Latent Cell Memory

Artistic impression of nucleosomes interaction.
Credit: Mette Høst, CMOL, Niels Bohr Institute, University of Copenhagen

New Danish research has examined the mechanisms behind latent cell memory, which can come to life and cause previously non-existent capacities suddenly to appear. Special yeast cells for example, can abruptly change from being of a single sex to hermaphrodite.

Researchers from the Niels Bohr Institute at the University of Copenhagen have used mathematical models and computer simulations to examine fundamental mechanisms of cell memory. The research is an interdisciplinary cooperation between molecular biologists and physicists and has just been published in the journal CELL (article by Dodd et al., 18 May issue).

Dormant capacities

Our genetic material - DNA -- is a blueprint for how we look and are. This genetic material is very stable and it is faithfully transmitted to our descendants. Once in a while though, a change occurs to the DNA, either large or small. Such changes are at the origin of the immense and varied animal and plant life on earth. Constructive changes in the DNA, that is, changes creating new functions, normally arise by a slow and gradual process that involves natural selection operating over many generations.

Sometimes however, dramatic and very sudden changes are observed in one individual in the absence of any kind of change to the DNA. This happens in fact in all of us as our body develops: cells with identical genetic information adopt very different fates, forming tissues that have apparently very little in common with each other, such as skin, brain, or bones. Mechanisms at the origin of this so-called cellular differentiation are those for which researchers at the University of Copenhagen have a possible clarification.

"The explanation for the sudden changes is that it is not the DNA itself that is altered - it is its immediate surroundings that change and thereby cause a cell to activate some of its dormant capacities" says Kim Sneppen, professor in Biophysics at the Niels Bohr Institute, University of Copenhagen .

The environment controls the DNA

The DNA coils itself around protein complexes called nucleosomes. Importantly, nucleosomes can carry various chemical modifications that either allow, or prevent, the expression of the DNA wrapped around them. Every time a cell divides into new cells, its double-stranded DNA splits into two single strands, which then each produce a new double-strand.

Nucleosomes though are not duplicated like the DNA-strands. Rather, they are distributed between the two new DNA double strands and the empty spaces are filled by new nucleosomes. Cell division is therefore an opportunity for changes in the nucleosomal composition of a specific DNA region. Changes can also happen during the lifetime of a cell due to chemical reactions allowing interconversions between the different nucleosome types. The effect of these changes can be that a latent capacity that was dormant comes to life, or, conversely, that a previously active capacity shuts down.

Same inheritance -- different traits

In the practical experiment molecular biologists used a mutant of a yeast cell which was bi-stable, in that it could become either of a single sex or hermaphrodite. The experiment showed that a spontaneous change occurred in the yeast cells about every 2000 cell-generations. By building a mathematical model based on positive feedback from the microscopic state of the nucleosomes, the research group could simulate the experimental results and in this way gained insight into the mechanisms by which living cells with identical DNA can achieve extreme differentiation.

The research at the 'Models of Life' Basic Research Center at the Niels Bohr Institute has shown that communication between nucleosomes and positive feedback are likely to constitute fundamental memory mechanisms in individual cells. The mechanism gives both stability and openness to new influences which the cell could need to change state. Nature has a partner which controls the cells latent memory.

Latent Memory Of Cells Comes To Life
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Nanomedicine & Nerve Cells

Nanomedicine Opens The Way For Nerve Cell Regeneration

Credit: Stockphoto - Sebastian Kaulitzki

The ability to regenerate nerve cells in the body could reduce the effects of trauma and disease in a dramatic way. In two presentations at the NSTI Nanotech 2007 Conference, researchers describe the use of nanotechnology to enhance the regeneration of nerve cells.

In the first method, developed at the University of Miami, researchers show how magnetic nanoparticles (MNPs) may be used to create mechanical tension that stimulates the growth and elongation of axons of the central nervous system neurons. The second method from the University of California, Berkeley uses aligned nanofibers containing one or more growth factors to provide a bioactive matrix where nerve cells can regrow.

