31 Mart 2014 Pazartesi

Self-healing bioengineered muscle grown in the laboratory

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Bioengineers have grown living skeletal muscle that looks a lot like the real thing. It contracts powerfully and rapidly, integrates into mice quickly, and for the first time, demonstrates the ability to heal itself both inside the laboratory and inside an animal.


Self-healing engineered muscle grown in the laboratory



Long, colorful strands of engineered muscle fiber have been stained to observe growth after implantation into a mouse. Credit: Duke University



The study conducted at Duke University tested the bioengineered muscle by literally watching it through a window on the back of living mouse. The novel technique allowed for real-time monitoring of the muscle’s integration and maturation inside a living, walking animal.


Both the lab-grown muscle and experimental techniques are important steps toward growing viable muscle for studying diseases and treating injuries, said Nenad Bursac, associate professor of biomedical engineering at Duke.


The results appear the week of March 25 in the Proceedings of the National Academy of Sciences Early Edition.


“The muscle we have made represents an important advance for the field,” Bursac said. “It’s the first time engineered muscle has been created that contracts as strongly as native neonatal skeletal muscle.”

Through years of perfecting their techniques, a team led by Bursac and graduate student Mark Juhas discovered that preparing better muscle requires two things—well-developed contractile muscle fibers and a pool of muscle stem cells, known as satellite cells.


makingmuscle2



This series of images shows the destruction and subsequent recovery of engineered muscle fibers that had been exposed to a toxin found in snake venom. This marks the first time engineered muscle has been shown to repair itself after implantation into a living animal.



Every muscle has satellite cells on reserve, ready to activate upon injury and begin the regeneration process. The key to the team’s success was successfully creating the microenvironments—called niches—where these stem cells await their call to duty.


“Simply implanting satellite cells or less-developed muscle doesn’t work as well,” said Juhas. “The well-developed muscle we made provides niches for satellite cells to live in, and, when needed, to restore the robust musculature and its function.”


To put their muscle to the test, the engineers ran it through a gauntlet of trials in the laboratory. By stimulating it with electric pulses, they measured its contractile strength, showing that it was more than 10 times stronger than any previous engineered muscles. They damaged it with a toxin found in snake venom to prove that the satellite cells could activate, multiply and successfully heal the injured muscle fibers.


makingmuscle3



This series of images shows the progress of veins slowly growing into implanted engineered muscle fibers.



With the help of Greg Palmer, an assistant professor of radiation oncology in the Duke University School of Medicine, the team inserted their lab-grown muscle into a small chamber placed on the backs of live mice. The chamber was then covered by a glass panel. Every two days for two weeks, Juhas imaged the implanted muscles through the window to check on their progress.


By genetically modifying the muscle fibers to produce fluorescent flashes during calcium spikes—which cause muscle to contract—the researchers could watch the flashes become brighter as the muscle grew stronger.


“We could see and measure in real time how blood vessels grew into the implanted muscle fibers, maturing toward equaling the strength of its native counterpart,” said Juhas.

The engineers are now beginning work to see if their biomimetic muscle can be used to repair actual muscle injuries and disease.


“Can it vascularize, innervate and repair the damaged muscle’s function?” asked Bursac. “That is what we will be working on for the next several years.”



Story Source:


The above story is based on materials provided by University of Duke University, Ken Kingery.


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Major breakthrough in stem cell manufacturing technology

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Scientists at The University of Nottingham have developed a new substance which could simplify the manufacture of cell therapy in the pioneering world of regenerative medicine.


Cell therapy is an exciting and rapidly developing area of medicine in which stem cells have the potential to repair human tissue and maintain organ function in chronic disease and age-related illnesses. But a major problem with translating current successful research into actual products and treatments is how to mass-produce such a complex living material.


Major breakthrough in stem cell manufacturing technology



Kevin Shakesheff, PhD, Head of The University of Nottingham’s School of Pharmacy and Professor of Drug Delivery and Tissue Engineerin



There are two distinct phases in the production of stem cell products; proliferation (making enough cells to form large tissue) and differentiation (turning the basic stem cells into functional cells). The material environment required for these two phases are different and up to now a single substance that does both jobs has not been available.


Now a multi-disciplinary team of researchers at Nottingham has created a new stem cell micro-environment which they have found has allowed both the self-renewal of cells and then their evolution into cardiomyocyte (heart) cells. The material is a hydrogel containing two polymers – an alginate-rich environment which allows proliferation of cells with a simple chemical switch to render the environment collagen-rich when the cell population is large enough. This change triggers the next stage of cell growth when cells develop a specific purpose.


