Brain Development Is Guided by Junk DNA That Isn't Really Junk

Brain Development Is Guided by Junk DNA That Isn't Really Junk

  8:02:00 AM    Science Lover

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Specific DNA once dismissed as junk plays an important role in brain development and might be involved in several devastating neurological diseases, UC San Francisco scientists have found.

UCSF researchers have uncovered a role in brain development and in neurological disease for little appreciated molecules called long noncoding RNA. In this image, fluorescent dyes track the presence of the RNA molecules and the genes they affect in the developing mouse brain. (Credit: Image courtesy of Alexander Ramos)

Their discovery in mice is likely to further fuel a recent scramble by researchers to identify roles for long-neglected bits of DNA within the genomes of mice and humans alike.

While researchers have been busy exploring the roles of proteins encoded by the genes identified in various genome projects, most DNA is not in genes. This so-called junk DNA has largely been pushed aside and neglected in the wake of genomic gene discoveries, the UCSF scientists said.

In their own research, the UCSF team studies molecules called long noncoding RNA (lncRNA, often pronounced as "link" RNA), which are made from DNA templates in the same way as RNA from genes.

"The function of these mysterious RNA molecules in the brain is only beginning to be discovered," said Daniel Lim, assistant professor of neurological surgery, a member of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, and the senior author of the study, published online April 11 in the journal Cell Stem Cell.

Alexander Ramos, a student enrolled in the MD/PhD program at UCSF and first author of the study, conducted extensive computational analysis to establish guilt by association, linking lncRNAs within cells to the activation of genes.

Ramos looked specifically at patterns associated with particular developmental pathways or with the progression of certain diseases. He found an association between a set of 88 long noncoding RNAs and Huntington's disease, a deadly neurodegenerative disorder. He also found weaker associations between specific groups of long noncoding RNAs and Alzheimer's disease, convulsive seizures, major depressive disorder and various cancers.

"Alex was the team member who developed this new research direction, did most of the experiments, and connected results to the lab's ongoing work," Lim said. The study was mostly funded through Lim's grant - a National Institutes of Health (NIH) Director's New Innovator Award, a competitive award for innovative projects that have the potential for unusually high impact.

Unlike messenger RNA, which is transcribed from the DNA in genes and guides the production of proteins, lncRNA molecules do not carry the blueprints for proteins. Because of this fact, they were long thought to not influence a cell's fate or actions.

Nonetheless, lncRNAs also are transcribed from DNA in the same way as messenger RNA, and they, too, consist of unique sequences of nucleic acid building blocks.

Evidence indicates that lncRNAs can tether structural proteins to the DNA-containing chromosomes, and in so doing indirectly affect gene activation and cellular physiology without altering the genetic code. In other words, within the cell, lncRNA molecules act "epigenetically" -- beyond genes -- not through changes in DNA.

The brain cells that the scientists focused on the most give rise to various cell types of the central nervous system. They are found in a region of the brain called the subventricular zone, which directly overlies the striatum. This is the part of the brain where neurons are destroyed in Huntington's disease, a condition triggered by a single genetic defect.

Ramos combined several advanced techniques for sequencing and analyzing DNA and RNA to identify where certain chemical changes happen to the chromosomes, and to identify lncRNAs on specific cell types found within the central nervous system. The research revealed roughly 2,000 such molecules that had not previously been described, out of about 9,000 thought to exist in mammals ranging from mice to humans.

In fact, the researchers generated far too much data to explore on their own. The UCSF scientists created a website through which their data can be used by others who want to study the role of lncRNAs in development and disease.

"There's enough here for several labs to work on," said Ramos, who has training grants from the California Institute for Regenerative Medicine (CIRM) and the NIH.

"It should be of interest to scientists who study long noncoding RNA, the generation of new nerve cells in the adult brain, neural stem cells and brain development, and embryonic stem cells," he said.

Other co-authors who worked on the study include UCSF postdoctoral fellows Aaron Diaz, PhD, Abhinav Nellore, PhD, Michael Oldham, PhD, Jun Song, PhD, Ki-Youb Park, PhD, and Gabriel Gonzales-Roybal, PhD; and MD/PhD student Ryan Delgado. Additional funders of the study included the Sontag Foundation and the Sandler Foundation.

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

Biological Transistor Enables Computing Within Living Cells

  10:14:00 AM    Science Lover

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When Charles Babbage prototyped the first computing machine in the 19th century, he imagined using mechanical gears and latches to control information. ENIAC, the first modern computer developed in the 1940s, used vacuum tubes and electricity. Today, computers use transistors made from highly engineered semiconducting materials to carry out their logical operations.

Artist's rendering of cells. (Credit: © Jezper / Fotolia)

And now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper to be published March 28 in Science, the team details a biological transistor made from genetic material -- DNA and RNA -- in place of gears or electrons. The team calls its biological transistor the "transcriptor."

