Neuronal Circuits Able To Rewire On The Fly To Sharpen Senses

Source:

http://www.sciencedaily.com/releases/2007/12/071216155630.htm

ScienceDaily (Dec. 22, 2007) — Researchers from the Center for the Neural Basis of Cognition (CNBC), a joint project of Carnegie Mellon University and the University of Pittsburgh, have for the first time described a mechanism called "dynamic connectivity," in which neuronal circuits are rewired "on the fly" allowing stimuli to be more keenly sensed.

This new, biologically inspired algorithm for analyzing the brain at work allows scientists to explain why when we notice a scent, the brain can quickly sort through input and determine exactly what that smell is.
"If you think of the brain like a computer, then the connections between neurons are like the software that the brain is running. Our work shows that this biological software is changed rapidly as a function of the kind of input that the system receives," said Nathan Urban, associate professor of biological sciences at Carnegie Mellon.
When a stimulus such as an odor is encountered, many neurons start to fire. When many neurons fire at the same time, the signals can be difficult for the brain to interpret. During lateral inhibition, the stimulated neurons send "cease-fire" messages to the neighboring neurons, reducing the noise and making it easier to precisely identify a stimulus. This process also facilitates accurate recognition of stimuli in many sensory areas of the brain.
In this project, Urban and colleagues specifically examine the process of lateral inhibition in an area of the brain called the olfactory bulb, which is responsible for processing scents. Until now, scientists thought that the connections made by the neurons in the olfactory bulb were dictated by anatomy and could only change slowly.
However, in this current study, Urban and colleagues found that the connections are, in fact, not set but rather able to change dynamically in response to specific patterns of stimuli. In their experiments, they found that when excitatory neurons in the olfactory bulb fire in a correlated fashion, this determines how they are functionally connected.
The researchers showed that dynamic connectivity allows lateral inhibition to be enhanced when a large number of neurons initially respond to a stimulus, filtering out noise from other neurons. By filtering out the noise, the stimulus can be more clearly recognized and separated from other similar stimuli.
"This mechanism helps to explain why you can walk into a room and recognize a smell that seems to be floral. As you continue to smell the odor, you begin to recognize that the scent is indeed flowers and even more specifically is the scent of roses," Urban said. "By understanding how the brain does this, we can then apply this mechanism to other problems faced by the brain."
Researchers converted this mechanism into an algorithm and used computer modeling to further show that dynamic connectivity makes it easier to identify and discriminate between stimuli by enhancing the contrast, or sharpness, of the stimuli, independent of the spatial patterns of the active neurons. This algorithm allows researchers to show the applicability of the mechanism in other areas of the brain where similar inhibitory connections are widespread. For example, the researchers applied the algorithm to a blurry picture and the picture appeared refined and in sharper contrast (see image).
The process is described in a paper in the January 2008 issue of Nature Neuroscience, and available online at http://dx.doi.org/10.1038/nn2030.
Coauthors of the study include Armen Arevian, a graduate student in the Center for Neuroscience at the University of Pittsburgh, and Vikrant Kapoor, a biological sciences graduate student at Carnegie Mellon. The study was funded through grants from the National Institute on Deafness and Other Communication Disorders, and the National Science Foundation.
Adapted from materials provided by Carnegie Mellon University.

Fausto Intilla

www.oloscience.com

New Gene Therapy Heals Growth Deficiency Disorder In Live Animal

Source:

http://www.sciencedaily.com/releases/2007/12/071218192020.htm

ScienceDaily (Dec. 20, 2007) — A team of Vanderbilt researchers have demonstrated for the first time that a new type of gene therapy, called RNA interference, can heal a genetic disorder in a live animal.

The study shows that RNA interference can "rescue" a strain of mouse that has been genetically engineered to express a defective human hormone that interferes with normal growth. When the gene that produces the defective human growth hormone is inserted into the mouse's genome, it also stunts the mouse's growth. But when a small snippet of RNA that interferes with the hormone's production is also added, the mouse is restored to normal.
"It has been very satisfying to figure out the underlying cause of this genetic disorder and then identify a way to prevent it," says John Phillips, the David T. Karzon Professor of Pediatrics at the Vanderbilt University Medical Center, who has been studying human growth deficiency disorders since 1978. He collaborated on the research with graduate students Nikki Shariat and Robin Ryther, who are directed by Professor of Biological Sciences James G. Patton.
Growth hormone deficiency has been estimated to occur in between one in 4,000 to 10,000 children. It has a number of different causes, but one that is genetically inherited is called Isolated Growth Hormone Deficiency type II, and this is the subject of the study.
Children with IGHD-II appear fairly normal at birth but do not gain weight or grow as fast as they should, and their bones do not mature properly. The current treatment consists of daily injections of growth hormone for years until the patients reach their adult height. Not only is this treatment extremely expensive, it also fails to correct the underlying source of the problem: deterioration and death of cells in the pituitary gland that produce growth hormone. As a result, this single hormone deficiency can develop into multi-hormonal deficiency over time.
IGHD-II is what geneticists call a dominant negative disorder. It is caused by a defective form of human growth hormone that not only can't stimulate growth itself but also blocks the action of normal growth hormone. "It acts like Aesop's dog in the manger ... which has no use for the hay but keeps the cows from eating," says Phillips. Some other common dominant negative diseases include forms of colon cancer, deafness, muscular dystrophy, brittle bone disease, kidney disease and retinitis pigmentosa.
The blueprint for a protein like growth hormone is genetically encoded in a series of special segments called exons. The instructions in the exons are first copied onto a length of special RNA, called messenger-RNA. The messenger-RNA is moved to a structure in the cell called a ribosome, which links amino acids together in the order specified by the RNA sequence to create the protein.
Normal growth hormone is produced by a series of five exons. The defective hormone is the result of a splicing error: It is made by combining the segments coded by the first two exons and the last two exons, mistakenly skipping the third exon.
"A normal person has a very small amount of this defective hormone -- about 1 percent -- but people in families with IGHD-II produce 10 to 20 to 50 percent. And the more they make the slower they grow," says Patton.
In 2003, co-author Iain Robinson at the National Institute for Medical Research in London created a transgenic mouse with the human growth hormone gene that duplicated growth hormone deficiency. Although the altered mice still contained the mouse growth hormone genes, he found that high levels of the defective human growth hormone not only stunted their growth but actually killed the cells in the pituitary that produce growth hormone.
"This came as a real surprise: We never thought that a splicing error would lead to cell death," says Patton.
Meanwhile, progress in RNA interference research gave Patton and Phillips an idea for a way to correct this disorder.
In the last 15 years, scientists have realized that short pieces of double-stranded RNA, called silencing-RNA, use a pathway that is normally used by cells to regulate genes. This has created an opportunity for developing highly targeted therapies for a number of genetic diseases including macular degeneration in the eye and to block viruses such as herpes and RSV respiratory viruses. "To the best of our knowledge, this is the first time it has been used to correct a dominant negative disorder in a living animal," says Patton.
The researchers realized that the messenger-RNA that produced the defective hormone had a unique signature created by skipping the third exon. This allowed the Patton lab to create a specific silencing-RNA, designed to bind uniquely with the defective messenger-RNA.
"You might call this the 'if you don't like the message, kill the messenger' approach," Phillips quips.
Having created the special silencing-RNA, the next problem was how to deliver it to the pituitary gland which, in the case of the mouse, is the size of a grain of uncooked rice and is located at the base of the brain. As a proof of concept, the researchers decided to create a second strain of mouse which carried the special silencing-RNA and mate them with the growth deficiency strain. Their offspring should have both the genetic defect that produces the defective growth hormone and the silencing-RNA that should inhibit its production, allowing the mouse growth hormone to act.
The experiment was successful. The offspring grew normally and showed no defects in their pituitaries.
Now the researchers are investigating ways to deliver their silencing-RNA to the pituitary gland that would be suitable for treating humans. The cells that produce growth hormone have special receptors that signal the cells to release their stocks of growth hormone. If they can figure out a way to attach the silencing-RNAs to a compound that binds to this receptor, they should be able to deliver them to the cells where they can interfere with the activity of the defective growth hormone.
This research was published online Nov. 15 by the journal Endocrinology.
Adapted from materials provided by Vanderbilt University.

Fausto Intilla

www.oloscience.com

Engineering Blood Vessels That Could Be Used In Human Body

Source:

http://www.sciencedaily.com/releases/2007/12/071217155248.htm

ScienceDaily (Dec. 19, 2007) — MIT scientists have found a way to induce cells to form parallel tube-like structures that could one day serve as tiny engineered blood vessels.

