Mammalian Clock Protein Responds Directly To Light

Source:

http://www.sciencedaily.com/releases/2008/06/080630200959.htm

ScienceDaily (July 1, 2008) — We all know that light effects the growth and development of plants, but what effect does light have on humans and animals? A new paper by Nathalie Hoang et al., published in PLoS Biology, explores this question by examining cryptochromes in flies, mice, and humans.

In plants, cryptochromes are photoreceptor proteins which absorb and process blue light for functions such as growth, seedling development, and leaf and stem expansion. Cryptochromes are present in humans and animals as well and have been proven to regulate the mechanisms of the circadian clock. But how they work in humans and animals is still somewhat of a mystery.
When plants are exposed to blue light, they experience a reduction in flavin pigments. This reduction activates the cryptochromes and thus allows for growth and seedling development. Hoang et al. sought to study the effect of blue light on fly, animal, and human cryptochromes by exposing them to blue light and measuring the change in the number of oxidized flavins. After a prolonged exposure to blue light, the authors found that the number of flavins did in fact decrease, as they do in plants.
While this research reveals a similarity in the responses of flies, mice, humans, and plants to blue light, the decrease in flavins affects circadian rhythms differently. The mouse cryptochromes, Mcry1 and Mcry2, interact with key parts of the circadian clock: mice with these cryptochromes missing exhibited a complete loss in circadian rhythm behaviors such as wheel-running. However, this change in behavior was independent of light exposure.
Although this paper by Hoang, et al, shows that cryptochromes in animals and humans do respond to light in a similar fashion to those in plants, the question as to how exactly light effects them is still open for further research. Although cryptochromes are mainly found in the retina of the eye, they are also present in many different tissues of the body that are close to the surface. This suggests that cryptochromes may have non-visual functions, and may also affect protein levels and behavior.

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Is sex necessary for reproduction?

Source:

http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2008/05/31/BU2810LQ1O.DTL

E-mail Bernadette Tansey at btansey@sfchronicle.com

Dr. Mark Hughes likes to startle audiences by declaring that sex may become outdated as a means of human reproduction. His field will replace it with technology, he submits.
"It is going to be, 'Sex is just for fun,' " Hughes will tell a crowd. "In vitro fertilization is going to be for making your children."
Hughes is joking - for the most part. But as head of a major embryo-screening company, Genesis Genetics Institute in Detroit, he also makes a compelling business argument that sex is in for some serious competition from assisted reproductive techniques.
By conceiving a child outside the womb, he says, parents gain the power to erase a hereditary disease from their family lineage. His company plucks a single cell from each of the embryos created for clients at in vitro fertilization clinics. After genetic testing of the sample cells, only the embryos found free of the disease gene are implanted to cause a pregnancy.
As the harvest of human genome studies continues, Hughes said, many more diagnostic tests for such genetic vulnerabilities are being developed. "The numbers of diseases we can do are just exploding," he said.
Pre-implantation genetic screening is just one of the offerings that can motivate even fertile individuals to make conception an affair surrounded by beakers and microscopes, rather than moonlight and roses.
The in vitro fertilization industry, which originated in the 1980s as a solution for infertile couples, has actively sought to expand its market scope by tapping social trends and collaborating with researchers in genetics and stem cell technology.
Assisted reproduction clinics have welcomed gay men, lesbians and older women who want to become parents. At some clinics, young women can freeze their eggs to boost the chance of a healthy child if they delay childbirth while building a career or searching for a soul mate. Some embryo-testing centers, though not Hughes' company, will help parents choose the gender of their child.
Genesis Genetics helped pioneer an avenue for parents who want a baby born with the right genetic traits to serve as a tissue or cell donor for a desperately ill brother or sister. Hughes calls this the "Save Your Siblings" technology. If the parents conceive in vitro, Genesis Genetics can pick the embryo that is most compatible with the ill sibling and reduce the danger of immune system rejection.
Beyond those developments, in vitro fertilization and stem cell technology are advancing in tandem. Researchers who see embryonic stem cells as possible future remedies for spinal cord injuries and degenerative diseases look to clinics for donations of surplus embryos from clients who have already completed their families. Now a stem cell company, StemLifeLine of San Carlos, is offering in vitro clients an additional service.

Stem cell line:
The company will convert the parents' extra embryos into a stem cell line for the family, on the chance that the cells might contribute to a future treatment for one of its members. Donor cells from surplus embryos might lower the risk that a related family member would suffer an immune system reaction, the company says. Critics are skeptical of the benefits, and some worry that parents will feel obligated to create a stem cell line for the family.
In fact, most of the new uses for in vitro fertilization have raised ethical or practical concerns. Technologies surrounding the birth of an individual lead to core questions about identity and familial responsibilities.
Even the advocates of assisted reproduction say it's hard for society to adjust its ethical frameworks to keep up with research developments. "The technologies are coming at a breakneck pace," said Anne Adams, a spokeswoman for the American Fertility Association, an advocacy group for in vitro clients.
Writers have been quick to predict drastic changes in society as new reproductive feats emerge from labs. One pivotal event was the birth in 1996 of the first cloned mammal, Dolly the sheep, who was conceived in a laboratory from only one parent, her mother. Soon after that, scholars posed the question "Is Sex Obsolete?" in a book about cloning.
The 1997 film "Gattaca" presented a cautionary vision of a future world in which few humans were conceived the old-fashioned way because it left the outcome up to a chance reshuffling of the parents' genes. Instead, genetically enhanced embryos were conceived in vitro. In the filmmaker's tale, society discriminated fiercely against people who were the natural products of "faith births."
So far, though, conceiving the traditional way is holding its ground. In vitro fertilization is expensive, and requires a woman to undergo hormone injections and a procedure to extract egg cells.
However, the number of births from assisted reproduction in the United States doubled between 1996 and 2005 to more than 52,000. Those infants made up 1 percent of the babies born in the United States in 2005, according to the unit that compiles the data for the U.S. Centers for Disease Control and Prevention.
The numbers for more recent years aren't yet available. Neither the CDC nor industry groups have been tracking the reasons parents chose in vitro fertilization, so it's hard to say whether its use is growing for reasons other than infertility.

Raising alarms:
The rapid pace of discoveries in reproductive medicine, however, is raising alarms among watchdog groups who fear the lightly regulated industry will reshape parenthood and culture before society has the chance to evaluate the new techniques. Defenders of the research, on the other hand, say the groups are unnecessarily concerned about recent work intended to develop embryonic stem cell lines for studies of disease.
Within the past nine months, groundbreaking advances have emerged with help from assisted reproduction companies. Stemagen Inc. of La Jolla (San Diego County) reported it had cloned human embryos from adult skin cells, using eggs donated by clients of the La Jolla branch of an in vitro fertilization consortium, the Reproductive Sciences Center. Genesis Genetics verified that the cells were clones.
Researchers at the Weill Medical College of Cornell University recently confirmed that they had genetically modified human embryos by inserting extra genes. Cells derived from cloned or modified embryos can be used to illuminate disease processes and test possible treatments. The scientists did not induce the embryos to develop into fetuses.
Early this year, Advanced Cell Technology of Los Angeles said it had derived stem cell lines from embryos without destroying those embryos, a step hailed because it might overcome ethical objections to embryonic stem cell research. But in addition, one of the research partners, StemLifeLine, said it hopes it can soon offer in vitro clinic clients the chance to have a stem cell line made that is an exact genetic match to their babies.
Cornell's foray into genetic engineering of human embryos caused an uproar among watchdog groups such as the Center for Genetics and Society in Oakland.
Marcy Darnovsky, associate executive director of the group, said the Cornell work should not have been done without a broad public policy debate. Whatever its intent, Darnovsky said, the research could help create the technological foundations for "a real-world Gattaca" of genetically enhanced offspring for the affluent and discrimination against unenhanced genetic castes.
"The technology and also the market dynamics are developing really quickly here," she said. "We don't want to be on the platform watching the train pull out of the station."
Hughes said genetic enhancement of children by adding genes to an embryo may not be feasible for many years, if ever. The technical challenges alone would be formidable, he said.

Favorable genes:
Similarly, enhancing favorable traits may not be possible by screening embryos conceived through in vitro fertilization, he said. Most desirable traits, such as intelligence, are the products of many different genes, he said. Parents would have to create large numbers of embryos to produce a single one with all the favorable genes, he said.
But Hughes said he does think that many more people will turn to assisted reproduction because of technology that is already in place - the use of embryo screening to eliminate genetic diseases.
For one thing, Hughes said, people are becoming much more aware of their familial disease risk as more genetic tests become available. And parents in the United States are having fewer children later in life, he said. They'll want less risk with the few they have, Hughes predicted. "They're going to use medical technology to at least stack the deck in favor of a healthy child."
But Hughes is also betting that his specialty - pre-implantation genetic screening - will become obsolete before sex does.
"I think we will hopefully find cures for these conditions and we won't have to avoid them," he said.

