doctorate in electrical engineering with advisor David Dill, PhD, professor of computer science, and co-advisor Sylvia Plevritis, PhD, associate professor of radiology, Sahoo took an immunology class and realized that many of the relationships in biology are not symmetric, but asymmetric. As an analogy, Sahoo noted that trees bearing fruit almost certainly have leaves, but trees outside of the fruiting season may or may not have leaves, depending on the time of year.

Sahoo and Dill realized that these asymmetric relationships could be found by applying Boolean logic, in which the researchers established a series of if/then rules and then searched data for candidates that satisfied all the rules. For example, scientists might know that gene A is very active at the beginning of cell development, and gene C is active much later. By screening large public databases, Sahoo can find the genes that are almost never active when A is active, and almost always active when C is active, in many other types of cells. Researchers can then test to determine whether these genes become active between the early and late stages of development.

In the paper, lead author Sahoo looked at gene expression patterns in the development of an immunological cell called a B cell. Starting with two known B-cell genes, Sahoo searched through databases with thousands of gene products in milliseconds and found 62 genes that matched the patterns he would expect to see for genes that got turned on in between the activation of the two genes he started with. He then examined databases involving 41 strains of laboratory mice that had been engineered to be deficient in one or more of the 62 genes. Of those 41 strains, 26 had defects in B cell development.

"This was the validation of the method," Sahoo said. "Biologists are really amazed that, with just a computer algorithm, in milliseconds I can find genes that it takes them a really long time to isolate in the lab." He added that he was especially gratified that the information comes from databases that are widely available and from which other scientists have already culled information.

Sahoo is now using the technique to find new genes that play a role in developing cancers.

"This shows that computational analysis of existing data can provide clues about where researchers should look next," he said. "This is something that could have an impact on cancer. It's exciting."

The interdisciplinary team that contributed to the findings involved researchers at both the School of Engineering and the School of Medicine. In addition to Dill (the paper's senior author) and Plevritis, the co-authors include Irving Weissman, MD, director of Stanford's stem cell institute, and postdoctoral scholars Jun Seita, PhD, Matthew Inlay, PhD, and Deepta Bhattacharya, PhD, who recently moved from Stanford to the Washington University School of Medicine in St. Louis.

Funding for this research came from the National Institutes of Health, the Siebel Stem Cell Institute, the Thomas and Stacey Siebel Foundation, the Cancer Research Institute, the National Cancer Institute and the California Institute for Regenerative Medicine.

Journal Reference:
Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Matthew A. Inlay, Irving L. Weissman, Sylvia K. Plevritis, and David L. Dill. MiDReG: A method of mining developmentally regulated genes using Boolean implications. Proceedings of the National Academy of Sciences, 2010;
DOI: 10.1073/pnas.0913635107


Breakthrough Blueprint for Studying Differentiation and Evolution With New Atlas of Transcription Factor Combinations

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ScienceDaily (Mar. 8, 2010) — In a significant leap forward in the understanding of how specific types of tissue are determined to develop in mammals, an international team of scientists has succeeded in mapping the entire network of DNA-binding transcription factors and their interactions. This global network, indicating which factors can combine to determine cell fate, will be published in the March 5 issue of the journal Cell.

Transcription factors (TFs) are proteins that bind to specific DNA sequences in order to direct which genes should be turned on or off in a tissue. Tissue specificity -- whether embryonic tissue develops into lungs or kidneys or skin, for example -- is determined by how and which TFs bind to genes. Between 2,000 and 3,000 transcription factor proteins are encoded by the human genome, potentially creating more than 4 million potential protein pairings.

It has long been appreciated that different combinations of TFs are active in different tissues. But given the enormous number of TFs and potential pairings, it has been difficult to precisely identify which combinations are functional, according to principal investigator Trey Ideker, PhD, chief of the Division of Genetics at the University of California, San Diego, School of Medicine.

The integrated approach to systematically map all possible combinations of TFs in mammals has generated large data sets in both humans and mice. The complete network contains 762 human and 877 mouse interactions between TFs, indicating TF pairs that can work in combination.

