Battling Bacteria: Antimicrobial 'Hole Puncher' Mechanism Described

Source:

http://www.sciencedaily.com/releases/2007/09/070920111411.htm

Science Daily — In the battle against bacteria, researchers have scored a direct hit. They have made a discovery that could shorten the road to new and more potent antibiotics.

The rapid development of bacterial resistance to conventional antibiotics (such as penicillin or vancomycin) has become a major public health concern. Because resistant strains of bacteria can arise faster than drug companies can create antibiotics, understanding how these molecules function could help companies narrow their focus on potential antibiotics and bring them to market sooner.
As reported in a paper accepted for publication in the Journal of the American Chemical Society and posted on its Web site, researchers have now deciphered the molecular mechanism behind selective antimicrobial activity for a prototypical class of synthetic compounds.
The compounds, which mimic antimicrobial peptides found in biological immune systems, "function as molecular 'hole punchers,' punching holes in the membranes of bacteria," said Gerard Wong, a professor of materials science and engineering, physics, and bioengineering at the U. of I., and a corresponding author of the paper. "It's a little like shooting them with a hail of nanometer-sized bullets -- the perforated membranes leak and the bacteria consequently die."
The researchers also determined why some compounds punch holes only in bacteria, while others kill everything within reach, including human cells.
"We can use this as a kind of Rosetta stone to decipher the mechanisms of much more complicated antimicrobial molecules," said Wong, who also is a researcher at the university's Beckman Institute.
"If we can understand the design rules of how these molecules work, then we can assemble an arsenal of killer molecules with small variations, and no longer worry about antimicrobial resistance."
In a collaboration between the U. of I. and the University of Massachusetts at Amherst, the researchers first synthesized a prototypical class of antimicrobial compounds, then used synchrotron small-angle X-ray scattering to examine the structures made by the synthetic compounds and cell membranes.
Composed of variously shaped lipids, including some that resemble traffic cones, the cell membrane regulates the passage of materials in and out of the cell. In the presence of the researchers' antimicrobial molecules, the cone-shaped lipids gather together and curl into barrel-shaped openings that puncture the membrane. Cell death soon follows.
The effectiveness of an antimicrobial molecule depends on both the concentration of cone-shaped lipids in the cell membrane, and on the shape of the antimicrobial molecule, Wong said. For example, by slightly changing their synthetic molecule's length, the researchers created antimicrobial molecules that would either kill nothing, kill only bacteria, or kill everything within reach.
"By understanding how these molecules kill bacteria, and how we can prevent them from harming human cells, we can provide a more direct and rational route for the design of future antibiotics," Wong said.
This work was supported by the National Science Foundation, the National Institutes of Health and the Office of Naval Research.
Note: This story has been adapted from a news release issued by University of Illinois at Urbana-Champaign.

Fausto Intilla

www.oloscience.com

Spaceflight Can Change Bacteria Into More Infectious Pathogens

Source:

http://www.sciencedaily.com/releases/2007/09/070924151126.htm

Science Daily — Space flight has been shown to have a profound impact on human physiology as the body adapts to zero gravity environments.

Now, a new study led by researchers from the Biodesign Institute at Arizona State University has shown that the tiniest passengers flown in space -- microbes -- can be equally affected by space flight, making them more infectious pathogens.
"Space flight alters cellular and physiological responses in astronauts including the immune response," said Nickerson, who led a project aboard NASA's space shuttle mission STS-115 (September 2006) involving a large, international collaboration between NASA, ASU and 12 other research institutions. "However, relatively little was known about microbial changes to infectious disease risk in response to space flight."
Cheryl Nickerson and lead author James Wilson, both professors in ASU's School of Life Sciences, have performed the first study of its kind to investigate the effect of space flight on the genetic responses and disease-causing potential, or virulence, of Salmonella typhimurium, the main bacterial culprit of food poisoning.
Their results, published in the journal Proceedings of the National Academy of Sciences, reveal a key role for a master regulator, called Hfq, in triggering the genetic changes that show an increase in the virulence of Salmonella as a result of spaceflight. The results of these studies hold potential to greatly advance infectious disease research in space and here on Earth, and may lead to the development of new therapeutics to treat and prevent infectious disease.
To study the effects of space flight, Nickerson and colleagues sent specially contained tubes of Salmonella in an experimental payload aboard the Space Shuttle Atlantis. The tubes of bacteria were placed in triple containment for safety and posed no threat to the health and safety of the crew during or after the mission.
During the flight, astronaut Heidemarie M. Stefanyshyn-Piper activated growth of the bacteria in sealed hardware and 'fixed' the cultures after a day of growth to determine changes in gene and protein expression levels.
"The bacterial cultures were taken up into space and activated to grow in a separate compartment of the tubes called the growth chamber," said Nickerson. "The bacteria didn't have access to the growth chamber until Heide pushed down on a plunger which introduced the bacteria into the growth media. Then they were grown for 24 hours, and at the end of 24 hours, Heide pushed down on the plunger again, which either "fixed" the bacteria with chemicals that preserved the gene expression message, or else introduced fresh media to keep the bacteria growing to perform the virulence studies."
As a synchronous control experiment back on Earth, Nickerson's team grew an identical set of bacteria in the same type of tubes used for flight and incubated them in a special room at the NASA Kennedy Space Center called the orbital environmental simulator.
"This simulator is linked in real-time to the shuttle, and duplicates the exact temperature, humidity and growth conditions of the shuttle, with the exception that they are not flying in space," said Nickerson. "In addition, we were also linked via real-time telecommunications with the shuttle crew when they were activating and terminating our experiments in flight, and we did the exact same things at the same time to the ground samples that the astronauts did to the flight samples -- thus we had perfectly matched synchronous ground controls."
After the bacteria returned to Earth, the group performed the first global analysis of Salmonella to measure the effect of space flight on gene and protein expression and virulence. By measuring the gene and protein patterns, the researchers could hone in on the key molecular players necessary for virulence from among thousands of potential candidates.
"We chose to measure gene expression at the mRNA level since the technique to do this, called microarray analysis, is a highly advanced and convenient way to quantitatively measure the expression of every gene in a single experiment," said Wilson, who coordinated the team's molecular profiling efforts for the Nickerson lab, and played a central role in the performance of these experiments, including data analysis. "It is a very powerful technique that was very applicable to the spaceflight experiment. The isolation of mRNA poses particular challenges since it is very sensitive to degradation, but we designed the experiment using a fixative that preserved the mRNA very well."
After logging in millions of miles in space, the invaluable and well-traveled bacterial samples were analyzed back on Earth, and for the protein profiling studies, were taken to the University of Arizona's core proteomics facility at its Center for Toxicology to measure the level of every protein that had been subjected to space flight.
"Working with the UA group was great and we obtained very nice data that complemented the microarray analysis very well," said Wilson. "Keep in mind also that our body of mRNA and protein expression data from this experiment is precious, since comprehensive analysis of an organism's molecular genetic response to space flight is very rare."
Compared to bacteria that remained on earth, the space-traveling Salmonella had changed expression of 167 genes. After the flight, animal virulence studies showed that bacteria that were flown in space were almost three times as likely to cause disease when compared with control bacteria grown on the ground.
The study discovered that an important regulatory protein, Hfq, may be a key molecule responsible for the increased virulence due to space flight. "Hfq is a protein that binds to and regulates a number of regulatory RNAs, which in turn, control gene expression," said Nickerson. "Our studies suggest that there may be a role for these regulatory RNAs in the cellular response to the physical and mechanical forces found in spaceflight, which are relevant to conditions that cells encounter here on Earth during the normal course of their lifecycles."
These results have important implications for human health since Salmonella (and other gut-related bacterial pathogens) are a leading cause of food-borne illness and infectious disease, especially in the developing world. Nickerson's group further highlights Hfq as a potential therapeutic target, since no vaccine currently exists for Salmonella food-borne infections in humans. In addition, the space flight studies may shed new light on why Salmonella has become increasingly resistant to antibiotic treatment.
"We also studied the morphology of the bacteria in response to space flight, and the change that we observed is consistent with what looks like formation of a biofilm. The ground grown samples did not show biofilm formation. Biofilms are associated with increased pathogenicity because the immune system can't clear the bacteria effectively and antibiotics don't treat them effectively."
The group will embark on another space shuttle mission likely next year to further understand the risks and mechanisms of infectious disease agents during space flight and how microbes cause infections on Earth.
Note: This story has been adapted from a news release issued by Arizona State University.

Fausto Intilla

www.oloscience.com

New Understanding Of Basic Units Of Memory

Source:

http://www.sciencedaily.com/releases/2007/09/070919123138.htm

Science Daily — A molecular "recycling plant" permits nerve cells in the brain to carry out two seemingly contradictory functions -- changeable enough to record new experiences, yet permanent enough to maintain these memories over time.