Fertilization timeline:
In vitro fertilization and other assisted reproductive techniques have tackled infertility and inherited disease, but advances in the technology have raised fears of sexless societies of genetically engineered children.
1932: "Brave New World" by Aldous Huxley published. Huxley's dark novel envisions the elimination of natural reproduction by a society that uses technology to produce humans divided into upper and lower classes or "genetic castes."
1960: Food and Drug Administration approves birth-control pills.
1970s: Emergence of commercial artificial insemination services.
1978: In vitro fertilization. The first test-tube baby, Louise Brown, born in England.
1989: Pre-implantation genetic screening. The first births of children from embryos screened to eliminate disease genes.
1996: First cloned mammal, Dolly the sheep, is born.
1997: "Gattaca" released. Filmmaker Andrew Niccol presents a future society in which sexual reproduction is nearly obsolete, and genetically enhanced humans discriminate against those with inherited limitations.
2000: Embryo screening for child tissue donor. The first baby is born from an embryo selected because he was a genetic match to an ill sibling who needed a tissue donation.
2005-06: Egg freezing. A growing number of clinics offer to freeze eggs for women who postpone childbirth.
2007: Genetically modified human embryo. Cornell scientists report they have inserted genes into a human embryo in order to derive stem cells for disease research.
January: Advanced Cell Technology of Los Angeles says it has derived stem cell lines from embryos without destroying the embryos.
Stemagen Inc. of La Jolla reports it has cloned a human embryo from a skin cell, in order to derive stem cells for disease research.

Fausto Intilla - www.oloscience.com

DNA Clues To Reproductive Behavior

Source:

http://www.sciencedaily.com/releases/2008/05/080523200910.htm

ScienceDaily (May 27, 2008) — A species of wild yeast goes through a cycle of sexual reproduction once in every 1,000 asexual generations, according to new research by Imperial biologists published in the PNAS journal in April.

The study focused on the wild yeast Saccharomyces paradoxus, which is able to reproduce both sexually and asexually. The scientific team used this yeast to examine how sexual and asexual reproduction cause different types of variations in an organism's DNA sequence. A DNA sequence is like an organism's 'blueprint' - a complete set of chemical instructions needed for it to grow and function.
The researchers analysed the DNA sequences of wild yeast and discovered how infrequently the yeast reproduces sexually by noting the unique 'signatures' sexual and asexual reproduction leave in the yeast's DNA sequence.
When the yeast reproduces asexually a mother cell generates a bud, which becomes detached, creating a new daughter cell, identical to the mother cell. During the budding process, the original DNA of the mother cell is copied, and occasionally mistakes are made, known as mutations. As these mutations occur in every generation, they can be used to distinguish asexual lineages and their total number can be used to estimate the number of asexual generations in a population.
On the other hand, if the yeast reproduces sexually, the mother cell's genetic material undergoes a process of division and recombination to create a new living organism. As a result of this recombining process new combinations of genes can be found in the offspring's DNA sequence, which indicate that the new organism was created by sexual, as opposed to asexual, reproduction.
Isheng Jason Tsai, a postgraduate student in Imperial's Department of Life Sciences, one of the authors of the paper, explains why being able to identify when different reproductive methods have occurred is important:
"Finding the unique signatures left by different types of reproduction on the yeast's DNA gives us valuable insights into the life cycle of this species, which is otherwise very difficult to study. This research has shed new light on the study of microbes, and their patterns of reproduction."
Jason and his colleagues analysed variations in the DNA sequence of one particular chromosome in two populations of the wild yeast Saccharomyces paradoxus.
By analysing the yeast's DNA sequences, the researchers were able to estimate rates of DNA variation caused by asexual reproduction, and rates of DNA variation caused by sexual reproduction. Both these two rates increase with the number of individuals in the population and can be used to estimate population size.
Comparing the estimates from these two different types of DNA variation enabled them to conclude that S. paradoxus goes through a sexual cycle approximately once every thousand asexual generations.
The paper, "Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle" was published online on 14 March. Download the paper.

Fausto Intilla - www.oloscience.com

Nanotechnology Risks: How Buckyballs Hurt Cells

Source:

http://www.sciencedaily.com/releases/2008/05/080527091910.htm

ScienceDaily (May 27, 2008) — A new study into the potential health hazards of the revolutionary nano-sized particles known as 'buckyballs' predicts that the molecules are easily absorbed into animal cells, providing a possible explanation for how the molecules could be toxic to humans and other organisms.

Using computer simulations, University of Calgary biochemist Peter Tieleman, post-doctoral fellow Luca Monticelli and colleagues modeled the interaction between carbon-60 molecules and cell membranes and found that the particles are able to enter cells by permeating their membranes without causing mechanical damage.
"Buckyballs are already being made on a commercial scale for use in coatings and materials but we have not determined their toxicity," said Tieleman, a Senior Scholar of the Alberta Heritage Foundation for Medical Research who specializes in membrane biophysics and biocomputing. "There are studies showing that they can cross the blood-brain barrier and alter cell functions, which raises a lot of questions about their toxicity and what impact they may have if released into the environment."
Tieleman's team used the high-powered computing resources of WestGrid, a partnership between 14 Western Canadian institutions, to run some of the cell behaviour simulations. The resulting model showed that buckyball particles are able to dissolve in cell membranes, pass into cells and re-form particles on the other side where they can cause damage to cells.
Spherical carbon-60 molecules were discovered in 1985, leading to the Nobel Prize in physics for researchers from the University of Sussex and Rice University who named the round, hollow molecules Buckminsterfullerene after renowned American architect Richard Buckminster Fuller, the inventor of the geodesic dome.
Popularly known as buckyballs, carbon-60 molecules form naturally in minute quantities under extreme conditions such as lightning strikes. They can also be produced artificially as spheres or oblong-shaped balls, known as fullerenes, and can be used to produce hollow fibers known as carbon nanotubes. Both substances are considered to be promising materials in the field of nanotechnology because of their incredible strength and heat resistance. Potential applications include the production of industrial materials, drug delivery systems, fuel cells and even cosmetics.
In recent years, much research has focused on the potential health and environmental impacts of buckyballs and carbon nanotubes. Fullerenes have been shown to cause brain damage in fish and inhaling carbon nanotubes results in lung damage similar to that caused by asbestos.
"Buckyballs commonly form into clumps that could easily be inhaled by a person as dust particles," Tieleman said. "How they enter cells and cause damage is still poorly understood but our model shows a possible mechanism for how this might occur."

Fausto Intilla - www.oloscience.com

First Female DNA Sequenced

Source:

http://www.sciencedaily.com/releases/2008/05/080526155300.htm

ScienceDaily (May 27, 2008) — Geneticists of Leiden University Medical Centre (LUMC) are the first to determine the DNA sequence of a woman. She is also the first European whose DNA sequence has been determined. Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings. The results will contribute to insights into human genetic diversity.

DNA of geneticist Marjolein Kriek:

The DNA is that of Dr. Marjolein Kriek, a clinical geneticist at LUMC. “If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.
Van Ommen continues: “Moreover, while women don’t have a Y-chromosome, they have two X-chromosomes. As the X-chromosome is present as a single copy in half the population, the males, it has undergone a harsher selection in human evolution. This has made it less variable. We considered that sequencing only males, for ‘completeness’, slows insight into X-chromosome varialibity. So it was time, after sequencing four males, to balance the genders a bit”. He smiles: “And after Watson we also felt that it was okay to do Kriek”.

Eight times coverage:

The DNA sequencing was done with the Illumina 1G equipment. This has been installed in January 2007 in the Leiden Genome Technology Center, the genomics facility of LUMC and CMSB. In total, approx. 22 billion base pairs (the ‘letters’ of the DNA language) were read. That is almost eight times the size of the human genome.’
Dr. Johan den Dunnen, project leader at the Leiden Genome Technology Center: 'This high coverage is needed to prevent mistakes, connect the separate reads and reduces the chance of occasional uncovered gaps.
Johan den Dunnen: 'The sequencing itself took about six months. Partly since it was run as a ‘side operation’ filling the empty positions on the machine while running other projects. Would such a job be done in one go, it would take just ten weeks”.
The cost of the project was approximately €40.000.- This does not include further in-depth bioinformatics analysis. This is estimated to take another six months.

History:
In 2001, the DNA sequence was published of a combination of persons. The DNA sequences of Jim Watson, discoverer of the DNA’s double helix structure, followed in 2007, and later the DNA of gene hunter Craig Venter. Recently the completion of the sequences of two Yoruba-Africans was announced.
This research was announced by the researchers May 26, at ‘Bessensap’, a yearly meeting of scientists and the press in the Netherlands.

Fausto Intilla - www.oloscience.com

Scientists Image A Single HIV Particle Being Born

Source:

http://www.sciencedaily.com/releases/2008/05/080525132345.htm

ScienceDaily (May 26, 2008) — A mapmaker and a mathematician may seem like an unlikely duo, but together they worked out a way to measure longitude -- and kept millions of sailors from getting lost at sea. Now, another unlikely duo, a virologist and a biophysicist at Rockefeller University, is making history of their own. By using a specialized microscope that only illuminates the cell's surface, they have become the first to see, in real time and in plain view, hundreds of thousands of molecules coming together in a living cell to form a single particle of the virus that has, in less than 25 years, claimed more than 25 million lives: HIV.