"The availability of this large combinatorial network of transcription factors will provide scientists with many opportunities to study gene regulation, tissue differentiation and evolution in mammals," said Ideker, professor in the Department of Medicine and at UCSD's Jacobs School of Engineering. He added that analysis of the network shows that highly connected TFs are broadly expressed across tissues, and that roughly half of the interactions are conserved between mouse and human.

The researcher team identified nearly 1,000 different pairs of TF proteins that can be wired together, representing the blueprint of all possible combinations that direct gene expression in mammals. The work may provide researchers with the clues necessary to one day determine how stem cells can be reprogrammed into a particular organ or tissue type.

The research team comprised 41 scientists from 17 different institutions around the world led by UC San Diego, the RIKEN Institute in Japan, and King Abdullah University of Science and Technology in Saudi Arabia. Members of UC San Diego were supported by a grant from the National Institute of Mental Health. Researchers at the RIKEN Omics Science Center were supported by the Japanese Ministry of Education, Culture, Sports, Science and Technology.

Journal Reference:
Timothy Ravasi, Harukazu Suzuki, Carlo Vittorio Cannistraci, Shintaro Katayama, Vladimir B. Bajic, Kai Tan, Altuna Akalin, Sebastian Schmeier, Mutsumi Kanamori-Katayama, Nicolas Bertin, Piero Carninci, Carsten O. Daub, Alistair R.R. Forrest, Julian Gough, Sean Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, Hideya Kawaji, Atsutaka Kubosaki, Timo Lassmann, Erik van Nimwegen, Chihiro Ogawa, Rohan D. Teasdale, Jesper Tegner, Boris Lenhard, Sarah A. Teichmann, Takahiro Arakawa, Noriko Ninomiya, Kayoko Murakami, Michihira Tagami, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ryoko Ishihara, Yayoi Kitazume, Jun Kawai, David A. Hume, Trey Ideker, Yoshihide Hayashizaki. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell, 2010; 140 (5): 744-752
DOI: 10.1016/j.cell.2010.01.044


Switch Mechanism for Controlling Traffic in Cells Discovered

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ScienceDaily (Mar. 18, 2010) — Scientists have identified a mechanism that switches on an extremely important process for the proper functioning and survival of our body's cells. Specifically, the fast-track transportation pathway of 'cargo' to and from the surface of the cell. Defects in this trafficking pathway can have severe consequences, leading to numerous diseases such as high cholesterol, neuropathies, sterility and complications in immune response. Understanding the mechanisms underlying these disorders is crucial to developing possible treatments and new therapeutic strategies.

Dr. Peter McPherson and Dr. Brigitte Ritter and their colleagues have discovered how a molecule called Rab35, which acts as a switch is turned on in order to activate the fast-track recycling pathway -- in which cargo that needs to be recycled back to the surface of the cell is rapidly selected and transported. The new study, published in the journal Molecular Cell, was conducted at The Montreal Neurological Institute and Hospital -- The Neuro, McGill University.

"The cells that make up our bodies are like a busy city," says Dr. McPherson, neuroscientist at The Neuro and the co-principal investigator for the study. "The cell surface is defined by a membrane that separates its interior from the external world, like the walls or borders of a city. Within this environment, there are simultaneous trafficking pathways that transport vital nutrients, receptors and other components required for cells to function, within cargo vehicles called 'vesicles.' Like traffic in a city, these 'cargo' vesicles travel at different speeds to numerous destinations within the cell with different purposes. For example, the receptors on the cell surface that bind to cholesterol are on the fast track pathway, so that once they deliver the cholesterol inside the cell, they move back to the surface quickly so that they can pick up some more. It is therefore crucial to understand the controls and switching mechanisms of trafficking inside cells, as this system is of vital importance to the proper functioning of the body."

The Rab35 molecule is the trafficking switch for the fast-track or high-priority recycling pathway signaling the quick return of cargo to the cell surface membrane. It is known that Rab35 exists in two forms, 'on' (GTP- bound) or off (GDP- bound). When Rab35 is turned 'on', it allows the cargo to go back up to the cell surface. What Dr. McPherson and Dr. Ritter and colleagues have discovered is the switch that turns Rab35 on.

