Biosingularity

Archive for January 2006

Stem cells are cells that have the remarkable potential to develop into many different cell types in the body. Serving as a sort of repair system for the body, they can theoretically divide without limit to replenish other cells for as long as the person or animal is still alive.

The most eagerly anticipated therapeutic use for stem cells is regenerative medicine. Biologists dream of the day they can take a stem cell and create any of the body’s cell types, producing pancreas or liver tissue that doctors could use to aid a failing organ. But to realize that dream, scientists must first understand the forces operating in stem cells — what makes some stem cells stay stem cells, while others grow into brain, liver, and skin cells?

Technology review magazine from MIT has a nice article on how scientists are learning how to control the two unique properties of stem cells.

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In a multifaceted study involving the Kuna Indians of Panama, an international team of scientists has pinpointed a chemical compound that is, in part, responsible, for the heart-healthy benefits of certain cocoas and some chocolate products.

The study showed that epicatechin, one of a group of chemicals known as flavanols, was directly linked to improved circulation and other hallmarks of cardiovascular health. The researchers, hope the findings will lead to new dietary or medicinal methods for improving and maintaining cardiovascular health.

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Ever since chemist Stanley Miller created organic compounds from simple building blocks like water, methane, and ammonia, the idea of creating life and thus peering into its possible origins, has fascinated biologists.

Is it possible to build a “protocell” or the most primitive life form from scratch? A cadre of pioneer scientists are trying to do just that. This fascinating quest and current advances in steps of creating life are described in a recent New Scientist article.

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My pick this week, Multipolarity Memes, is a very interesting blog that is  dedicated to guide us to an accelerating, truly self-fulfilling future.

The topics covered are highly diverse from robotics, physics to biological advances. All posted stories accompany visually stimulating thematic pictures or surreal graphics. There are also some very interesting commentaries about futuristic social, political and philosphical issues or dilemmas.

Multipolarity Memes is one of the few blogs that does a great job guiding us to our accelerating future, highly recommended.

Knocking out a gene that helps repair nicks in DNA causes young mice to develop many of the degenerative characteristics of their wizened elders. Mice lacking the gene develop hunchback, thinning skin, decreasing bone density, and a declining immune system — all in the span of a month.

The researchers do not know whether the accelerated aging-like effects of losing the gene, called SIRT6, relate to its role in DNA repair. Nor do they know whether the degenerative effects are relevant to the natural aging process. However, they said, the discovery offers an intriguing new model for studying DNA repair, as well as its possible role in aging-related degeneration.

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A group, led by Dr. Paul Frenette at Mount Sinai School of Medicine, found that the sympathetic–or “fight or flight” branch–of the nervous system plays a critical role in coaxing bone marrow stem cells into the bloodstream. Bone marrow cells known as hematopoietic stem cells are the source for blood and immune cells.

New study by Mount Sinai researchers may lead to improved stem cell therapies for patients with compromised immune systems due to intensive cancer therapy or autoimmune disease. Read the rest of this entry »

Single walled carbon nanotubes wrapped with DNA can be placed inside living cells and detect trace amounts of harmful contaminants using near infrared light, report researchers at the University of Illinois at Urbana-Champaign. Their discovery opens the door to new types of optical sensors and biomarkers that exploit the unique properties of nanoparticles in living systems.

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Two studies in the Jan. 27, 2006 issue of Cell have yielded evidence that could prove a boon for stem cell therapies aimed at patients with Parkinson’s disease and those with compromised immune systems due to intensive cancer therapy or autoimmune disease, according to researchers. The basic findings in mice revealed critical factors that determine the fate of one type of nerve cell progenitor and that set bone marrow stem cells into action.