Major priority


Professor of Advanced Drug Delivery and Tissue Engineering, Kevin Shakesheff, said:


“Our new combination of hydrogels is a first. It allows dense tissue structures to be produced from human pluripotent stem cells (HPSC) in a single step process never achieved before. The discovery has important implications for the future of manufacturing in regenerative medicine. This field of healthcare is a major priority for the UK and we are seeing increasing investment in future manufacturing processes to ensure we are ready to deliver real treatments to patients when HPSC products and treatments go to trial and become standard.”


The research, Combined hydrogels that switch human pluripotent stem cells from self-renewal to differentiation, is published in the Proceedings of the National Academy of Sciences (PNAS).


Story Source:

The above story is based on materials provided by University of Nottingham, Emma Rayner.


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Experts create intelligent ‘plaster’ to monitor patients

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Medical engineers said Sunday they had created a device the size of a plaster which can monitor patients by tracking their muscle activity before administering their medication.


Experts create intelligent 'plaster' to monitor patients



High performance multifunctional wearable electronics integrated with nanoparticles are conformally attached to the skin for the diagnosis and therapy of motion-related neurological disorders. The image shows the multifunctional wearable devices partially peeled away from the skin. Credit: Donghee Son and Jongha Lee



Methods for monitoring so-called “movement disorders” such as epilepsy and Parkinson’s disease have traditionally included video recordings or wearable devices, but these tend to be bulky and inflexible.

The new gadget, which is worn on the skin, looks like a Band-Aid but uses nanotechnology—in which building blocks as small as atoms and molecules are harnessed to bypass problems of bulkiness and stiffness— to monitor the patient.


Scientists have long hoped to create an unobtrusive device able to capture and store medical information as well as administer drugs in response to the data.


This has proved difficult due to the large amount of onboard electronics and storage space required, high power consumption, and the lack of a mechanism for delivering medicine via the skin.


But although monitoring helps to track disease progression and allows better treatment, until now the electronics used in the devices have been hard and brittle, and not ideal for an on-the-skin device.

But the team from South Korea and the United States said they had found the solution in nanomaterials, creating a flexible and stretchable device that resembles an adhesive plaster, about one millimetre (0.04 inches) thick.


Still a prototype, the gadget comprises multiple layers of ultrathin nanomembranes and nanoparticles, the creators wrote in the journal Nature Nanotechnology.


“The team use silicon nanomembranes in the motion sensors, gold nanoparticles in the non-volatile memory and silica nanoparticles, loaded with drugs, in a thermal actuator,” they wrote in a summary.

The study showed that when worn on the wrist of a patient, the patch could measure and record muscle activity.


The recorded data then triggered the release, with the aid of a wafer-thin internal heater, of drugs stored inside the nanoparticles.


A temperature sensor made of silicon nanomembranes monitored the skin temperature to prevent burns during drug delivery.


“This platform overcomes the limitations of conventional wearable devices and has the potential to improve compliance, data quality and the efficacy of current clinical procedures,” the authors wrote.

Dae-Hyeong Kim from the Center for Nanoparticle Research in Seoul said that the device currently needs a microprocessor from an external computer, which could be in a wristwatch, to which it is attached with thin wires.


“But in the future wireless components will be incorporated,” to make the device independent and fully mobile, he told AFP.


Story Source:


The above story is based on materials provided by AFP, Nicholas Tufnell.


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29 Mart 2014 Cumartesi

Cybathlon 2016: first ‘Olympics’ for bionic athletes

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Cybathlon, a Swiss-hosted Olympics for bionic athletes, will be held in October 2016.The Cybathlon is a championship for racing pilots with disabilities (i.e. parathletes) who are using advanced assistive devices including robotic technologies, explains the event’s website.


Cybathlon 2016 first Olympics for bionic athletes


There will be numerous competitions for a broad selection of disciplines that will allow those with powered knee prostheses, wearable arm prostheses, powered exoskeletons, powered wheelchairs, electrically stimulated muscles and novel brain-computer interfaces to take part.


Many different forms of assistive devices will be accepted, including little-known prototypes from research labs as well as familiar commercial products. Each competition will award two medals — one for the pilot and one for the individual(s) responsible for providing the device.


Story Source:


The above story is based on materials provided by Wired, Nicholas Tufnell.


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BIOSTEC 2015

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The purpose of BIOSTEC is to bring together researchers and practitioners, including engineers, biologists, health professionals and informatics/computer scientists, interested in both theoretical advances and applications of information systems, artificial intelligence, signal processing, electronics and other engineering tools in knowledge areas related to biology and medicine.