"Transcriptors are the key component behind amplifying genetic logic -- akin to the transistor and electronics," said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper's lead author.

The creation of the transcriptor allows engineers to compute inside living cells to record, for instance, when cells have been exposed to certain external stimuli or environmental factors, or even to turn on and off cell reproduction as needed.

"Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics," said Drew Endy, PhD, assistant professor of bioengineering and the paper's senior author.

The biological computer

In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.

"We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic," said Endy.

Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.

They refer to their transcriptor-based logic gates as "Boolean Integrase Logic," or "BIL gates" for short.

Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.

Despite their outward differences, all modern computers, from ENIAC to Apple, share three basic functions: storing, transmitting and performing logical operations on information.

Last year, Endy and his team made news in delivering the other two core components of a fully functional genetic computer. The first was a type of rewritable digital data storage within DNA. They also developed a mechanism for transmitting genetic information from cell to cell, a sort of biological Internet.

It all adds up to creating a computer inside a living cell.

Boole's gold

Digital logic is often referred to as "Boolean logic," after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It's that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.

"AND" and "OR" are just two of the most basic Boolean logic gates. An "AND" gate, for instance, is "true" when both of its inputs are true -- when "a" and "b" are true. An "OR" gate, on the other hand, is true when either or both of its inputs are true.

In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. "You could test whether a given cell had been exposed to any number of external stimuli -- the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not," he said.

By the same token, you could tell the cell to start or stop reproducing if certain factors were present. And, by coupling BIL gates with the team's biological Internet, it is possible to communicate genetic information from cell to cell to orchestrate the behavior of a group of cells.

"The potential applications are limited only by the imagination of the researcher," said co-author Monica Ortiz, a PhD candidate in bioengineering who demonstrated autonomous cell-to-cell communication of DNA encoding various BIL gates.

Building a transcriptor

To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes -- the integrases mentioned earlier -- that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.

"The choice of enzymes is important," Bonnet said. "We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms."

On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.

With transcriptors, a very small change in the expression of an integrase can create a very large change in the expression of any two other genes.

To understand the importance of amplification, consider that the transistor was first conceived as a way to replace expensive, inefficient and unreliable vacuum tubes in the amplification of telephone signals for transcontinental phone calls. Electrical signals traveling along wires get weaker the farther they travel, but if you put an amplifier every so often along the way, you can relay the signal across a great distance. The same would hold in biological systems as signals get transmitted among a group of cells.

"It is a concept similar to transistor radios," said Pakpoom Subsoontorn, a PhD candidate in bioengineering and co-author of the study who developed theoretical models to predict the behavior of BIL gates. "Relatively weak radio waves traveling through the air can get amplified into sound."

Public-domain biotechnology

To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.

"Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together," Bonnet said.

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U of T researchers build an antenna for light

U of T researchers build an antenna for light

  9:53:00 AM    Science Lover

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University of Toronto researchers have derived inspiration from the photosynthetic apparatus in plants to engineer a new generation of nanomaterials that control and direct the energy absorbed from light.

Their findings are reported in a forthcoming issue of Nature Nanotechnology, which will be released on July 10, 2011.

The U of T researchers, led by Professors Shana Kelley and Ted Sargent, report the construction of what they term "artificial molecules."

"Nanotechnologists have for many years been captivated by quantum dots – particles of semiconductor that can absorb and emit light efficiently, and at custom-chosen wavelengths," explained co-author Kelley, a Professor at the Leslie Dan Faculty of Pharmacy, the Department of Biochemistry in the Faculty of Medicine, and the Department of Chemistry in the Faculty of Arts & Science. "What the community has lacked – until now – is a strategy to build higher-order structures, or complexes, out of multiple different types of quantum dots. This discovery fills that gap."

The team combined its expertise in DNA and in semiconductors to invent a generalized strategy to bind certain classes of nanoparticles to one another.

"The credit for this remarkable result actually goes to DNA: its high degree of specificity – its willingness to bind only to a complementary sequence – enabled us to build rationally-engineered, designer structures out of nanomaterials," said Sargent, a Professor in The Edward S. Rogers Sr. Department of Electrical & Computer Engineering at the University of Toronto, who is also the Canada Research Chair in Nanotechnology. "The amazing thing is that our antennas built themselves – we coated different classes of nanoparticles with selected sequences of DNA, combined the different families in one beaker, and nature took its course. The result is a beautiful new set of self-assembled materials with exciting properties."



Traditional antennas increase the amount of an electromagnetic wave – such as a radio frequency – that is absorbed, and then funnel that energy to a circuit. The U of T nanoantennas instead increased the amount of light that is absorbed and funneled it to a single site within their molecule-like complexes. This concept is already used in nature in light harvesting antennas, constituents of leaves that make photosynthesis efficient. "Like the antennas in radios and mobile phones, our complexes captured dispersed energy and concentrated it to a desired location. Like the light harvesting antennas in the leaves of a tree, our complexes do so using wavelengths found in sunlight," explained Sargent.