It is known that injured neurons in the central nervous system (CNS) do not regenerate, but it is not clear why. Adult CNS neurons may lack an intrinsic capacity for rapid regeneration, and CNS glia create an inhibitory environment for growth after injury. Can these challenges be overcome even before we fully understand them at a molecular level?

Dr. Mauris N. De Silva describes the novel nanotechnology based approach designed that includes the use of magnetic nanoparticles and magnetic fields for addressing the challenges associated with regeneration of central nervous system after injury. "By providing mechanical tension to the regrowing axon, we may be able to enhance the regenerative axon growth in vivo." This mechanically induced neurite outgrowth may provide a possible method for bypassing the inhibitory interface and the tissue beyond a CNS related injury.

Using optic nerve and spinal cord tissues as in vivo models and dissociated retinal ganglion neurons as an in vitro model, De Silva and his colleagues are currently investigating how these magnetic nanoparticles can be incorporated into neurons and axons at the site of injury. Although, this study is at a very preliminary stage to explore the possibility of using magnetic nanoparticles for enhancing in vivo axon regeneration, this work may have significant implications for the treatment of spinal cord injuries, and is a vital "next step" in bringing this new technology to clinical use.

The second presentation focuses on peripheral nerve injury, which affects 2.8% of all trauma patients and quite often results in lifelong disability. Since peripheral nerves relay signals between the brain and the rest of the body, injury to these nerves results in loss of sensory and motor function. Upper extremity paralysis alone affects more than 300,000 individuals annually in the US. The most serious form of peripheral nerve injury is complete severance of the nerve.

The severed nerve can regenerate; the nerve fibers from the nerve end closest to the spinal cord have to grow across the injury gap, enter the other nerve segment and then work their way through to their end targets (skin, muscle, etc). Usually, when the gap between the severed nerve endings is larger than a few millimeters, the nerve does not regenerate on its own. If left untreated, the end result is permanent sensory and motor paralysis. A few hundred thousand people suffer from this debilitating condition annually in the US.

Currently, the most successful form of treatment is to take a section of healthy nerve (autograft) from another part of the patient's body to bridge the damaged one. This autograft then serves as a guide for nerve fibers to cross the injury gap. Although successful, this autograft procedure has major drawbacks including loss of function at the donor site, multiple surgeries and, quite often, it's just not possible to find a suitable nerve to use as a graft. Various synthetic nerve grafts are currently available but none work better than the autograft and can't bridge gaps larger than 4 centimeters.

Researchers at the University of California, Berkeley have developed a technology that has the potential to serve as a better alternative than currently available synthetic nerve grafts. The graft material is composed entirely of aligned nanoscale polymer fibers. These polymer fibers act as physical guides for regenerating nerve fibers. They have also developed a way to make these aligned nanofibers bioactive by attaching various biochemicals directly onto the surfaces of the nanofibers. Thus, the bioactive aligned nanofiber technology mimics the nerve autograft by providing both physical and biochemical cues to enhance and direct nerve growth.

This technology has been tested by culturing rat nerve tissue ex vivo on our bioactive aligned nanofiber scaffolds. When the nerve tissue was cultured on unaligned nanofibers there was no nerve fiber growth onto the scaffolds. However, on aligned nanofiber scaffolds, they not only observed nerve fibers growing from the tissue but the nerve fibers were aligned in the same orientation as the nanofibers. Furthermore, when there were biochemicals present on the nanofibers, the nerve fiber growth was enhanced 5 fold. In a matter of just 5 days, nerve fibers had extended 4 millimeters from the nerve tissue in a bipolar fashion on the bioactive aligned nanofiber scaffolds. Thus, this technology can induce, enhance and direct nerve fiber regeneration in a straight and organized manner.

In order to make the technology clinically viable, they have also developed a novel graft fabrication technology in their laboratory. The most common method for fabricating polymer nanofibers is to use an electrical field to "spin" very thin fibers. This technique is called electrospinning and can be used to make nanofiber scaffolds in various shapes such as sheets and tubes. They have made a key innovation to this technology that enables us to fabricate tubular nerve grafts composed entirely of polymer nanofibers aligned along the length of tubes. This technology also allows customization of the length, diameter and thickness of the aligned tubular nanofiber grafts. The group will evaluate the performance of these aligned nanofiber nerve grafts in small animal pre-clinical studies starting in mid-May.