Researchers at the Karolinska Institutet in Sweden discovered a “master determinant” that turns embryonic stem cells into bona fide dopamine neurons, brain cells that degenerate in those with Parkinson’s disease. The findings hold promise for the future of cell replacement therapy for the debilitating and incurable disease characterized by tremors, said study authors Thomas Perlmann and Johan Ericson. The results also underscore the general importance of a thorough understanding of development for producing authentic cells of a desired type from stem cells.
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In an article appearing online today in the journal Nature Methods, researchers at the EPFL (Ecole Polytechnique Fédérale de Lausanne) unveil a powerful new tool that will facilitate genetic research and open up new avenues for the clinical treatment of genetic disease.

An all-in-one tool like this – efficiently combining techniques that each previously required separate delivery – will likely see wide use in genetic research and in clinical gene therapy applications. It is particularly applicable for use in stem cells, embryonic cells and tissues and organs that are amenable to genetic transduction.
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When activated, a specific protein in the brain enhances long-term storage of fearful memories and strengthens previously established fearful memories, Yale School of Medicine researchers report this week in Nature Neuroscience.

“This report is the first to demonstrate evidence of enhancements in memory reconsolidation in the brain,” said the senior author, Jane Taylor, associate professor in the Department of Psychiatry. “Understanding these molecular mechanisms may provide critical insights into psychiatric disorders.”
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Adult stem cells may be free of the ethical concerns that hamper embryonic stem cell research, but they still pose formidable scientific challenges. Chief among these is the doggedness with which adult stem cells differentiate into mature tissue the moment they’re isolated from the body. This makes it nearly impossible for researchers to multiply them in the laboratory. And because adult stem cells are so rare, that makes it difficult to use them for treating disease.

Now, researchers in the lab of Whitehead Institute Member and MIT professor of biology Harvey Lodish have discovered a way to multiply an adult stem cell 30-fold, an expansion that offers tremendous promise for treatments such as bone marrow transplants and perhaps even gene therapy.

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Researchers from Germany announce they have finished the first complete analysis of the “molecular machines” in one of biology’s most important model organisms: S. cerevisiae (baker’s yeast).

The study combined a method of extracting complete protein complexes from cells (tandem affinity purification, developed in 2001 by Bertrand Séraphin at EMBL), mass spectrometry and bioinformatics to investigate the entire protein household of yeast, turning up 257 machines that had never been observed. It also revealed new components of nearly every complex already known.
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This week’s cool blog site is Al Fin .The primary interest of the author is to see best of humanity survives long enough to reach the next level.

The site features cool new technological advances, many in biology, in a unique and clean fashion, which are occasionally accompanied with visually stimulating pictures. Most posts also contain well written commentaries that provide interesting perspectives to stories.

Al Fin also has one of the most extensive and well organized links of interest I have seen. There are many interesting links from machine intelligence to outer space, meticulously found and listed.

Al Fin is a great blog that I highly recommend.

Scientists at Virginia Tech have developed a single-step process for creating nonwoven fibrous mats from a small organic molecule – creating a new nanoscale material with potential applications where biocompatible materials are required, such as scaffolds for tissue growth and drug delivery. Read the rest of this entry »

When a human looks at a number, letter or other shape, neurons in various areas of the brain’s visual center respond to different components of that shape, almost instantaneously fitting them together like a puzzle to create an image that the individual then “sees” and understands, researchers at The Johns Hopkins University report.
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Researchers have identified a new and unusual tumor suppressor gene that may be important in cancers of the lung and head and neck. The study shows that restoring the inactivated gene can slow the growth of tumor cells.

The gene, known as TCF21, is silenced in tumor cells through a chemical change known as DNA methylation, a process that is potentially reversible.
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Just imagine listening to someone talk and also hearing the buzz of the overhead lights, the hum of your computer and the muffled conversation down the hallway. To focus on the person speaking to you, your brain clearly can’t give equal weight to all incoming sensory information. It has to attend to what is important and ignore the rest.