The discovery of this molecular recycling plant, detailed in a study appearing early online Sept. 19 in the journal Neuron, provides new insights into how the basic units of learning and memory function. Individual memories are "burned onto" hundreds of receptors that are constantly in motion around nerve synapses -- gaps between individual nerve cells crucial for signals to travel throughout the brain.
According to the study's leader, Duke University Medical Center neurobiologist Michael Ehlers, M.D., Ph.D., these receptors are constantly moving around the synapse and often times they disappear or escape. Ehlers discovered that a specific set of molecules catch these elusive receptors, take them to the recycling plant where they are reprocessed and returned to the synapse intact.
"These receptors constantly escape the synapse and are in a perpetual state of recycling," said Ehlers, who is also a Howard Hughes Medical Institute investigator. "This process occurs on a time scale of minutes or hours, so the acquisition of new neurotransmitter receptors and their recycling is an on-going process. Memory loss may result from receptors escaping from the synapse."
All this activity takes place on millions of tiny "nubs," or protrusions in the synapses known as dendritic spines. The recycling plants are located within the body of these dendritic spines.
"We believe that the existence of this recycling ability explains in part how individual dendritic spines retain their unique identity amidst this constant molecular turnover," Ehlers said. "The system is simultaneously dynamic and stable."
While these findings should be able to help neurobiologists as they attempt to understand the molecular foundations of learning and memory, Ehlers believes that this knowledge could also be helpful in explaining what happens in certain neurological disorders, such as Alzheimer's disease, schizophrenia, or learning disorders like autism.
For example, it appears that in animal models of the early phases of Alzheimer's disease, often before any symptoms become apparent, the dendritic spines gradually lose their ability to transport and recycle the receptors.
"If the receptors don't get recycled, you see a gradual loss of synaptic function that is associated with reduced cognitive ability," Ehlers said. "These dendritic spines are where learning and memories reside. These are the basic units of memory."
Other Duke members of the team were Jiuyi Lu, Thomas Helton, Thomas Blanpied, Bence Racz and Thomas Newpher. Richard Weinberg of the University of North Carolina -- Chapel Hill was also a member of the team. The research was supported by the National Institutes of Health.
Note: This story has been adapted from a news release issued by Duke University Medical Center.

Fausto Intilla

www.oloscience.com

The Petri Dish Is Taken To New Dimensions

Source:

http://www.sciencedaily.com/releases/2007/09/070919115955.htm

Science Daily — A team of Brown University biomedical engineers has invented a 3-D Petri dish that can grow cells in three dimensions, a method that promises to quickly and cheaply produce more realistic cells for drug development and tissue transplantation.

The technique employs a new dish – cleverly crafted from a sugary substance long used in science laboratories – that allows cells to self-assemble naturally and form “microtissues.” A description of how the 3-D dish works appears in the journal Tissue Engineering.
“It’s a new technology with a lot of promise to improve biomedical research,” said Jeffrey Morgan, a Brown professor of medical science and engineering.
Morgan conceived and created the 3-D Petri dish with a team of Brown students led by Anthony Napolitano, a Ph.D. candidate in the biomedical engineering program. Napolitano spent two years perfecting the new dish and recently won a $15,000 award from the National Collegiate Inventors and Innovators Alliance to develop the patent-pending technology into a commercially viable product.
“This technology is an inexpensive and easy-to-use alternative to current 3-D cell culture methods,” Napolitano said. “It’s the next generation.”
The technology tackles a topic of increasing interest to scientists: creating hothouse cells that look and behave more like cells grown in the human body. Since 1877, scientists have relied on the Petri dish to grow, or culture, cells. The cells stick to the bottom of the dishes and spread out as they multiply. In the body, however, cells don’t grow that way. They are surrounded by other cells in three dimensions, forming tissues such as skin, muscle, and bone. This is what happens in Morgan’s 3-D dish.
The clear, rubbery dish is the size of a silver dollar. It is made from a water-based gel made of agarose, a complex carbohydrate long used in molecular biology. This gel has a few benefits. It is porous, allowing nutrients and waste to circulate. And it is non-adhesive, so cells won’t stick to it. At the bottom of the dish sit 820 tiny recesses or wells. When cells are added to the dish –about 1 million at a time – roughly 1,000 sink to the bottom of each well and form a pile. These close quarters allow cells to self-assemble, or form natural cell-to-cell connections, a process not possible in traditional Petri dishes.
The result: microtissues consisting of hundreds of cells, even of different types. In Tissue Engineering, the Brown team describes how they combined human fibroblasts, which make connective tissue, and endothelial cells, which line the heart and blood vessels. The cells came together to form spheres and doughnut-shaped clusters. The process was quick – self-assembly took place in less than 24 hours.
“These microtissues have several potential uses,” Morgan said. “They can be used to test new cancer compounds and other drugs. And they can be transplanted into the body to regenerate tissue, such as pancreatic cells for diabetics. While there are other methods out there for making microtissues, our 3-D technology is fast, easy and inexpensive. It can make hundreds of thousands of microtissues in a single step.”
Differences in culture techniques matter in biomedicine, according to a growing body of research. Studies show sometimes dramatic differences in the shape, function and growth patterns of cells cultured in 2-D compared with cells cultured in 3-D. For example, a recent Brown study found that nerve cells grown in 3-D environments grew faster, had a more realistic shape and deployed hundreds of different genes compared to cells grown in 2-D environments.
That’s why several laboratories are pursuing 3-D cell culture methods. Brown Technology Partnerships has filed a patent application based on the technology developed in the Morgan lab and is actively pursuing licensing partners.
Napolitano was lead author of the Tissue Engineering article, and Morgan was senior author. Other members of the research team included Peter Chai, a student at The Warren Alpert Medical School of Brown University and Dylan Dean, an M.D./Ph.D. graduate student in the molecular pharmacology and physiology program.
The National Science Foundation funded the research.
Note: This story has been adapted from a news release issued by Brown University.

Fausto Intilla

www.oloscience.com

Personal Genomes: Mainstream In Five Years, But Who Should Have Access?

Source:

http://www.sciencedaily.com/releases/2007/09/070920145356.htm

Science Daily — Imagine this: you visit your clinician, undergo genetic testing, and then you are handed a miniature hard drive containing your personal genome sequence, which is subsequently uploaded onto publicly accessible databases. This may sound like science fiction, but it is scientific fact, and it is already happening.

In an article published in the upcoming issue of Science, University of Alberta researcher Tim Caulfield and co-authors highlight the need to proceed with caution when it comes to personal genomics projects that represent research milestones but are also fraught with ethical, social and clinical implications. Caulfield, who is the Canada Research Chair in Health Law at the U of A and professor and research director in public health sciences, is recognized as one of the foremost experts in health law research in Canada.
Scientists predict that within five years DNA sequencing technologies will be affordable enough that personal genomics will be integrated into routine clinical care. Companies are responding by offering their services for ancestry tracing, forensics, nutritional advice and reproductive assistance. It won't be long before companies are able to offer Facebook-like social networking services centred around our genomes.
Once we have our personal genomic information, what will we do with it and how might this information be used outside the medical context? How will physicians educate patients about the significance of genetic risk information? Will already-strained health-care systems be able to cope with the inevitable influx of "worried well" patients seeking follow-up investigations for genetic risks that are not clinically meaningful?
Caulfield and his colleagues pose these questions and warn that the routine generation of individual genome sequences will pose challenges to our health-care system.
They argue that only clinically meaningful genomic test results should be integrated into medical decision-making--however, this will require clear standards, multidisciplinary collaboration and careful consideration of the ethical, social and clinical implications.
Note: This story has been adapted from a news release issued by University of Alberta.

Fausto Intilla

www.oloscience.com

Mystery Behind How Nuclear Membrane Forms During Mitosis Solved

Source:

http://www.sciencedaily.com/releases/2007/09/070915100302.htm

Science Daily — Just how a dividing cell rebuilds the nuclear envelope, the protective, functional wrapping that encases both the original and newly copied genetic material, has been a source of controversy for the last 20 years.