The technology presented herein is being patented by the University of California, Berkeley and has been licensed to NanoNerve, Inc.

According to Principal Investigator, Shyam Patel, "Speed is the key to successful nerve regeneration. Our aligned nanofiber technology takes full advantage of the fact that the shortest distance between damaged nerve endings is a straight line. It directs straightforward nerve growth and never lets them stray from the fast lane."

The presentation on magnetic nanoparticles is "Developing Super-Paramagnetic Nanoparticles for Central Nervous System Axon Regeneration" by M.N. De Silva, M.V. Almeida and J.L. Goldberg, from the University of Miami. The talk on aligned nanofibers is "Bioactive Aligned Nanofibers for Nerve Regeneration" by S. Patel and S. Li, from the University of California, Berkeley, CA.

Story adapted from a news release by Elsevier Health Sciences.
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Circadian Clocks

Graphic of the ribbon structure of the vivid protein with a rising sun signifies the circadian clock (24-hour cycle). (Credit: Image courtesy of Cornell University)

Circadian clocks regulate the timing of biological functions in almost all higher organisms. Anyone who has flown through several time zones knows the jet lag that can result when this timing is disrupted.

Now, new research by Cornell and Dartmouth scientists explains the biological mechanism behind how circadian clocks sense light through a process that transfers energy from light to chemical reactions in cells. Circadian clocks in cells respond to differences in light between night and day and thereby allow organisms to anticipate changes in the environment by pacing their metabolism to this daily cycle.

The clocks play a role in many processes: timing when blooming plants open their petals in the morning and close them at night; or setting when fungi release spores to maximize their reproductive success. In humans, the clocks are responsible for why we get sleepy at night and wake in the morning, and they control many major regulatory functions.

Disruptions of circadian rhythms can cause jet lag, mental illness and even some forms of cancer.
"These clocks are highly conserved in all organisms, and in organisms separated by hundreds of millions of years of evolution," said Brian Crane, the paper's senior author and an associate professor in Cornell's Department of Chemistry and Chemical Biology.

The study revealed how a fungus (Neurospora crassa) uses circadian clock light sensors to control production of carotenoids, which protect against damage from the sun's ultraviolet radiation just after sunrise. The researchers studied a protein called vivid, which contains a chromophore or "light-absorbing molecule".

The chromophore captures a photon or particle of light, and the captured energy from the light triggers a series of interactions that ultimately lead to conformational changes on the surface of the vivid protein. These structural changes on the protein's surface kick off a cascade of events that affect the expression of genes, such as those that turn carotenoid production on and off.

By substituting a single atom (sulphur for oxygen) on the surface of the vivid protein, the researchers were able to shut down the chain of events and prevent the structural changes on the protein's surface, thereby disrupting the regulation of carotenoid production.

"We can now show that this conformational change in the protein is directly related to its function in the organism," said Brian Zoltowski, the paper's lead author and a graduate student at Cornell in chemical biology.

The circadian clock allows the fungus to regulate and produce carotenoids only when they are needed for protection against the sun's rays. A similar "switch" may be responsible for timing the sleep cycle in humans.

"We were interested in trying to understand behavior at the molecular level," said Crane. "This a great example of chemical biology, in that we can perturb the chemistry of a single molecule in a particular way and actually change the behavior of a complex organism."

The study was supported by grants from the National Institutes of Health.
The research is published in the May 18 issue of the journal Science.
Story adapted from a news release issued by Cornell University
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Event Structure Perception

Thinking Thing by Thinkingthing


In order to comprehend the continuous stream of cacophonies and visual stimulation that battle for our attention, humans will breakdown activities into smaller, more digestible chunks, a phenomenon that psychologists describe as "event structure perception."

Event structure perception was originally believed to be confined to our visual system, but new research shows that a similar process occurs when reading about everyday events as well.

Nicole Speer and her colleagues at Washington University examined event structure perception by having subjects read narratives about everyday activities while undergoing functional Magnetic Resonance Imaging (fMRI) to measure neural activity. The subjects were then invited back a few days later to reread these same narratives, this time without the fMRI scan. Instead, they were asked to divide the narrative where they believed one segment of narrative activity ended and another segment began.