Two scientists at the Stanford University School of Medicine have taken a big step toward sorting out how the brain accomplishes this task. In the Jan. 19 issue of Nature, the researchers show that a mechanism for prioritizing information – previously reported only in primates – is also used by birds.
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Non-coding regions of the genome – those that don’t code for proteins – are now known to include important elements that regulate gene activity. Among those elements are microRNAs, tiny, recently discovered RNA molecules that suppress gene expression. Increasing evidence indicates a role for microRNAs in the developing nervous system, and researchers from Children’s Hospital Boston now demonstrate that one microRNA affects the development of synapses – the points of communication between brain cells that underlie learning and memory.

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Regular exercise is associated with a delay in the onset of dementia and Alzheimer’s disease, according to a University of Washington study. The study–the most definitive investigation of exercise and dementia to date–also found that the more frail a person is, the more he or she may benefit from exercise.

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Scientists generally agree that all cloned animals are biologically flawed. But they don’t agree about what that means for stem cells derived from cloned embryos, the basis for therapeutic cloning.

Also known as somatic cell nuclear transfer, therapeutic cloning is a promising approach to create individually customized cellular therapies for treating certain disorders. Demonstrated in mice but not in humans, it begins with stem cells derived from a cloned embryo. But if cloned embryos can’t produce normal organisms, how can they produce normal stem cells?

Analyzing the complete gene-expression profiles of both cloned and fertilization-derived stem cells in mice, scientists at Whitehead Institute for Biomedical Research now have concluded that the two are, in fact, indistinguishable.
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A team of scientists at the Weizmann Institute of Science, has come up with new findings that may have implications in delaying and slowing down cognitive deterioration in old age. The basis for these developments is, published today in the February issue of Nature Neuroscience, that immune cells contribute to maintaining the brain’s ability to maintain cognitive ability and cell renewal throughout life.
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A component of many proteins has been found to constitute one of the most powerful and resilient molecular “springs” in nature, researchers have discovered.

The scientists say their discovery could lead to a new understanding of mechanical processes within the living cell. The discovery also could provide potent nanoscale “shock absorbers” or “gate-opening springs” in tiny nanomachines.

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Researchers have found that the curry spice turmeric holds real potential for the treatment and prevention of prostate cancer, particularly when combined with certain vegetables.

The scientists tested turmeric, also known as curcumin, along with phenethyl isothiocyanate (PEITC), a naturally occurring substance particularly abundant in a group of vegetables that includes watercress, cabbage, winter cress, broccoli, Brussels sprouts, kale, cauliflower, kohlrabi and turnips. PEITC and curcumin, alone or in combination, demonstrate significant cancer-preventive qualities in laboratory mice, and the combination of PEITC and curcumin could be effective in treating established prostate cancers.
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Researchers knew that a subset of kidney cancer patients responded well to an experimental targeted therapy, but they didn’t know why. If they could determine the mechanism behind the response, they would be able to predict which patients would respond and personalize their treatment accordingly.

Extrapolating from the clinical responses, scientists at UCLA uncovered the cascade of molecular events by which the cancer cells in a subset of patients became sensitized to the experimental drug CCI-779. Armed with this information, UCLA researchers are developing a test to identify which patients will benefit from receiving CCI-779.

The research, published this month in Nature Medicine, takes researchers a step closer to personalized medicine – treating cancer patients not with a one-size-fits-all therapy but with a treatment based on the specific molecular signature of their cancer cells.

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Researchers at The University of Texas M. D. Anderson Cancer Center say they have jumped a significant hurdle in the use of RNA interference (RNAi), believed by many to be the ultimate tool to both decode the function of individual genes in the human genome and to treat disease.

Reporting in the journal Genes and Development, investigators have developed a simple way to use the RNAi approach to silence a selected gene in a specific tissue in a mouse to determine the function of that targeted gene.

This is another major breakthrough related to RNA interferene that was the topic of my prior post.
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This is first in series of mini-commentaries that I hope will provide background and context to the importance some of the major discoveries that I have posted.

This week’s feature is RNA interference (RNAi). There is a great mini-tutorial about RNAi at PBS Nova site. The the wiki on RNAi is also useful for providing simple background.