The answer matters because the architecture established during formation of the envelope is regarded as key to future regulation of gene expression.
Now scientists at the Salk Institute of Biological Studies, reporting in the September 9 advanced online edition of Nature Cell Biology, lay the debate to rest. Studying frog eggs, they discovered that the endoplasmic reticulum (ER), a key cellular organelle shaped like a network of tubes, flattens part of itself during mitosis to form a double-sided sheet, which then bends around what will become the nucleus, the control hub of the cell.
“The process is simple and elegant,” says Martin W. Hetzer, Ph.D., an assistant professor in the Molecular and Cell Biology Laboratory, who explains, “the membrane tubules are flattened as they associate with chromatin. Our model does not involve vesicle fusion.”
The most dramatic event during nuclear assembly following replication and separation of chromosomes is the reformation of the nuclear envelope, a highly structured barrier that separates the nuclear interior from the rest of the cell, say Hetzer and Daniel J. Anderson, a graduate student in Hetzer’s lab and co-author of the study. The envelope is the gateway into the nucleus and, thus, restricts access to the genome; it is composed of a concentric double membrane that is penetrated by nuclear pores, which serve as transport channels between the nucleus and the cytoplasm.
Just as chromosomes duplicate, the cell’s organelles, including the ER, also reproduce themselves. “The ER is always there and remains an intact network of tubes,” says Hetzer. In a mature cell the ER works closely with the genome, synthesizing and transporting the proteins produced under the direction of genes housed inside the nucleus.
Some scientists have believed that the ER in the sister cells help form the nuclear envelope, although proof of the process has been lacking. Others have argued that the new membrane is resurrected from bits of the “old” nuclear membrane that disintegrates when nuclear chromosomes duplicate and pull apart during mitosis.
“The problem with this theory, however, is that these fragments would then have to be fused together in the newly produced cells, and that would require massive membrane fusion and a dedicated protein machinery,” Hetzer says. “But no one has ever found it. Our data suggests that the search for this fusion machinery is now obsolete,” he says.
Hetzer and Anderson used a popular scientific model of mitosis, the eggs of Xenopus, an African frog, to determine how the nuclear envelope is restored. They found that the tubules of the ER are connected to each other in a three-way junction that allows them to constantly move and change position relative to each other.
During the early phases of mitosis, the end of the tubes bind directly to DNA found at the surface of the chromatin, the tightly bundled coil of genetic material and proteins that form chromosomes after DNA replication. Then, as mitosis proceeds, extra DNA binding proteins that reside in the ER are employed to progressively immobilize some of the tubules, flattening them out to create the nuclear membrane
“The tubules are squeezed into flat sheets that merge with each other, forming large membrane sheets that cover the entire surface of the chromatin,” Hetzer says. Why this matters, according to Hetzer, is because it is becoming increasingly clear that the nuclear envelope plays an important role in cell function.
“Anchorage of chromatin at the nuclear periphery and its three-dimensional organization within the nuclear interior helps regulate gene expression, and we know that mutations in nuclear envelope proteins cause a variety of different human diseases,” he says. “So knowing how the nuclear membrane is assembled will help us understand nuclear architecture and, in the long run, gene expression.”
The study was funded by NIH and a Pew Scholar Award.
Animation available: http://www.salk.edu/video/Sec61-U2OS-1/Sec61-U2OS-1.html
Note: This story has been adapted from a news release issued by Salk Institute for Biological Studies.

Fausto Intilla

www.oloscience.com

Brain Network Related To Intelligence Identified

Source:

http://www.sciencedaily.com/releases/2007/09/070911092117.htm

Science Daily — A primary mystery puzzling neuroscientists – where in the brain lies intelligence? – just may have a unified answer.

In a review of 37 imaging studies related to intelligence, including their own, Richard Haier of the University of California, Irvine and Rex Jung of the University of New Mexico have uncovered evidence of a distinct neurobiology of human intelligence. Their Parieto-Frontal Integration Theory (P-FIT) identifies a brain network related to intelligence, one that primarily involves areas in the frontal and the parietal lobes.
“Recent neuroscience studies suggest that intelligence is related to how well information travels throughout the brain,” said Haier, a professor of psychology in the School of Medicine and longtime human intelligence researcher. “Our review of imaging studies identifies the stations along the routes intelligent information processing takes. Once we know where the stations are, we can study how they relate to intelligence.”
The data suggest that some of the brain areas related to intelligence are the same areas related to attention and memory and to more complex functions like language. Haier and Jung say this possible integration of cognitive functions suggests that intelligence levels might be based on how efficient the frontal-parietal networks process information.
Brain imaging studies of intelligence are relatively new, with Haier doing some of the first ones only 20 years ago. Although there is still discussion about how to define and measure intelligence, Haier and Jung found surprising consistency in the studies they reviewed despite the fact the studies represented a variety of approaches.
A detailed report on this research including peer commentary from 19 researchers appears online in the journal Behavioral and Brain Sciences.
In his peer commentary, University of Washington psychologist Earl Hunt writes: “The Jung & Haier P-FIT model shows how far we have progressed toward understanding the biological basis of intelligence. Twenty-five years ago researchers in the field were engaged in an unedifying discussion of the relation between skull sizes and intelligence test scores. By taking advantage of the huge advances in measurement of the brain that have occurred in the past quarter century, [Jung and Haier] can take the far more sophisticated view that individual differences in intelligence depend, in part, upon individual differences in specific areas of the brain and in the connections between them.”
Haier and Jung have made some of the seminal findings in intelligence studies. In a 2004 study, they found that regions related to general intelligence are located throughout the brain and that a single “intelligence center,” such as the frontal lobe, is unlikely. And in a 2005 study, they found that while there are essentially no disparities in general intelligence between the sexes, women have more white matter and men more gray matter related to intelligence test scores, suggesting that no single neuroanatomical structure determines general intelligence and that different types of brain designs can produce equivalent intellectual performance.
“Genetic research has demonstrated that intelligence levels can be inherited, and since genes work through biology, there must be a biological basis for intelligence,” Haier said. “We have a long way to go before we understand the details, but our P-FIT model provides a framework for testing new hypotheses in future experiments.”
Note: This story has been adapted from a news release issued by University of California - Irvine.

Fausto Intilla

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New Method Can Reveal Ancestry Of All Genes Across Many Different Genomes

Source:

http://www.sciencedaily.com/releases/2007/09/070911155206.htm

Science Daily — The wheels of evolution turn on genetic innovation -- new genes with new functions appear, allowing organisms to grow and adapt in new ways. But deciphering the history of how and when various genes appeared, for any organism, has been a difficult and largely intractable task.

Now a team led by scientists at the Broad Institute of MIT and Harvard has broken new ground by developing a method, described in the September 6 advance online edition of Nature, that can reveal the ancestry of all genes across many different genomes. First applied to 17 species of fungi, the approach has unearthed some surprising clues about why new genes pop up in the first place and the biological nips and tucks that bolster their survival.
"Having the ability to trace the history of genes on a genomic scale opens the doors to a vast array of interesting and largely unexplored scientific questions," said senior author Aviv Regev, an assistant professor of biology at MIT and a core member of the Broad Institute. Although the principles laid out in the study pertain to fungi, they could have relevance to a variety of other species as well.
It has been recognized for decades that new genes first arise as carbon copies of existing genes. It is thought that this replication allows one of the gene copies to persist normally, while giving the other the freedom to acquire novel biological functions. Though the importance of this so-called gene duplication process is well appreciated -- it is the grist for the mill of evolutionary change -- the actual mechanics have remained murky, in part because scientists have lacked the tools to study it systematically.
Driven by the recent explosion of whole genome sequence data, the authors of the new study were able to assemble a natural history of more than 100,000 genes belonging to a group of fungi known as the Ascomycota. From this, the researchers gained a detailed view of gene duplication across the genomes of 17 different species of fungi, including the laboratory model Saccharomyces cerevisiae, commonly known as baker's yeast.
The basis for the work comes from a new method termed "SYNERGY", which first author Ilan Wapinski and his coworkers developed to help them reconstruct the ancestry of each fungal gene. By tracing a gene's lineage through various species, the method helps determine in which species the gene first arose, and if -- and in what species -- it became duplicated or even lost altogether. SYNERGY draws its strength from the use of multiple types of data, including the evolutionary or "phylogenetic" tree that depicts how species are related to each other, and the DNA sequences and relative positions of genes along the genome.
Perhaps most importantly, the method does not tackle the problem of gene origins in one fell swoop, as has typically been done, but rather breaks it into discrete, more manageable bits. Instead of treating all species at once, SYNERGY first focuses on a pair of the most recently evolved species -- those at the outer branches of the tree -- and works, two-by-two, toward the more ancestral species that comprise the roots.
From this analysis, Regev and her colleagues were able to identify a set of core principles that govern gene duplication in fungi. The findings begin to paint a picture of how new genes are groomed over hundreds of millions of years of evolution.
The study was supported by grants from the Burroughs Wellcome Fund and the National Institute of General Medical Sciences.
Note: This story has been adapted from a news release issued by Massachusetts Institute Of Technology.