"Professors Kelley and Sargent have invented a novel class of materials with entirely new properties. Their insight and innovative research demonstrates why the University of Toronto leads in the field of nanotechnology," said Professor Henry Mann, Dean of the Leslie Dan Faculty of Pharmacy.

"This is a terrific piece of work that demonstrates our growing ability to assemble precise structures, to tailor their properties, and to build in the capability to control these properties using external stimuli," noted Paul S. Weiss, Fred Kavli Chair in NanoSystems Sciences at UCLA and Director of the California NanoSystems Institute.

Kelley explained that the concept published in today's Nature Nanotechnology paper is a broad one that goes beyond light antennas alone.

"What this work shows is that our capacity to manipulate materials at the nanoscale is limited only by human imagination. If semiconductor quantum dots are artificial atoms, then we have rationally synthesized artificial molecules from these versatile building blocks."

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The Future of Metabolic Engineering: Designer Molecules, Cells and Microorganisms

The Future of Metabolic Engineering: Designer Molecules, Cells and Microorganisms

  5:22:00 PM    Science Lover

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Will we one day design and create molecules, cells and microorganisms that produce specific chemical products from simple, readily-available, inexpensive starting materials? Will the synthetic organic chemistry now used to produce pharmaceutical drugs, plastics and a host of other products eventually be surpassed by metabolic engineering as the mainstay of our chemical industries? Yes, according to Jay Keasling, chemical engineer and one of the world's foremost practitioners of metabolic engineering.

Metabolic engineering - the practice of 
altering genes and metabolic pathways 
within a cell or microorganism -- could 
one day be used to mass-produce biofuels, 
pharmaceuticals and other chemical 
products from inexpensive and renewable 
starting materials. (Credit: Flavio Robles, 
Berkeley Lab Public Affairs)

In a paper published in the journal Science Keasling discusses the potential of metabolic engineering -- one of the principal techniques of modern biotechnology -- for the microbial production of many of the chemicals that are currently derived from non-renewable resources or limited natural resources. Examples include, among a great many other possibilities, the replacement of gasoline and other transportation fuels with clean, green and renewable biofuels.

"Continued development of the tools of metabolic engineering will be necessary to expand the range of products that can be produced using biological systems, Keasling says. "However, when more of these tools are available, metabolic engineering should be just as powerful as synthetic organic chemistry, and together the two disciplines can greatly expand the number of chemical products available from renewable resources."

Keasling is the chief executive officer for the Joint BioEnergy Institute, a U.S. Department of Energy (DOE) bioenergy research center. He also holds joint appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab), where he oversees that institute's biosciences research programs, and the University of California (UC), Berkeley, where he serves as director of the Synthetic Biology Engineering Research Center, and is the Hubbard Howe Jr. Distinguished Professor of Biochemical Engineering.

Metabolic engineering is the practice of altering genes and metabolic pathways within a cell or microorganism to increase its production of a specific substance. Keasling led one of the most successful efforts to date in the application of metabolic engineering, when he combined it with synthetic organic chemistry techniques to develop a microbial-based means of producing artemisinin, the most potent of all anti-malaria drugs. He and his research group at JBEI are now applying that same combination to the synthesis of liquid transportation fuels from lignocellulosic biomass. In all cases, the goal is to engineer microbes to perform as much of the chemistry required to produce a desired final product as possible.

"To date, microbial production of natural chemical products has been achieved by transferring product-specific enzymes or entire metabolic pathways from rare or genetically intractable organisms to those that can be readily engineered," Keasling says. "Production of non-natural specialty chemicals, bulk chemicals, and fuels has been enabled by combining enzymes or pathways from different hosts into a single microorganism, and by engineering enzymes to have new function."

These efforts have utilized well-known, industrial microorganisms, but future efforts, he says, may include designer molecules and cells that are tailor-made for the desired chemical and production process.

"In any future, metabolic engineering will soon rival and potentially eclipse synthetic organic chemistry," Keasling says.

Keasling cites the production of active pharmaceutical ingredients as one area where metabolic engineering enjoys a distinct advantage over synthetic organic chemistry. This includes three specific classes of chemicals -- alkaloids, which are primarily derived from plants; polyketides and non-ribosomal peptides, which are produced by various bacteria and fungi; and isoprenoids, which also are typically produced by microbes.

"Many of these natural products are too complex to be chemically synthesized and yet have a value that justifies the cost of developing a genetically engineered microorganism," Keasling says. "The cost of starting materials is generally a small fraction of the complete cost of these products, and relatively little starting material is necessary so availability is not an issue."

Keasling also says that metabolic engineering could provide a valuable alternative means of producing variations of terpenes, the hydrocarbon compounds common to the resins of conifers, in a form that could yield pharmaceuticals that are more effective for the treatment of human disease than the forms that nature has provided.