RNAi is arguably the most important molecular biology discovery of the last decade and was declared breakthrough of the year by Science magazine in 2002. This technology has the potential to transform medicine but providing us the tool to regulate expression of genes. RNAi mediated treatments may also become the next big thing in biotech.

I recently reported about the structure of the key RNAi component, Dicer protein. This story revealed new insight into the intricate mechanism of RNAi. Several other discoveries posted here also involved RNAi.

This is first in series, where I will mention blogs or web links I find interesting.

This week’s recommended blog site is Technological Event Horizon. The author is an independent philosopher, Micah Glasser, and writes thoughtful and sometimes philosophical opinions on accelerated technological advancement.

The title of recent blog was “When Machines Transcend the Mechanical” where Micah argued that humans will not transcend biology, per se. Rather machines will transcend the mechanical. I agreed with this argument.
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A team of scientists has peeled back some of the mystery of how cells are able to turn off genes selectively to control critical events of development. The new insights arise from the first clear molecular images of the structure of Dicer, an enzyme that enables cells to dissect genetic material precisely.

The findings provides scientists with new information about a mechanism that enables cells to silence genes, a process that governs key developmental events ranging from brain development to stem cell differentiation.

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Photodynamic therapy (PDT), which uses a light-sensitive chemical known as a photosensitizer to produce cell-killing “reactive oxygen,” has become an important option for the treatment of esophageal cancer and non-small cell lung cancer. Current photosensitizers, however, produce significant side effects, including sensitivity to the sun, that limits their wider use in treating cancer.

In an attempt to both eliminate those side effects and increase the anticancer activity of photosensitizers, researchers from MIT-Harvard Center of Cancer Nanotechnology Excellence, has developed a polymer nanoparticle to ferry photosensitizers into cancer cells, where they can then unleash their potent cell-killing effects.

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Harvard University biologists have identified a molecular pathway active in neurons that interacts with RNA to regulate the formation of long-term memory in fruit flies. The same pathway is also found at mammalian synapses, and could eventually present a target for new therapeutics to treat human memory loss.

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Eating a very low-calorie yet nutritionally balanced diet is good for your heart. Studying heart function in members of an organization called the Caloric Restriction Society, investigators at Washington University School of Medicine in St. Louis found that their hearts functioned like the hearts of much younger people.

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A protein that guides the early development of creatures as diverse as fruit flies and humans also plays a role in regulating fat and bone formation in adult organisms, researchers at UT Southwestern Medical Center have discovered.

The findings, reported in the January issue of the journal Cell Metabolism, open an avenue for potential therapy in humans for obesity, diabetes, osteoporosis and lipodystrophy, a disorder characterized by a selective loss of body fat.
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A quarter century after they discovered it, researchers have identified the job of one of the most common DNA-damage response proteins. The enzyme has puzzled scientists because it is present in nearly every organism, which suggests that it is crucial to life, and yet, in laboratory experiments, its function has remained a mystery.

The discovery suggests that the enigmatic enzyme known as DinB DNA polymerase is specialized for proficient and accurate replication of a particular kind of damaged DNA, reports Graham Walker, an HHMI professor at the Massachusetts Institute of Technology.
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Based on overwhelmingly positive comments and constructive critiques I received over the last several weeks, I will try to implement some additions here that I hope will be an improvement. Of course, this will depend on finding sufficient time during my extremely busy schedule.

One of the changes requested was to link the stories to the original scientific articles, if they are published results. I will try to link most of the discoveries to Pubmed database abstracts, which then links to the original journal articles.

Second, I will try to post comments/opinions once a week, summarizing why I think the stories posted that week are important and try to add my personal input. I could also include some of the comments made to these stories, which could further enhance the discussions.

Finally, again on weekly basis, I will try to either feature the web or blog sites that I like or link to commentary/opinion blogs related to the theme of this site. In addition, you can email me if you like to write a commentary/opinion article that you would like to be posted here. I will try my best to accomodate that if it is within the context of the mission of biosingularity.