This work, published in the May 25 advanced online issue of Nature, may not only prove useful in developing treatments for the millions around the globe still living with the lethal virus but the technique created to image its assembly may also change the way scientists think about and approach their own research.
"The use of this technique is almost unlimited," says Nolwenn Jouvenet, a postdoc who spearheaded this project under the direction of HIV expert Paul Bieniasz and cellular biophysicist Sandy Simon, who has been developing the imaging technique since 1992. "Now that we can actually see a virus being born, it gives us the opportunity to answer previously unanswered questions, not only in virology but in biology in general."
Unlike a classical microscope, which shines light through a whole cell, the technique called total internal reflection microscopy only illuminates the cell's surface where HIV assembles. "The result is that you can see, in exquisite detail, only events at the cell surface. You never even illuminate anything inside of the cell so you can focus on what you are interested in seeing the moment it is happening," says Simon, professor and head of the Laboratory of Cellular Biophysics.
When a beam of light passes through a piece of glass to a cell's surface, the energy from the light propagates upward, illuminating the entire cell. But when that beam is brought to a steeper angle, the light's energy reflects off the cell's surface, illuminating only the events going on at its most outer membrane. By zeroing in at the cell's surface, the team became the first to document the time it takes for each HIV particle, or virion, to assemble: five to six minutes. "At first, we had no idea whether it would take milliseconds or hours," says Jouvenet. "We just didn't know."
"This is the first time anyone has seen a virus particle being born," says Bieniasz, who is an associate professor and head of the Laboratory of Retrovirology at Rockefeller and a scientist at the Aaron Diamond AIDS Research Center. "Not just HIV," he clarifies, "any virus."
To prove that what they were watching was virus particles assembling at the surface (rather than an already assembled virion coming into their field of view from inside the cell), the group tagged a major viral protein, called the Gag protein, with molecules that fluoresce, but whose color would change as they packed closer together. Although many different components gather to form a single virion, the Gag protein is the only one necessary for assembly. It attaches to the inner face of the cell's outer membrane and when enough Gag molecules flood an area, they coalesce in a way that spontaneously forms a sphere.
Simon, Bieniasz and Jouvenet found that the Gag molecules are recruited from the inside of the cell and travel to the cell's surface. When enough Gag molecules get close and start bumping into each other, the cell's outer membrane starts to bulge outward into a budding virion and then pinches off to form an individual, infectious particle. At this point, the researchers showed that the virion is a lone entity, no longer exchanging resources with the cell. By using tricks from optics and physiology, they were able to watch the steps of viral assembly, budding, and even scission off the cell surface. With such a view they can start to describe the entire lifeline in the birth of the virus.
"I think that you can begin to understand events on a different level if you actually watch them happen instead of inferring that they might occur using other techniques," says Bieniasz. "This technique and this collaboration made that possible."
This research was supported in part by the National Institutes of Health, the National Science Foundation and amFAR, the Foundation for AIDS Research.

Fausto Intilla - www.oloscience.com

Many Paths, Few Destinations: How Stem Cells Decide What They'll Become

Source:

http://www.sciencedaily.com/releases/2008/05/080521131552.htm

ScienceDaily (May 24, 2008) — How does a stem cell decide what specialized identity to adopt -- or simply to remain a stem cell? A new study suggests that the conventional view, which assumes that cells are "instructed" to progress along prescribed signaling pathways, is too simplistic. Instead, it supports the idea that cells differentiate through the collective behavior of multiple genes in a network that ultimately leads to just a few endpoints -- just as a marble on a hilltop can travel a nearly infinite number of downward paths, only to arrive in the same valley.

The findings, published in the May 22 issue of Nature, give a glimpse into how that collective behavior works, and show that cell populations maintain a built-in variability that nature can harness for change under the right conditions. The findings also help explain why the process of differentiating stem cells into specific lineages in the laboratory has been highly inefficient.
Led by Sui Huang, MD, PhD, a Visiting Associate Professor in the Children's Hospital Boston Vascular Biology Program (now also on the faculty of the University of Calgary), and Hannah Chang, an MD/PhD student in Children's Vascular Biology Program, the researchers examined how blood stem cells "decide" to become white blood cell progenitors or red blood cell progenitors.
They began by examining populations of seemingly identical blood stem cells, and found that a cell marker of "stemness," a protein called Sca-1, was actually present in highly variable amounts from cell to cell -- in fact, they found a 1,000-fold range. One might think that low Sca-1 cells are simply those cells that have spontaneously differentiated. However, when Huang and Chang divided the cells expressing low, medium and high levels of Sca-1 and cultured them, each descendent cell population recapitulated the same broad range of Sca-1 levels over nine days or more, regardless of what levels they started with.
"We then asked, are these cells also biologically different?" says Huang, the paper's senior author. "And it turned out they were dramatically different in differentiation."
Blood stem cells with low levels of Sca-1 differentiated into red blood cell progenitors seven times more often than cells high in Sca-1 when exposed to erythropoietin, a growth factor that promotes red blood cell production. Conversely, when stem cells were exposed to granulocyte--macrophage colony-stimulating factor, which stimulates white blood cell formation, those that were highest in Sca-1 were the most likely to become white cells. Yet, in both experiments, all three groups of cells retained characteristics of stem cells.
Huang and Chang then looked at the proteins GATA1 and PU.1, transcription factors that normally favor differentiation into red and white blood cells, respectively. Blood stem cells that were low in Sca-1 (and most prone to become red blood cells) had much more GATA1 than did the high- and medium-Sca-1 cells. Stem cells high in Sca-1 (and least prone to become red blood cells) had the highest levels of PU.1.
But most important, the differences in Sca-1, GATA1 and PU.1 levels across the three cell groups became less pronounced over time, as did the variability in the cells' propensity to differentiate, suggesting that the differences are transient.
In a final step, Huang and Chang used microarrays to look at the cells' entire genome. Again, they found tremendous variability within the apparently uniform cell population: more than 3,900 genes were differentially expressed (turned "on" or "off") between the low- and high-Sca-1 cells. And again, this variability was dynamic: the differences diminished over time, with gene activity in both the low- and high-Sca-1 cells becoming more like that in the middle group.
Together, the findings make the case that a slow fluctuation or cycling of gene activity tends to maintain cells in a stable state, while also priming them to differentiate when conditions are right.
"Even if cells are officially genetically identical and belong to the same clone, individual members of that population are quite different at any given time," says Huang. "This heterogeneity has usually been seen as random 'measurement noise,' and, more recently, as 'gene expression noise.' But it turns out to be very important, and is the basis for stem cells' multipotency -- their ability to differentiate into multiple lineages."
"Nature has created an incredibly elegant and simple way of creating variability, and maintaining it at a steady level, enabling cells to respond to changes in their environment in a systematic, controlled way," adds Chang, first author on the paper.
Practically speaking, the work suggests that stem cell biologists may need to change their approach to differentiating stem cells in the laboratory for therapeutic applications.
"So far the process has been highly inefficient -- only 10 to 50 percent of cells respond to the hormone or whatever is given to make them differentiate," Huang says. "That is because of the cells' inherent heterogeneity. People have been finding more and more sophisticated stimulator cocktails, but we could make the process more efficient by harnessing the heterogeneity and identifying cells that are already highly poised to differentiate."
Chang has already done follow-up experiments showing that stem cell differentiation can be made dramatically more efficient by choosing the right subpopulation of stem cells and stimulating them promptly, while they are most apt to differentiate. "I'm not doing anything complicated -- just using what nature already has," she says.
But the findings also challenge biologists to change how they think about biological processes. The work supports the idea of biological systems moving toward a stable "attractor state," a concept borrowed from physics. In this case, blood stem cells tend to remain blood stem cells, yet they experience inherent fluctuations in gene activity and protein production that can sometimes be enough to tip the balance and cause them to fall into other attractor states -- namely, red or white blood cell progenitors. Specific growth factors can tip the balance, but these factors are part of an overall landscape that guides cells toward different destinies. A marble going downhill will eventually end up in a valley, but which valley it falls into depends on the shape of the landscape.
"Growth or differentiation factors merely increases the probability that a cell will grow or differentiate," says Donald Ingber, MD, PhD, a co-author on the paper who, with Huang, served as Chang's mentor on the project. "Cell differentiation is an ensemble property, a collective behavior, inherent in the system's architecture and set of regulatory interactions."
A previous study by Huang established, for the first time, that a given cell can exhibit a very different pattern of gene activity from its neighbor, taking a very different path through the landscape, yet end up in the same valley. He and his colleagues exposed precursor cells to two completely different drugs (DMSO and retinoic acid) and closely monitored the cells' gene expression. Both groups of cells eventually differentiated to become neutrophils (a type of white blood cell), but the molecular paths they took and their patterns of gene expression were completely different until day seven, when they finally converged.
The landscape analogy and collective "decision-making" are concepts unfamiliar to biologists, who have tended to focus on single genes acting in linear pathways. This made the work initially difficult to publish, notes Huang. "It's hard for biologists to move from thinking about single pathways to thinking about a landscape, which is the mathematical manifestation of the entirety of all the possible pathways," he says. "A single pathway is not a good way to understand a whole process. Our goal has been to understand the driving force behind it."
This study was funded by the Air Force Office of Scientific Research, the National Institutes of Health, the Presidential Scholarship, the Ashford Fellowship of Harvard University, and the Army Research Office.