The researchers found that they can control the cells' development by growing them on a surface with nano-scale patterning.
Engineered blood vessels could one day be transplanted into tissues such as the kidneys, liver, heart or any other organs that require large amounts of vascular tissue, which moves nutrients, gases and waste to and from cells.
"We are very excited about this work," said Robert Langer, MIT Institute Professor and an author of the paper. "It provides a new way to create nano-based systems with what we hope will provide a novel way to someday engineer tissues in the human body." A paper on the work was posted this month in an online issue of Advanced Materials.
The work focuses on vascular tissue, which includes capillaries, the tiniest blood vessels, and is an important part of the circulatory system. The team has created a surface that can serve as a template to grow capillary tubes aligned in a specific direction.
The researchers built their template using microfabrication machinery at Draper Laboratory in Cambridge. Normally such technology is used to build micro-scale devices, but the researchers adapted it to create nano-scale patterns on a silicone elastomer substrate. The surface is patterned with ridges and grooves that guide the cells' growth.
"The cells can sense (the patterns), and they end up elongated in the direction of those grooves," said Christopher Bettinger, MIT graduate student in materials science and engineering and lead author of the paper.
The cells, known as endothelial progenitor cells (EPCs), not only elongate in the direction of the grooves, but also align themselves along the grooves. That results in a multicellular structure with defined edges, also called a band structure.
Once the band structures form, the researchers apply a commonly used gel that induces cells to form three-dimensional tubes. Unlike cells grown on a flat surface, which form a network of capillary tubes extending in random directions, cells grown on the nano-patterned surface form capillaries aligned in the direction chosen by the researchers.
The researchers believe the technique works best with EPCs because they are relatively immature cells. Earlier attempts with other types of cells, including mature epithelial cells, did not produce band structures.
Growing tissue on a patterned surface allows researchers a much greater degree of control over the results than the classic tissue engineering technique of mixing cell types with different growth factors and hoping that a useful type of tissue is produced, said Bettinger.
"With this technique, we can take the guesswork out of it," he said.
The next step is to implant capillary tubes grown in the lab into tissues of living animals and try to integrate them into the tissues.
Other authors of the paper are Jeffrey Borenstein, director of the Biomedical Engineering Center at Draper Laboratory; Zhitong Zhang, an MIT senior in the Department of Chemical Engineering; and Sharon Gerecht of Johns Hopkins University.
The research was funded by the National Institutes of Health, Draper Laboratory and the Juvenile Diabetes Research Foundation.
Adapted from materials provided by Massachusetts Institute of Technology.

Fausto Intilla

www.oloscience.com

Sperm's Immune-protection Properties Could Provide Link To How Cancers Spread

Source:

http://www.sciencedaily.com/releases/2007/12/071213101352.htm

ScienceDaily (Dec. 19, 2007) — Sugar-based markers on human sperm cells which may prevent them from being attacked by the female immune system could provide a vital clue to how some cancers spread in the human body, according to new research.

The new research analysed these markers which are believed to tell the female immune system that the sperm are not dangerous pathogens, and therefore should not be attacked by the woman's white blood cells during the reproductive process. The study*, led by Imperial College London and the University of Missouri, suggests that these sugar markers, found on N-glycans which are part of human sperm glycoproteins, can be universally recognised by all human immune systems, regardless of the individual.
Professor Anne Dell from Imperial College London's Department of Life Sciences, one of the study's lead authors, said: "Normal human cells carry chemical markers made of proteins which tell the immune system not to attack them. In the case of organ transplants, for example, doctors try to match these markers in both the donor and the recipient to prevent rejection. However, in the case of sperm cells, their sugar-based markers are different: they are recognised by everyone's immune system, meaning that no immune response is triggered during reproduction between any two people."
This kind of marker is also found on some types of cancer cells, some bacterial cells, some parasitic worms and HIV infected white blood cells. The scientists believe that these markers allow such dangerous cells and pathogens to evade destruction by the human immune system, leading to serious -- sometimes fatal - illness.
Professor Dell explains that understanding how this basic biology works on sperm cells may lead to greater knowledge of how some serious diseases and infections manage to win the battle with the human immune system. She says:
"If aggressive cancers and pathogens are using the same system of universally-recognisable markers to trick the immune system into thinking they're harmless, we need to work out exactly how this interaction works. This is where we're planning to take this research next. Understanding how these markers work at a basic biological and chemical level could lead to new ways to treat or prevent cancers and other diseases in the future."
*The study, 'Expression of Bisecting Type and Lewisx/Lewisy Terminated N-Glycans on Human Sperm', was published on 14 December 2007 in the Journal of Biological Chemistry.
Adapted from materials provided by Imperial College London.

Fausto Intilla

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New Hope For Sleep Disorders: Genetic Switch For Circadian Rhythms Discovered

Source:

http://www.sciencedaily.com/releases/2007/12/071212201458.htm

ScienceDaily (Dec. 18, 2007) — University of California, Irvine researchers have identified the chemical switch that triggers the genetic mechanism regulating our internal body clock.

The finding, which uncovers the most specific information about the body's circadian rhythms to date, identifies a precise target for new pharmaceuticals that can treat sleep disorders and a host of related ailments.
Paolo Sassone-Corsi, Distinguished Professor and Chair of Pharmacology, found that a single amino acid activates the genes that regulate circadian rhythms. Amino acids are the building blocks of proteins, and Sassone-Corsi was surprised to find that only a single amino acid activates the body-clock mechanism because of the complex genes involved.
"Because the triggering action is so specific, it appears to be a perfect target for compounds that could regulate this activity," Sassone-Corsi said. "It is always amazing to see how molecular control is so precise in biology."
Circadian rhythms are the body's intrinsic time-tracking system, which anticipates environmental changes and adapts to the appropriate time of day. They regulate a host of body functions, from sleep patterns and hormonal control to metabolism and behavior. About 10 percent to 15 percent of all human genes are regulated by circadian rhythms. Disruption of these rhythms can profoundly influence human health and has been linked to insomnia, depression, heart disease, cancer and neurodegenerative disorders.
The gene CLOCK and its partner BMAL1 trigger circadian rhythms. Sassone-Corsi and his research team discovered last year that CLOCK functions as an enzyme that modifies chromatin, the protein architecture of a cell's DNA.
In this current study, the Sassone-Corsi team learned that a single amino acid in the BMAL1 protein undergoes a modification that triggers the genetic chain of events involved with circadian rhythms.
Sassone-Corsi notes that if this amino-acid modification is impaired in any way, the switching mechanism can be thrown off, which can be the genetic underpinning of circadian-rhythm-related ailments. Currently, Sassone-Corsi is testing antibodies that can target this BMAL1 amino-acid activity.
The study appears in the Dec. 13 issue of Nature.
Jun Hirayama, Saurabh Sahar, Benedetto Grimaldi and Yasukazu Nakahata of UC Irvine, and Teruya Tamaru and Ken Takamatsu of Toho University in Tokyo participated in the study, which received support from the Cancer Research Coordinating Committee of the University of California and the National Institutes of Health.
Adapted from materials provided by University of California - Irvine.

Fausto Intilla

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Laser Beam 'Fire Hose' Used To Sort Cells; Could Enable New Kinds Of Biological Research

Source:

http://www.sciencedaily.com/releases/2007/12/071210163008.htm

ScienceDaily (Dec. 17, 2007) — Separating particular kinds of cells from a sample could become faster, cheaper and easier thanks to a new system developed by MIT researchers that involves pushing up the cells with a laser beam "fire hose."