Fausto intilla

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Synthetic Biology? Memory In Yeast Cells Synthesized

Source:

http://www.sciencedaily.com/releases/2007/09/070915081448.htm

Science Daily — Harvard Medical School researchers have successfully synthesized a DNA-based memory loop in yeast cells, findings that mark a significant step forward in the emerging field of synthetic biology.
After constructing genes from random bits of DNA, researchers in the lab of Professor Pamela Silver, a faculty member in Harvard Medical School's Department of Systems Biology, not only reconstructed the dynamics of memory, but also created a mathematical model that predicted how such a memory "device" might work.
"Synthetic biology is an incredibly exciting field, with more possibilities than many of us can imagine," says Silver, lead author of the paper to be published in the September 15 issue of the journal Genes and Development. "While this proof-of-concept experiment is simply one step forward, we've established a foundational technology that just might set the standard of what we should expect in subsequent work."
Like many emerging fields, there's still a bit of uncertainty over what, exactly, synthetic biology is. Ask any three scientists for a definition, and you'll probably get four answers.
Some see it as a means to boost the production of biotech products, such as proteins for pharmaceutical uses or other kinds of molecules for, say, environmental clean-up. Others see it as a means to creating computer platforms that may bypass many of the onerous stages of clinical trials. In such a scenario, a scientist would type the chemical structure of a drug candidate into a computer, and a program containing models of cellular metabolism could generate information on how people would react to that compound.
Either way, at it's core, synthetic biology boils down to gleaning insights into how biological systems work by reconstructing them. If you can build it, it forces you to understand it.
A team in Silver's Harvard Medical School lab led by Caroline Ajo-Franklin, now at Lawrence Berkeley National Laboratory, and postdoctoral scientist David Drubin decided to demonstrate that not only could they construct circuits out of genetic material, but they could also develop mathematical models whose predictive abilities match those of any electrical engineering system.
"That's the litmus test," says Drubin, "namely, building a biological device that does precisely what you predicted it would do."
The components of this memory loop were simple: two genes that coded for proteins called transcription factors.
Transcription factors regulate gene activity. Like a hand on a faucet, the transcription factor will grab onto a specific gene and control how much, or how little, of a particular protein the gene should make.
The researchers placed two of these newly synthesized, transcription factor-coding genes into a yeast cell, and then exposed the cell to galactose (a kind of sugar). The first gene, which was designed to switch on when exposed to galactose, created a transcription factor that grabbed on to, and thus activated, the second gene.
It was at this point that the feedback loop began.
The second gene also created a transcription factor. But this transcription factor, like a boomerang, swung back around and bound to that same gene from which it had originated, reactivating it. This caused the gene to once again create that very same transcription factor, which once again looped back and reactivated the gene.
In other words, the second gene continually switched itself on via the very transcription factor it created when it was switched on.
The researchers then eliminated the galactose, causing the first synthetic gene, the one that had initiated this whole process, to shut off. Even with this gene gone, the feedback loop continued.
"Essentially what happened is that the cell remembered that it had been exposed to galactose, and continued to pass this memory on to its descendents," says Ajo-Franklin. "So after many cell divisions, the feedback loop remained intact without galactose or any other sort of molecular trigger."
Most important, the entire construction of the device was guided by the mathematical model that the researchers developed.
"Think of how engineers build bridges," says Silver. "They design quantitative models to help them understand what sorts of pressure and weight the bridge can withstand, and then use these equations to improve the actual physical model. We really did the same thing. In fact, our mathematical model not only predicted exactly how our memory loop would work, but it informed how we synthesized the genes."
For synthetic biology, this kind of specificity is crucial. "If we ever want to create biological black boxes, that is, gene-based circuits like this one that you can plug into a cell and have it perform a specified task, we need levels of mathematical precision as exact as the kind that go into creating computer chips," she adds.
The researchers are now working to scale-up the memory device into a larger, more complex circuit, one that can, for example, respond to DNA damage in cells.
"One day we'd like to have a comprehensive library of these so-called black boxes," says Drubin. "In the same way you take a component off the shelf and plug it into a circuit and get a predicted reaction, that's what we'd one day like to do in cells."
For an animation of how to construct a synthetic memory loop see http://hms.harvard.edu/public/video/silver_illustration.mov
Full Citation: Caroline M. Ajo-Franklin(1), David A. Drubin(1), Julian A. Eskin(1), Elaine P.S. Gee(2), Dirk Landgraf(1), Ira Phillips(1), and Pamela A. Silver(1), "Rational design of memory in eukaryotic cells", Genes and Development, Volume 21, Issue 18: September 15, 2007
1-Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston MA 2-Harvard University Program in Biophysics, Massachusetts Institute of Technology, Cambridge, MA
Note: This story has been adapted from a news release issued by Harvard Medical School.

Fausto Intilla
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Making Gene Therapy Safer: Delivering Genes Via Polymers

Source:

http://www.sciencedaily.com/releases/2007/09/070907095614.htm

Science Daily — In work that could lead to safe and effective techniques for gene therapy, MIT researchers have found a way to fine-tune the ability of biodegradable polymers to deliver genes.

Gene therapy, which involves inserting new genes into patients' cells to fight diseases like cancer, holds great promise but has yet to realize its full potential, in part because of safety concerns over the conventional technique of using viruses to carry the genes.
The new MIT work, published this week in Advanced Materials, focuses on creating gene carriers from synthetic, non-viral materials. The team is led by Daniel Anderson, research associate in MIT's Center for Cancer Research.
"What we wanted to do is start with something that's very safe-a biocompatible, degradable polymer-and try to make it more effective, instead of starting with a virus and trying to make it safer," said Jordan Green, a graduate student in biological engineering and co-first author of the paper.
Gregory Zugates, a former graduate student in chemical engineering now at WMR Biomedical, Inc., is also a co-first author of the paper.
Gene therapy has been a field of intense research for nearly 20 years. More than 1,000 gene-therapy clinical trials have been conducted, but to date there are no FDA-approved gene therapies. Most trials use viruses as carriers, or vectors, to deliver genes.
However, there are risks associated with using viruses. As a result, many researchers have been working on developing non-viral methods to deliver therapeutic genes.
The MIT scientists focused on three poly(beta-amino esters), or chains of alternating amine and diacrylate groups, which had shown potential as gene carriers. They hoped to make the polymers even more efficient by modifying the very ends of the chains.
When mixed together, these polymers can spontaneously assemble with DNA to form nanoparticles. The polymer-DNA nanoparticle can act in some ways like an artificial virus and deliver functional DNA when injected into or near the targeted tissue.
The researchers developed methods to rapidly optimize and test new polymers for their ability to form DNA nanoparticles and deliver DNA. They then chemically modified the very ends of the degradable polymer chains, using a library of different small molecules.
"Just by changing a couple of atoms at the end of a long polymer, one can dramatically change its performance," said Anderson. "These minor alterations in polymer composition significantly increase the polymers' ability to deliver DNA, and these new materials are now the best non-viral DNA delivery systems we've tested."
The polymers have already been shown to be safe in mice, and the researchers hope to ultimately run clinical trials with their modified polymers, said Anderson.
Non-viral vectors could prove not only safer than viruses but also more effective in some cases. The polymers can carry a larger DNA payload than viruses, and they may avoid the immune system, which could allow multiple therapeutic applications if needed, said Green.
One promising line of research involves ovarian cancer, where the MIT researchers, in conjunction with Janet Sawicki at the Lankenau Institute for Medical Research, have demonstrated that these polymer-DNA nanoparticles can deliver DNA at high levels to ovarian tumors without harming healthy tissue.
Other MIT authors on the paper are Nathan Tedford, a former graduate student in biological engineering now at Epitome Biosystems; Linda Griffith, professor of biological engineering; Douglas Lauffenberger, head of biological engineering, and Institute Professor Robert Langer. Sawicki and Yu-Hung Huang of the Lankenau Institute are also co-authors.
The research was funded by the National Institutes of Health, the Department of Defense and the National Science Foundation.
Note: This story has been adapted from a news release issued by Massachusetts Institute of Technology.

Fausto Intilla

www.oloscience.com

Skin As A Living Coloring Book

Source:

http://www.sciencedaily.com/releases/2007/09/070906132823.htm

Science Daily — The pigment melanin, which is responsible for skin and hair color in mammals, is produced in specialized cells called melanocytes and then distributed to other cells. But not every cell in the complex layers of skin becomes pigmented. The question of how melanin is delivered to appropriate locations may have been answered by a study from researchers at the Massachusetts General Hospital (MGH) Cutaneous Biology Research Center (CBRC).