Fausto Intilla - www.oloscience.com

Exploring The Mechanics Of Judgment, Beliefs: Technique Images Brain Activity When We Think Of Others

Source:

http://www.sciencedaily.com/releases/2008/05/080515212112.htm

ScienceDaily (May 18, 2008) — How do we know what other people are thinking? How do we judge them, and what happens in our brains when we do?

MIT neuroscientist Rebecca Saxe is tackling those tough questions and many others. Her goal is no less than understanding how the brain gives rise to the abilities that make us uniquely human--making moral judgments, developing belief systems and understanding language.
It's a huge task, but "different chunks of it can be bitten off in different ways," she says.
Saxe, who joined MIT's faculty in 2006 as an assistant professor of brain and cognitive sciences, specializes in social cognition--how people interpret other people's thoughts. It's a difficult subject to get at, since people's thoughts and beliefs can't be observed directly.
"These are extremely abstract kinds of concepts, although we use them fluently and constantly to get around in the world," says Saxe.
While it's impossible to observe thoughts directly, it is possible to measure which brain regions are active while people are thinking about certain things. Saxe probes the brain circuits underlying human thought with a technique called functional magnetic resonance imaging (fMRI), a type of brain scan that measures blood flow.
Using fMRI, she has identified an area of the brain (the temporoparietal junction) that lights up when people think about other people's thoughts, something we do often as we try to figure out why others behave as they do.
That finding is "one of the most astonishing discoveries in the field of human cognitive neuroscience," says Nancy Kanwisher, the Ellen Swallow Richards Professor of Brain and Cognitive Sciences at MIT and Saxe's PhD thesis adviser.
"We already knew that some parts of the brain are involved in specific aspects of perception and motor control, but many doubted that an abstract high-level cognitive process like understanding another person's thoughts would be conducted in its own private patch of cortex," Kanwisher says.
Breaking down the brain
Because fMRI reveals brain activity indirectly, by monitoring blood flow rather than the firing of neurons, it is considered a fairly rough tool for studying cognition. However, it still offers an invaluable approach for neuroscientists, Saxe says.
More precise techniques, such as recording activity from single neurons, can't be used in humans because they are too invasive. fMRI gives a general snapshot of brain activity, offering insight into what parts of the brain are involved in complex cognitive activities.
Saxe's recent studies use fMRI to delve into moral judgment--specifically, what happens in the brain when people judge whether others are behaving morally. Subjects in her studies make decisions regarding classic morality scenarios such as whether it's OK to flip a switch that would divert a runaway train onto a track where it would kill one person instead of five people.
Judging others' behavior in such situations turns out to be a complex process that depends on more than just the outcome of an event, says Saxe.
"Two events with the exact same outcome get extremely different reactions based on our inferences of someone's mental state and what they were thinking," she says.
For example, judgments often depend on whether the judging person is in conflict with the person performing the action. When a soldier sets off a bomb, an observer's perception of whether the soldier intended to kill civilians depends on whether the soldier and observer are on the same side of the conflict.
In a future study, Saxe and one of her postdoctoral associates plan to study how children develop beliefs regarding groups in longstanding conflict with their own group (for example, Muslims and Serbs in the former Yugoslavia, or Sunnis and Shiites in parts of the Middle East).
They hope to first identify brain regions that are active while people think about members of a conflict group, then observe any changes in brain activity following mediation efforts such as "peace camps" that bring together children from two conflict groups.
Big questions
Saxe earned her PhD from MIT in 2003, and recently her first graduate student, Liane Young, successfully defended her PhD thesis. That extends a direct line of female brain and cognitive scientists at MIT that started with Molly Potter, professor of psychology, who advised Kanwisher.
"It is thrilling to see this line of four generations of female scientists," Kanwisher says.
Saxe, a native of Toronto, says she wanted to be a scientist from a young age, inspired by two older cousins who were biochemists.
At first, "I wanted to be a geneticist because I thought it was so cool that you could make life out of chemicals. You start with molecules and you make a person. I thought that was mind-blowing," she says.
She was eventually drawn to neuroscience because she wanted to explore big questions, such as how the brain gives rise to the mind.
She says that approach places her right where she wants to be in the continuum of scientific study, which ranges from tiny systems such as a cell-signaling pathway, to entire human societies. At each level, there is a tradeoff between the size of the questions you can ask and the concreteness of answers you can get, Saxe says.
"I'm doing this because I want to pursue these more-abstract questions, maybe at the cost of never finding out the answers," she says.

Fausto Intilla - www.oloscience.com

Simple Artificial Cell Created From Scratch To Study Cell Complexity

Source:

http://www.sciencedaily.com/releases/2008/05/080515171023.htm

ScienceDaily (May 16, 2008) — A team of Penn State researchers has developed a simple artificial cell with which to investigate the organization and function of two of the most basic cell components: the cell membrane and the cytoplasm--the gelatinous fluid that surrounds the structures in living cells. The work could lead to the creation of new drugs that take advantage of properties of cell organization to prevent the development of diseases. The team's findings will be published later this month in the Journal of the American Chemical Society.

"Many scientists are trying to understand cells by turning off genes, one at a time, and are observing the effects on cell function, but we're doing the opposite," said Associate Professor of Chemistry Christine D. Keating, who led the research. "We're starting from scratch, adding in components to find out what is needed to simulate the most basic cell functions. Our goal is to find out how much complexity can be observed in very simple collections of molecules."
Building on previous work that was published in the 16 January 2008 issue of Journal of the American Chemical Society, Keating and her colleagues built a model cell using as the cytoplasm a solution of two different polymers: polyethyleneglycol (PEG) and dextran. The researchers encapsulated this polymer solution inside a cell membrane and, because the two polymers do not mix, one of the phases surrounded the other like the white of an egg around a yolk. The team then exposed the cell to a concentrated solution of sugar. Through a process known as osmosis--in which water diffuses across a cell membrane from a region of higher water concentration to a region of lower water concentration--water traveled from the relatively diluted polymer solution inside the cell to the more concentrated sugar solution outside the cell. As a result, the volume of the polymer solution inside the membrane was reduced.
With a cell membrane that was now too large and also unconstrained by its spherical shape, the cell converted to a budded form. A dextran-rich mixture filled the bud while a PEG-rich mixture remained inside the body of the cell. This new structure exhibited the type of complexity that the team had been looking for; it exhibited polarity. "Polarity is critical to development," said Keating. "It is an important first step in the development of a complex multi-cellular organism, like a human being, in which different cells perform different functions."
In previous work, the team created a membrane that was entirely uniform, but in their most recent paper, they describe an asymmetric membrane containing a mixture of lipid molecules. Some of these lipid molecules contained tiny pieces of PEG, which interacted with the PEG in the cytoplasm, thus generating polarity in the model cell. "Our work demonstrated the interrelationship of the cytoplasm and the cell membrane," said Keating.
The team's next step is to create a cascade in polarity. "By creating a model cytoplasm with different compositions, we demonstrated that we can control the behavior of cell membranes," said Keating. "Now we want to find out what will happen if, for example, we add an enzyme whose activity depends on the compositions of the cytoplasm and cell membrane."
Although Keating and her colleagues plan to continue adding components to their model cell, they don't expect to make a real cell. "We aren't trying to generate life here. Rather, we want to understand the physical principles that govern biological systems," said Keating. "For me the big picture is trying to understand how the staggering complexity observed in biological systems might have arisen from seemingly simple chemical and physical principles."
The research team includes Ann-Sofie Cans, a former postdoctoral researcher in the Department of Chemistry who is now at Chalmers University of Technology in Sweden, and M. Scott Long and Meghan Andes, both graduate students in the Department of Chemistry. The work was primarily supported by a grant from the National Science Foundation and by the Arnold and Mabel Beckman Foundation.

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Genetic Variation Linked To Preference Sugary Food

Source:

http://www.sciencedaily.com/releases/2008/05/080514064928.htm

ScienceDaily (May 14, 2008) — A new study in Physiological Genomics finds that individuals with a specific genetic variation consistently consume more sugary foods. The study offers the first evidence of the role that a variation in the GLUT2 gene -- a gene that controls sugar entry into the cells -- has on sugar intake, and may help explain individual preferences for foods high in sugar.