The system, which can sort up to 10,000 cells on a conventional glass microscope slide, could enable a variety of biological research projects that might not have been feasible before, its inventors say. It could also find applications in clinical testing and diagnosis, genetic screening and cloning research, all of which require the selection of cells with particular characteristics for further testing.
Joel Voldman, an associate professor in MIT's Department of Electrical Engineering and Computer Science, and Joseph Kovac, a graduate student in the department, developed the new system, which is featured as the cover story in the Dec. 15 issue of the journal Analytical Chemistry.
Present methods allow cells to be sorted based on whether or not they emit fluorescent light when mixed with a marker that responds to a particular protein or other compound. The new system allows more precise sorting, separating out cells based not just on the overall average fluorescent response of the whole cell but on responses that occur in specific parts of the cell, such as the nucleus. The system can also pick up responses that vary in how fast they begin or how long they last.
"We've been interested in looking at things inside the cell that either change over time, or are in specific places," Voldman said. Separating out cells with such characteristics "can't be done with traditional cell sorting."
For example, if cells differ in how quickly they respond to a particular compound used in the fluorescent labeling, the new system would make it possible to "select out the ones that are faster or slower, and see what's different," said Voldman, who also has appointments in MIT's Research Laboratory of Electronics and the Microsystems Technology Laboratories.
"It seems like that should be easy, but it isn't," he said. There are other ways of accomplishing the same kind of cell separation, but they require complex and expensive equipment, or are limited in the number of cells they can process.
The new system uses a simple transparent silicone layer bonded to a conventional glass microscope slide. Fabricated in the layer are a series of tiny cavities, or traps, in which cells settle out after being added to the slide in a solution. Up to 10,000 cells could be sorted on a single slide.
Looking through the microscope, either a technician or a computerized system can check each cell to determine whether it has fluorescence in the right area or at the right time to meet the selection criteria. If so, its position is noted by the computer. At the end of the selection process, all of the cells whose positions were recorded are then levitated out of their traps using the pressure of a beam of targeted light from a low-cost laser. A flowing fluid then sweeps the selected cells off to a separate reservoir.
The laser levitation of the cells acts like "a fire hose pushing up a beach ball," Voldman said. But the laser method is gentle enough that the living cells remain viable after the process is complete, allowing further biological testing.
Voldman and Kovac are continuing to refine the system, working on making it easier to use and on improving its ability to keep samples sterile. Voldman said that unlike expensive separation techniques such as optical tweezers, the new system could cost only a few thousand dollars. As a result, it could be employed in a variety of biological research laboratories or clinical settings, not just in big, centralized testing facilities.
The research was funded by the National Institutes of Health and the Singapore-MIT Alliance; Kovac is supported by an ASEE National Defense Science and Engineering Graduate Fellowship.
Adapted from materials provided by Massachusetts Institute of Technology.

Fausto Intilla

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Losses Of Long-established Genes Contribute To Human Evolution

Source:

http://www.sciencedaily.com/releases/2007/12/071214094129.htm

ScienceDaily (Dec. 15, 2007) — While it is well understood that the evolution of new genes leads to adaptations that help species survive, gene loss may also afford a selective advantage. A group of scientists at the University of California, Santa Cruz led by biomolecular engineering professor David Haussler has investigated this less-studied idea, carrying out the first systematic computational analysis to identify long-established genes that have been lost across millions of years of evolution leading to the human species.

Haussler and five others in his group--postdoc Jingchun Zhu, graduate students Zack Sanborn and Craig Lowe, technical projects manager Mark Diekhans, and evolutionary biologist Tom Pringle--are co-authors on the paper*.
"The idea that gene losses might contribute to adaptation has been kicked around, but not well studied," said Zhu, who is first author of the paper. "We found three examples in the literature, and all of them could have medical implications."
To find gene losses, Zhu employed a software program called TransMap that Diekhans had developed. The program compared the mouse and human genomes, searching for genes having changes significant enough to render them nonfunctional somewhere during the 75 million years since the divergence of the mouse and the human.
"This is the first study designed to search the entire genome for recent loss of genes that do not have any near-duplicate copies elsewhere in the genome," said Haussler. "These are likely to be the more important gene losses."
Genes can be lost in many ways. This study focused on losses caused by mutations that disrupt the open reading frame (ORF-disrupting mutations). These are either point mutations, where events such as the insertion or substitution of a DNA base alter the instructions delivered by the DNA, or changes that occur when a large portion of a gene is deleted altogether or moves to a new place on the genome.
"We used the dog genome as an out-group to filter out false positives," Sanborn explained, because the dog diverged from our ancient common ancestor earlier than the mouse. "If a gene is still living in both dog and mouse but not in human, it was probably living in the common ancestor and then lost in the human lineage."
Using this process, they identified 26 losses of long-established genes, including 16 that were not previously known.
The gene loss candidates found in this study do not represent a complete list of gene losses of long-established genes in the human lineage, because the analysis was designed to produce more false negatives than false positives.
Next they compared the identified genes in the complete genomes of the human, chimpanzee, rhesus monkey, mouse, rat, dog, and opossum to estimate the amount of time the gene was functional before it was lost. This refined the timing of the gene loss and also served as a benchmark for whether the gene in question was long-established, and therefore probably functional, or merely a loss of a redundant gene copy. Through this process, they found 6 genes that were lost only in the human.
One previously unknown loss, the gene for acyltransferase-3 (ACYL3), particularly caught their attention. "This is an ancient protein that exists throughout the whole tree of life," said Zhu. Multiple copies of the ACYL3 gene are encoded in the fly and worm genomes. "In the mammalian clade there is only one copy left, and somewhere along primate evolution, that copy was lost."
"In our analysis, we found that this gene contains a nonsense mutation in human and chimp, and it appears to still look functional in rhesus," said Sanborn. Further, they found that the mutation is not present in the orangutan, so the gene is probably still functional in that species.
"On the evolutionary tree leading to human, on the branch between chimp and orangutan sits gorilla," explained Sanborn. Knowing if the gene was still active in gorilla would narrow down the timing of the loss.
Sanborn took to the wet laboratory to sequence the corresponding region in a DNA sample from a gorilla. The gorilla DNA sequence showed the gene intact, without the mutation, so the loss likely occurred between the speciation of gorilla and chimpanzee.
"Acyltransferase-3 was not the only lost gene that doesn't have any close functional homologues in the human genome. A highlight of our research was that we were able to find a list of these 'orphan losses,'" said Zhu. "Some of them have been functional for more than 300 million years, and they were the last copies left in the human genome." While the copies of these genes remaining in the human genome appear to be nonfunctional, functional copies of all of them exist in the mouse genome.
"These orphan genes may be interesting candidates for experimental biologists to explore," said Zhu. "It would be interesting to find out what was the biological effect of these losses. Once their function is well characterized in species that still have active copies, we could maybe speculate about their effects on human evolution."
*Their findings appear in the December 14 issue of PLoS Computational Biology.
This research was funded by the National Human Genome Research Institute, the National Institutes of Health, the National Cancer Institute, and the Howard Hughes Medical Institute.
Adapted from materials provided by University of California - Santa Cruz.

Fausto Intilla

www.oloscience.com

Scientists Overcome Major Obstacles To Stem Cell Heart Repair

Source:

http://www.sciencedaily.com/releases/2007/12/071212201501.htm

ScienceDaily (Dec. 13, 2007) — Scientists at Imperial College London have overcome two significant obstacles on the road to harnessing stem cells to build patches for damaged hearts. Presenting the research at a UK Stem Cell Initiative conference December 13 in Coventry, research leader Professor Sian Harding has explained how her group have made significant progress in maturing beating heart cells (cardiomyocytes) derived from embryonic stem cells and in developing the physical scaffolding that would be needed to hold the patch in place in the heart in any future clinical application.

From the outset the Imperial College researchers have been aiming to solve two problems in the development of a stem cell heart patch. The first is undesirable side effects, such as arrhythmia, that can result from immature and undeveloped cardiomyocytes being introduced to the heart. The second is the need for a scaffold that is biocompatible with the heart and able to hold the new cardiomyocytes in place while they integrate into the existing heart tissue. Matching the material to human heart muscle is also hoped to prevent deterioration of heart function before the cells take over.
The stem cell team, led by Dr Nadire Ali, co-investigator on the grant*, have managed to follow beating embryonic stem cell-derived cardiomyocytes for up to seven months in the laboratory and demonstrate that these cells do mature. In this period the cells have coordinated beating activity, and they adopt the mature controls found in the adult heart by approximately four months after their generation from embryonic stem cells. These developed cardiomyocytes will then be more compatible with adult heart and less likely to cause arrhythmias.
The team have also overcome hurdles in the development of a biocompatible scaffold. Working closely with a group of biomaterial engineers, led by Dr Aldo Boccaccini and Dr Qizhi Chen, co-investigators on the grant, in the Department of Materials, Imperial College London, they have developed a new biomaterial with high level of biocompatibility with human tissue, tailored elasticity and programmable degradation. The latter quality is important as any application in the heart needs to be able to hold cells in place long enough for them to integrate with the organ but then degrade safely away. The researchers have found that their material, which shares the elastic characteristics of heart tissue, can be programmed to degrade in anything from two weeks upwards depending on the temperatures used during synthesis.
Professor Harding said: "Although we are still some way from having a treatment in the clinic we have made excellent progress on solving some of the basic problems with stem cell heart therapies. The work we have done represents a step forward in both understanding how stem cell-derived developing heart cells can be matured in the laboratory and how materials could be synthesised to form a patch to deliver them to damaged areas of the heart.
"A significant amount of hard work and research remains to be done before we will see this being used in patients but the heart is an area where stem cell therapies offer promise. We know that the stem cell-derived cardiomyocytes will grow on these materials, and the next step is to see how the material and cell combination behave in the long term."
Professor Nigel Brown, BBSRC Director of Science and Technology, commented: "This research shows that although embryonic stem cell therapies are still some way away from the clinic, progress is being made on the basic biological developments. As with all new biomedical applications, an understanding of the underpinning fundamental science is essential to successfully moving forward."
*This research was funded by the Biotechnology and Biological Sciences Research Council.
Adapted from materials provided by Biotechnology and Biological Sciences Research Council.