"In this study we identified that a particular region of the vesicle-bound protein connecden, , called the DENN domain, is the 'finger' that flips the switch," says Dr. Ritter. "The DENN domain connects with the Rab35 molecule and through enzymatic activity converts Rab35 from the inactive to the active form, in essence, turning on the switch."

DENN domains are found in multiple protein products encoded by 16 human genes. Mutations in the DENN domain cause humans diseases such as sterility and Charcot-Marie-Tooth neuropathy, yet until now the function of this common module has been unknown. The DENN domain is evolutionarily ancient and bioinformatics studies suggest that it is present in all eukaryotic, or multi-compartmental cells, indicating that the DENN domain has mediated crucial functions throughout evolution.

"If the finger or the switch itself is mutated or missing, cargo can't recycle, which has dire consequences," adds Dr. McPherson. "For example a very important cargo transported by this specific fast track recycling pathway, controlled by Rab35 is the MHC class I receptor involved in the immune system response. If a cell becomes infected by a virus, the MHC receptor is loaded with fragments of the virus that have infected the inside of a cell. The MHC receptor needs to be taken back to the cell surface quickly so that so that it can act as a signpost indicating to circulating immune cells that this particular cell has been infected by a virus and needs to be destroyed, preventing viral infection to other cells."

This critical new insight into the control mechanisms for the cells' trafficking system provide a deeper understanding of diseases that result from complications in trafficking, as well as provide new therapeutic targets for the development of treatments.

This study was supported by the Fonds de la recherche en sante du Quebec (FRSQ), the Canadian Institutes of Health Research (CIHR) and the National Institutes of Health (NIH).

Journal Reference:
Patrick D. Allaire, Andrea L. Marat, Claudia Dall'Armi, Gilbert Di Paolo, Peter S. McPherson, Brigitte Ritter. The Connecdenn DENN Domain: A GEF for Rab35 Mediating Cargo-Specific Exit from Early Endosomes. Molecular Cell, 2010; 37 (3): 370-382
DOI: 10.1016/j.molcel.2009.12.037


Wednesday, March 17, 2010

EFF Posts Documents Detailing Law Enforcement Collection of Data From Social Media Sites

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EFF has posted documents shedding light on how law enforcement agencies use social networking sites to gather information in investigations. The records, obtained from the Internal Revenue Service and Department of Justice Criminal Division, are the first in a series of documents that will be released through a Freedom of Information Act (FOIA) case that EFF filed with the help of the UC Berkeley Samuelson Clinic.

One of the most interesting files is a 2009 training course that describes how IRS employees may use various Internet tools -- including social networking sites and Google Street View -- to investigate taxpayers.

The IRS should be commended for its detailed training that clearly prohibits employees from using deception or fake social networking accounts to obtain information. Its policies generally limit employees to using publicly available information. The good example set by the IRS is in stark contrast to the U.S. Marshalls and the Bureau of Alcohol, Tobacco, Firearms and Explosives. Neither organization found any documents on social networking sites in response to EFF's request suggesting they do not have any written policies or restrictions upon the use of these websites.

The documents released by the IRS also include excerpts from the Internal Revenue Manual explaining that employees aren't allowed to use government computers to access social networking sites for personal communication, and cautioning them to be careful to avoid any appearance that they're speaking on behalf of the IRS when making personal use of social media.

The Justice Department released a presentation entitled "Obtaining and Using Evidence from Social Networking Sites." The slides, which were prepared by two lawyers from the agency's Computer Crime and Intellectual Property Section, detail several social media companies' data retention practices and responses to law enforcement requests. The presentation notes that Facebook was “often cooperative with emergency requests” while complaining about Twitter’s short data retention policies and refusal to preserve data without legal process. The presentation also touches on use of social media for undercover operations.

Over the next few months, EFF will be getting more documents from several law enforcement and intelligence agencies concerning their use of social networking sites for investigative purposes. We'll post those files here as they arrive.

by Marcia Hofmann


Wednesday, March 10, 2010

Sonic Hedgehog Gene Found in an Unexpected Place During Limb Development

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ScienceDaily (Mar. 9, 2010) — Sonic hedgehog, a gene that plays a crucial rule in the positioning and growth of limbs, fingers and toes, has been confirmed in an unexpected place in the embryos of developing mice -- the layer of cells that creates the skin.