The study was conducted by Ahmed El-Sohemy, Karen M. Eny, Thomas M.S. Wolever and Benedicte Fontaine-Bisson, all of the Department of Nutritional Sciences, University of Toronto, Toronto, Canada. *
Summary of the Study
Food preferences are influenced by the environment as well as genetics. Cravings for foods high in sugar vary from person to person, but the reasons why are still unclear. To better understand the mechanism, the research team examined the effect of a common variation in a gene that controls the entry of sugar (glucose) into cells. The gene is called glucose transporter type 2 or GLUT2.
The researchers tested the effects of the genetic variation in two distinct populations. One population consisted of older adults who were all either overweight or obese. The other population consisted of generally healthy young adults who were mostly lean.
The diet of the participants in the first population was assessed by recording all of the foods and beverages consumed over a three day period, and repeating this 3-day food record two weeks later to ensure that the effect was reproducible. All participants were interviewed face-to-face during the two visits to the research centers. For the second population, the study participants used a questionnaire that asked about the foods and beverages typically consumed during a one month period.
Blood was drawn from each participant, and their DNA extracted. The researchers examined the genotype distribution and compared the food intake data each participant provided between individuals with the variation and those without the variation in GLUT2. The DNA samples that carried the variation in GLUT2 were associated with consuming more sugars in both populations studied.
Findings
The results of the study showed that a genetic variation of GLUT2 is associated with differences in the habitual consumption of sugars both within and between two distinct populations. Specifically:
those individuals with the GLUT2 variation consistently consumed more sugars (sucrose (table sugar)), fructose (simple sugar such as corn syrup) and glucose (carbohydrates), regardless of age or sex.
the two sets of food records from the older group showed that the older individuals with the variation consumed more sugars than their non-variant older counterparts (112± 9 vs. 86±4 grams of sugar per day and 111±8 vs. 82± 4 grams per day).
the individuals in the younger population who carried the variant were found to consume more sweetened beverages (0.49±0.05 vs. 0.34±0.02 servings per day) and more sweets (1.45±0.10 vs. 1.08±0.05 servings per day) than their non-variant counterparts.
there were no differences in the amount of protein, fat, starch or alcohol that was consumed by those either with or without the variant.
Conclusions
According to Dr. El-Sohemy, the study's senior researcher, "We have found that a variation in the GLUT2 gene is associated with a higher intake of sugars among different populations. These findings may help explain some of the individual variations in people's preference for sugary foods. It's especially important given the soaring rates of obesity and diabetes throughout much of the world."
The study was funded by the Advanced Food and Materials Network (AFMNet) and the Canadian Institutes of Health Research (CIHR).
*The study, entitled Genetic Variant in the Glucose Transporter Type 2 (GLUT 2) is Associated with Higher Intakes of Sugars in Two Distinct Populations, appears in the May 2008 edition of Physiological Genomics (http://physiolgenomics.physiology.org/).

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Architecture For Fundamental Processes Of Life Discovered

Source:

http://www.sciencedaily.com/releases/2008/05/080513103957.htm

ScienceDaily (May 14, 2008) — A team of Canadian researchers has completed a massive survey of the network of protein complexes that orchestrate the fundamental processes of life. In the online edition of the journal Science, researchers from the Université de Montréal describe protein complexes and networks of complexes never before observed -- including two implicated in the normal mechanisms by which cells divide and proliferate and another that controls recycling of the molecular building blocks of life called autophagy.

These processes are implicated in diseases such as cancers and autophagy has recently been shown to be involved in degenerative neurological disorders such as Alzheimer's and Huntington's diseases. The discovery will fill gaps in basic knowledge about the workings and evolutionary origins of the living cell and provide new avenues to explore in linking these fundamental processes to human disease.
The study was led by Stephen Michnick, a Université de Montréal biochemistry professor and Canada Research Chair in Integrative Genomics, along with Université de Montréal co-first authors: Kirill Tarassov, Vincent Messier, Christian Landry and Stevo Radinovic. Collaborators from McGill's Department of Biology included Canadian genomics pioneer Prof. Howard Bussey and Prof. Jackie Vogel.
"Our team systematically analyzed the interactions of proteins of bakers yeast, a unicellular organism confirmed to provide insight into fundamental processes shared by most living cells including those of humans," explained Prof. Michnick.
New technology makes discovery possible
The examination of protein complexes was made possible by a unique technology developed by Prof. Michnick with his post-doctoral fellows and graduate students. The novel technology allows interactions between proteins to be studied in their nearly natural state in the cell. With this technology, the scientists performed approximately 15 million pair-wise tests to identify about 3,000 interactions between protein pairs.
Since protein-to-protein association largely defines their function, this is a major advancement towards scientific understanding of the inner life of human cells. Thanks to Prof. Michnick's technology, the researchers also uncovered the architecture of protein complexes -- key information necessary to determine how proteins work together to orchestrate complex biochemical processes.
"The technologies and resources developed for this study can be applied to investigate protein networks in more complex organisms including crop plant and human cells," said Prof. Michnick. "They may also be used to link multiple genes implicated in complex human diseases to common cellular processes. What's more, applications to diagnostic tests and the development of drugs and antibodies against human cancers can be readily envisioned."
Professor Michnick's research was supported by the Canadian Institutes of Health Research (CIHR), Institute of Genetics and the Natural Sciences and Engineering Research Council of Canada (NSERC). The research was also funded by Genome Canada and Génome Québec.
Journal reference:
An in Vivo Map of the Yeast Protein Interactome. Kirill Tarassov, Vincent Messier, Christian R. Landry, Stevo Radinovic, Mercedes M. Serna Molina, Igor Shames, Yelena Malitskaya, Jackie Vogel, Howard Bussey, Stephen W. Michnick. Science. May 8, 2008.

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How Embryonic Stem Cells Develop Into Tissue-specific Cells Demonstrated

Source:

http://www.sciencedaily.com/releases/2008/05/080512105729.htm

ScienceDaily (May 13, 2008) — While it has long been known that embryonic stem cells have the ability to develop into any kind of tissue-specific cells, the exact mechanism as to how this occurs has heretofore not been demonstrated. Now, researchers at the Hebrew University of Jerusalem and elsewhere have succeeded in graphically revealing this process, resolving a long-standing question as to whether the stem cells achieve their development through selective activation or selective repression of genes.
The collaborative research group, which included Dr. Eran Meshorer of the Department of Genetics at the Silberman Institute of Life Sciences at the Hebrew University of Jerusalem, has revealed that the embryonic stem (ES) cells express large proportions of their genome "promiscuously." This permissive expression includes lineage-specific and tissue-specific genes, non-coding regions of the genome that are normally "silent," and repetitive sequences in the genome, which comprise the majority of the mammalian genome but are also normally not expressed.
When ES cells differentiate into specific cell tissue-types, they undergo global genetic silencing. But until this occurs, the ES cells maintain an open and active genome. This might very well be the secret of their success, since by maintaining this flexibility they maintain their capacity to become any cell type. Once silencing, or genetic repression, occurs, this ability is gone.
Thus, one can say that the ES cells stand at the ready until the "last minute" -- prepared to engage in selective activation into specific cells -- holding "in abeyance" their ability to become any kind of cells at the point and time required.
To reveal the process as to how this occurs, the researchers created the first full-mouse genomic platform of DNA microarrays. Microarrays are glass-based chips that allow simultaneous detection of thousands of genes. The microarrays used in the study were not confined to specific genes only but spanned the entire genome.
Hundreds of such microarrays were required in the study to cover the entire genome in different time points during stem cell differentiation. It was by observation of these sequences that the researchers were able to establish exactly how and at what point the stem cells developed into specific tissue cells and when the silencing occurs.
The project carried out by the researchers appears in the latest issue of the journal Cell Stem Cell. The collaborators in addition to Dr. Meshorer who participated in the project include Tom Misteli, Ron McKay, Stuart Le Grice, Sol Efroni and Kenneth Buetow of the US National Institutes of Health, Thomas Gingeras of Affymetrix Inc. of Santa Clara, Calif., and David Bazett-Jones of The Hospital for Sick Children, Toronto.

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Molecule With 'Self-control' Synthesized

Source:

http://www.sciencedaily.com/releases/2008/05/080512172317.htm

ScienceDaily (May 13, 2008) — Plants have an ambivalent relationship with light. They need it to live, but too much light leads to the increased production of high-energy chemical intermediates that can injure or kill the plant.