Fausto Intilla

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Researchers Can Read Thoughts To Decipher What A Person Is Actually Seeing

Source:

http://www.sciencedaily.com/releases/2007/12/071206222634.htm

ScienceDaily (Dec. 11, 2007) — Following ground-breaking research showing that neurons in the human brain respond in an abstract manner to particular individuals or objects, University of Leicester researchers have now discovered that, from the firing of this type of neuron, they can tell what a person is actually seeing.

The original research by Dr R Quian Quiroga, of the University’s Department of Engineering, showed that one neuron fired to, for instance, Jennifer Aniston, another one to Halle Berry, another one to the Sydney Opera House, etc.
The responses were abstract. For example, the neuron firing to Halle Berry responded to several different pictures of her and even to the letters of her name, but not to other people or names.
This result, published in Nature in 2005 came from data from patients suffering from epilepsy. As candidates for epilepsy surgery, they are implanted with intracranial electrodes to determine as accurately as possible the area where the seizures originate. From that, clinicians can evaluate the potential outcome of curative surgery.
Dr Quian Quiroga’s latest research, which has appeared in the Journal of Neurophysiology, follows on from this.
Dr Quian Quiroga explained: “For example, if the 'Jennifer Aniston neuron' increases its firing then we can predict that the subject is seeing Jennifer Aniston. If the 'Halle Berry neuron' fires, then we can predict that the subject is seeing Halle Berry, and so on.
“To do this, we used and optimised a 'decoding algorithms', which is a mathematical method to infer the stimulus from the neuronal firing. We also needed to optimise our recording and data processing tools to record simultaneously from as many neurons as possible. Currently we are able to record simultaneously from up to 100 neurons in the human brain.
“In these experiments we presented a large database of pictures, and discovered that we can predict what picture the subject is seeing far above chance. So, in simple words, we can read the human thought from the neuronal activity.
“Once we reached this point, we then asked what are the most fundamental features of the neuronal firing that allowed us to make this predictions. This gave us the chance of studying basic principles of neural coding; i.e. how information is stored by neurons in the brain.
“For example, we found that there is a very limited time window in the neuronal firing that contains most of the information used for such predictions. Interestingly, neurons fired only 4 spikes in average during this time window. So, in another words, only 4 spikes of a few neurons are already telling us what the patient is seeing.”
Potential applications of this discovery include the development of Neural Prosthetic devices to be used by paralysed patients or amputees. A patient with a lesion in the spinal cord (as with the late Christopher Reeves), can still think about reaching a cup of tea with his arm, but this order is not transmitted to the muscles.
The idea of Neural Prostheses is to read these commands directly from the brain and transmit them to bionic devices such as a robotic arm that the patient could control directly from the brain.
Dr Quian Quiroga’s work showing that it is possible to read signals from the brain is a good step forward in this direction. But there are still clinical and ethical issues that have to be resolved before Neural Prosthetic devices can be applied in humans.
In particular, these would involve invasive surgery, which would have to be justified by a clear improvement for the patient before it could be undertaken.
Adapted from materials provided by University of Leicester.

Fausto Intilla

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'Oosight' Microscope Enables Embryonic Stem Cell Breakthrough

Source:

http://www.sciencedaily.com/releases/2007/11/071129183731.htm

ScienceDaily (Dec. 3, 2007) — A noninvasive, polarized light microscope invented at the Marine Biological Laboratory (MBL) played a crucial role in a recent breakthrough in embryonic stem-cell research aimed at developing medical therapies.

A team led by Shoukhrat Mitalipov, Ph.D., of Oregon Health & Science University reported the successful derivation of stem cells from cloned monkey embryos in the November 22 issue of Nature. While embryonic stem cells have been made from cloned embryos in a mouse, this is the first time they have been produced in a primate.
In humans, this method for deriving stem cells is a potential way to make "custom" tissues that are genetically identical to a patient, which would avoid rejection by the patient's immune system. Stem cells, in theory, can be induced to become any type of cell, tissue or organ. However, in recent years, some investigators had claimed it wouldn't be technically possible to make embryonic stem cells from monkeys or humans using this method (somatic cell nuclear transfer, or therapeutic cloning).
Mitalipov's stem-cell derivation succeeded, he says, largely due to the Oosight ™ microscope system developed by Cambridge Research & Instrumentation Inc. (CRi) of Woburn Mass., using technology invented at the MBL by senior scientist Rudolf Oldenbourg, Ph.D., and research associate Guang Mei, Ph.D. Former MBL research scientists David L. Keefe, M.D., and Lin Liu, Ph.D., both of whom teach in the MBL's Frontiers in Reproduction course, worked with Oldenbourg to adapt the technology for somatic cell nuclear transfer and embryology.
"The use of the Oosight was one of the major modifications we made in our present work," Mitalipov says.
The Oosight allowed Mitalipov's team to clearly see and remove the meiotic spindle from 304 female rhesus monkey eggs. This is the first step in therapeutic cloning, called enucleation. Next, they inserted the genetic material from the skin cells of an adult male rhesus monkey into the eggs and allowed them to grow to the blastocyst stage. From these cloned embryos, the researchers obtained two viable stem cell lines that are genetically identical to the adult male monkey.
"We are thrilled that the Oosight worked for enucleating monkey eggs," says Keefe. "We already had shown at the MBL, in 2000, that the technology developed by Dr. Oldenbourg facilitated noninvasive enucleation of mice eggs." At that time, Keefe operated a research lab at the MBL and directed the Division of Reproductive Medicine and Infertility at Women & Infants Hospital in Providence, R.I. Keefe is presently professor and chair of the Department of Obstetrics and Gynecology at the University of South Florida College of Medicine.
"Before, the problem was always that you could not see the spindle in the egg," Mitalipov says. "The only way to see it was to stain it with dyes. And that, we found, was very detrimental for egg quality." The Oosight uses liquid-crystal polarized light technology to image the spindle noninvasively, with high contrast and quality.
"You can actually look in the Oosight microscope and see the spindle with your eyes, not frozen as a computer screen image," says Mitalipov, which is critical for the next step: taking the spindle out of the egg. "You can't manipulate the egg while looking at a computer screen. You have to look at the egg. The Oosight, plus very skilled micromanipulations of the eggs, gave us a 100% success rate with enucleating."
The Oosight is based on technology that is the result of decades of MBL research pioneered by Distinguished Scientist Shinya Inoué. In the 1950s, Inoué was one of the first cytologists to make extensive use of the polarized light microscope to observe birefringent components of the cell, which led to his landmark discovery in 1951 of the meiotic spindle fibers in living cells. He later showed that dynamic disassembly of the spindle fibers can produce force that moves the chromosomes toward the poles of the cell during mitosis or meiosis.
In 1957, Inoué added a polarization rectifier to his custom-built microscope, which dramatically decreased distortion and improved the contrast of the image. Rudolf Oldenbourg further improved the polarizing microscope in the mid-1990s, adding liquid crystals with electro-optical controls and software. This version, called the LC-PolScope, allows one to simultaneously measure the birefringence in every resolved specimen point across the entire viewing field of the microscope; traditional models could only measure a single point of the specimen at a time. The LC-PolScope continues to be refined and expanded for live cell imaging at the MBL. Its technology is being adapted to different application areas by Cambridge Research & Instrumentation and is sold under trademarks such as Oosight and Abrio.
In the mid-1990s, David Keefe set up a lab at the MBL in order to collaborate with Oldenbourg and Inoué. Keefe was interested in finding out if the noninvasive LC-PolScope could be used in clinical settings to evaluate the quality of human eggs prior to in vitro fertilization procedures, and thus reduce the number of nonviable embryos created; and to improve the efficiency of therapeutic cloning in animals.
"When I was training as an ob-gyn at Yale in the mid 1980s, we were one of the first places to use ultrasound to assess the health of babies in utero," Keefe says. "As a student in the MBL Physiology Course, I learned of Drs. Inoué's and Oldenbourg's work, and realized we could use the polarizing microscope to assess health even earlier during development -- back to the beginning, at the egg stage -- without hurting the egg," Keefe says.
Using the LC-PolScope, Keefe, Oldenbourg and collaborators reported for the first time on layers of birefringence in the egg's zona pellucida in 1997. In 2000, Lin Liu, Keefe, Oldenbourg and collaborators reported that the polarized light microscope also helped enucleate mouse eggs, the critical step during somatic cell nuclear transfer, and proposed that this approach would improve the efficiency and safety of therapeutic cloning (Nature Biotech. 18: 223-225).
The LC-PolScope was commercialized first as the SpindleView in 1999, later as the Oosight in 2005, with improvements for fast viewing contributed by Michael Shribak, Ph.D., associate research scientist at the MBL. The Oosight has the same optical components and the algorithms as the LC-PolScope, but it is simplified for routine operation. While polarized light microscopy is now used throughout the world in infertility clinics, and was proposed as an aid to cloning research, its actual application to cloning research was not appreciated until the recent Nature paper by Mitalipov et al.
"In spirit and in application, the Oosight really expands on what Shinya Inoué started in the 1950s," says Oldenbourg. "And it was David Keefe's vision that the LC-PolScope could be used for in vitro fertilization or for enucleation, since it can be used to visualize the spindle without staining it with dyes."
"It's very significant that the Oosight and its applications were developed at the MBL," says Keefe. "The MBL is such a special and unique place. We had Shinya Inoué, Rudolf Oldenbourg, and our group of mammalian embryologists and clinicians, all working literally 25 feet from each other's labs. That's why this work was accomplished."
Journal citations:
Byrne, J.A., D.A. Pedersen, L.L. Clepper, M. Nelson, W.G. Sanger, S. Gokhale, D.P. Wolf, and S.M. Mitalipov (2007). Producing primate embryonic stem cells by somatic cell nuclear transfer. Nature 450: 497-502.
Liu, L., R. Oldenbourg, J.R. Trimarchi, and D.L. Keefe. 2000. A reliable, noninvasive technique for spindle imaging and enucleation of mammalian oocytes. Nature Biotech. 18: 223-225.
Adapted from materials provided by Marine Biological Laboratory.