Speer, surmised that if changes in neural activity occurred at the same points that the subjects divided the stories, then it could be safe to suggest that humans are physiologically disposed to break down activities into narratives (remember that the same subjects had no idea during the first part of the experiment that they would later be asked to segment the story).

As expected, activity in certain areas of the brain increased at the points that subjects had identified as the beginning or end of a segment, otherwise known as an "event boundary." Consistent with previous research, such boundaries tended to occur during transitions in the narrative such as changes of location or a shift in the character's goals. Researchers have hypothesized that readers break down narrated activities into smaller chunks when they are reading stories. However, this is the first study to demonstrate that this process occurs naturally during reading, and to identify some of the brain regions that are involved in this process.

The fact that these results occurred with narratives that described mundane events is particularly important to our understanding of how humans comprehend everyday activity. Speer writes that the findings "provide evidence not only that readers are able to identify the structure of narrated activities, but also that this process of segmenting continuous text into discrete events occurs during normal reading."

In addition, a subset of the network of brain regions that also responds to event boundaries while subjects view movies of everyday events was activated. Speer believes that "this similarity between processing of visual and narrated activities may be more than mere coincidence, and may reflect the existence of a general network for understanding event structure." Future research will ultimately address the relationship between the two perception systems, and whether a global mechanism underlies event structure perception.

Article: "Human Brain Activity Time-Locked to Narrative Event Boundaries " May issue of Psychological Science, a journal of the Association for Psychological Science.
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Human Brain Breaks Down Events Into Smaller Units From Science Daily
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Green Tea

A new study from the University of Michigan Health System suggests that a compound in green tea may provide therapeutic benefits to people with rheumatoid arthritis. Credit: Stockphoto Science Daily


The compound from green tea was found to suppress the inflammatory products in the connective tissue of people with rheumatoid arthritis.

The study, presented April 29 at the Experimental Biology 2007 in Washington, D.C., looks at a potent anti-inflammatory compound derived from green tea. Researchers found that the compound – called epigallocatechin-3-gallate (EGCG) – inhibited the production of several molecules in the immune system that contribute to inflammation and joint damage in people with rheumatoid arthritis.

To conduct the research, the scientists isolated cells called synovial fibroblasts from the joints of patients with rheumatoid arthritis. These fibroblasts – cells that form a lining of the tissue surrounding the capsule of the joints – then were cultured in a growth medium and incubated with the green tea compound.

The fibroblasts were then stimulated with pro-inflammatory cytokine IL-1b, a protein of the immune system known to play an important role in causing joint destruction in people with rheumatoid arthritis. The researchers looked at whether the green tea compound has the capability to block the activity of two potent molecules, IL-6 and cyclooxygenase-2 (COX-2), which also are actively involved in causing boneerosion in the joints of people with rheumatoid arthritis.

When untreated cells were stimulated with IL-1b, a sequence of molecular events occurred that resulted in production of the bone-destructive molecules. But the scientists found that pre-incubation with EGCG was capable of inhibiting the production of these molecules. EGCG also inhibited the production of prostaglandin E2, a hormone-like substance that causes inflammation in the joints.

The cell signaling pathways that regulate levels of these immune system molecules under both normal and rheumatoid arthritis situations are well studied, and the researchers were able to trace the effects of the green tea compound infusion to see that it worked by inhibiting these pathways.

Green Tea Compound, May Be A Therapy For Rheumatoid Arthritis
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Weighing living cells

New MIT technique weighs single living cells.
For the first time, MIT researchers have found a way to measure the mass of single cells with high accuracy.

The new technique, which is based on a micromechanical detector, could allow researchers to develop inexpensive, portable diagnostic devices and might also offer a unique glimpse into how cells change as they undergo cell division.

Unlike conventional methods, the MIT technique allows cells to remain in fluid while they are being measured, opening up a new realm of possible applications, says Scott Manalis, senior author of a paper on the work that will appear in the April 26 issue of Nature.