"Pigment recipient cells essentially tell melanocytes where to deposit melanin, and the pattern of those recipients determines pigment patterns," says Janice Brissette, PhD, who led the study. "Recipient cells act like the outlines in a child's coloring book; as recipient cells develop, they form a 'picture' that is initially colorless but is then 'colored in' by the melanocytes."
In humans, melanin is deposited in both the skin and the hair; but in some other mammals such as mice, melanin is primarily deposited in the coat, leaving the skin beneath the coat unpigmented. Melanocytes deposit melanin via cellular extensions called dendrites that reach out to other cells in the epidermis (the outer layer of skin) or the hair follicles. But the mechanism determining whether melanin is delivered to a particular cell has been unknown.
The MGH-CBRC researchers theorized that a mouse gene known as Foxn1 might play a role. Lack of Foxn1 is responsible for so-called 'nude mice,' which have hair that is so brittle it breaks off, resulting in virtually total hairlessness, and other defects of the skin. A similar phenomenon exists in humans with inactivation of the corresponding gene.
When the researchers developed a strain of transgenic mice in which Foxn1 is misexpressed in cells that do not usually contain melanin, they found those normally colorless areas became pigmented. Examining the skin of the transgenic mice revealed that melanocytes were contacting and delivering melanin to the cells in which Foxn1 was abnormally activated. No pigment was observed in the corresponding tissues of normal mice. Examination of human skin samples showed that the human version of Foxn1 was also expressed in cells known to be pigment recipients. Further experiments revealed that Foxn1 signals melanocytes through a protein called Fgf2, levels of which rise as Foxn1 expression increases.
"Foxn1 makes epithelial cells into pigment recipients, which attract melanocytes and stimulate pigment transfer, engineering their own pigmentation," says Brissette, an associate professor of Dermatology at Harvard Medical School. She and her colleagues note that the Foxn1/Fgf2 pathway probably has additional functions in the skin and that it is probably not the only pathway responsible for the targeting of pigment.
"We know that Foxn1 and Fgf2 act in concert with other factors and function within a larger network of genes. Our next step will be to identify other genes that can confer the pigment recipient phenotype or control the targeting of pigment," Brissette adds. Her research may eventually be relevant to disorders such as vitiligo -- in which pigment disappears from patches of skin -- age spots, the greying of hair and even the deadly melanocyte-based skin cancer melanoma.
The report appears in the Sept. 7 issue of Cell.
The co-first authors of the Cell report are Lorin Weiner, PhD, and Rong Han, PhD, both of the MGH-CBRC. Additional co-authors are Jian Li, PhD, Kiyotaka Hasegawa, MS, and David Lee, MGH-CBRC; Bianca Scicchitano, PhD, now at La Sapienza/University of Rome; and Maddalena Grossi, PhD, University of Lausanne, Switzerland. The study was supported by the National Institutes of Health and by the CBRC.
Note: This story has been adapted from a news release issued by Massachusetts General Hospital.

Fausto Intilla

www.oloscience.com

Color Night Vision In The Aye-Aye, A Most Unusual Primate

Source:

http://www.sciencedaily.com/releases/2007/09/070904114535.htm

Science Daily — A quest to gain a more complete picture of color vision evolution has led Biodesign Institute researcher Brian Verrelli to an up-close, genetic encounter with one of the world's most rare and bizarre-looking primates.
Verrelli and his ASU team have performed the first sweeping study of color vision in the aye-aye (pronounced "eye-eye"), a bushy-tailed, Madagascar native primate with a unique combination of physical features including extremely large eyes and ears, and elongated fingers for reaching hard to access insects and other foods. Verrelli, lead author George Perry, and collaborator Robert Martin's results, published in the journal Molecular Biology and Evolution, have led to some surprising conclusions on how this nocturnal primate may have retained color vision function.
Verrelli's group focuses on color vision to better understand genetic variation between human and other primate populations and the truly big evolutionary questions as to what makes us human. "At least within humans and some other primates, we know that there are three different genes responsible for color vision," said Verrelli. The genes, called opsins, come in three forms that shape our color vision palette, one for blue, another for green, and a third for red.
"What makes that very interesting is that the green and red are found on the X chromosome [sex chromosome], and it is the manipulation of those two genes alone which is related to color blindness for eight to ten percent of the male population," explains Verrelli. In a 2004 study in the American Journal of Human Genetics by Verrelli and collaborator Sarah Tishkoff of the University of Maryland, they suggested that natural genetic selection has provided women with a frequent ability to better discriminate between colors than men.
"These three genes may explain all the variation that we might see across human populations in color vision," said Verrelli. "But how did our range of color vision variation come to be in the first place?"
To help trace back the evolution of color vision, Verrelli's collaborator Perry turned to the endangered aye-aye, a primate representative of lemurs. These primates split from other groups including humans, apes, and monkeys more than sixty million years ago, and are thought to be in some ways representative of the early primates that lived at that time. "We chose the aye-aye specifically because it has a very interesting behavior in that it is fully nocturnal, and so, it raises an obvious and straightforward question: If you are an animal that lives at night, do you need color vision?"
In a simple case of 'use it or lose it,' the prevailing theory suggested that nocturnal primates cannot use color vision to see, and so the genes that they have for color vision accumulated mutations and degraded over evolutionary time.
From a practical standpoint, studying color vision in the aye-aye proved to be a daunting endeavor. Since the aye-aye is an endangered species, obtaining DNA samples in the wild was not possible. The group turned to a few rare international research institutions and colleagues that have aye-ayes to obtain DNA samples for their study.
In all total, they obtained samples from eight aye-ayes for their study. It took a year and a half to analyze the samples, since Perry and Verrelli had to invent the methodology to perform the first wide-range genetic analysis on the aye-aye. "From a conservation, population and functional viewpoint, it was the first study of its kind," said Verrelli.
The results his team found were so startling that they had to recheck them twice. "When examining these genes in the aye-aye, we realized that they are not degrading," said Verrelli. "In fact, for the green opsin gene, we did not find a single mutation in it. The opsin genes look to be absolutely fully functional, which is completely counter to how we had believed color vision evolved in nocturnal mammals."
The authors plan to collaborate with others to perform behavioral studies to see if aye-ayes can respond to colors and further molecular studies to identify the exact color absorption by the opsin proteins to see how this may differ from other primates that are not nocturnal.
The study has not only proved important to understanding color vision evolution, but also has shown the value of examining the dazzling diversity of life, especially in endangered species.
"We not only need to focus on organisms that are related to us and are common, but also organisms that are uncommon and endangered, for there may be behaviors and physical features that, once they are lost, we may never understand."
The study was completed in collaboration with the Biodesign Institute's Center for Evolutionary Functional Genomics, ASU's School of Life Sciences and School of Human Evolution and Social Change, and the Department of Anthropology at the Field Museum of Chicago.
Note: This story has been adapted from a news release issued by Arizona State University.

Fausto Intilla
www.oloscience.com

Pivotal Hearing Structure Revealed

Source:

http://www.sciencedaily.com/releases/2007/09/070905133615.htm

Science Daily — Scientists have shed light on how our bodies convert vibrations entering the ear into electrical signals that can be interpreted by the brain. Exactly how the electrical signal is generated has been the subject of ongoing research interest.