Perhaps the ripest targets of opportunity for future metabolic engineering efforts are petroleum-based bulk chemical products, including gasoline and other fuels, polymers and solvents. Because such products can be inexpensively catalyzed from petroleum, microbial production has until now been rare, but with fluctuating oil prices, dwindling resources and other considerations, the situation, Keasling says, has changed.

"It is now possible to consider production of these inexpensive bulk chemicals from low-cost starting materials, such as starch, sucrose, or cellulosic biomass with a microbial catalyst," he says. "The key to producing these bulk chemicals in metabolically-engineered cells will be our ability to make the exact molecule needed for existing products rather than something 'similar but green' that will require extensive product testing before it can be used."

In his Science paper, Keasling discusses the formidable roadblocks that stand in the way of a future in which microorganisms and molecules can be tailor-made through metabolic engineering, including the need for "debugging routines" that can find and fix errors in engineered cells. However, he is convinced these roadblocks can and will be overcome.

"One can even envision a day when cell manufacturing is done by different companies, each specializing in certain aspects of the synthesis, with one company constructing the chromosome, one company building the membrane and cell wall bag, and one company filling this bag with the basic molecules needed to boot up the cell."

The Joint BioEnergy Institute (JBEI) is one of three Bioenergy Research Centers funded by the U.S. Department of Energy to advance the development of the next generation of biofuels. It is a scientific partnership led by Berkeley Lab and including the Sandia National Laboratories, the University of California campuses of Berkeley and Davis, the Carnegie Institution for Science, and the Lawrence Livermore National Laboratory.

The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution partnership, funded by the National Science Foundation, that is aimed at "making biology easier to engineer." The SynBERC partnership is led by UC Berkeley and includes UC San Francisco, Harvard, MIT, Stanford, and Prairie View A&M University.

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Stem Cells from Amniotic Fluid: Reprogrammed Amniotic Fluid Cells Can Generate All Types of Body Cells

Stem Cells from Amniotic Fluid: Reprogrammed Amniotic Fluid Cells Can Generate All Types of Body Cells

  10:06:00 AM    Science Lover

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Reprogrammed amniotic fluid cells can generate all types of body cells. High hopes rest on stem cells: one day, they may be used to treat many diseases. To date, embryos are the main source of these cells, but this raises ethical problems. Scientists at the Max Planck Institute for Molecular Genetics in Berlin have now managed to convert amniotic fluid cells into pluripotent stem cells. These amniotic fluid-derived iPS cells are hardly distinguishable from embryonic stem cells. However, they "remember" where they came from.

Top: Before their reprogramming into amniotic fluid iPS cells, 
human amniotic fluid cells are outwardly distinguishable from 
embryonic stem cells. Bottom left: Amniotic fluid iPS cells 
produce OCT4 (green), one of the most important marker 
proteins for embryonic stem cells. Bottom right: Starting from 
this embryonic stem cell phase, the amniotic fluid iPS cells can 
form hepatocyte-like cells and others. They produce the plasma
protein alpha-fetoprotein (red), which is abundant in fetal 
liver. (Credit: Max Planck Institute for Molecular Genetics)

The research appears in the online journal PLoS ONE, published by the Public Library of Science.

The special abilities of embryonic stem cells can today be used in multiple "grown-up" cells (e.g. skin and hair cells). This is done by reprogramming the cells and converting them to "induced pluripotent stem cells" (iPS cells). These then possess the typical properties of embryonic stem cells, meaning they can generate any of the cell types of the human body (pluripotency), and they can multiply endlessly.

Stem cells with memory
 
The scientists have shown that the amniotic fluid iPS cells can form different human cell types. They have also discovered that induced pluripotent stem cells can remember the original cell type from which they were generated. During cellular reprogramming, various genes that control the development of stem cells are apparently switched on or remain active. This confirms other current research results, which show that iPS cells derived from distinct tissues are prone to follow their pre-destined developmental path upon spontaneous differentiation. "We don't know just yet whether this donor-cell type memory will have an impact on possible medical treatment, or which type of somatic cell-derived iPS cell will be most suitable for treatment," cautions Katharina Wolfrum of the Max Planck Institute for Molecular Genetics.

Amniotic fluid cells have a number of advantages over other cell types. For one thing, amniotic fluid cells are routinely harvested in antenatal examinations to enable the early detection of disease. In most cases, more cells are obtained than are actually needed. In addition, the amniotic fluid mixture contains different types of cells from the unborn child, including stem-cell-like cells. As they are not very old, they have fewer environmentally-induced mutations, making them genetically more stable. "This may mean that it is possible to reprogram these amniotic fluid cells faster and more easily than other cell types, making amniotic fluid-derived iPS cells an interesting complement to embryonic stem cells," explains James Adjaye of the Max Planck Institute in Berlin.