Named for a video game character, Sonic hedgehog describes both a gene and the protein it produces in the body. Its study is important to increase understanding of human birth defects.

It was thought to be exclusively present in the cell layer that builds bone and muscle, called the mesoderm. But University of Florida Genetics Institute researchers have discovered that Sonic hedgehog is also at work in mice limb buds in what is known as the ectoderm, the cell layer that gives rise to the skin in vertebrates.

Finding Sonic hedgehog in this layer of cells is loosely akin to discovering that yeast has crept from the batter to the frosting, where it has the surprising effect of limiting how much the cake will rise. More literally, instead of causing appendages to grow, Sonic hedgehog seems to act as a failsafe mechanism to keep additional digits from developing.

"Sonic hedgehog protein determines how your limbs form, and why your pinky is at the bottom of your hand and your thumb is at the top," said Brian D. Harfe, an associate professor of molecular genetics and microbiology at the UF College of Medicine. "But what's been previously published is only part of the picture. We determined that Sonic hedgehog signaling is required in the ectoderm to have normal digit formation. Get rid of it, and an extra digit forms."

In this case, when scientists disrupted Sonic hedgehog signaling in a small region of the limb buds of embryonic mice, an additional digit began to arise in what would be the mouse paw.

The discovery, recently published in the Proceedings of the National Academy of Sciences, suggests that Sonic hedgehog's role in the growth of appendages is far more complex than originally thought. Developmental biologists may have to rethink established theories about how limbs are patterned in vertebrates -- an effort that could provide insight into human birth defects.

"We used technology where a viral protein seeks out specific sequences of DNA," said Cortney M. Bouldin, a graduate student in the Interdisciplinary Program in Biomedical Sciences in the department of molecular genetics and microbiology. "We concentrated on disabling a protein essential for Sonic hedgehog signaling. Although it has been removed from the limb before, we wanted to specifically remove it from the ectoderm. When we did that, in the latter stages of development, we saw extra cartilage and the early beginnings of another digit."

Sonic hedgehog signaling in the ectoderm of limb buds may act as a buffering system that prevents unneeded growth, Bouldin said.

The UF research was sparked by studies of gene activity in the limb buds of mice by William J. Scott, a professor of pediatrics at the University of Cincinnati. Scott used a microarray experiment to examine gene expression levels in the ectoderm of mice limb buds, finding activity that could not be possible without the presence of Sonic hedgehog.

UF researchers were able to advance this investigation from cell studies to developing mice embryos by knocking out gene expression in a small region of the ectodermal layer. It allowed them to observe early limb development in the absence of Sonic hedgehog signaling.

"The view had been if you reduce signaling, if anything you would get fewer fingers," said Scott, who did not participate in the UF research. "We now know we can't disregard Sonic hedgehog signaling in the ectoderm. It still has its predominant effect in the tissue where it is made, but it does something more than we thought it did previously. When we try to understand problems that arise with limb growth in humans, we will be able to examine those possibilities."

Harfe said the next phase of the work will be to observe what happens when Sonic hedgehog signaling is disrupted through larger segments of the ectodermal layer. Ultimately, researchers hope the work will lead to quality of life improvements for people.

"We would like to repair limb defects in humans and enhance regeneration of limbs, helping people who might cut off fingers in an accident, for example," Harfe said.

The work was funded by the UF College of Medicine.

Journal Reference:
Bouldin et al. Shh pathway activation is present and required within the vertebrate limb bud apical ectodermal ridge for normal autopod patterning. Proceedings of the National Academy of Sciences, March 8, 2010; DOI: 10.1073/pnas.0912818107


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Saturday, March 6, 2010

LHC News - Full Steam Ahead!

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Following the completion of the campaign to improve the reliability of the cabling for the new Quench Protection System, the main dipoles and quadrupoles of the eight LHC sectors have now been commissioned up to a current of 6 kAmps. In the early hours of Sunday 28 February, the beams were circulating again in the LHC: the longest run in CERN's history has just started!