When a noise occurs, such as a car honking or a person laughing, sound vibrations entering the ear first bounce against the eardrum, causing it to vibrate. This, in turn, causes three bones in the middle ear to vibrate, amplifying the sound. Vibrations from the middle ear set fluid in the inner ear, or cochlea, into motion and a traveling wave to form along a membrane running down its length.
Sensory cells (called hair cells) sitting atop the membrane "ride the wave" and in doing so, bump up against an overlying membrane. When this happens, bristly structures protruding from their tops (called stereocilia) deflect, or tilt to one side. The tilting of the stereocilia cause pore-sized channels to open up, ions to rush in, and an electrical signal to be generated that travels to the brain, a process called mechanoelectrical transduction.
Most scientists believe that the channel gates are opened and closed by microscopic bridges--called "tip links"--that connect shorter stereocilia to taller ones positioned behind them. If scientists could determine what the tip links are made of, they'd be one step closer to understanding what causes the channel gates to open. This is no easy feat, however, because stereocilia are extremely small, scarce, and difficult to handle. Several proteins had been reported to occur at the tip link in earlier studies, but results have been conflicting to this point.
In a study published in the September 6, 2007, issue of the journal Nature, researchers showed that two key proteins join together at the precise location where energy of motion is turned into electrical impulses. These proteins, cadherin 23 and protocadherin 15, are part of a complex of proteins called "tip links" that are on hair cells in the inner ear. The tip link is believed to have a central function in the conversion of physical cues into electrochemical signals.
"Mutations in [the genes] cadherin 23 and protocadherin 15 can cause deafness as well as Usher syndrome, the leading cause of deaf-blindness in humans," says Professor Ulrich Mueller, of the Scripps Research Department of Cell Biology and Institute for Childhood and Neglected Diseases. "Age-related hearing loss in humans may also be related to problems in the tip links."
"This team has helped solve one of the lingering mysteries of the field," says James F. Battey, Jr., director of the National Institute on Deafness and Other Communication Disorders (NIDCD), one of the National Institutes of Health (NIH). "The better we understand the pivotal point at which a person is able to discern sound, the closer we are to developing more precise therapies for treating people with hearing loss, a condition that affects roughly 32.5 million people in the United States alone."
Physiology of hearing and deafness
Childhood and age-related hearing impairment is a major issue in our society. According to the NIDCD, one in three people older than 60 and about half of all people over 75 suffer some form of hearing loss. And about four out of every 100,000 babies born in the United States have Usher syndrome, the major cause of deaf-blindness.
Hearing is a classic example of a phenomenon called mechanotransduction, a process that is important not only for hearing, but also for a number of other bodily functions, such as the pereception of touch. It is a complicated process whereby spatial and physical cues are transduced into electrical signals that run along nerve fibers to areas in the brain where they are interpreted.
"Hearing is the least well understood of the senses," notes Mueller.
We do know that sound starts as waves of mechanical vibrations that travel through the air from their source to a person's ear through the compression of air molecules. When these vibrational waves hit a person's outer ear, they go down the ear canal into the middle ear and strike the ear drum. The vibrating ear drum moves a set of delicate bones that communicate the vibrations to a fluid-filled spiral structure in the inner ear known as the cochlea. When sound causes these bones to move, they compress a membrane on one entrance of the cochlea and this causes the fluid inside to move accordingly.
Inside the cochlea are specialized "hair" cells that have symmetric arrays of stereocilia extending out from their surface. The movement of the fluid inside the cochlea causes the stereocilia to move. This physical change creates an electrical change and causes ion channels to open. The opening of these channels is monitored by sensory neurons surrounding the hair cells, and these neurons then communicate the electrical signals to neurons in the auditory association cortex of the brain.
In Usher syndrome and some other "sensory neuronal" diseases that cause deafness, the hair cells in the cochlea are unable to maintain the symmetric arrays of stereocilia.
A few decades ago, a molecular complex called the tip link was discovered in the stereocilia. These tip links connect the tips of stereocilia and are also thought to be important for the transmission of physical force to mechanically gated ion channels. For years, in part because stereocilia are extremely small, scarce, and difficult to handle, the molecules that made up the tip link remained elusive.
But a few years ago, Mueller and his colleagues identified one of the key proteins that formed the tip link-the protein cadherin 23. In their March 26, 2004, Nature article, Mueller and colleagues showed that the protein cadherin 23 was expressed in the right place in the hair cell to be part of the tip link, that it had the correct biochemistry, and that it seemed to be responsible for opening the ion channels. They also showed that cadherin 23 protein formed a complex with another protein called myosin 1c, which helped to close the channel once open.
"The current study provides a higher degree of resolution than the 2004 study, thanks to a collaboration with NIH Researcher Bechara Kachar and Scripps Research Professor Ron Milligan and his advanced imaging facilities," says Mueller. "Now, we put to rest any doubts about the details of our findings."
Three lines of evidence
The current study used three lines of evidence to demonstrate that cadherin 23 and protocadherin 15 unite and adhere to one another to form the tip link.
The researchers first created antibodies that would bind to and label short segments on the cadherin 23 and protocadherin 15 proteins in the inner ears of rats and guinea pigs. Using immuno-fluorescence and electron microscopy studies, they showed that cadherin 23 was located on the side of the taller stereocilium and protocadherin 15 was present on the tip of the shorter one, with their loose ends overlapping in between.
The researchers were able to identify both proteins by removing an obstacle to the antibody-binding process: calcium. Under normal conditions, cadherin 23 and protocadherin 15 are studded with calcium ions, which prevent antibodies from binding to the targeted sites. When calcium was removed through the addition of a chemical known as BAPTA, both labels became visible.
Next, the researchers built a structure resembling a tip link by expressing the cadherin 23 and protocadherin 15 proteins in the laboratory and watching how they interacted. When conditions were right, the two proteins wound themselves tightly together from one end to the other in a configuration that mirrored a naturally occurring tip link. As with normal tip links, the structure thrived in calcium concentrations that paralleled those found in fluid of the inner ear, while a drastic reduction in calcium disrupted the structure.
Lastly, the scientists found that one mutation of protocadherin 15 that causes one form of deafness inhibited the interaction of the two proteins, leading them to conclude that the mutation reduces the adhesive properties of the two proteins and prevents the formation of the tip link. In a second mutation of protocadherin 15, the tip link was not destroyed; the scientists suggested that the deafness is not likely caused by the breakup of the tip link but by interference with its mechanical properties.
Knowing precisely the composition and configuration of the tip link, scientists can now explore how these proteins interact with other components to form the rest of the transduction machinery. In addition, scientists can study how new treatments might be developed to address the breaking up of tip links through environmental factors, such as loud noise.
In addition to Mueller, other authors of the study, "Cadherin 23 and protocadherin 15 interact to form tip-link filaments in sensory hair cells," were: Piotr Kazmierczak, Elizabeth M. Wilson-Kubalek, and Ronald A. Milligan of The Scripps Research Institute, and Hirofumi Sakaguchi,, Joshua Tokita, and Bechara Kachar of the Laboratory of Cellular Biology, National Institute on Deafness and other Communication Disorders, National Institutes of Health.
Funding for the study was principally provided by the NIDCD. Other NIH institutes and centers that contributed funding were the National Institute of General Medical Sciences (NIGMS), the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and the National Center for Research Resources (NCRR).
Note: This story has been adapted from a news release issued by Scripps Research Institute.

Fausto Intilla

www.oloscience.com

New View Of DNA Repair: Enzyme Alerts Cell's Powerful Army To Repair DNA Damage

Source:

http://www.sciencedaily.com/releases/2007/09/070905173151.htm

Science Daily — Scientists know that inside each cell, a little engine called RNA polymerase II does one essential job: It copies instructions from genes in the nucleus that get carried to production units in the rest of the cell to support our daily needs. Now researchers at the University of Michigan Medical School have shown that RNA polymerase II also constantly scans the cell's DNA for damage. When certain types of damage in DNA halt the action of RNA polymerase II, a stress signal is generated that alerts a key tumor-suppressor protein called p53.

The activities of p53, a master protein that responds to DNA damage by marshaling hundreds of genes to repair or eliminate damaged cells, have been the subject of thousands of studies. Mutations in the p53 gene occur in more than half of all cancers.
"We have come up with a new paradigm for how cells protect themselves against cancer-producing DNA lesions," says Mats Ljungman, Ph.D., a U-M researcher and lead author of a recent study in the Proceedings of the National Academy of Sciences.
"Much is known already about p53, but this adds a significant piece of knowledge about how it is activated," Ljungman adds. He is an associate professor in the Department of Radiation Oncology in the Division of Radiation and Cancer Biology at the U-M Comprehensive Cancer Center and associate professor of Environmental Health Sciences at the U-M School of Public Health.
A commentary in the journal praised the U-M study and urged more attention to RNA polymerases as major sensors "for all DNA damage response reactions."
Ljungman says the findings have implications for the study of cancer, aging and neurological diseases. Figuring out precisely how cells detect and repair damage is crucial in understanding what goes wrong in cancer, in which harmful mutations can elude the body's ability to control cell division.
Finding and repairing DNA lesions is a non-stop job for cells.
As many as 20,000 lesions occur daily in a cell's DNA, Ljungman says. Many stresses result from oxidation and other internal cell processes. In addition, our DNA is also challenged by sunlight, radiation and reactive chemicals found in food.
"So much damage happens all the time," Ljungman says. "That puts pressure on cells to efficiently scan the DNA and do something about it. That's what we think the transcription machinery is doing."
RNA polymerase II is the main enzyme involved in transcription, the process of reading the genetic code. The U-M team did a series of experiments to find out what happens when transcription is blocked. They found that using transcription-blocking agents such as ultraviolet light resulted in activation of the p53 stress response, independent of other cell processes.
When they micro-injected an anti-RNA polymerase agent into human cell nuclei, they found that p53 proteins then accumulated in the cell nucleus -- one aspect of the stress response -- even when no DNA damage occurred. Ljungman and his colleagues also discovered what happens when RNA polymerase II gets stuck on a kink or other lesion in the DNA. It sends a signal via two proteins that activate p53.
"These two proteins are saying, 'Transcription has stopped,'" says Ljungman. These early triggers act like the citizen who smells smoke and sounds a fire alarm, alerting the fire department. Then p53, like a team of fire fighters, arrives and evaluates what to do. To reduce the chance of harmful mutations that may result from DNA damage, p53 may kill cells or stop them temporarily from dividing, so that there is time for DNA repair.
Learning more about the processes involved in transcription could pay off in improved treatments in years to come. Cisplatin, a drug used to treat testicular and ovarian cancer, acts by stopping transcription and causing cells to die. Some other chemotherapy drugs block transcription too. But these types of drugs also damage a cancer patient's DNA in normal tissues, sometimes leading to other cancers later.
The study's findings eventually could lead to better drugs that might target transcription directly without those ill effects, Ljungman believes.
In addition to Ljungman, other authors who worked on the U-M study include graduate students Frederick A. Derheimer, Heather M. O'Hagan, Heather M. Krueger, and Sheela Hanasoge, and Research Associate Michelle T. Paulsen, all from the Department of Radiation Oncology, Division of Radiation and Cancer Biology, U-M Comprehensive Cancer Center.
The study was funded by the National Institutes of Health, the University of Michigan and the Department of Radiation Biology.
Citation: Proceedings of the National Academy of Sciences, July 31, 2007, vol. 104, no. 31, 12778--12783
Note: This story has been adapted from a news release issued by University of Michigan Health System.

Fausto Intilla

www.oloscience.com

Parasitic Battles Can Involve Gene Transfer That Aids Evolution

Source:

http://www.sciencedaily.com/releases/2007/09/070905134534.htm

Science Daily — Scientists at MIT's Department of Civil and Environmental Engineering and the Technion Israel Institute of Technology have for the first time recorded the entire genomic expression of both a host bacterium and an infecting virus over the eight-hour course of infection.

