Bioengineers Create Genetic ‘Bio-Transistor’ – Will Permit Cell Programming, Disease Monitoring

Bioengineers Create Genetic ‘Bio-Transistor’ – Will Permit Cell Programming, Disease Monitoring (via Planetsave)

Stanford University scientists working in the new discipline of synthetic biology have devised a “genetic transistor” that mimics the classic three terminal transistor found in many electronic devices and computers. The new device is intended to have broad applications for a variety of “cellular…


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Stash of stem cells found in a human parasite

A composite image of a scanning electron micrograph of a pair of male and female Schistosoma mansoni with the outer tegument (skin) of the male worm “peeled back” (digitally) to reveal the stem cells (orange) underneath. (Credit: Jim Collins, Ana Vieira and Phillip Newmark, Howard Hughes Medical Institute and University of Illinois at Urbana-Champaign)

Feb. 22, 2013 — The parasites that cause schistosomiasis, one of the most common parasitic infections in the world, are notoriously long-lived. Researchers have now found stem cells inside the parasite that can regenerate worn-down organs, which may help explain how they can live for years or even decades inside their host.

Schistosomiasis is acquired when people come into contact with water infested with the larval form of the parasitic worm Schistosoma, known as schistosomes. Schistosomes mature in the body and lay eggs that cause inflammation and chronic illness. Schistosomes typically live for five to six years, but there have been reports of patients who still harbor parasites decades after infection.

According to new research from Howard Hughes Medical Institute (HHMI) investigator Phillip Newmark, collections of stem cells that can help repair the worms’ bodies as they age could explain how the worms survive for so many years. The new findings were published online on February 20, 2013, in the journal Nature.

The stem cells that Newmark’s team found closely resemble stem cells in planaria, free-living relatives of the parasitic worms. Planaria rely on these cells, called neoblasts, to regenerate lost body parts. Whereas most adult stem cells in mammals have a limited set of possible fates—blood stem cells can give rise only to various types of blood cells, for example —planarian neoblasts can turn into any cell in the worm’s body under the right circumstances.

Newmark’s lab at the University of Illinois at Urbana-Champaign has spent years focused on planaria, so they knew many details about planarian neoblasts —what they look like, what genes they express, and how they proliferate. They also knew that in uninjured planarians, neoblasts maintain tissues that undergo normal wear and tear over the worm’s lifetime.

“We began to wonder whether schistosomes have equivalent cells and whether such cells could be partially responsible for their longevity,” says Newmark.

Following this hunch, and using what they knew about planarian neoblasts, post-doctoral fellow Jim Collins, Newmark, and their colleagues hunted for similar cells in Schistosoma mansoni, the most widespread species of human-infecting schistosomes.

Their first step was to look for actively dividing cells in the parasites. To do this, they grew worms in culture and added tags that would label newly replicated DNA as cells prepare to divide; this label could later be visualized by fluorescence. Following this fluorescent tag, they saw a collection of proliferating cells inside the worm’s body, separate from any organs.

The researchers isolated those cells from the schistosomes and studied them individually. They looked like typical stem cells, filled with a large nucleus and a small amount of cytoplasm that left little room for any cell-type-specific functionality. Newmark’s lab observed the cells and found that they often divided to give rise to two different cells: one cell that continued dividing, and another cell that did not.

“One feature of stem cells,” says Newmark, “is that they make more stem cells; furthermore, many stem cells undergo asymmetric division.” The schistosomes cells were behaving like stem cells in these respects. The other characteristic of stem cells is that they can differentiate into other cell types.

To find out whether the schistosome cells could give rise to multiple types of cells, Newmark’s team added the label for dividing cells to mice infected with schistosomes, waited a week, and then harvested the parasites to see where the tag ended up. They could detect labeled cells in the intestines and muscles of the schistosomes, suggesting that stem cells incorporating the labels had developed into both intestinal and muscle cells.

Years of previous study on planarians by many groups paved the way for this type of work on schistosomes, Newmark says.