BIOSTEC 2015



“The Present and Future of Devices for Neural Recording” Dr. Adam Kampff (BIOSTEC 2013)



Dates: 12-15 January 2015

Venue: Lizbon, Portugal

Website: http://www.biostec.org/


Important Dates


Regular Papers

Paper Submission: July 29, 2014

Authors Notification: November 3, 2014

Camera Ready and Registration: November 17, 2014


Position Papers

Paper Submission: September 30, 2014

Authors Notification: November 6, 2014

Camera Ready and Registration: November 17, 2014


Special Sessions

Paper Submission: November 7, 2014

Authors Notification: November 24, 2014

Camera Ready and Registration: December 3, 2014


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Post-Doctoral Research Fellow : Seattle, WA, United States

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A Postdoctoral Research Fellow position is available immediately in the Clinical Research Division of the Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA. The successful applicant will work with Dr. Matthias Stephan (http://ift.tt/1fwKgKa) to explore the fast-developing and highly interdisciplinary field of immunobioengineering for adoptive T-cell therapy.


Stephan Lab



Stephan Lab photo, February 2014



Using next-generation immunomodulatory synthetic materials, the postdoctoral fellow will develop new approaches – beyond existing T-cell-based therapies – to therapeutically manipulate the immune system against cancer.


The successful applicant will fabricate stimulatory biomaterial devices, drug delivery systems and bioactive substances and test their therapeutic potential in preclinical tumor models of adoptive T-cell therapy. The FHCRC provides a highly interactive and supportive environment for junior investigators to grow and develop their future career; it consistently ranks in the top 20 best places to work for postdocs, as surveyed by The Scientist.


Suitable applicants should have a PhD degree in immunology or bioengineering.


The candidate must have a strong knowledge of primary immune cell isolation and culture, flow cytometry, and advanced training in animal procedures such as tail vein injections and the establishment of advanced in vivo murine tumor models. The position further requires a basic understanding of genetic engineering and protein expression. The successful candidate will be a scientifically driven, well organized self-starter. We are a VEVRAA Federal Contractor.


To apply for this position, please CLICK HERE


Job details

Employer: Fred Hutchinson Cancer Research Center

Location:Seattle, WA, United States

Expires: April 27, 2014

Job type: Postdoctoral

Salary: Unspecified

Qualifications: Postgraduate – Doctorate/PhD

Employment type: Permanent

Job hours: Full-time


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Embryonic stem cells: Reprogramming in early embryos

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An Oregon Health & Science University scientist has been able to make embryonic stem cells from adult mouse body cells using the cytoplasm of two-cell embryos that were in the “interphase” stage of the cell cycle. Scientists had previously thought the interphase stage — a later stage of the cell cycle — was incapable of converting transplanted adult cell nuclei into embryonic stem cells.


Embryonic stem cells- Reprogramming in early embryos



Shoukhrat Mitalipov, Ph.D.



The findings by OHSU’s Shoukhrat Mitalipov, Ph.D., and his team could have major implications for the science of generating patient-matched human embryonic stem cells for regenerative medicine. Human embryonic stem cells are capable of transforming into any cell type in the body. Scientists believe stem cell therapies hold promise for someday curing or treating a wide range of diseases and conditions — from Parkinson’s disease to cardiac disease to spinal cord injuries — by replacing cells damaged through injury or illness.


Mitalipov’s findings will be published March 26 in the online edition of Nature. If the new findings in mice hold true for humans, it could significantly help efforts to make rejection-proof human embryonic stem cells for regenerative therapies. That’s because embryonic cells that Mitalipov’s team used for reprogramming — cells in the “interphase” stage — are more accessible than the traditional egg cells that are in short supply. Scientists previously had believed embryonic stem cells were capable of being produced only using the metaphase stage of egg cytoplasm.


Embryonic stem cells can be made using a process called somatic cell nuclear transfer, or SCNT, in which the nucleus from an adult cell is transferred into the cytoplasm of an unfertilized egg cell. The cytoplasmic machinery then “reprograms” that nucleus and cell into becoming an embryonic stem cell capable of transforming to any type of cell in the body.


“It has always been thought that this capacity for reprogramming ended with metaphase,” said Mitalipov, senior scientist at OHSU’s Oregon National Primate Research Center. “Our study shows that this reprogramming capacity remains in the later embryonic cell cytoplasm even during interphase. It looks like the factors continue working and they efficiently reprogram the cells — just as they do in metaphase.”


Many scientists have attempted to reprogram cells by interphase cytoplasm. Mitalipov and his team found success by carefully synchronizing the cell cycles of the adult cell nucleus and the recipient embryonic cytoplasm. Both had to be at an almost identical point in their respective cell cycles for the process to work, Mitalipov said.