The results of this research likely will encourage scientists in several fields to rethink their approach to the study of host-virus systems, which are believed to play a key evolutionary role by facilitating the transfer of genes between species.
Professors Debbie Lindell of the Technion and Sallie Chisholm of MIT and co-authors report in the Sept. 6 issue of Nature that their study of a system involving the marine bacteria, Prochlorococcus, leads them to speculate that viral infection may play a role in shaping the genetic repertoire of families of bacteria, even though individual infected bacteria die.
This could indicate that the meeting between a marine bacterial host and its virus may not be just a battle between two individuals, but an evolutionarily significant exchange that helps both species become more fit for life in the ocean environment.
"The current status of host-virus relations has been influenced by a rich history of interactions," said Lindell. "While we can't definitively pin down the sequence of past co-evolutionary events, our findings suggest a novel means through which the exchange of beneficial genes between host and virus have been triggered."
And, because the pattern of genomic expression in this host-virus system differed significantly from that in the more commonly studied system of intestinal bacteria such as E. coli and a virus called T7, the research will likely lead to increased appreciation for the need to study diverse types of marine bacteria, rather than relying on a single system as a broad model.
"We hope this work will encourage scientists to explore a wide range of host-pathogen systems and thus lead to a significant broadening of our understanding of the diversity of the host-pathogen interactions existing in nature," said Chisholm, one of the discoverers of Prochlo-rococcus in 1985. "More importantly, these studies will help us understand the role these interactions play in shaping microbial ecosystems."
Researchers have only in the past few decades begun discovering and studying ecologically relevant ocean bacteria, such as Prochlorococcus, which play a very important role in our lives. These single-celled photosynthetic bacteria use light energy to produce oxygen and organic carbon --supplying a significant portion of the oxygen we breathe--and forming the basis for the ocean food chain.
In previously studied host-virus systems, a virus hijacks the bacterial host cell and shuts down genome expression immediately, preventing the bacterium from conducting its own metabolic processes. The attacking virus redirects expression to its own genome and activates the genes beneficial for its activity, which is to replicate itself quickly at the cost of the host.
But uncharacteristically, in the system of Prochlorococcus and virus P-SSP7, an unprecedented 41 of the bacteria's 1,717 genes were upregulated. That is, the researchers detected increased quantities of the messenger RNA encoded by these genes in the cell during the infection process. The upregulation of so many host genes during infection is a phenomenon unseen before in the world of bacteriology.
Moreover, many of the host genes upregulated during infection are among those that are found in genomic islands in the host, variable regions that appear to be hot-spots for genetic exchange between bacterial hosts and viruses. In this case, some of the genes that have been transferred back and forth encode for proteins that affect the bacteria's ability to adapt to changes in environmental factors, such as nutrient deprivation and light stress. The scientists hypothesize that modifications made to the bacterial genes when they were in the virus led to new versions of the proteins that may provide the bacteria with an increased ability to withstand environmental changes. It is also possible that multiple copies of a gene provide some benefit.
Another unusual occurrence is that the viral genome contains genes transferred from bacterial hosts that encode energy-producing proteins, including photosynthesis genes that cyanobacteria need for metabolism and DNA replication. Although these genes are positioned far apart in the viral genome, they are transcribed at the same time during infection rather than in the usual left-to-right order. This leads the researchers to surmise that the virus is trying to keep its host alive longer so that the host continues to provide the energy needed for the virus's own DNA replication.
Lindell and Chisholm believe the most plausible scenario to explain the gene upregulation and gene trading is that the bacterium activates certain genes in response to infection as a means of self-protection. The virus has "learned" to use those genes to its own advantage and so incorporates them into its own genome. Later, when infecting another bacterium, the virus upregulates those genes itself to facilitate its own reproduction within the host bacterium. When a bacterium survives an infection, those viral modified genes are incorporated back into the bacterial DNA in genome islands, making that bacterium and its descendants more likely to survive in the harsh ocean environment.
"These viral parasites cooperate with their hosts during infection, providing proteins that probably function within host metabolic pathways, to squeeze every bit of energy out them before killing them off," said Lindell. "Yet on evolutionary scales, such host-pathogen interactions are influencing the evolution of gene content in both host and virus, which in turn is likely impacting their ability to colonize new niches."
Next steps in the research are to see if the host-like genes in the virus really do confer a fitness advantage to the virus and then to the host bacterium when transferred back.
Funding for this research came from the Department of Energy's GTL Program, the Gordon and Betty Moore Foundation, and the National Science Foundation.
Lindell performed the research as a postdoctoral associate in Chisholm's lab before joining the Technion faculty in the Department of Biology in October 2006. It builds on previous work in Chisholm's lab at MIT, including research by Lindell and co-author Matthew Sullivan, who in 2004 noted the presence of host genes in the viruses and their transfer back to the host, and by Maureen Coleman, who in 2006 found genomic islands in the host that had most likely come from viruses.
Other authors are MIT graduate students Gregory Kettler and Coleman; MIT postdoctoral associate Sullivan; Jacob Jaffe of the Broad Institute; Matthias Futschik and Ilka Axmann of Humboldt University; Trent Rector, Robert Steen and George Church of Harvard Medical School; and Wolfgang Hess of the University of Freiburg.
Note: This story has been adapted from a news release issued by Massachusetts Institute of Technology.

Fausto Intilla

www.oloscience.com

Human-Animal Hybrid Embryos Approved For Research In Britain

Source:

http://www.sciencedaily.com/releases/2007/09/070906104037.htm

Science Daily — The following is the statement by the Human Fertilisation and Embryo Authority, the body which oversees human embryo research in Britain. The group will allow the creation of part-human, part-animal hybrid embryos for research purposes. British regulations already require that human embryos for research purposes are destroyed within 14 days of their creation.

Statement:
"The decision on how the HFEA should approach the licensing of human - animal hybrids and chimera research has presented a particular challenge as this research is so novel in legal, scientific and ethical terms.
"In order to ensure that the Authority was able to make an appropriate and reasoned decision, we needed to ensure we had a comprehensive and robust evidence base as a foundation for that decision.
"Once we had established that such research would legally fall within the HFEA's remit to license, we were then able to start to assess whether such research would, in principle, be necessary and desirable in both scientific and ethical terms.
"As such the HFEA, working with support from the Government's Sciencewise programme, put together a detailed and comprehensive consultation gathering evidence from scientists and the wider public about the issues raised by this research. This has been far more than just opinion polling and has involved a series of detailed deliberative sessions where the full range of issues raised by such research were discussed. This enabled participants to make their own informed judgements, asking questions and challenging their own views.
"Having looked at all the evidence the Authority has decided that there is no fundamental reason to prevent cytoplasmic hybrid research. However, public opinion is very finely divided with people generally opposed to this research unless it is tightly regulated and it is likely to lead to scientific or medical advancements.
"This is not a total green light for cytoplasmic hybrid research, but recognition that this area of research can, with caution and careful scrutiny, be permitted. Individual research teams should be able to undertake research projects involving the creation of cytoplasmic hybrid embryos if they can demonstrate, to the satisfaction of an HFEA licence committee, that their planned research project is both necessary and desirable. They must also meet the overall standards required by the HFEA for any embryo research.
"Having looked at the principles behind this kind of research, an HFEA licence committee will now look at the details of the two specific research applications that were submitted earlier this year. We would hope to have a decision on both applications in November.
"In general, people who do not fundamentally oppose embryo research are prepared to accept that human animal research may have some value. But there is a clear demand from people to know more about what researchers are doing and their plans for future work, highlighting a need for better communication about science and research from both the scientific community and ourselves as regulator. In the coming months we will be looking to see how this can be delivered.
"In terms of other kinds of hybrid and chimera research, it became very clear that not only did the scientific community not wish to perform such research at present but that the prospect was so distant that they could not envisage what form this research would possibly take in the future.
"The Authority felt it would be completely wrong to make a decision on broader hybrid and chimera research without an adequate evidence base. However, the HFEA will continue to monitor the potential for this wider research and any emerging evidence through its 'horizon scanning' programme."
Note: This story has been adapted from a news release issued by Human Fertilisation and Embryo Authority.

Fausto Intilla
www.oloscience.com

New Species May Form WIth A Little Help From Immune System

Source:

http://www.sciencedaily.com/releases/2007/09/070905103023.htm

Science Daily — Plant geneticists and animal breeders alike know the problem: single individuals or entire broods will not thrive, some die early, or remain, even if they survive, the runts of the litter and thus not useful for continued breeding programs. What is annoying for the breeder, fascinates geneticists and molecular biologists. The unfit offspring are an example that genetic material cannot always be combined at will.