Moreover, amniotic fluid cells could be extracted for cellular reprogramming before the birth of a child and be prepared for their intended use while the pregnancy is still ongoing. "This would make it possible to test which drugs work for a baby and whether they are tolerated, before that baby is born. Moreover, in the future, sick newborns can be treated with cells from their own body," says Adjaye.

Admin's Note: This article is not intended to provide medical advice, diagnosis or treatment.

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A New Way to Make Stem Cells Using RNA instead of DNA could avoid the health risks--and the political pitfalls--of stem-cell treatments.

A New Way to Make Stem Cells Using RNA instead of DNA could avoid the health risks--and the political pitfalls--of stem-cell treatments.

  1:27:00 AM    Science Lover

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A Harvard researcher has developed a way to make pluripotent stem cells that solves several of the major impediments to using them to treat human diseases.

New cell: This microscope image shows neurons
(colored green) created from pluripotent stem
cells using modified RNA.
Credit: Phil Manos, Cell Press

Derrick Rossi, an assistant professor at Harvard Medical School, created pluripotent stem cells--which can turn into virtually any other type of cell in the body--from non-stem cells without using viruses to tinker with a cell's genome, as conventional methods do. This means that Rossi's method could be substantially safer for treating disease. The work is published today in the journal Cell Stem Cell.

"Rossi has figured out how to turn a skin cell into a stem cell without genetic modifications, and to do it efficiently," said Doug Melton, codirector of the Harvard Stem Cell Institute, where Rossi is a principal faculty member, at a press conference.

Rossi's innovation, which has not yet been tested in people, was to use messenger RNA instead of DNA to produce the four proteins needed to reprogram the cell. He has started a company called ModeRNA to commercialize this use of messenger RNA. He said the approach may also have potential in gene therapy, which also relies on viruses to deliver treatment, but he declined to talk further about the company or possible gene therapy applications because the work is at such an early stage.

Improving the usability of man-made stem cells is key to helping patients and ending the political morass that has slowed stem-cell research. On Tuesday, a U.S. federal appeals court allowed federal funding of embryonic stem-cell research to continue while a legal case against such funding proceeds.

The human embryonic stem cells used in research were mostly derived from embryonic tissue grown a decade ago. These are the most versatile cells in the body, and the gold standard by which man-made cells are judged.

Four years ago, Japanese researcher Shinya Yamanaka showed that regular cells could be turned into embryonic-like stem cells--called induced pluripotent stem (iPS) cells--through the introduction of four specific proteins. Theoretically, this meant that doctors could take skin cells from a sick or disabled person, transform them into stem cells, and then into a specialized cell to treat them--an insulin-producing islet cell for someone with diabetes or a nerve cell for someone who is paralyzed, for instance. Using iPS cells avoids the need to destroy embryos and, because they can be derived from the patient's own cells, means less risk of rejection.

But only one in 1,000 or one in 10,000 skin cells could be transformed into a stem cell using Yamanaka's method. It also changes a cell's genes in ways that might trigger cancer or other problems.

Rossi 's idea was to produce Yamanaka's four proteins in a different way. Instead of using the DNA that holds the instructions for making proteins, he wanted to use RNA, which carries those instructions to the place in a cell where proteins are made.

His first several attempts were miserable failures. When he tried to change the messages the RNA carried, he triggered a serious immune response and most of the cells shut down or self-destructed. Rossi then tried modifying the RNA chemically and eventually figured out a way to allow his changes to escape immune detection while delivering the message. "This was key to our success," said Rossi, who is also a researcher at Children's Hospital Boston. "We could encode RNA for any protein we wanted to express and insert it into a cell."

Rossi said it was a happy coincidence that using RNA instead of changing the DNA was as much as 100-fold more efficient. He said the effect was possibly because the process more closely reflects how cells themselves transform.

Rossi successfully differentiated his stem cells into muscle cells using RNA, a process that may offer promise in gene therapy and other treatments. His method does not alter the cell's underlying genome, though Rossi admits that he does not yet understand what it does to the cell's epigenome, which controls expression of genes.

Rossi said that his cells, which he's named RiPS, for "RNA induced Pluripotent Stem" cells, are more like embryonic stem cells than traditional iPS cells because they have not been genetically altered.

Melton said the Harvard Stem Cell Institute, which includes several hundred stem-cell researchers from across Harvard University and its affiliated hospitals, will now be making its standard iPS cells with Rossi's method.

In a prepared statement, Yamanaka, now at the University of California, San Francisco, said Rossi's approach to generating stem cells seems promising, and he would like to have someone in his lab try it.

"The quality of the induced pluripotent stem cells generated by this method should be carefully examined because their characteristics vary depending on the induction methods and the origins of the resulting cells," he said. "The standard method to generate iPSCs for clinical applications has yet to be established. I think this method has the potential for it."

Jacob Hanna, a postdoctoral fellow at the Whitehead Institute for Biomedical Research in Cambridge, said he's also eager to begin working with the cells.