“That was the secret,” Mitalipov said. “When we did that matching, then everything worked.”


Mitalipov said the next step to further his research will be to test the process in rhesus macaques.


Mitalipov has become a world scientific leader in embryonic stem cell research and in somatic cell nuclear transfer. He recently was named the director of a newly created research center at OHSU — the Center for Embryonic Cell and Gene Therapy. The center will help Mitalipov and his team accelerate their research, with expanded support from private philanthropy.


Story Source:


The above story is based on materials provided by Oregon Health & Science University, Todd Murphy.


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28 Mart 2014 Cuma

Researchers identify good bacteria that protects against HIV

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Researchers at the University of Texas Medical Branch at Galveston by growing vaginal skin cells outside the body and studying the way they interact with “good and bad” bacteria, think they may be able to better identify the good bacteria that protect women from HIV infection and other sexually transmitted infections.


Researchers identify good bacteria that protects against HIV



Photo Credits: Alexey Kashpersky



The health of the human vagina depends on a symbiotic/mutually beneficial relationship with “good” bacteria that live on its surface feeding on products produced by vaginal skin cells. These good bacteria, in turn, create a physical and chemical barrier to bad bacteria and viruses including HIV.


A publication released today from a team of scientists representing multiple disciplines at UTMB and the Oak Crest Institute of Science in Pasadena, Calif., reports a new method for studying the relationship between the skin cells and the “good” bacteria.


The researchers are the first to grow human vaginal skin cells in a dish in a manner that creates surfaces that support colonization by the complex good and bad communities of bacteria collected from women during routine gynecological exams. The bacteria communities have never before been successfully grown outside a human.


The research group led by Richard Pyles at UTMB reports in the journal PLOS One that by using this model of the human vagina, they discovered that certain bacterial communities alter the way HIV infects and replicates. Their laboratory model will allow careful and controlled evaluation of the complex community of bacteria to ultimately identify those species that weaken the defenses against HIV. Pyles also indicated that this model “will provide the opportunity to study the way that these mixed species bacterial communities change the activity of vaginal applicants including over-the-counter products like douches and prescription medications and contraceptives. These types of studies are very difficult or even impossible to complete in women who are participating in clinical trials.”


In fact, the team’s report documented the potential for their system to better evaluate current and future antimicrobial drugs in terms of how they interact with “good and bad” bacteria. In their current studies a bacterial community associated with a symptomatic condition called bacterial vaginosis substantially reduced the antiviral activity of one of the leading anti-HIV medicines.


Conversely, vaginal surfaces occupied by healthy bacteria and treated with the antiviral produced significantly less HIV than those vaginal surfaces without bacteria treated with the same antiviral. Dr. Marc Baum, the lead scientist at Oak Crest and co-author of the work, stated “this model is unique as it faithfully recreates the vaginal environment ex vivo, both in terms of the host cellular physiology and the associated complex vaginal microbiomes that could not previously be cultured. I believe it will be of immense value in the study of sexually transmitted infections.”


Story Source:


The above story is based on materials provided by he University of Texas Medical Branch, Raul Reyes.


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Brain implant to be developed as a novel treatment for epilepsy

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A new technique which could revolutionise the treatment of epilepsy is to be tested thanks to a £10 million grant from the Wellcome Trust and the Engineering and Physical Sciences Research Council (EPSRC).


Brain implant to be developed as a novel treatment for epilepsy



Credits: Timeslive



Led by Newcastle University, and including teams from Imperial College London and UCL, the CANDO project seeks to develop a brain implant that uses light waves to try to counteract the disrupted brain activity which causes epileptic seizures.


The project will last seven years and will involve designing a small device, about the size of a drawing pin, to be implanted into the patient’s brain. It will continually monitor and interact with brain activity to stabilise disrupted networks of neurons. The technique will also involve a form a gene therapy called optogenetics, which will be used to make the specific neurons that need to be targeted light-sensitive.


In the UK there are around 600,000 people who have the condition. The usual treatment is through drugs, but for about a third of patients they have limited impact.For these patients surgery can be an option. For that to be possible the area of the brain from where the seizures are originating needs to be found and removed. However, often a single area causing seizures cannot be found, or if ti can it may lie within a region of the brain that cannot be removed without causing unacceptable side-effects. And even in patients who are able to have surgery, the seizures can come back after a few years.


The only other possible treatment is the use of implants. Current implants work in such a way that means they only start to operate once a seizure has started, and it is often too late by then. However, the new device will monitor the brain’s neurons to try to act before a seizure starts, providing a more effective solution.