Fausto Intilla

www.oloscience.com

Human Genome Has Four Times More Imprinted Genes Than Previously Identified

Source:

http://www.sciencedaily.com/releases/2007/11/071130075016.htm

ScienceDaily (Nov. 30, 2007) — Scientists at Duke University have created the first map of imprinted genes throughout the human genome, and they say a modern-day Rosetta stone -- a form of artificial intelligence called machine learning -- was the key to their success. The study revealed four times as many imprinted genes as had been previously identified.

In classic genetics, children inherit two copies of a gene, one from each parent, and both actively shape how the child develops. But in imprinting, one of those copies is turned off by molecular instructions coming from either the mother or the father. This process of "imprinting" information on a gene is believed to happen during the formation of an egg or sperm, and it means that a child will inherit only one working copy of that gene. That's why imprinted genes are so vulnerable to environmental pressures: If the only functioning copy is damaged or lost, there's no backup to jump in and help out.
Many of the newly-identified imprinted genes lie within genomic regions linked to the development of major diseases like cancer, diabetes, autism, and obesity. Researchers say that if some of these genes are later shown to be active in these disorders, they may offer clues to better disease prevention or management.
"Imprinted genes have always been something of a mystery, partly because they don't follow the conventional rules of inheritance," says Dr. Randy Jirtle, a genetics researcher in the departments of radiation oncology and pathology at Duke and a senior author of the study. "We're hoping this new roadmap will help us and others find more information about how these genes affect our health and well-being."
The technical wizardry needed to find the genes fell to Dr. Alexander Hartemink, the other senior author of the study and an assistant professor in Duke's department of computer science, and Philippe Luedi, the first author of the study. They fed sequence data from two types of genes -- ones known to be imprinted and ones believed not to be imprinted -- into a computer and asked it to discover the differences. This machine learning approach led to an algorithm, which was able -- like the original Rosetta stone -- to decode seemingly impenetrable data, in this case, specific DNA sequences that pointed to the presence of imprinted genes.
"We can't say for certain that we identified all of them, but we think we found a large number," says Hartemink.
Jirtle, who has studied imprinting for years, notes that imprinting is an epigenetic event, meaning it's something that can change a gene's function without altering the sequence of its DNA. "Imprinted genes are unusually vulnerable to pressures in our environment -- even what we eat, drink, and breathe. On top of that, epigenetic changes can be inherited. I don't think people realize that."
Several years ago, Jirtle showed that Agouti mice -- normally fat and yellow -- when fed certain dietary supplements, would produce brown, normal weight babies. The babies' Agouti genes, the ones responsible for color, were the same as the mother's, yet they looked different. "That's epigenetics in action," says Jirtle.
It's estimated that imprinted genes comprise about 1 percent of the human genome, and until now, only several dozen had been identified. Using their new "Rosetta stone", however, Jirtle and Hartemink found 156 new likely imprinted genes, and validated two particularly interesting ones on chromosome 8, where none had been found before. One of them, KCNK9, is mostly active in the brain, is known to cause cancer, and may also be linked to bipolar disorder and epilepsy. The second, DLGAP2, is a possible bladder cancer tumor suppressor gene.
Hartemink says experiments to confirm that all 156 new genes are truly imprinted -- and not just statistically likely candidates -- will be difficult, mostly because gene expression varies from tissue to tissue and most genes turn on and off over time. "We've certainly narrowed the field, but we have a whole lot of work ahead of us."
This research is published in the December 3 issue of Genome Research.
Grants from the National Institutes of Health, National Science Foundation, U.S. Department of Energy and the Alfred Sloan Foundation supported the research.
Duke colleagues who also contributed to the work include Fred Dietrich, from the department of molecular genetics and microbiology; Jennifer Weidman, from the department of radiation oncology and Jason Bosko, an undergraduate in the department of computer science.
Adapted from materials provided by Duke University Medical Center.

Fausto Intilla

www.oloscience.com

Vascular Biologists Make A Significant Discovery In Neurobiology

Source:

http://www.sciencedaily.com/releases/2007/11/071129142714.htm

ScienceDaily (Nov. 30, 2007) — Researchers investigating blood vessels at Barts and The London School of Medicine have hit upon a new discovery in neurobiology that could have implications for patients experiencing peripheral nerve disorders.
Lead by Professor Sussan Nourshargh the research reports on the previously unknown expression and function of a particular cell adhesion molecule, junctional adhesion molecule-C (JAM-C), in peripheral nerves. JAM-C, largely associated to date with inflammatory disorders, was found to play a critical role in maintaining the integrity and function of peripheral nerves by forming an integral part of the insulating sheath that surrounds these nerves -- the myelin.
The work, which was conducted in close collaboration with scientists at Imperial College London, University College London, Cancer Research UK and the University of Geneva, is published in the journal Science.
Together with their collaborators, Professor Nourshargh and team member Christoph Scheiermann, discovered that mice in which the JAM-C gene had been deleted showed neuronal functional defects -- specifically, impaired nerve conduction and behavioural abnormalities indicating muscle weakness.
The findings of the study also indicated that in nerves from patients with particular peripheral nerve disorders the expression of JAM-C was defective. Collectively this study describes a previously unrecognised role for JAM-C and identifies this molecule as a key player in regulating the structural integrity and function of peripheral nerves. The study also potentially provides insight into the causes of some peripheral nerve disorders and presents a strong platform for further research into this area.
There are more than 100 kinds of peripheral nerve disorders affecting approximately 1 in 20 people, symptoms of which -- often starting gradually and steadily worsening -- include numbness, pain, tingling, muscle weakness and sensitivity to touch.
Commenting on the significance of the research findings Professor Nourshargh said: "The discovery of JAM-C in peripheral nerves has made a major contribution to the field of neurobiology at a fundamental molecular level, but has also raised the possibility that defective expression and/or function of this molecule may be associated with the pathology of certain peripheral nerve disorders."
This research was conducted in close collaboration with neurologist Professor Praveeen Anand of Imperial College London.
The paper; 'Expression and Function of Junctional Adhesion Molecule-C in Myelinated Peripheral Nerves,' is published in Science on 30 November 2007.
Adapted from materials provided by Queen Mary, University of London.

Fausto Intilla
www.oloscience.com

Gene Study Supports Single Main Migration Across Bering Strait

Source:

http://www.sciencedaily.com/releases/2007/11/071126170543.htm

ScienceDaily (Nov. 28, 2007) — Did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?