During the campaign that the LHC teams carried out over the last few weeks to ensure the correct functioning of the LHC magnets at high current, the several thousand channels of the new Quench Protection System were verified and the resistance of the 10,000 splices connecting the magnets was precisely measured, showing no unacceptably anomalous values.

In order to operate the LHC without risk to the magnet system, it must be possible to switch off the magnets and extract the stored energy in about ten seconds at all times. At the same time, efforts have been concentrated on correctly tuning the parameters of the Quench Protection System in order to avoid it triggering the beam dump when not technically necessary.

Having completed the magnet-powering tests at 6 kAmps, the hardware commissioning team has handed the machine over to the operation team. The initial operations have included tests without beams to verify the correct functioning of all the systems (magnets, radiofrequency, collimators, injection and beam abort systems, etc.) in unison.

By midnight on Saturday 27 February the machine was ready to receive the beams, and injection started. By early the next morning both beams were circulating again in the LHC (see figure). Sunday was then dedicated to the optimization of the beam trajectory and of the other optical parameters, as well as to the control of the beams by the radio-frequency cavities that keep the protons bunched.

In the CERN Control Centre, the operators are now working on optimising the beam parameters and improving the beam lifetime. The energy of the proton beams is currently 450 GeV. The first energy ramp-up is expected in the next few days. High-energy collisions are planned for the end of March.

(LHC News)

Friday, March 5, 2010

Key Piece of Puzzle Sheds Light on Function of Ribosomes

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ScienceDaily (Jan. 13, 2010) — When ribosomes produce protein in all living cells, they do so through a chemical reaction that happens so fast that scientists have been puzzled. Using large quantum mechanical calculations of the reaction center of the ribosome, researchers at Uppsala University in Sweden can now provide the first detailed picture of the reaction.

It was previously known how the chemical reaction goes about adding amino acids to the growing protein. Both computer simulations and x-ray crystallographic experiments have identified a hydrogen bonding network that appears to be the main explanation for the high speed of the reaction. What is especially remarkable is the presence of a couple of "trapped" water molecules seem to be the only parts of the ribosome that are in contact with the reacting chemical groups.

Doctoral candidate Goran Wallin and Professor Johan Aqvist at the Department of Cell and Molecular Biology at Uppsala University have carried out large-scale calculations of the ribosome reaction center, and this has enabled them to monitor the changes electronic structure during the reaction. With about a thousand quantum mechanical optimizations, they have succeeded in establishing exactly what the highest point of the energy surface looks like, the point that determines the speed of the reaction.

"Our calculations provide a detailed picture of the reaction and show that the two water molecules play a central role in ribosome catalysis. One of the molecules participates directly in the reaction by 'shuffling' protons around, while the other one helps increase the speed of the reaction," explains Johan Aqvist.

The findings surprisingly show that it is just a few components in the ribosome's reaction center that induce the catalytic effect, whereas the surrounding structure mainly holds them in place.

"An exciting question for future research is whether these components are a vestige of a primordial and much simpler ribosome," says Johan Aqvist.

Journal Reference:
Wallin et al. The transition state for peptide bond formation reveals the ribosome as a water trap. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0914192107


How ATP, Molecule Bearing 'the Fuel of Life,' Is Broken Down in Cells

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ScienceDaily (Mar. 1, 2010) — Researchers at the Louisiana State University Health Sciences Center have figured out how ATP is broken down in cells, providing for the first time a clear picture of the key reaction that allows cells in all living things to function and flourish.

Discovered some 80 years ago, adenosine triphosphate is said to be second in biological importance only to DNA. Each cell in the human body contains about a billion ATP molecules, and the power derived from the breakdown of them is used to deliver substances to their cellular homes, build needed complex molecules and even make muscles contract.

"ATP is the fuel of life. It's an energy currency molecule -- the most important source of chemical and mechanical energy in living systems," explains Sunyoung Kim, the associate professor who oversaw the research published Feb. 19 in the Journal of Biological Chemistry.