The intermediates do this because the efficient conversion of sunlight into chemical energy cannot keep up with sunlight streaming into the plant.
"The intermediates don't have anywhere to go because the system is jammed up down the line," says ASU chemist Devens Gust. Plants employ a sophisticated process to defend against damage.
To better understand this process, Gust, along with fellow ASU researchers Thomas Moore and Ana Moore, both professors of chemistry and biochemistry, designed a molecule that mimics what happens in nature.
In nature, plants defend against this sunlight overload process using non-photochemical quenching (NPQ). This process drains off the excess light excitation energy as heat so that it cannot generate the destructive high-energy species.
The ASU-designed molecule works in a similar fashion in that it converts absorbed light to electrochemical energy but reduces the efficiency of the conversion as light intensity increases. The ASU-designed molecule has several components including two light gathering antennas -- a porphyrin electron donor, a fullerene acceptor and a control unit that reversibly photoisomerizes between a dihydroindolizine (DHI) and a betaine (BT).
When white light (sunlight) shines on a solution of the molecules, light absorbed by the porphyrin (or by the antennas) is converted to electrochemical potential energy. When the white light intensity is increased, the DHI on some molecules change to a different molecular structure, BT, that drains light excitation energy out of the porphyrin and converts it to heat, avoiding the generation of excess electrochemical potential. As the light becomes brighter, more molecules switch to the non-functional form, so that the conversion of light to chemical energy becomes less efficient. The molecule adapts to its environment, regulating its behavior in response to the light intensity.
"One hallmark of living cells is their ability to sense and respond to surrounding conditions," explains Thomas Moore. "In the case of metabolic control this process involves molecular-level recognition events that are translated into control of a chemical process."
"Functionally, this mimics one of the processes in photosynthesis that severely limits the energy conversion efficiency of higher plants," he added. "One way in which this work is important is that by understanding these events at the molecular level one can imagine redesigning photosynthesis to improve energy conversion efficiency and thereby come closer to meeting our energy needs."
The research is also important to one aspect of the exploding field of nanotechnology, that of regulation, Gust adds. Biological systems are known for their ability to engage in adaptive self-regulation. The nanoscale components respond to other nanoscale systems and to external stimuli in order to keep everything in balance and functioning properly. The ASU research shows how a bio-regulation system has been captured in a non-biological molecular scale analog process.
"Achieving such behavior in human-made devices is vital if we are to realize the promise of nanotechnology," adds Gust. "Although the mechanism of control used in the ASU molecule is different from that employed in NPQ, the overall effect is the same as occurs in the natural photosynthetic process."
Results were reported in the advanced online publication of Nature Nanotechnology (May 4, 2008).
In addition to Gust, Thomas Moore and Ana Moore, the ASU work was carried out by Stephen Straight, Gerdenis Kodis, Yuichi Terazono and Michael Hambourger.

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Gene Linked To Alcohol And Cocaine Dependence

Source:

http://www.sciencedaily.com/releases/2008/05/080505162829.htm

ScienceDaily (May 12, 2008) — Previous family-based research had linked a broad region on chromosome 4q with alcohol dependence (AD). A new study has found that nine of the single nucleotide polymorphisms (SNPs) -- DNA sequence variations -- in the 3' region of the tachykinin receptor 3 gene (TACR3), located within chromosome 4q, have a significant association with AD, particularly those with more severe AD, and co-existing cocaine dependence.
"We believe it is important to identify genes contributing to AD for two primary reasons," said Tatiana M. Foroud, director of the division of hereditary genomics at the Indiana University School of Medicine and first author of the study.
"First, better treatments can be developed which would improve the success rate for those wishing to end their AD," she said. "Second, being able to identify those at greater risk for AD at a young age would allow interventions to be initiated earlier, potentially reducing the likelihood that the individual will become AD."
"The past few years have been an incredibly exciting time in gene identification," added Danielle Dick, assistant professor of psychiatry, psychology, and human and molecular genetics at Virginia Commonwealth University.
"Scientists are now entering an era where genes are being associated with AD and, importantly, these findings are replicating across samples," she said. "We know that AD shows a lot of variability, with affected individuals differing on many dimensions, such as age of onset, severity of symptoms and other co-occurring psychiatric and drug problems. This study makes an effort to understand how the TACR3 gene might contribute to some of this variability, rather than simply treating all AD as the same."
This study is part of the larger Collaborative Study on the Genetics of Alcoholism (COGA), said Foroud, which had previously detected a link between AD and a region on chromosome 4q. "We believe it is likely that multiple genes contributing to AD lie within this chromosomal region," she said. "Given that several lines of evidence suggested that TACR3 was a good candidate gene, we decided to not only test for an association with AD, but also expand our analyses to include additional phenotypes, such as cocaine dependence."
Using COGA data, researchers searched for an association between AD and 30 SNPs throughout TACR3 among 219 European American families (n=1,923 genotyped individuals). Researchers also looked for any association with cocaine dependence.
"We have identified a gene that we believe contributes to the risk for AD," said Foroud, "and is, furthermore, particularly important for those individuals who meet not only the DSM-IV criteria for AD but also the more stringent ICD-10 criteria. Furthermore, we found that this gene was also strongly associated with cocaine dependence."
Foroud said these results help support the theory that there are many genes, each with small individual effects, that contribute to the risk for AD. "Furthermore, this study highlights the importance of studying multiple phenotypes -- such as alcohol and cocaine dependence -- to try to understand how a gene might contribute to multiple disease risk." She and her colleagues plan to continue analyzing TACR3 in the COGA sample.
Dick is optimistic about the potential returns on future genetic research. "While any one gene on its own just has a very small effect in altering risk," she said, "once we catalog many of the genes involved in the development of dependence, this could lead to better individual-risk assessment, which may lead to improved prevention and intervention programs."
Results will be published in the June issue of Alcoholism: Clinical & Experimental Research and are currently available at OnlineEarly. Co-authors of the ACER paper, "The Tachykinin Receptor 3 (TACR3) is Associated with Alcohol and Cocaine Dependence," were: Leah Flury Wetherill, John I. Nurnberger, Jr., Xiaoling Xuei and Howard J. Edenberg of the Indiana University School of Medicine; John Kramer of the University of Iowa Carver College of Medicine in Iowa City; Jay A. Tischfield of the Human Genetics Institute at Rutgers University; and Marc A. Schuckit of the University of California, San Diego. The study was funded by the National Institute on Alcohol Abuse and Alcoholism, and the National Institute on Drug Abuse.

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Surprising Discovery: Multicellular Response Is 'All For One'

Source:

http://www.sciencedaily.com/releases/2008/05/080508143317.htm

ScienceDaily (May 10, 2008) — Real or perceived threats can trigger the well-known "fight or flight response" in humans and other animals. Adrenaline flows, and the stressed individual's heart pumps faster, the muscles work harder, the brain sharpens and non-essential systems shut down. The whole organism responds in concert in order to survive.

At the molecular level, it has been widely assumed that, in single-celled organisms, each cell perceives its environment -- and responds to stress conditions -- individually, each on its own to protect itself. Likewise, it had been thought that cells in multicellular organisms respond the same way, but a new study by scientists at Northwestern University reports otherwise.
The Northwestern researchers demonstrated something very unexpected in their studies of the worm C. elegans: Authority is taken away from individual cells and given to two specialized neurons to sense temperature stress and organize an integrated molecular response for the entire organism.
The study, with results that show a possible parallel with the orchestrated "fight or flight response," will be published in the May 9 issue of the journal Science.
"This was surprising -- that two neurons control the response of the 957 other cells in C. elegans," said Richard I. Morimoto, Bill and Gayle Cook Professor of Biochemistry, Molecular Biology and Cell Biology in Northwestern's Weinberg College of Arts and Sciences. He led the research team.
"It is well established that single cells respond to physiological stress on their own, cell by cell. Now we've shown this is not the case when individual cells become organized to form a multicellular organism. Now it is all for one -- an integrated system where the cells and tissues only respond to stress when the neuronal signal says to respond as an organism."
The findings have implications for new ways of thinking about diseases that affect the stress pathways, says Morimoto. Neurons that sense the environment govern such important pathways as stress response and molecular chaperones, which play a significant role in aging and neurodegenerative diseases.
In their experiments, the researchers genetically blocked the two thermosensory neurons (known as AFDs) and their ability to sense temperature and discovered there was no response to stress in any cell in the organism without them. (C. elegans is a transparent roundworm whose genome, or complete genetic sequence, is known and is a favorite organism of biologists.)
"This shows, for the first time, that the molecular response to physiological stress is organized by specific neurons and suggests similarities to the neurohormonal response to stress," said Morimoto, who was the first to clone a human heat shock gene in 1985. "The two neurons control how all the other cells in the animal sense and respond to physiological stress."
The team also checked the "machinery" of the 957 other cells (those that are not thermosensory neurons) in the mutant animals and determined that the individual cells could sense an increase in temperature. But, because the thermosensory neurons were not working properly and sending signals, the cells did not initiate a heat shock response. No signal, no response.
The researchers proposed a model whereby this loss of cell autonomy serves to integrate behavioral, metabolic and stress-related responses to establish an organismal response to environmental change.
The researchers would predict, considering the study's results, that other organisms including humans might have similar classes of neurons that organize and orchestrate a response to stress -- a central neuronal control switch for regulating temperature and the expression of genes that protect the health of proteins.
In addition to Morimoto, other authors of the paper, titled "Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons," are Veena Prahlad, a postdoctoral fellow, and Tyler Cornelius, an undergraduate student, both from Northwestern.