Or did the ancestors of today's native peoples come from other parts of Asia or Polynesia, arriving multiple times at several places on the two continents, by sea as well as by land, in successive migrations that began as early as 30,000 years ago?
The questions -- featured on magazine covers and TV specials -- have agitated anthropologists, archaeologists and others for decades.
University of Michigan scientists, working with an international team of geneticists and anthropologists, have produced new genetic evidence that's likely to hearten proponents of the land bridge theory. The study, published online in PLoS Genetics, is one of the most comprehensive analyses so far among efforts to use genetic data to shed light on the topic.
The researchers examined genetic variation at 678 key locations or markers in the DNA of present-day members of 29 Native American populations across North, Central and South America. They also analyzed data from two Siberian groups. The analysis shows:
o genetic diversity, as well as genetic similarity to the Siberian groups, decreases the farther a native population is from the Bering Strait -- adding to existing archaeological and genetic evidence that the ancestors of native North and South Americans came by the northwest route.
o a unique genetic variant is widespread in Native Americans across both American continents -- suggesting that the first humans in the Americas came in a single migration or multiple waves from a single source, not in waves of migrations from different sources. The variant, which is not part of a gene and has no biological function, has not been found in genetic studies of people elsewhere in the world except eastern Siberia.
The researchers say the variant likely occurred shortly prior to migration to the Americas, or immediately afterwards.
"We have reasonably clear genetic evidence that the most likely candidate for the source of Native American populations is somewhere in east Asia," says Noah A. Rosenberg, Ph.D., assistant professor of human genetics and assistant research professor of bioinformatics at the Center for Computational Medicine and Biology at the U-M Medical School and assistant research professor at the U-M Life Sciences Institute.
"If there were a large number of migrations, and most of the source groups didn't have the variant, then we would not see the widespread presence of the mutation in the Americas," he says.
Rosenberg has previously studied the same set of 678 genetic markers used in the new study in 50 populations around the world, to learn which populations are genetically similar and what migration patterns might explain the similarities. For North and South America, the current research breaks new ground by looking at a large number of native populations using a large number of markers.
The pattern the research uncovered -- that as the founding populations moved south from the Bering Strait, genetic diversity declined -- is what one would expect when migration is relatively recent, says Mattias Jakobsson, Ph.D., co-first author of the paper and a post-doctoral fellow in human genetics at the U-M Medical School and the U-M Center for Computational Medicine and Biology. There has not been time yet for mutations that typically occur over longer periods to diversify the gene pool.
In addition, the study's findings hint at supporting evidence for scholars who believe early inhabitants followed the coasts to spread south into South America, rather than moving in waves across the interior.
"Assuming a migration route along the coast provides a slightly better fit with the pattern we see in genetic diversity," Rosenberg says.
The study also found that:
Populations in the Andes and Central America showed genetic similarities.
Populations from western South America showed more genetic variation than populations from eastern South America.
Among closely related populations, the ones more similar linguistically were also more similar genetically.
Citation: PLoS Genet 3(11): e185. doi:10.1371/journal.pgen.0030185
In addition to Rosenberg and Jakobsson, study authors include Cecil M. Lewis, Jr., former post-doctoral fellow in the U-M Department of Human Genetics, and 24 researchers at U.S., Canadian, British, Central and South American universities.
Adapted from materials provided by University of Michigan Health System.

Fausto Intilla

www.oloscience.com

New Microscope Peers Into Secret Lives Of Cells

Source:

http://www.sciencedaily.com/releases/2007/11/071121094738.htm

ScienceDaily (Nov. 26, 2007) — “See those white sparks?” asks Kirk Czymmek, as he points to the video on his computer screen of a highly magnified heart cell in action. Tiny fireworks flash across the screen with every pulsation of the cell.

“That's calcium,” Czymmek notes. “Scientists have discovered that there is a large release of calcium with every heartbeat. If we don't see those sparks,” he notes, “you have a major problem--perhaps even heart failure.”
Czymmek has a bird's-eye view into the fascinating and rarely seen world of the microscopic, as director of the University of Delaware's Bio-imaging Center.
The center, a component of UD's Delaware Biotechnology Institute, is equipped with the latest technology for microscopic explorations into a diversity of intriguing subjects under investigation by University researchers, from plants that can decontaminate soils of toxic metal pollutants, to carbon nano-bombs for destroying cancer cells.
Czymmek, who also is an associate professor of biological sciences at UD, recently showcased the latest addition to the University's suite of high-tech imaging tools--a state-of-the-art laser-scanning confocal microscope. UD is among a handful of universities that own one of the million-dollar instruments.
The device, known as the LSM 510 DUO, manufactured by Carl Zeiss MicroImaging Inc., typically uses a laser beam to observe a single focal point at a time on its subject--acquiring over a quarter-million picture elements, or pixels, in a single scan, which takes about one second. However, if the laser beam is shaped into a line and swept across the sample, it can scan an image over 100 times faster.
The microscope is particularly useful in examining thick samples such as muscle tissue at high resolution, Czymmek says, because a series of scans may be made at different depths within the sample and assembled automatically in minutes, yielding breathtakingly detailed, three-dimensional images, much like an MRI of the human body reveals.
“It has been my experience, that advances in analytical science often open the door to new scientific inventions and innovations,” said David Weir, director of the Delaware Biotechnology Institute. “The capability we now have with this new microscope, which allows us to observe natural processes as they occur and in great detail, will surely result in new, important discoveries.”
Currently, Czymmek and his staff--associate scientist Liz Adams and research associates Deborah Powell and Shannon Modla--are assisting UD researchers with a broad range of scientific projects on plants and fungi, vocal cords, bone health, biofilms, DNA repair, and gel-like synthetic polymers, among others.
An average of 175 users per year have been served at the center since it opened in 2001, according to Czymmek. UD faculty, staff and students, as well as research collaborators from industry and governmental agency partners, have all been trained in the safe and proper operation of the center's sophisticated “eyes.”
UD's Bio-Imaging Center also is an important resource for scientists beyond Delaware's borders, with colleagues from the National Institutes of Health, Johns Hopkins University, DuPont, Georgetown University, Merck and Virginia Commonwealth University attending microscopy training workshops hosted by Czymmek and his staff.
Czymmek, who refers to himself as a “jack of all trades,” has been using confocal microscopes on almost a daily basis since 1990 when they helped illuminate his doctoral studies of plant diseases and fungi.
One of the things he most likes about his position at UD is its cross-disciplinary focus. He has assisted scientists in examining the hard exoskeleton of an insect, for example, to learn how to make new and improved materials.
“I like being able to help tie together the biology and engineering and help people figure out the best way to solve a problem,” he says.
With each new and improved tool for revealing hidden worlds, Czymmek and his staff gain a front-row seat into the formerly unknown and help put dozens of UD research studies literally into sharper focus.
“It's kind of like going out in space,” Czymmek says with a smile. “We get to see things that no one else has ever seen before.”
Adapted from materials provided by University of Delaware.

Fausto Intilla

www.oloscience.com

Scientists Melt Million-year-old Ice In Search Of Ancient Microbes

Source:

http://www.sciencedaily.com/releases/2007/11/071126115305.htm

ScienceDaily (Nov. 26, 2007) — Researchers from the University of Delaware and the University of California at Riverside have thawed ice estimated to be at least a million years old from above Lake Vostok, an ancient lake that lies hidden more than two miles beneath the frozen surface of Antarctica.

The scientists will now examine the eons-old water for microorganisms, and then through novel genomic techniques, try to figure out how these tiny, living “time capsules” survived the ages in total darkness, in freezing cold and without food and energy from the sun.
The research is designed to provide insight into how organisms adapted to live in extreme environments.
“It's some of the coolest stuff I have ever worked on,” said Craig Cary, professor of marine biosciences at UD. “We are going to gain access to the genetics of organisms isolated for possibly as long as 15 million years.”
The collaborative research team includes Cary and doctoral student Julie Smith from UD's College of Marine and Earth Studies; project leader Brian Lanoil, assistant professor of environmental sciences at the University of California at Riverside, and doctoral student James Gosses; and Philip Hugenholtz and postdoctoral fellows Victor Kunin and Brian Rabkin at the U.S. Department of Energy's Joint Genome Institute.
Last week in Lanoil's laboratory in California, segments of a tube-like ice core were thawed under meticulous, “clean lab” conditions to prevent accidental contamination, a process that required nearly a year of preparation.
“It was very exciting to see the Vostok ice, knowing how old it is and how much it took to get that ice to the lab,” Smith said. “The ice core itself was incredibly clear and glasslike, reflecting the light like a prism.”
The segments of ice were cut from an 11,866-foot ice core drilled in 1998 through a joint effort involving Russia, France and the United States. The core was taken from approximately two miles below the surface of Antarctica and 656 feet (200 meters) above the surface of Lake Vostok and has since been stored at -35 degrees C at the National Ice Core Laboratory in Denver.
“This ice was once water in the lake that refroze onto the bottom of the ice sheet,” Cary explained. “We have no direct samples of the lake itself, only this indirect sampling of the refrozen ice above it because drilling into the lake without taking extensive precautions could lead to the lake's contamination. The borehole made to collect the ice is filled with a mixture of jet fuel, kerosene, and CFCs to keep it from closing,” Cary noted. “Since the lake has not had direct contact with the surface world for at least 15 million years, this would be a contamination of one of the most pristine environments on Earth,” he said.
Cary said the decontamination procedure was “the most complicated and complete ever attempted,” requiring the use of an isolation chamber for the actual melting, concentration of the meltwater through a special filtering system, use of bleaching solutions for the destruction of any contaminating bacteria or DNA from the outside of the core, and the wearing of sterile jump suits for all of the laboratory personnel, among other measures.
Although other scientific projects have identified the microorganisms living in the Vostok water, they have not revealed what these little one-celled organisms do or how they have become adapted to an environment that is eternally dark, cold and so isolated that food and energy sources are likely rare and hard to come by.
“This research is important because it will give us insight into how microbes can survive in a very energy-limited system,” Smith said. She intends to pursue a career in academia after she completes her doctorate at UD's College of Marine and Earth Studies.
“Most of our planet is permanently cold and dark, so it makes sense that we should study how life exists under these conditions. In addition, enzymes produced by these microorganisms may be useful in industrial applications down the road,” Smith noted.
The Vostok water contains only between 10-100 microbes per milliliter compared to approximately 1 million microbes per milliliter for most lakes, Cary said.
Novel “whole genome amplification” techniques will be applied, which provide insight into the genetic diversity of a community of organisms when only small numbers of organisms are available.
A veteran of research expeditions around the globe, Cary is an expert on “extremophiles”--organisms that thrive in the harshest environments on the planet, ranging from the dry, frigid desert of Antarctica, to geyser-like hydrothermal vents spewing toxic chemicals from the ocean floor.
In the case of Lake Vostok, scientists speculate that it stays in a liquid state underneath miles of ice due to one of the Earth's natural “furnaces”--hydrothermal vents. Superheated water erupts from these cracks in the seafloor which form where the plates that form the Earth's crust pull apart.
“We hope that by being so isolated for millions of years, these microorganisms from Vostok will be able to tell us about their life and conditions through the ages,” Cary said.
This research is sponsored by the National Science Foundation and is part of the International Polar Year.
Adapted from materials provided by University of Delaware.