“The cells we found in the schistosome look remarkably like planarian neoblasts. They aren’t associated with any one organ, but can give rise to multiple cell types. People often wonder why we study the ‘lowly’ planarian, but this work provides an example of how basic biology can lead you, in unanticipated and exciting ways, to findings that are directly relevant to important public health problems.”

Newmark says the stem cells aren’t necessarily the sole reason schistosome parasites survive for so many years, but their ability to replenish multiple cell types likely plays a role. More research is needed to find out how the cells truly affect lifespan, as well as what factors in the mouse or human host spur the parasite’s stem cells to divide, and whether the parasites maintain similar stem cells during other stages of their life cycle.

The researchers hope that with more work, scientists will be able to pinpoint a way to kill off the schistosome stem cells, potentially shortening the worm’s lifespan and treating schistosome infections in people.

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Newt Finding Might Set Back Efforts to Regrow Human Limbs: Scientific American

Unique proteins in these amphibians cast doubt on the existence of any latent potential for limb regeneration

By Zoe Cormier and Nature magazine

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The Eastern, or red-spotted, newt may have evolved the ability to regenerate organs and limbs in relatively recent times Image: Flickr/StoneHorse Studios

The ability of some animals to regenerate tissue is generally considered to be an ancient quality of all multicellular animals. A genetic analysis of newts, however, now suggests that it evolved much more recently.

Tiny and delicate it may be, but the red spotted newt (Notophthalmus viridescens) has tissue-engineering skills that far surpass the most advanced biotechnology labs. The newt can regenerate lost tissue, including heart muscle, components of its central nervous system and even the lens of its eye.

Doctors hope that this skill relies on a basic genetic program that is common — albeit often in latent form — to all animals, including mammals, so that they can harness it in regenerative medicine. Mice, for instance, are able to generate new heart cells after myocardial injury.

The newt study, by Thomas Braun at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, Germany, and his colleagues, suggest that it might not be so simple.

Attempts to analyze the genetics of newts in the same way as for humans, mice and flies have so far been hampered by the enormous size of the newt genome, which is ten times larger than our own. Braun and his colleagues therefore looked at the RNA produced when genes are expressed — known as the transcriptome — and used three analytical techniques to compile their data.

The team compiled the first catalogue of all the RNA transcripts expressed in N. viridescens, looking at both primary and regenerated tissue in the heart, limbs and eyes of both embryos and larvae.

The researchers found more than 120,000 RNA transcripts, of which they estimate 15,000 code for proteins. Of those, 826 were unique to the newt. What is more, several of those sequences were expressed at different levels in regenerated tissue than in primary tissue. Their results are published in Genome Biology.

Modern or ancestral?
The findings add to existing evidence that the ability evolved recently, says Jeremy Brockes of University College London, whose research provided the first evidence that regenerating tissue in salamanders express proteins that are not found in other vertebrates.

“I no longer believe that there is an ancestral program that is waiting to be reawakened,” Brockes says. “However, I absolutely do believe it’s possible to coax mammal tissues into regenerating to a greater degree with the lessons we learn from newts.”

But saying that the trait is either ancestral or recent is probably too “black and white”, says Elly Tanaka of the Center for Regenerative Therapies in Dresden, Germany. The truth, she says, could be somewhere in the middle. “It may in fact be that regeneration is ancestral, but that newts have species-specific adaptations that allow it to have such spectacular regenerative capacities compared with other vertebrates.”

Moreover, Tanaka adds, scientists would do well to look for more grey zones in the potential for harnessing the regenerative capacities of newts (and of other animals, such as fish). Rather than focusing on spectacular, but perhaps unlikely, scenarios in which amputees could regrow entire limbs, researchers should instead focus on more plausible options, such as improving the healing of scars and burns or increasing the speed of organ regeneration.

This article is reproduced with permission from the magazine Nature. The article was first published on February 21, 2013.