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Human Aging Gene Found In Flies

Source:

http://www.sciencedaily.com/releases/2008/05/080511205328.htm

ScienceDaily (May 12, 2008) — Scientists funded by the Biotechnology and Biological Sciences Research Council (BBSRC) have found a fast and effective way to investigate important aspects of human aging. Working at the University of Oxford and The Open University, Dr Lynne Cox and Dr Robert Saunders have discovered a gene in fruit flies that means flies can now be used to study the effects aging has on DNA. In new work published today in the journal Aging Cell, the researchers demonstrate the value of this model in helping us to understand the aging process. This exciting study demonstrates that fruit flies can be used to study critical aspects of human aging at cellular, genetic and biochemical levels.
Dr Lynne Cox from the University of Oxford said: "We study a premature human aging disease called Werner syndrome to help us understand normal aging. The key to this disease is that changes in a single gene (called WRN) mean that patients age very quickly. Scientists have made great progress in working out what this gene does in the test tube, but until now we haven’t been able to investigate the gene to look at its effect on development and the whole body. By working on this gene in fruit flies, we can model human aging in a powerful experimental system."
Dr Robert Saunders from The Open University added: "This work shows for the first time that we can use the short-lived fruit fly to investigate the function of an important human aging gene. We have opened up the exciting possibility of using this model system to analyse the way that such genes work in a whole organism, not just in single cells.”
Dr Saunders, Dr Cox and colleagues have identified the fruit fly equivalent of the key human aging gene known as WRN. They find that flies with damage to this gene share important features with people suffering from the rapid aging condition Werner syndrome, who also have damage to the WRN gene. In particular, the DNA, or genetic blueprint, is unstable in the flies that have the damaged version of the gene and the chromosomes are often altered. The researchers show that the fly’s DNA becomes rearranged, with genes being swapped between chromosomes. In patients with Werner syndrome, this genome instability leads to cancer. Cells derived from Werner syndrome patients are extremely sensitive to a drug often used to treat cancers: the researchers show that the flies that have the damaged gene are killed by even very low doses of the drug.
Professor Nigel Brown, Director of Science and Technology, Biotechnology and Biological Sciences Research Council said: "The aging population presents a major research challenge to the UK and we need effort to understand normal aging and the characteristics that accompany it."
"Fruit flies are already used as a model for the genetics behind mechanisms that underlie normal functioning of the human body and it is great news that this powerful research tool can be applied to such an important area of study into human health."

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Aust researchers discover epilespy mutant gene

Source:

http://www.abc.net.au/worldtoday/content/2008/s2241983.htm

The World Today - Monday, 12 May , 2008 13:48:00
Reporter: Nance Haxton

ELEANOR HALL: Researchers in Adelaide have discovered the mutant gene responsible for epilepsy in women.It’s a groundbreaking discovery and the team from the University of Adelaide and the Adelaide Women's and Children's Hospital has had its findings published today in the journal, Nature Genetics.One of the lead researchers, Dr Leanne Dibbens, has been speaking to Nance Haxton.

LEANNE DIBBENS: We came across a number of families in which only the females in the family suffered from epilepsy and intellectual disability, and it showed a very unusual inheritance pattern in these families, and that led us to look at what the genetic defect in these families was.

NANCE HAXTON: And what did you find?

LEANNE DIBBENS: We found that these families carry different mutations in the one gene, protocadherin 19, and that when females who carry one good copy and one bad copy of the gene, they are actually affected, whereas males, even when they carry only a bad copy of the gene, they are not affected.

NANCE HAXTON: Is the research now looking at why men don't seem to be affected by this condition, even though they carry the gene that's responsible?LEANNE DIBBENS: Exactly. We're looking at why males aren't affected with this condition, and we have a lead in that we know that there's a related gene on the Y chromosome, and only males carry a Y chromosome, and so we think that this gene is perhaps protecting or rescuing the males in these families from this condition.

NANCE HAXTON: What sort of ramifications would that have once you actually confirm those reasons? Could it be a possible treatment or a prevention for this disorder, and also for epilepsy in a wider range of people?

LEANNE DIBBENS: The most immediate ramification is that we can now offer genetic counselling to these families that suffer ESMR and people can choose to have pre-natal testing if that's what they desire and make decisions on whether they have daughters with this condition.And the wider implications are that we now know that this gene family is involved in epilepsy and intellectual disability, and so we'll be looking to see whether this gene or other related genes also play a role in these more common disorders.

NANCE HAXTON: So it's really opened up a whole new realm of research into other related disorders, even such as autism or obsessive disorders as well?

LEANNE DIBBENS: That's right. We'll now be looking at larger groups of patients with epilepsy, intellectual disability, and a number of the females affected in these families have autistic features and obsessive features, and so we'll also be looking at patient cohorts with those features.

NANCE HAXTON: The cause of many of these disorders has ultimately been a mystery for a while hasn't it?

LEANNE DIBBENS: That's right. Very little is known about the genetic causes of epilepsy, even the common epilepsies, intellectual disability. We have come a way in understanding causes of that, but in particular, autism and obsessive traits really, very little is known about the genetic causes of those disorders.

NANCE HAXTON: And particularly given that there's a rise in the occurrence of these conditions, that this has certainly come at a very pivotal or interesting time?

LEANNE DIBBENS: That's right. It gives us a chance now to dive in and look at the roles of the types of genes and what roles are playing in the brain and what happens when these processes go wrong, and why it leads to autism and obsessive traits.

NANCE HAXTON: So it could lead to a treatment and a prevention, or would it be really concentrating on one of those two options?

LEANNE DIBBENS: It's always difficult to predict where the research will go and what it would lead to, but we hope that it will enable more genetic counselling and possibly treatments and ultimately prevention. But that's a few years off yet.

ELEANOR HALL: Dr Leanne Dibbens speaking to Nance Haxton in Adelaide.

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Glowing Zebrafish Help Researchers Track Role Of Sugars In The Cell

Source:

http://www.sciencedaily.com/releases/2008/05/080505094133.htm

ScienceDaily (May 6, 2008) — Using artificial sugar and some clever chemistry, University of California, Berkeley, researchers have made glow-in-the-dark fish whose internal light comes from the sugar coating on their cells.
This novel method of fluorescently tagging the sugar chains, or carbohydrates, that coat cells is a new tool for those studying development in the zebrafish, a laboratory organism popular because its transparent embryos allow easy observation of living cells as they develop over time.
"Most people think of carbohydrates as food, but the surface of any cell in our body is adorned with a ton of sugars as well as proteins that allow cells to communicate with other cells and invading pathogens," said UC Berkeley graduate student Jeremy M. Baskin. "People have had for many years the ability to image specific proteins, but not carbohydrates. We have developed for the first time methods for labeling and imaging carbohydrates inside an intact animal."
"An understanding of how, when and where cells dust themselves with sugar may shed light on how stem cells develop into tissues, as well as turn up markers of disease, such as cancer, or strategies for battling infectious organisms," said first author Scott T. Laughlin, who, like Baskin, is a graduate student in the Department of Chemistry.
One big advantage of the technique is that it is non-toxic and can be used to study living cells, Baskin said, whereas other methods of tagging cell-surface carbohydrates cannot be performed on living specimens.
Baskin and Laughlin, together with Carolyn Bertozzi, UC Berkeley professor of chemistry and of molecular and cell biology, and developmental geneticist Sharon L. Amacher, associate professor of molecular and cell biology, reported their results in the May 2 issue of the journal Science. Bertozzi also is director of the Molecular Foundry at Lawrence Berkeley National Laboratory, a Howard Hughes Medical Institute investigator, a faculty affiliate of the California Institute for Quantitative Biosciences (QB3) and the T.Z. and Irmgard Chu Distinguished Professor of Chemistry at UC Berkeley.
"We have genes in our body coding for proteins, but proteins get modified in lots of different ways, one of which is by addition of sugars that stick out on the cell surface and change the way the protein interacts with the environment," Amacher said. "One of the big mysteries is how the pattern of sugar modification changes during development, or in cancer cells versus non-cancer cells, for example. The exciting work Carolyn is now doing is finding ways that we can actually see the sugar labels on proteins."
Scientists have known for more than a century how to attach fluorescent dyes to proteins, and have used the technique to study protein trafficking in cell culture and even in whole organisms, though often at the expense of killing the cells or organism. Bertozzi has focused on making it just as easy to study the sugars on cells, in part to investigate their role in such diseases as tuberculosis and influenza. In the latter, the flu virus enters cells by way of hemagglutinin, a sugar-protein complex on the viral surface that attaches to sugars on the surface of host cells. But sugars clearly have roles in cell-to-cell communication that have yet to be discovered.
One technique Bertozzi has developed is to feed cells an artificial sugar that looks so much like the real thing that cells are tricked into incorporating the sugar into their carbohydrate chains. Once the sugar becomes part of the forest of carbohydrates adorning a living cell, she then uses a non-toxic chemical reaction to attach small organic labels to it. Simple, highly selective and non-toxic chemical reactions like this have come to be called click chemistry.
In their work on zebrafish, Baskin, Bertozzi and their colleagues soaked zebrafish embryos in the artificial sugar N-azidoacetylgalactosamine, which the embryo cells then used as a carbohydrate building block to replace the natural sugar N-acetylgalactosamine. The researchers then modified a chemical reaction that is normally toxic to cells to eliminate the toxic copper catalyst and employed this reaction to attach a small fluorescent molecule, a fluorophore, to the "azido" part of the unnatural sugar.
The copper-free click chemistry worked with three separate fluorophores, enabling the researchers to make two-to five-day-old zebrafish cells glow red, green and even near infrared, which is invisible to the eye but can be detected by some microscopes. They were able to observe differences over time in when and where on a single cell the sugar appeared, sugar movement through the cell interior, and in which tissues the sugar showed up.
"We're hoping to extend the technique to other sugars, too," Baskin said, noting that of the nine sugars used by vertebrates to build carbohydrates, Bertozzi's lab has found artificial surrogates for four of them. "We also want to try getting (artificial sugar) to work in different organisms and different disease models, such as cancer models in mice. Basically, we are providing this as a tool for the general community to use."
Amacher, who studies tissue patterning in the very early zebrafish embryo, is anxious to work with the labeling technique, but is waiting until Bertozzi's group gets it to work in hours-old embryos, at a stage when muscles and organs begin to form.
"Once they get the labeling technique to work at very early times, it is going to be an even more exciting collaboration, and hopefully, a continuing one," she said.
The work was supported by the National Institutes of Health.
Adapted from materials provided by University of California - Berkeley.