Fausto Intilla

www.oloscience.com

Flip-flopping Gene Expression Can Be Advantageous

Source:

http://www.sciencedaily.com/releases/2007/11/071126103616.htm

ScienceDaily (Nov. 26, 2007) — One gene for pea pod color generates green pods while a variant of that gene gives rise to the yellow-pod phenotype, a feature that helped Gregor Mendel, the 19th century Austrian priest and scientist, first describe genetic inheritance. However, many modern-day geneticists are focused on the strange ability of some genes to be expressed spontaneously in either of two possible ways.

In order to better understand this phenomenon of epigenetic multistability, a major complication for Mendelian genetics, scientists at UC San Diego grew virtual bacterial cells in a computer experiment. They created a two-phenotype model system programmed to grow in ways that matched natural growth. In a deceptively simple experiment, they then recorded the degree to which the two phenotypes varied over time in individual cells, and then repeated the experiment over and over. They reported in the Nov. 19 online edition of Proceedings of the National Academy of Sciences that variability due to epigenetic multistability is larger and persists much longer than they had expected.
While the phenomenon is yet to be discovered in the human genome, the new results suggest that researchers studying bacteria should carefully design their experiments to measure variability due to epigenetic multistability. Even in human cells, multistability may play a role in genes can alternate between “on” and “off” settings.
“Scientists studying bacteria have simply not had the tools to understand phenotypic variability,” said Ting Lu, lead author of the study who was a physics graduate student in the lab of bioengineering professor Jeff Hasty. (Lu is currently a postdoctoral fellow at Princeton University.) “We’ve arrived at a theoretical framework that allows experimenters to measure the ephemeral nature of epigenetics.”
Epigenetic multistability may be vital to cells that are outwardly different, but genetically identical. Only one of the two phenotypes might thrive in a given environmental condition; however, the less advantageous phenotype could come in handy if the environmental conditions unexpectedly changed. By having both phenotypes, the chances would be better that the best one will be present when needed.
Researchers in many labs recently have demonstrated that gene expression can be surprisingly random. The framework established in the UCSD study evaluates how such noisy gene expression affects the properties of developing cellular colonies, such as the progression of bacterial infections or the growth of a population of cancerous cells.
The PNAS paper also documented that the time it takes for a population of cells to reach a stable variance depends on the initial growth conditions and how easily those conditions support cell growth.
“Different results can emerge depending on how cells are grown,” said Jeff Hasty, a professor of bioengineering at UCSD and senior author of the paper. “Our results should allow all researchers studying bacteria to better understand the variability they routinely see from one experiment to the next."
This work is supported by the National Institutes of Health. While a student at UCSD, Lu was affiliated with the Center for Theoretical Biological Physics, a $10 million National Science Foundation-financed center designed to apply the mathematical tools of theoretical physics to biology.
Adapted from materials provided by University of California - San Diego.

Fausto Intilla

www.oloscience.com

Key Nerve Navigation Pathway Identified

Source:

http://www.sciencedaily.com/releases/2007/11/071121145008.htm

ScienceDaily (Nov. 26, 2007) — Newly launched nerve cells in a growing embryo must chart their course to distant destinations, and many of the means they use to navigate have yet to surface. In a study published in the current issue of the journal Neuron, scientists at the Salk Institute for Biological Studies have recovered a key signal that guides motor neurons -- the nascent cells that extend from the spinal cord and must find their way down the length of limbs such as arms, wings and legs.

The Salk study, led by Samuel Pfaff, Ph.D, a professor in the Gene Expression Laboratory, identifies a mutation they christened Magellan, after the Portuguese mariner whose ship Victoria was first to circumnavigate the globe. The Magellan mutation occurs in a gene that normally pilots motor neurons on the correct course employing a newly discovered mechanism, their results demonstrate.
In the mutants, growing neurons can be seen leaving the spinal cord normally but then appear to lose direction. The elongating cells develop "kinks" and sometimes fold back on themselves or become entwined in a spiral, forming coils outside the spinal cord. "They appear to become lost in a traffic roundabout," described Pfaff, who observed the growing neurons with fluorescent technology.
Understanding how motor neurons reach the appropriate targets is necessary for the implementation of novel therapies, including embryonic stem cell replacement for the treatment of presently incurable disorders such as Lou Gehrig's disease, in which motor neurons undergo irreversible decay.
"Embryonic studies provide useful insights on how to replicate the system in an adult," said Pfaff. And, as he also pointed out, the mechanisms used by motor neurons are likely to be similar to those used in other parts of the central nervous system, such as the brain. The Magellan mutation discovered by Pfaff's group was found in mice, but the affected gene, called Phr1, has also been identified in other model systems, including fruit flies and the worm species C. elegans.
A growing nerve bears at its bow a structure called the growth cone, a region rich in the receptor molecules whose job is to receive cues from the environment, much as ancient mariners who observed the stars and set their course accordingly. During development, the growth cone continuously pushes forward, while the lengthening neuron behind it matures into the part of the cell called the axon. Once the growing cell "lands" at its target in a muscle cell, it is the axon that will relay the messages that allow an animal to control and move its limbs at will.
In Magellan mutants, Pfaff's team discovered that the growth cone becomes disordered. Rather than forming a distinct "cap" on the developing neuron, the cone is dispersed in pieces along both the forward end and the axon extending behind it.
"The defect is found in the structure of the neuron itself," said Pfaff, noting that the fundamental pieces, such as the receptors capable of reading cues, all seem to be present. Without the correct orientation of receptors, however, signals cannot be read accurately, resulting in growth going off course.
"A precise gradient normally exists across the cone," said Pfaff, "which is disrupted in the Magellan mutants." As a result, cells lose their polarity. They literally do not know the front end from the back end, according to Pfaff. This sense of polarity is a universal feature common to all growing neurons. Therefore, "Phr1 is likely to play a role in most growing neurons to ensure their structure is retained at the same time they are growing larger," he said.
Pfaff and his group identified Magellan using a novel system they had developed, in which individual motor neurons and axons can be visualized fluorescently. They were able to screen more than a quarter of a million mutations, and the mutations of interest were rapidly mapped to known genes as a result of the availability of the sequenced mouse genome -- a byproduct of the effort to sequence entire genomes such as that in the human.
The Magellan mutation is located in a gene known as Phr1, which is also active in other parts of the nervous system, indicating that it most likely functions to steer other types of neurons, such as those that enervate sensory organs or connect different regions of the brain. Studies of Magellan may therefore shed light on how a variety of neurological disorders might be treated with cell replacement strategies.
Lead author on the study is Joseph W. Lewcock, formerly a postdoctoral fellow in Pfaff's laboratory and currently at Genentech, Inc. Additional Salk authors include postdoctoral fellow Nicolas Genoud and senior research assistant Karen Lettieri.
The study, titled "The ubiquitin ligase Phr1 regulates axon outgrowth through modulation of microtubule dynamics," was supported by the National Institute for Neurological Disorders and Stroke.
Adapted from materials provided by Salk Institute.