Calcium is initial trigger in our immune response to healing

“White blood cells are a little like ‘Jeckyll and Hyde’ in that they help us heal but are also the reason behind why we scar so we really need to know how they are regulated at wounds in order to learn how to control their behaviours for future therapeutic intervention,” said Paul Martin. (Credit: © Vivian Seefeld / Fotolia)

Feb. 14, 2013 — For the first time scientists studying the cellular processes underlying the body’s response to healing have revealed how a flash of calcium is the very first step in repairing damaged tissue. The findings, published in Current Biology, could lead to new therapies that speed up the healing process following injury or surgery.

Until recently, very little was known about how damaged tissue activates and attracts the first white blood cells to the wound — the first stage in the healing process. However, researchers from the University of Bristol’s School of Biochemistry in collaboration with a team from the University of Bath, have shown that the very first trigger in this process is a flash of calcium which spreads like a wave back from the wound edge through gap junctions that connect all the cells.

This flash of calcium signal goes on to activate an enzyme known as DUOX that synthesises hydrogen peroxide, which, in turn, attracts the first white blood cells to the wound. This white blood cell invasion, which is initiated during our inflammatory responses, is needed to kill off invading microbes and stop the onset of septicaemia following tissue damage.

The findings indicate that the wound-induced calcium flash represents the earliest identified signal following wounding and might therefore orchestrate the rapid recruitment of immune cells.

To assess the impact of a reduced calcium flash upon the inflammatory response the team used Drosophila (fruit fly) embryos because they are translucent which makes it easy to image the inflammatory response and because of their simple genetics. The team found that blocking the calcium flash inhibited H2O2 release at the wound site leading to a reduction in the number of immune cells migrating to the wound.

Paul Martin, Professor of Cell Biology and an expert in wound healing at the University, said: “White blood cells are a little like ‘Jeckyll and Hyde’ in that they help us heal but are also the reason behind why we scar so we really need to know how they are regulated at wounds in order to learn how to control their behaviours for future therapeutic intervention.”

Will Razzell, the lead PhD researcher on this study, added: “We are more than ever understanding the pathways that lead to immune cell attraction to wounds. As calcium represents the immediate inflammatory signal, we now have a good foundation to investigate this complicated process further.”

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Modifications of a nanoparticle can change chemical interactions with cell membranes


In a recent article published along with cover art engineers showed how simple shape and charge modifications of a nanoparticle can cause tremendous changes in the chemical interactions between the nanoparticle and a cell membrane. (Credit: Image courtesy of Syracuse University)

Jan. 23, 2013 — Researchers at Syracuse University’s Department of Biomedical and Chemical Engineering at L.C. Smith College of Engineering and Computer Science are studying the toxicity of commonly used nanoparticles, particles up to one million times smaller than a millimeter that could potentially penetrate and damage cell membranes.

In a recent article published along with cover art in the journal Langmuir, researchers Shikha Nangia, assistant professor of biomedical and chemical engineering (BMCE), and Radhakrishna Sureshkumar, Department Chair of BMCE and professor of physics, showed how simple shape and charge modifications of a nanoparticle can cause tremendous changes in the chemical interactions between the nanoparticle and a cell membrane.

Nanomaterials, which are currently being used as drug carriers, also pose a legitimate concern, since no universal standards exist to educate and fully protect those who handle these materials. Nanoparticles are comparable to chemicals in their potential threat because they could easily penetrate the skin or be inhaled.

“Nanotechnology has immense potential that is starting to be being realized; a comprehensive understanding of toxicity of nanoparticles will help develop better safe handling procedures in nanomanufacturing and nano-biotechnology” says Sureshkumar and Nangia, In addition, the toxicity levels of various nanoparticles can be used to our advantage in targeting cancer cells and absorbing radiation during cancer therapy. Nanotoxicity is becoming a major concern as the use of nanoparticles in imaging, therapeutics, diagnostics, catalysis, sensing and energy harvesting continues to grow dramatically.

This research project has taken place over the past year utilizing a state of the art 448 core parallel computer nicknamed “Prophet” housed in Syracuse University’s Green Data Center. The research was funded by the National Science Foundation.

Langmuir is a notable, interdisciplinary journal of American Chemical Society publishing articles in: colloids, interfaces, biological interfaces, nano-materials, electrochemistry and devices and applications.