Apparently there are reproductive barriers that not only prevent the exchange of genes between well established species, but also between varieties of one and the same species. How these barriers arise is of central importance if one wants to understand the origin of biodiversity. A research team led by Detlef Weigel from the Max Planck Institute of Developmental Biology in Germany and Jeff Dangl from the University of North Carolina has now shown that a mis-regulated immune system can establish reproductive barriers and might be a first step toward speciation. The international collaboration studied a genetic incompatibility known as hybrid necrosis, using thale cress, Arabidopsis thaliana.
The new work, reported in PLoS Biology, was based on the observation that unfit hybrids from different plant species are very similar. Their growth is retarded, the leaves become yellow and necrotic, the tissue collapses and they often do not survive to make flowers; the syndrome is generally known as hybrid necrosis. "We suspected that hybrid necrosis is always caused by the same biochemical mechanism," explains Weigel, director at the Max Planck Institute.
To test this hypothesis, the scientists took 280 genetically different strains of Arabidopsis from all over the world, which they crossed in 861 different combinations. Most of the hybrid plants were strong and grew normally, but 20 - or two percent - of the crosses produced only small necrotic and unhealthy plants. Genomics-based experiments showed that these hybrids all had a comparable profile of gene activity:
A common group of some 1000 genes were either more strongly or more weakly active in the hybrids than in their healthy parents. Moreover, this pattern was very similar to what is seen with a strong immune response mounted against pathogens during a normal infection. The plant immune response typically involves the sacrifice of a few cells at and around the infection site. But in the wimpy hybrids, healthy tissue also suffered - without pathogen infection. The hybrid plants apparently mistook their own cells for dangerous germs.
Although the genes that determined the abnormal autoimmunity were different in most crosses, the researchers discovered that often only two genes were required to cause the necrotic hybrid response. One of the fatal genes came from the father, the other from the mother. In one case that the researchers studied in more detail, they found that the gene that causes necrosis in hybrids, but not in the parents, is normally used to sense the presence of a pathogen.
The scientists emphasize, however, that the hybrids are not the victims of malfunctioning genes: in contrast to many hereditary diseases, the necrosis is not due to each parent carrying a defective copy of the same gene. Rather, there is a destructive interaction between two different genes, each of which evolved differently in the two parents. The genes on their own are harmless or even beneficial, since the parents are healthy. Only the combination of the altered gene variants creates problems. These types of genetic malfunction are often known as Dobzhanshy-Muller incompatibilities, after the two giants of early modern genetics who first studied these necrotic hybrids in fruit flies.
The results of the German-American team challenge the classical definition of a species, according to which individuals of one species can mate at will and produce fertile offspring. Apparently there are barriers to the free interchange of genes even within a species; after all, one out of 50 crosses in this study was not successful. "The formation of new species thus needs to be understood as a gradual process, where barriers within a species continually increase, until two groups cannot be crossed at all anymore" says Weigel.
While this view is widely accepted today, it is mostly unclear, why such genetic barriers arise in the first place. Which advantage has the plant, when sometimes all seeds from a cross die? The current study offers a possible explanation. The plant genome changes under pressure from pathogens.
"Plant and pathogen are locked in a race," says Dangl, professor and expert in the genetics of plant pathology at the University of North Carolina. The pathogens tirelessly develop new strategies to attack the plant and evade its immune system. The plant, in turn, tries to be prepared against as many new microbe "weapons" as possible. Armed to the teeth, it can happen that a harmless protein variant from a more distant relative is all of a sudden classified as dangerous and attacked.
The scientists are optimistic that their insights can be applied to other species. Common traits indicate that hybrid necrosis in crops such as wheat is caused by the same mechanisms as in tale cress. Dangl therefore believes that Arabidopsis can serve as a useful model for the understanding of hybrid necrosis in general. "Such a model would be very useful for breeding, since such genetic incompatibilities prevents some of the crosses breeders would like to make," according to Dangl.
The finding that only a few genes are responsible for each case of hybrid necrosis is particularly encouraging. It seems that only a few genetic changes are required to circumvent crossing barriers und to achieve a desired new combination of genetic traits. The flip side of the coin is that only minimal modifications in the genome can be sufficient to suppress the free exchange of genes between relatives, and that perhaps not much is needed to form a new species.
Authors of the study were Detlef Weigel, Kirsten Bomblies, Janne Lempe, Norman Warthmann and Christa Lanz from the Max Planck Institute for Developmental Biology, Tübingen, Germany; and Petra Epple und Jeffery L. Dangl from the University of North Carolina in Chapel Hill, North Carolina, USA.
Reference: Detlef Weigel, Kirsten Bomblies, Janne Lempe, Norman Warthmann, Christa Lanz and Petra Epple und Jeffery L. Dangl "Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants" PLoS Biology 5, e236 (4. September 2007)
Note: This story has been adapted from a news release issued by Max-Planck-Gesellschaft.

Fausto Intilla

www.oloscience.com

Microfluidic Chambers Advance The Science Of Growing Neurons

Source:

http://www.sciencedaily.com/releases/2007/08/070830160803.htm

Science Daily — Researchers at the University of Illinois have developed a method for culturing mammalian neurons in chambers not much larger than the neurons themselves. The new approach extends the lifespan of the neurons at very low densities, an essential step toward developing a method for studying the growth and behavior of individual brain cells.

The technique is described this month in the journal of the Royal Society of Chemistry – Lab on a Chip.
“This finding will be very positively greeted by the neuroscience community,” said Martha Gillette, who is an author on the study and the head of the cell and developmental biology department at Illinois. “This is pushing the limits of what you can do with neurons in culture.”
Growing viable mammalian neurons at low density in an artificial environment is no easy task. Using postnatal neurons only adds to the challenge, Gillette said, because these cells are extremely sensitive to environmental conditions.
All neurons rely on a steady supply of proteins and other “trophic factors” present in the extracellular fluid. These factors are secreted by the neurons themselves or by support cells, such as the glia. This is why neurons tend to do best when grown at high density and in the presence of other brain cells. But a dense or complex mixture of cells complicates the task of characterizing the behavior of individual neurons.
One technique for keeping neural cultures alive is to grow the cells in a medium that contains serum, or blood plasma. This increases the viability of cells grown at low density, but it also “contaminates” the culture, making it difficult to determine which substances were produced by the cells and which came from the serum.
Those hoping to understand the cellular origins of trophic factors in the brain would benefit from a technique that allows them to measure the chemical outputs of individual cells. The research team made progress toward this goal by addressing a few key obstacles.
First, the researchers scaled down the size of the fluid-filled chambers used to hold the cells. Chemistry graduate student Matthew Stewart made the small chambers out of a molded gel of polydimethylsiloxane (PDMS). The reduced chamber size also reduced – by several orders of magnitude – the amount of fluid around the cells, said Biotechnology Center director Jonathan Sweedler, an author on the study. This “miniaturization of experimental architectures” will make it easier to identify and measure the substances released by the cells, because these “releasates” are less dilute.
“If you bring the walls in and you make an environment that’s cell-sized, the channels now are such that you’re constraining the releasates to physiological concentrations, even at the level of a single cell,” Sweedler said.
Second, the researchers increased the purity of the material used to form the chambers. Cell and developmental biology graduate student Larry Millet exposed the PDMS to a series of chemical baths to extract impurities that were killing the cells.
Millet also developed a method for gradually perfusing the neurons with serum-free media, a technique that resupplies depleted nutrients and removes cellular waste products. The perfusion technique also allows the researchers to collect and analyze other cellular secretions – a key to identifying the biochemical contributions of individual cells.
“We know there are factors that are communicated in the media between the cells,” Millet said. “The question is what are they, and how can we get at those?”
This combination of techniques enabled the research team to grow postnatal primary hippocampal neurons from rats for up to 11 days at extremely low densities. Prior to this work, cultured neurons in closed-channel devices made of untreated, native PDMS remained viable for two days at best.
The cultured neurons also developed more axons and dendrites, the neural tendrils that communicate with other cells, than those grown at low densities with conventional techniques, Gillette said.
“Not only have we increased the cells’ viability, we’ve also increased their ability to differentiate into what looks much more like a mature neuron,” she said.
Sweedler noted that the team’s successes are the result of a unique collaboration among scientists with very different backgrounds.
“(Materials science and engineering professor) Ralph Nuzzo is one of the pioneers in self-assembled monolayers and surface chemistry,” Sweedler said. “Martha Gillette’s expertise is in understanding how these neurons grow, and in imaging them. My lab does measurement science on a very small scale. It’s almost impossible for any one lab to do all that.”
Nuzzo and Sweedler are William H. and Janet Lycan professors of chemistry. Gillette is Alumni Professor of Cell and Developmental Biology. All are appointed in the Institute for Genomic Biology. Sweedler and Gillette are affiliates of the Beckman Institute and the Neuroscience Program. Sweedler is a professor in the Bioengineering Program and Gillette in the College of Medicine.
Note: This story has been adapted from a news release issued by University of Illinois at Urbana-Champaign.

Fausto Intilla

www.oloscience.com