Fausto Intilla - www.oloscience.com

New Technique Accelerates Biological Image Analysis

Source:

http://www.sciencedaily.com/releases/2008/05/080501093523.htm

ScienceDaily (May 3, 2008) — Researchers in Carnegie Mellon University's Lane Center for Computational Biology have discovered how to significantly speed up critical steps in an automated method for analyzing cell cultures and other biological specimens.
The new technique, published online in the Journal of Machine Learning Research, promises to enable higher accuracy analysis of the microscopic images produced by today's high-throughput biological screening methods, such as the ones used in drug discovery, and to help decipher the complex structure of human tissues.
Improved accuracy could reduce the cost and the time necessary for these screening methods, make possible new types of experiments that previously would have required an infeasible amount of resources, and perhaps uncover interesting but subtle anomalies that otherwise would go undetected, the researchers said.
The technique also will be applicable in fields beyond biology because it improves the efficiency of the belief propagation algorithm, a widely used method for drawing conclusions about interconnected networks.
"Current automated screening systems for examining cell cultures look at individual cells and do not fully consider the relationships between neighboring cells," said Geoffrey Gordon, associate research professor in the School of Computer Science's Machine Learning Department. "This is in large part because simultaneously examining many cells with existing methods requires impractical amounts of computational time."
In many cases, computer vision systems have been shown to distinguish patterns that are difficult for humans to detect, he added. However, even automated systems may confuse two similar patterns, and the confusion may be resolvable by considering neighboring cells.
Gordon and his fellow authors, biomedical engineering student Shann-Ching "Sam" Chen and computational biologist Robert F. Murphy, were able to expand their focus from single to multiple cells by increasing the efficiency of the belief propagation algorithm. The algorithm has become a workhorse for researchers because it enables a computer to make inferences about a set of data by drawing on multiple sources of information. In the case of biological specimens, for instance, it can be used to infer which parts of the image are individual cells or to determine whether the distributions of particular proteins within each cell are abnormal.
But as the number of variables increase, the belief propagation algorithm can grow unwieldy and require an impractical amount of computing time to solve these problems.
The belief propagation algorithm assumes that neighbors -- whether they are cells, or bits of text -- have effects on each other. So the algorithm represents each piece of evidence used to make inferences as a node in an interconnected network, and exchanges messages between nodes. The Carnegie Mellon researchers found shortcuts for generating these messages, which significantly improved the speed of the entire network.
Murphy, director of the Lane Center for Computational Biology, said this technique could improve the performance of belief propagation algorithms in many applications, including text analysis, Web analysis and medical diagnosis. For this paper, the researchers applied their techniques to analysis of protein patterns within HeLa cells. They found the technique speeded analysis by several orders of magnitude.
In high-throughput screening processes used for drug discovery and other research, tens of thousands of wells -- each containing tens or hundreds of cells -- need to be analyzed each day, Murphy said. Automated analysis of the cellular relationships within so many wells would be impossible without the sort of speedups achieved in the new study, he added.
Chen, who graduated with his Ph.D. in biomedical engineering last year, is now a postdoctoral researcher at the Scripps Research Institute in La Jolla, Calif.
Adapted from materials provided by Carnegie Mellon University.

Fausto Intilla - www.oloscience.com

Trojan Horse Of Viruses Revealed

Source:

http://www.sciencedaily.com/releases/2008/04/080425065354.htm

ScienceDaily (Apr. 28, 2008) — Viruses use various tricks and disguises to invade cells. Researchers have now discovered yet another strategy used by viruses: the vaccinia virus disguises itself as cell waste, triggers the formation of evaginations in cells and is suspected to enter the cell interior before the immune defense even notices. The research results have been published in Science.
The vaccinia virus has a problem: it is a giant among viruses and needs a special strategy in order to infiltrate a cell and reproduce. Professor Ari Helenius and Postdoc Jason Mercer from ETH Zurich's Institute for Biochemistry have now discovered what this strategy is. In the process, they stumbled upon new and surprising findings.
The invasion strategy
In order to infiltrate a cell, the vaccinia virus exploits the cellular waste disposal mechanism. When a cell dies, other cells in the vicinity ingest the remains, without needing waste disposal experts such as macrophages. The cells recognize the waste via a special molecule, phosphatidylserine, which sits on the inner surface of the double membrane of cells. This special molecule is pushed out as soon as the cell dies and is broken into parts. The vaccinia virus itself also carries this official waste tag on its surface. "The substance accumulates on the shell of vaccinia viruses", Jason Mercer explained. The pathogen disguises itself as waste material and tricks cells into digesting it, just as they normally would with the remains of dead cells. As the immune response is simultaneously suppressed, the virus can be ingested as waste without being noticed.
The uptake into the cell itself is via macropinocytosis. The ETH Zurich researchers have demonstrated that the vaccinia virus moves along actin-rich filamentous extensions towards the cell. As soon as they impinge upon the cell membrane, an evagination forms, a bleb. The virus itself is the trigger for the formation of the evagination. Using a messenger substance to "knock on the door", the virus triggers a signaling chain reaction inside the cell so that the bleb forms, catches the virus and smuggles it into the cell.
Proteins as unsuspecting allies
"The viruses are the Trojan horses that want to enter Troy; the Trojans are the many proteins that transmit the signals and open the 'city gates' to the unwelcome guest", Ari Helenius said. Aided by Professor Lukas Pelkmans' team, Jason Mercer examined over 7000 different proteins in order to find out not only which Trojans let the virus in, but which as well are chiefly involved in the supply chain. Using definitive methods, the researchers de-activated each one of the suspected proteins to examine their function,and narrowed the vast number of proteins down to 140 potential culprits. The enzyme kinase PAK1 turned out to be an especially "helpful" citizen of Troy. Without PAK1, the pathogen's trick did not work and the cell did not form any evaginations.
Until now, very little has been known about the mechanism vaccinia viruses use to infiltrate a cell. Professor Helenius, whose research objective is to find out what methods and strategies various different viruses employ to invade somatic cells, clarified "This strategy is a new one". Other viruses, such as herpes, adeno and H1 viruses use macropinocytosis. However the vaccinia virus is the first one identified that uses apoptotic mimicry as an entry strategy.
Knowledge of the virus strategies and the signal proteins involved in the ingestion of a virus by a cell is crucial to finding and developing new agents against the pathogens. Until now, antiviral medication has targeted the virus itself. Ari Helenius, however, is looking for substances that interrupt the signaling chain and halt the communication between the virus and the cell. If the cell does not ingest a virus, the virus cannot reproduce and is quickly eliminated by the immune system. This process also has another big advantage: "Viruses cannot adapt to the obstruction of the signal chain all that quickly", he said.
Smallpox: a bioterrorist attack?
The vaccinia virus belongs to a family of particularly dangerous viruses, namely the pox viruses. The most infamous member, Variola, the casitive agent of smallpox constituted a global pandemic disease in the Middle Ages, causing the deaths of millions of people, especially among the indigenous population of North America who became infected by European settlers. Pox was the first viral disease against which a vaccination was developed. In 1771, the first rudimentary vaccine was produced from cowpox viruses, which protected people from the sequelae of the disease. Since 1978, the disease has been classed as eradicated and officially is preserved in only two laboratories; one in Atlanta, the other in Novosibirsk. US authorities, however, fear bioterrorist attacks with pox viruses. Research on these dangerous pathogens is thus encouraged.
Adapted from materials provided by ETH Zurich/Swiss Federal Institute of Technology.

Fausto Intilla - www.oloscience.com