Scientists for decades have worked to understand the critically important reaction but, until now, did not know how proteins in a cell extract and use the energy from ATP.

In its original form, an ATP molecule has three phosphate groups. While it has been known for some time that, for ATP breakdown to occur, the third phosphate group must be attacked by a hydroxide, or a water molecule that has lost one of its protons, it was unknown what actually stripped away that proton, allowing the release of ATP's stores.

The team chose to investigate one particular family of protein machines that break down ATP -- the kinesins.

Kinesins are tiny biological machines that work a lot like car engines, Kim says, travelling up and down cellular roadways in support of several functions, such as cellular division and cargo transport.

"We picked kinesins because they're the simplest known motor proteins. Usually, proteins that break down ATP are very large and have a lot of moving parts for mechanical work." Kim says. "The simpler and the smaller the system is, the more likely you can capture information about it in detail."

The team narrowed its study further to the human kinesin Eg5, which is essential for cell division -- normal and abnormal -- and is touted as an attractive target for next- generation cancer drugs. Inhibition of Eg5 kinesin, by disrupting its ability to break down ATP, may be able to block cancer progression, and a number of Eg5 inhibitors are in clinical trials.

To get a clear picture of how the kinesin and ATP interact, the team set out to use X- ray crystallography to develop a three-dimensional structure that would detail all the bonds and atomic contacts, explains assistant professor David Worthylake, one of the co -authors.

The challenge, though, was trapping the protein in the middle of the energy-releasing chain of events by coaxing it to hold onto a chemical mimic of ATP, in which the final phosphate cannot be removed as usual, and examining the "jammed" protein up close.

According to Courtney Parke, a graduate student and the first author of the team's paper, successfully trapping an ATP mimic is quite difficult. Before her team achieved it, only three other attempts had been successful. Still, all those successes were a bit unsatisfying, she says, because they didn't show how that first step in ATP breakdown occurred.

Further complicating matters, purified kinesin proteins typically are found bound to product of ATP breakdown, adenosine diphosphate, or ADP.

"We said, `You know what? We don't think that you can just insert the mimic of ATP into this purified protein with ADP already bound to it. We think ADP has to be taken out first. That's what the protein does naturally,'" Kim says. "So, instead of forcing the protein out of its normal sequence of steps in breaking down ATP, we pulled out the ADP first and then asked the Eg5 kinesin to bind the ATP mimic. And, lo and behold, we got the answer."

The surprising result was that the protein uses a string of water molecules to harness the energy of the reaction.

"Conventional wisdom pointed toward the reactive agent that starts the ATP breakdown process as being something in the protein, such as an amino acid," notes Edward Wojcik, an assistant professor and another co-author on the paper.

But, it wasn't an amino acid at all: It was a second water molecule that pulled the proton off the first water molecule.

"Each of these water molecules is attached to different part of the protein. And, normally, they hold tightly to each other as well, keeping two very distant parts of the protein connected by a molecular bridge," Kim explains. "Our data show, when the second water molecule takes the proton from the first one, the proton is transferred across this bridge. This causes the two different parts of the protein that the bridge holds together to unfurl, and you have motion in the protein."

That internal motion propels the nanomachine along its assigned roadway, allowing it to do its assigned duties.

"For such a relatively simple molecule, water still has some tricks to teach us, and I am still amazed that we found it to play such a pivotal role in the motor protein machinery," Wojcik says.

The team hopes that, with a clearer understanding of how these biological machines work, scientists will better understand how and why things are moved around inside cells, allowing them to figure out how to turn things on and off at will with novel drugs to help combat diseases.

"We believe many, if not all, proteins that use the energy from ATP breakdown may work the same way," Kim says.

The project was supported by funding from the Louisiana Board of Regents and from the National Institutes of Health. By being named a "Paper of the Week" by the Journal of Biological Chemistry, the team's article has been categorized in the top 1 percent of papers reviewed by the editorial board in terms of significance and overall importance.

It also has been named a "Must Read" by the Faculty of 1000 Biology, an online research service that reviews the most interesting papers published in the biological sciences, based on the recommendations of leading researchers.


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