Editing genome with high precision: New method to insert multiple genes in specific locations, delete defective genes

Jan. 3, 2013 — Researchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and to develop new therapies, among other potential applications.

To create their new genome-editing technique, the researchers modified a set of bacterial proteins that normally defend against viral invaders. Using this system, scientists can alter several genome sites simultaneously and can achieve much greater control over where new genes are inserted, says Feng Zhang, an assistant professor of brain and cognitive sciences at MIT and leader of the research team.

“Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,” says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

Zhang and his colleagues describe the new technique in the Jan. 3 online edition of Science. Lead authors of the paper are graduate students Le Cong and Ann Ran.

Early efforts

The first genetically altered mice were created in the 1980s by adding small pieces of DNA to mouse embryonic cells. This method is now widely used to create transgenic mice for the study of human disease, but, because it inserts DNA randomly in the genome, researchers can’t target the newly delivered genes to replace existing ones.

In recent years, scientists have sought more precise ways to edit the genome. One such method, known as homologous recombination, involves delivering a piece of DNA that includes the gene of interest flanked by sequences that match the genome region where the gene is to be inserted. However, this technique’s success rate is very low because the natural recombination process is rare in normal cells.

More recently, biologists discovered that they could improve the efficiency of this process by adding enzymes called nucleases, which can cut DNA. Zinc fingers are commonly used to deliver the nuclease to a specific location, but zinc finger arrays can’t target every possible sequence of DNA, limiting their usefulness. Furthermore, assembling the proteins is a labor-intensive and expensive process.

Complexes known as transcription activator-like effector nucleases (TALENs) can also cut the genome in specific locations, but these complexes can also be expensive and difficult to assemble.

Precise targeting

The new system is much more user-friendly, Zhang says. Making use of naturally occurring bacterial protein-RNA systems that recognize and snip viral DNA, the researchers can create DNA-editing complexes that include a nuclease called Cas9 bound to short RNA sequences. These sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA.

This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut.

Each of the RNA segments can target a different sequence. “That’s the beauty of this — you can easily program a nuclease to target one or more positions in the genome,” Zhang says.

The method is also very precise — if there is a single base-pair difference between the RNA targeting sequence and the genome sequence, Cas9 is not activated. This is not the case for zinc fingers or TALEN. The new system also appears to be more efficient than TALEN, and much less expensive.

The new system “is a significant advancement in the field of genome editing and, in its first iteration, already appears comparable in efficiency to what zinc finger nucleases and TALENs have to offer,” says Aron Geurts, an associate professor of physiology at the Medical College of Wisconsin. “Deciphering the ever-increasing data emerging on genetic variation as it relates to human health and disease will require this type of scalable and precise genome editing in model systems.”

The research team has deposited the necessary genetic components with a nonprofit called Addgene, making the components widely available to other researchers who want to use the system. The researchers have also created a website with tips and tools for using this new technique.

Engineering new therapies

Among other possible applications, this system could be used to design new therapies for diseases such as Huntington’s disease, which appears to be caused by a single abnormal gene. Clinical trials that use zinc finger nucleases to disable genes are now under way, and the new technology could offer a more efficient alternative.

The system might also be useful for treating HIV by removing patients’ lymphocytes and mutating the CCR5 receptor, through which the virus enters cells. After being put back in the patient, such cells would resist infection.

This approach could also make it easier to study human disease by inducing specific mutations in human stem cells. “Using this genome editing system, you can very systematically put in individual mutations and differentiate the stem cells into neurons or cardiomyocytes and see how the mutations alter the biology of the cells,” Zhang says.

In the Science study, the researchers tested the system in cells grown in the lab, but they plan to apply the new technology to study brain function and diseases.

The research was funded by the National Institute of Mental Health; the W.M. Keck Foundation; the McKnight Foundation; the Bill & Melinda Gates Foundation; the Damon Runyon Cancer Research Foundation; the Searle Scholars Program; and philanthropic support from MIT alumni Mike Boylan and Bob Metcalfe, as well as the newscaster Jane Pauley.

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