Fausto Intilla

www.oloscience.com

Bioclocks Work By Controlling Chromosome Coiling

Source:

http://www.sciencedaily.com/releases/2007/11/071121144914.htm

ScienceDaily (Nov. 23, 2007) — There is a new twist on the question of how biological clocks work.

In recent years, scientists have discovered that biological clocks help organize a dizzying array of biochemical processes in the body. Despite a number of hypotheses, exactly how the microscopic pacemakers in every cell in the body exert such a widespread influence has remained a mystery. Now, a new study provides direct evidence that biological clocks can influence the activity of a large number of different genes in an ingenious fashion, simply by causing chromosomes to coil more tightly during the day and to relax at night.
"The idea that the whole genome is oscillating is really cool," enthuses Vanderbilt Professor of Biological Sciences Carl Johnson, who headed the research that was published online Nov. 13 in the Proceedings of the National Academy of Sciences. "The fact that oscillations can act as a regulatory mechanism is telling us something important about how DNA works: It is something DNA jockeys really need to think about."
Johnson's team, which consisted of Senior Lecturer Mark A Woelfle, Assistant Research Professor Yao Xu and graduate student Ximing Qin, performed the study with cyanobacteria (blue-green algae), the simplest organism known to possess a biological clock. The chromosomes in cyanobacteria are organized in circular molecules of DNA. In their relaxed state, they form a single loop. But, within the cell, they are usually "supercoiled" into a series of small helical loops. There are even two families of special enzymes, called gyrases and topoisomerases, whose function is coiling and uncoiling DNA.
The researchers focused on small, non-essential pieces of DNA in the cyanobacteria called plasmids that occur naturally in the cyanobacteria. Because a plasmid should behave in the same fashion as the larger and more unwieldy chromosome, the scientists consider it to be a good proxy of the behavior of the chromosome itself.
When the plasmid is relaxed, it is open and uncoiled and, when it is supercoiled, it is twisted into a smaller, more condensed state. So, the researchers used a standard method, called gel electrophoresis, to measure the extent of a plasmid's supercoiling during different points in the day/night cycle.
The researchers found a distinct day/night cycle: The plasmid is smaller and more tightly wound during periods of light than they are during periods of darkness. They also found that this rhythmic condensation disappears when the cyanobacteria are kept in constant darkness.
"This is one of the first pieces of evidence that the biological clock exerts its effect on DNA structure through the coiling of the chromosome and that this, in turn, allows it to regulate all the genes in the organism," says Woelfle.
Some cyanobacteria use their biological clocks to control two basic processes. During the day, they use photosynthesis to turn sunlight into chemical energy. During the night, they remove nitrogen from the atmosphere and incorporate it into a chemical compound that they can use to make proteins.
According to the Johnson lab's "oscilloid model," the genes that are involved in photosynthesis should be located in regions of the chromosome that are "turned on" by the tighter coiling in the DNA during the day and "turned off" during the night when the DNA is more relaxed. By the same token, the genes that are involved in nitrogen fixation should be located in regions of the chromosome that are "turned off" during the day when the DNA is tightly coiled and "turned on" during the night when it is more relaxed.
The researchers see no reason why the bioclocks in higher organisms, including humans, do not operate in a similar fashion. "This could be a universal theme that we are just starting to decipher," says Woelfle.
The DNA in higher organisms is much larger than that in cyanobacteria and it is linear, not circular. Stretched end-to-end, the genome in a mammalian cell is about six feet long. In order to fit into a microscopic cell, the DNA must be tightly packed into a series of small coils, something like microscopic Slinkies.
Previous studies have shown that in higher organisms between 5 to 10 percent of genes in the genome are controlled by the bioclock, compared to 100 percent of genes in the cyanobacteria. In the case of the higher organisms, the bioclock's control is likely to be local rather than the global situation in cyanobacteria.
With a circular chromosome (as in cyanobacteria), twisting it at any point affects the entire molecule. When you twist a linear chromosome at a certain point, however, the effect only extends for a limited distance in either direction because the ends are not connected. That fits neatly with the idea that the bioclock's influence on linear chromosomes is limited to certain specific regions, regions where the specific genes that it regulates are located.
Adapted from materials provided by Vanderbilt University.

Fausto Intilla

www.oloscience.com

Evolutionary Comparison Finds New Human Genes

Source:

http://www.sciencedaily.com/releases/2007/11/071120111538.htm

ScienceDaily (Nov. 23, 2007) — Using supercomputers to compare portions of the human genome with those of other mammals, researchers at Cornell have discovered some 300 previously unidentified human genes, and found extensions of several hundred genes already known.
The discovery is based on the idea that as organisms evolve, sections of genetic code that do something useful for the organism change in different ways.
The research is reported by Adam Siepel, Cornell assistant professor of biological statistics and computational biology, Cornell postdoctoral researcher Brona Brejova and colleagues at several other institutions in the online version of the journal Genome Research, and it will appear in the December print edition.
The complete human genome was sequenced several years ago, but that simply means that the order of the 3 billion or so chemical units, called bases, that make up the genetic code is known. What remains is the identification of the exact location of all the short sections that code for proteins or perform regulatory or other functions.
More than 20,000 protein-coding genes have been identified, so the Cornell contribution, while significant, doesn't dramatically change the number of known genes. What's important, the researchers say, is that their discovery shows there still could be many more genes that have been missed using current biological methods. These methods are very effective at finding genes that are widely expressed but may miss those that are expressed only in certain tissues or at early stages of embryonic development, Siepel said.
"What's exciting is using evolution to identify these genes," Siepel said. "Evolution has been doing this experiment for millions of years. The computer is our microscope to observe the results."
Four different bases -- commonly referred to by the letters G, C, A and T -- make up DNA. Three bases in a row can code for an amino acid (the building blocks of proteins), and a string of these three-letter codes can be a gene, coding for a string of amino acids that a cell can make into a protein.
Siepel and colleagues set out to find genes that have been "conserved" -- that are fundamental to all life and that have stayed the same, or nearly so, over millions of years of evolution.
The researchers started with "alignments" discovered by other workers -- stretches up to several thousand bases long that are mostly alike across two or more species. Using large-scale computer clusters, including an 850-node cluster at the Cornell Center for Advanced Computing, the researchers ran three different algorithms, or computing designs -- one of which Siepel created -- to compare these alignments between human, mouse, rat and chicken in various combinations.
Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.
After eliminating predictions that matched already known genes, the researchers tested the remainder in the laboratory, proving that many of the genes could in fact be found in samples of human tissue and could code for proteins. The researchers were sometimes able to identify the proteins by comparison with databases of known proteins. The discovered genes mainly have to do with motor activity, cell adhesion, connective tissue and central nervous system development, functions that might be expected to be common to many different creatures.
The entire project, from building and testing the mathematical models to running final laboratory tests, took about three years, Siepel said. The work was supported by the National Cancer Institute, a National Science Foundation Early Career Development Grant and a University of California graduate research fellowship.
Adapted from materials provided by Cornell University.

Fausto Intilla
www.oloscience.com

Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth

Source:

http://www.sciencedaily.com/releases/2007/11/071122151148.htm

ScienceDaily (Nov. 23, 2007) — A team led by the University of Colorado at Boulder and the University of Milan has discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.

CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life's molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that "self-orient" parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic "soup" solution of ancient organic molecules.
Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, Clark said, scientists have been seeking effective ways for simple molecules to spontaneously self-select, "chain-up" and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.
"We found that even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules," Clark said. "Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules."
Liquid crystals -- organic materials related to soap that exhibit both solid and liquid properties -- are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.
RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.
Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA's elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.
A paper on the subject was published in the Nov. 23 issue of Science. The paper was authored by Clark, Michi Nakata and Christopher Jones from CU-Boulder, Giuliano Zanchetta and Tommaso Bellini of the University of Milan, Brandon Chapman and Ronald Pindak of Brookhaven National Laboratory and Julie Cross of Argonne National Laboratory. Nakata died in September 2006.
The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.
Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together "end-to-end," forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way -- much like magnetic buttons -- as they expelled water in between them, Clark said.
A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The team using a machine called the Argonne Advanced Photon Source synchrotron that enabled probing of the "nano DNA" molecular organization in single liquid crystal orientation domains only a few microns in size. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.
"The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes," Clark said. "In a sample of chains in which the bases don't match and the chains can't form helical duplexes, we did not observe liquid crystal ordering."
Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments, said Clark. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.
"We found this to be a remarkable result," Clark said. "It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.
"In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order."
Adapted from materials provided by University of Colorado at Boulder.

Fausto Intilla

www.oloscience.com