"I think it's a very exciting paper with a very promising method," said Hanna, who was not involved in the research. When asked if he was jealous that Rossi had developed the method first, Hanna said, "Yes, of course! It's a very nice paper," quickly adding, "Jealous in a very positive and supporting way."

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Better Way to Grow Stem Cells Developed

Better Way to Grow Stem Cells Developed

  10:59:00 PM    Science Lover

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Human pluripotent stem cells, which can become any other kind of body cell, hold great potential to treat a wide range of ailments, including Parkinson's disease, multiple sclerosis and spinal cord injuries. However, scientists who work with such cells have had trouble growing large enough quantities to perform experiments -- in particular, to be used in human studies. Furthermore, most materials now used to grow human stem cells include cells or proteins that come from mice embryos, which help stimulate stem-cell growth but would likely cause an immune reaction if injected into a human patient.

This image shows human embryonic stem cells grown on a synthetic surface developed by MIT researchers. The cells at top (blue) are stained to reveal their nuclei, while the cells in the middle and bottom are stained for proteins that are known to be present when cells are pluripotent. Green cells are stained for Oct4 (using green fluorescent protein) and red cells are stained for SSEA-4. (Credit: Ying Mei, Krishanu Saha, Robert Langer, Rudolf Jaenisch, and Daniel G. Anderson)

To overcome those issues, MIT chemical engineers, materials scientists and biologists have devised a synthetic surface that includes no foreign animal material and allows stem cells to stay alive and continue reproducing themselves for at least three months. It's also the first synthetic material that allows single cells to form colonies of identical cells, which is necessary to identify cells with desired traits and has been difficult to achieve with existing materials.

The research team, led by Professors Robert Langer, Rudolf Jaenisch and Daniel G. Anderson, describes the new material in the Aug. 22 issue of Nature Materials. First authors of the paper are postdoctoral associates Ying Mei and Krishanu Saha.

Human stem cells can come from two sources -- embryonic cells or body cells that have been reprogrammed to an immature state. That state, known as pluripotency, allows the cells to develop into any kind of specialized body cells.

It also allows the possibility of treating nearly any kind of disease that involves injuries to cells. Scientists could grow new neurons for patients with spinal cord injuries, for example, or new insulin-producing cells for people with type 1 diabetes.

To engineer such treatments, scientists would need to be able to grow stem cells in the lab for an extended period of time, manipulate their genes, and grow colonies of identical cells after they have been genetically modified. Current growth surfaces, consisting of a plastic dish coated with a layer of gelatin and then a layer of mouse cells or proteins, are notoriously inefficient, says Saha, who works in Jaenisch's lab at the Whitehead Institute for Biomedical Research.

"For therapeutics, you need millions and millions of cells," says Saha. "If we can make it easier for the cells to divide and grow, that will really help to get the number of cells you need to do all of the disease studies that people are excited about."

Previous studies had suggested that several chemical and physical properties of surfaces -- including roughness, stiffness and affinity for water -- might play a role in stem-cell growth. The researchers created about 500 polymers (long chains of repeating molecules) that varied in those traits, grew stem cells on them and analyzed each polymer's performance. After correlating surface characteristics with performance, they found that there was an optimal range of surface hydrophobicity (water-repelling behavior), but varying roughness and stiffness did not have much effect on cell growth.

They also adjusted the composition of the materials, including proteins embedded in the polymer. They found that the best polymers contained a high percentage of acrylates, a common ingredient in plastics, and were coated with a protein called vitronectin, which encourages cells to attach to surfaces.

Using their best-performing material, the researchers got stem cells (both embryonic and induced pluripotent) to continue growing and dividing for up to three months. They were also able to generate large quantities of cells -- in the millions.

The MIT researchers hope to refine their knowledge to help them build materials suited to other types of cells, says Anderson, from the MIT Department of Chemical Engineering, the Harvard-MIT Division of Health Sciences and Technology, and the David H. Koch Institute for Integrative Cancer Research. "We want to better understand the interactions between the cell, the surface and the proteins, and define more clearly what it takes to get the cells to grow," he says.

Other MIT authors of the paper are Said Bogatyrev, Z. Ilke Kalcioglu, Maisam Mitalipova, Neena Pyzocha, Fredrick Rojas and Krystyn Van Vliet. Jing Yang, Andrew Hook, Martyn Davies and Morgan Alexander of the University of Nottingham (United Kingdom) and Seung-Woo Cho of Yonsei University (Korea) are also authors of the paper.

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Toward Deafness Cure: Inner-Ear Cells Created

Toward Deafness Cure: Inner-Ear Cells Created

  9:47:00 PM    Science Lover

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Deep inside the ear, specialized cells called hair cells detect vibrations in the air and translate them into sound. Ten years ago, Stefan Heller, PhD, professor of otolaryngology at the Stanford University School of Medicine, came up with the idea that if you could create these cells in the laboratory from stem cells, it would go a long way toward helping scientists understand the molecular basis of hearing in order to develop better treatments for deafness.