In addition to weighing cells, the technology can be used to "weigh nanoparticles or sub-monolayers of biomolecules with a resolution in solution that is six orders of magnitude more sensitive than commercial mass sensor methods. One direction we're pursuing is mass-based flow cytometry, a way to weigh and count specific cells," said Manalis, an associate professor in MIT's Departments of Biological Engineering and Mechanical Engineering.

Current mass-measurement methods achieve a resolution down to a zeptogram (10 to the minus 21 grams) but only work with non-living things because the procedure must be performed inside a vacuum. So, the MIT researchers decided to turn the conventional system inside out.

In the traditional method, the molecules to be weighed are placed on top of a tiny slab, or cantilever, made of silicon. The slab vibrates at its resonant frequency (the frequency at which the material naturally tends to vibrate) inside a vacuum. When a molecule sits on the slab, the frequency changes slightly, and the mass of the molecule can be calculated by measuring that change.

This measurement must be performed in a vacuum to prevent air (or fluid) from interfering with the frequency of oscillation. However, cells cannot survive in a vacuum, so they must be measured in fluid, which diminishes the accuracy of the measurement.

The researchers solved this dilemma by placing the fluid containing the sample inside the silicon slab, which still oscillates within a vacuum surrounding it. The biological sample is pumped through a microchannel that runs across the slab, without impairing its ability to vibrate.

"The resonator is sealed in a tiny vacuum cavity inside the chip, so there is virtually no resistance to the vibration," said co-lead author Thomas Burg, a research associate in biological engineering. "This lets us measure a mass change, say 10 parts in a billion, of the already very light microcantilever."

So far, the researchers have weighed particles with a resolution down to slightly below a femtogram (10 to the minus 15 grams), but Manalis believes that with refinements, the sensitivity could potentially be lowered by several orders of magnitude within a few years. "Every step along the way will open up new possibilities."

The researchers can also measure the mass density of particles or cells "by varying the density of the surrounding solution," said Michel Godin, co-lead author.

The research team is already looking into several applications for the new technique. One area of great promise is creating a device that would mimic the cell-counting capabilities of flow cytometers. However, flow cytometry devices, which work by bouncing light off a flowing stream of cells, are too large and expensive to be useful in developing countries.

A tiny chip that could count cells using the new MIT weighing method would be a "cheap and robust" alternative to commercially available flow cytometers, which typically cost more than $20,000, Manalis said. "Since the device is batch-fabricated by conventional semiconductor processing techniques, it could potentially be used in a disposable format."

"Simply put, a cheap, simple CD4 counting device that can be used by a community health worker … would be a breakthrough advance in global health," according to Rodriguez.

Manalis is also planning a collaboration with MIT associate professor of biology Angelika Amon, who is interested in studying how the mass density of a single cell changes as it goes through cell division. Using the new method, scientists can ultimately trap a single cell and observe it over a long period of time. Changes in mass could correlate to production of proteins, offering a new way to study what the cell does during division, Manalis said.

Another application of the new technology is to measure small particles, or beads. It's important to know the size of particles used in paint, drug-delivery devices, coatings and nanocomposite materials, said Manalis, who added that the new technology could become the "gold standard" way to measure these particles one by one.

This illustration shows an artistic depiction of the concept that enables measuring the mass of a single bacterium and single nanoparticles in fluid with a very high resolution. A hollow resonator, represented by a hollow, fluid-filled guitar, vibrates while small particles, represented here by a bacterium, flow through it. As the particles flow through the resonator, they change the frequency (tone) of the vibration. (Credit: Image courtesy Thomas Burg)

Other authors on the Nature paper are Scott Knudsen, MIT postdoctoral associate in biological engineering; Wenjiang Shen, Greg Carlson and John S. Foster of Innovative Micro Technology in Santa Barbara, Calif.; and Ken Babcock of Innovative Micro Technology and Affinity Biosensors in Santa Barbara.

The research was funded by the National Institutes of Health Cell Decision Process Center, the Institute for Collaborative Biotechnologies from the U.S. Army Research Office, the Air Force Office of Sponsored Research, the National Science Foundation and the Natural Sciences and Engineering Research Council of Canada.
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The Max Planck Society Press Releases
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