Please continue your input and wish everyone happy new year.

Scientists have developed a new technique for crystallising proteins, a discovery which could help speed up the development of new medicines and treatments.

Crystallisation is the process which converts materials, such as proteins, into three dimensional crystals, thus enabling their atomic structure to be studied. The three dimensional structure of the crystals indicates the proteins function, and from this, researchers hope to be able to develop more effective treatments.
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Chemists have identified a new approach for the possible treatment of Alzheimer’s disease that they say has the potential to destroy beta-amyloid fibrils and plaque — hypothesized to contribute to the mental decline of Alzheimer’s patients. The researchers say the new technique, which they call a type of “molecular surgery,” could halt or slow the disease’s progress without harming healthy brain cells.

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Scientists from The Walter and Eliza Hall Institute, using a mouse model, have discovered the rare stem cell that drives the formation of all breast tissue. This discovery lays an important foundation for understanding how normal breast tissue develops. The identification of the breast stem cell is also likely to provide clues about how breast cancer develops and how rogue cells evade current therapies.

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A team of cancer researchers has shown that a gene commonly lost during neuroblastoma tumor formation, one of the most aggressive cancers in babies and children, is in fact a “metastasis suppressor” gene. The researchers now also describe how the gene, caspase 8, works.

The findings, published in the January 5 issue of the journal Nature, provide important new insights into the biology of metastatic disease and lay the necessary groundwork for developing targeted therapies designed to halt the spread of neuroblastoma, and possibly other cancers.

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For the more than 18 million Americans who suffer from depressive illnesses, the best pharmacological treatments are those that increase levels of serotonin, the brain chemical that regulates mood, sleep and memory. New research by an international team of scientists, led by Rockefeller University researchers in Nobel prize winner Paul Greengard’s laboratory, shows that a gene called p11 is closely related to serotonin transmission in the brain — and may play a key role in determining a person’s susceptibility to depression.

The newly discovered link between depression and the serotonin system, reported in the January 6 issue of the journal Science, could lead to new treatments for these mental disorders.

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Physicists from the University of Oxford have designed the first structurally robust, self-assembling DNA building blocks. The DNA tetrahedra, 10,000,000,000 (ten thousand million) of which could fit on the head of a pin, could lead to the manufacture of complex nanostructures such as powerful electrical circuits. Read the rest of this entry »

Scientists working at the WiCell Research Institute, a private laboratory affiliated with the University of Wisconsin-Madison, have developed a precisely defined stem cell culture system free of animal cells and used it to derived two new human embryonic stem cell lines.

The new work, which is reported at Jan. 1, 2006 issue of the journal Nature Biotechnology, helps move stem cells a small step closer to clinical reality by completely ridding the culture medium in which they are grown of animal products that could harbor viruses or other deleterious agents.

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Synthetic Genomics, Inc., a company founded by the genome sequencing pioneer Dr. J. Craig Venter, is developing new scientific processes to enable industry to design and test desired genetic modifications. Using the genome as a bio-factory, a custom designed, modular “cassette” system will be developed so that the organism executes specific molecular functions. Synthetically produced organisms with reduced or reoriented metabolic needs will enable new, powerful, and more direct methods of bio-engineered industrial production.

According to Dr. Venter: “Work in creating a synthetic chromosome/genome will give us a better understanding of basic cellular processes. Genome composition, regulatory circuits, signaling pathways and numerous other aspects of organism gene and protein function will be better understood through construction of a synthetic genome. Not only will this basic research lead to better understanding of these pathways and components in the particular organisms, but also better understanding of human biology. The ability to construct synthetic genomes may lead to extraordinary advances in our ability to engineer microorganisms for many vital energy and environmental purposes.”

This is a very exciting new step towards biosingularity. Dr. Venter is a true visionary who has been relentlessly pushing the technology to decode the complex program of biological systems.
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