Section through the organ of corti, 
showing inner and outer hair cells. 
(Credit: Courtesy of Wikimedia Commons)

After years of lab work, researchers in Heller's lab will report in the May 14 issue of Cell that they have found a way to develop mouse cells that look and act just like the animal's inner-ear hair cells -- the linchpin to our sense of hearing and balance -- in a petri dish.

If they can further perfect the recipe to generate hair cells in the millions, it could lead to significant scientific and clinical advances along the path to curing deafness in the future, they said.

"This gives us real hope that there might be some kind of therapy for regenerating hair cells," said David Corey, PhD, professor of neurobiology at Harvard University who was not involved in the study. "It could take a decade or more, but it's a possibility."

Using both embryonic stem cells from mice as well as reprogrammed mouse fibroblasts (a type of relatively undifferentiated cell found in many parts of the body), the researchers present a step-by-step guide on how to coax these cells into the sensory cells that normally reside in the inner ear.

"We knew it was really working when we saw them in the electron microscope," Heller said. "They really looked like they were more or less taken out of the ear."

Humans are born with 30,000 cochlear and vestibular hair cells per ear. (By contrast, one retina harbors about 120 million photoreceptors.) When a significant number of these cells are lost or damaged, hearing loss occurs. The major reason for hearing loss and certain balance disorders is that -- unlike other species such as birds -- humans and other mammals are unable to spontaneously regenerate these hearing cells.

As the population has aged and noise pollution has grown more severe, health experts now estimate that one in three adults over the age of 65 has developed a handicapping hearing loss due to the destruction of these limited number of hair cells.

One of the roadblocks to understanding the molecular basis of hearing is the paucity of hair cells available for study, Heller said. While researchers will ultimately need human hair cells, the mouse version is a good model for the initial phases of experimentation, he said. In addition to using mouse embryonic stem cells, the researchers used fibroblasts that had been reprogrammed to behave like stem cells: These are known as induced pluripotent stem cells, or iPS cells.

"Our study offers a protocol to generate millions of functional hair cells from a renewable source," Heller said. "We can now generate these cells and don't have to go through dozens of mice for a single experiment. This allows us to do molecular studies with much higher efficiency."

The study details how the researchers succeeded in coaxing the mouse embryonic stem cells and the iPS cells through different phases of development that occur in the womb. According to lead author Kazuo Oshima, MD, PhD, a research instructor at Stanford who works in Heller's lab, they started by turning the stem and iPS cells into the type of cells that form a young embryo's ectoderm -- the embryo's outer layer of cells that eventually differentiate into many tissues and structures, such as skin and nerve cells. Next they used specific growth factors to transform them into "otic-progenitor" cells (otic means ear). And after that, they varied the chemical soup in the dish, so that the cells clustered in a manner similar to hair cells and developed stereociliary bundles, which are also characteristic of hair cells.

"We looked at how the ear develops in an embryo, at the developmental steps, and mimicked these steps in a culture dish," Heller said.

Hair cells in the inner ear contain tiny clumps of hair-like projections, known as stereocilia. Sound vibrations cause the stereocilia to bend slightly, causing mechanical vibrations that are then converted into an electrochemical signal that the brain interprets as sound.

The cells in the petri dish, under close examination, had this same structure.

"These cells have a very intriguing structure," Heller said. "They look like they have hair tufts of stereocilia."

More importantly, further study showed that the cells also responded to mechanical stimulation by producing currents just like hair cells. Using a probe, researchers stimulated the bundles and recorded the currents that were evoked. Co-author Anthony Ricci, PhD, associate professor of otolaryngology, was responsible for this step of the work.

Heller, a leader in stem-cell based research on the inner ear, has recently been focused on two paths for possible cures for deafness: drug therapy -- which could be as simple as an application of ear drops -- and stem cell transplantation into the inner ear.

Both paths could be further advanced by the ability to develop hair-cell-like cells, he said. "We could now test thousands of drugs in a culture dish," he explained. "It is impossible to achieve such a scale in animals. Within a decade or so we could reap the benefits of this type of screening."

The lab's research into the regeneration of hair cells for transplantation into the inner ear to cure deafness will also continue.

"We made hair-cell-like cells in a petri dish," said Oshima. "This is an important step toward development of future therapies."

The study was funded by grants from the National Institute of Health, the California Institute for Regenerative Medicine and by a Neuroscience of Brain Disorders Award from the McKnight Endowment Fund for Neuroscience.

Other Stanford co-authors include postdoctoral scholars Kunyoo Shin, PhD; Mark Diensthuber, MD; and Anthony Peng, PhD.

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New Nerve Cells -- Even in Old Age: Researchers Find Different Types of Stem Cells in the Brains of Mature and Old Mice

New Nerve Cells -- Even in Old Age: Researchers Find Different Types of Stem Cells in the Brains of Mature and Old Mice

  10:25:00 AM    Science Lover

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After birth the brain loses many nerve cells and this continues throughout life -- most neurons are formed before birth, after which many excess neurons degenerate. However, there are some cells that are still capable of division in old age -- in the brains of mice, at least. According to scientists from the Max Planck Institute of Immunobiology in Freiburg, different types of neuronal stem cells exist that can create new neurons. While they divide continuously and create new neurons in young animals, a large proportion of the cells in older animals persist in a state of dormancy. However, the production of new cells can be reactivated, for example, through physical activity or epileptic seizures. What happens in mice could also be applicable to humans as neurons that are capable of dividing also occur in the human brain into adulthood.

Different types of stem cells in the brain of mature mice. 
(Credit: Verdon Taylor (from: Lugert et al., 
Cell Stem Cell, May 7th, 2010))

The research is published in the journal Cell Stem Cell.

You can't teach an old dog new tricks. The corresponding view that the brain loses learning and memory capacity with advancing age prevailed for a long time. However, neuronal stem cells exist in the hippocampus -- a region of the brain that plays a central role in learning and memory functions -- that can produce new nerve cells throughout life. It is known from tests on mice that the newly formed cells are integrated into the existing networks and play an important role in the learning capacity of animals. Nonetheless, the formation of new cells declines with age and the reasons for this were unknown up to now.

Together with colleagues from Dresden and Munich, the Freiburg researchers have now succeeded in explaining for the first time why fewer new neurons are formed in the adult mouse brain. They managed to identify different populations of neuronal stem cells, thereby demonstrating that the hippocampus has active and dormant or inactive neuronal stem cells. "In young mice, the stem cells divide four times more frequently than in older animals. However, the number of cells in older animals is only slightly lower. Therefore, neuronal stem cells do not disappear with age but are kept in reserve," explains Verdon Taylor from the Max Planck Institute of Immunobiology.

The precise factors that influence the reactivation of dormant stem cells are not yet clear. The cells can, however, be stimulated to divide again. The scientists observed more newborn hippocampal neurons in physically active mice than in their inactive counterparts. "Consequently, running promotes the formation of new neurons," says Verdon Taylor. Pathological brain activity, for example that which occurs during epileptic seizures, also triggers the division of the neuronal stem cells.

Horizontal and radial stem cells

The different stem cell populations are easy to distinguish under the microscope. The first group comprises cells which lie perpendicular to the surface of the hippocampus. Most of these radial stem cells are dormant. As opposed to this, over 80% of the cells in the group of horizontal stem cells -- cells whose orientation runs parallel to the hippocampus surface -- continuously form new cells; the remaining 20% are dormant but sporadically become activated. The activity of genes such as Notch, RBP-J and Sox2 is common to all of the cells.

Radial and horizontal stem cells differ not only in their arrangement, apparently they also react to different stimuli. When the animals are physically active, some radial stem cells abandon their dormant state and begin to divide, while this has little influence on the horizontal stem cells. The result is that more radial stem cells divide in active mice. The horizontal stem cells, in contrast, are also influenced by epileptic seizures.

It would appear that neuronal stem cells are not only found in the brains of mice. The presence of neurons that are formed over the course of life has also been demonstrated in the human hippocamus. Therefore, scientists suspect that different types of active and inactive stem cells also arise in the human brain. It is possible that inactive stem cells in humans can also be activated in a similar way to inactive stem cells in mice. "There are indicators that the excessive formation of new neurons plays a role in epilepsy. The use of neuronal brain stem cells in the treatment of brain injuries or degenerative diseases like Alzheimers may also be possible one day," hopes Verdon Taylor.

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Major Step Forward In Cell Reprogramming, Researchers Report

Major Step Forward In Cell Reprogramming, Researchers Report

  3:02:00 AM    Science Lover

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A team of Harvard Stem Cell Institute (HSCI) researchers has made a major advance toward producing induced pluripotent stem cells, or iPS cells, that are safe enough to use in treating diseases in patients.

Lee Rubin, director of translational medicine at HSCI and the other senior author on the research team, said that "our goals were to try to as discretely and specifically as possible guide the cells through the deprogramming process" from the adult state to the embryonic-like state. (Credit: Photograph by Kris Snibbe/Harvard Staff Photographer)

“This demonstrates that we’re halfway home, and remarkably we got halfway home with just one chemical,” said Kevin Eggan, an HSCI principal faculty member who is the senior author of the paper being published online today by the journal Cell Stem Cell.

“There are four genes that do this, and with just one chemical we replaced half the genes,” said Eggan, who is also an assistant professor in Harvard’s Department of Stem Cell and Regenerative Biology. “The one chemical replaces those two genes in different ways at different times in the experiment. The experiments we performed not only led to discovery of the chemical, but they also explained how it works,” he said.

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