Dr Andrew Jackson, a Wellcome Trust Fellow in neuroscience, and Professor Anthony O’Neill, Siemens Professor of Microelectronics, will lead the research at Newcastle University. Dr Jackson said: “This is a new way of trying to prevent seizures before they happen. Currently implants only kick in once the seizure has started, which is often too late. If our technique works then it should be more effective and make a real difference to patients’ lives.”


The implant will be tested using human brain slices removed during surgery, computer modelling, and animal models.


Dr Roger Whittaker, Clinical Senior Lecturer and Honorary Consultant Clinical Neurophysiologist in the Newcastle upon Tyne NHS Hospitals Foundation Trust, who leads the clinical aspects of the project, said: “Patients who can’t rely on drugs to help them with their epilepsy can really suffer. This innovative approach could offer a better long-term solution for that group and really have a positive impact on their lives.”


Emma Dowling, 28, has lived with epilepsy since she was a girl. When she was diagnosed at eight years old she was put on drug treatment, and then later had surgery to remove part of her brain. Emma said: “I started hearing voices and would suddenly stop what I was doing when I was younger, which can be an early sign of epilepsy. The drugs I was put on have quite severe side-effects and were affecting my memory, which made it harder at school.


“They also became less effective as I got older and I started having seizures more frequently. Some would be ‘grand mal’ seizures where I’d shake on the floor but others would be lower-key ones where my brain just zoned out. I had a couple of those during job interviews. It really affects your confidence.


“Eventually I had surgery when I was 25 but I still have auras and take some drugs as well. I have been offered more surgery, but there are side-effects to that as well, and it just feels funny that they are removing parts of your brain.


“Something like this project, which could stop seizures before they happen and doesn’t involve removing brain cells, would be amazing for epilepsy sufferers like me. I have managed to get on with my life and I have a job now but it has been a lot harder for me because of my condition.”


Dr Ted Bianco, Director of Technology Transfer at the Wellcome Trust, said: “It was the express purpose of this funding competition to support the development of adventurous new technologies that push the boundaries of what will be possible in tomorrow’s medicine. Such an ambition is writ large in this project that brings together engineering, the basic neurosciences and clinical management to ameliorate the disabling effects of epilepsy.Should the research be successful, the underlying technology may open the way to advances in the treatment of other neurological disorders.”


Story Source:


The above story is based on materials provided by Wellcome Trust, Clare Ryan.


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27 Mart 2014 Perşembe

Scientists Move Closer to Inventing Artificial Life

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An international team of scientists led by Jef Boeke, PhD, director of NYU Langone Medical Center’s Institute for Systems Genetics, has synthesized the first functional chromosome in yeast, an important step in the emerging field of synthetic biology, designing microorganisms to produce novel medicines, raw materials for food, and biofuels.


Scientists Move Closer to Inventing Artificial Life 2



Jef Boeke, PhD, director of NYU Langone Medical Center’s Institute for Systems Genetics



Over the last five years, scientists have built bacterial chromosomes and viral DNA, but this is the first report of an entire eukaryotic chromosome, the threadlike structure that carries genes in the nucleus of all plant and animal cells, built from scratch. Researchers say their team’s global effort also marks one of the most significant advances in yeast genetics since 1996, when scientists initially mapped out yeast’s entire DNA code, or genetic blueprint.


“Our research moves the needle in synthetic biology from theory to reality,” says Dr. Boeke, a pioneer in synthetic biology who recently joined NYU Langone from Johns Hopkins University.


“This work represents the biggest step yet in an international effort to construct the full genome of synthetic yeast,” says Dr. Boeke. “It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell. We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot.”


In this week’s issue of Science online March 27, the team reports how, using computer-aided design, they built a fully functioning chromosome, which they call synIII, and successfully incorporated it into brewer’s yeast, known scientifically as Saccharomyces cerevisiae.


The seven-year effort to construct synIII tied together some 273, 871 base pairs of DNA, shorter than its native yeast counterpart, which has 316,667 base pairs. Dr. Boeke and his team made more than 500 alterations to its genetic base, removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins, and “jumping gene” segments known to randomly move around and introduce mutations. Other sets of base pairs were added or altered to enable researchers to tag DNA as synthetic or native, and to delete or move genes on synIII.


“When you change the genome you’re gambling. One wrong change can kill the cell,” says Dr. Boeke. “We have made over 50,000 changes to the DNA code in the chromosome and our yeast still live. That is remarkable. It shows that our synthetic chromosome is hardy, and it endows the yeast with new properties.”


The Herculean effort was aided by some 60 undergraduate students enrolled in the “Build a Genome” project, founded by Dr. Boeke at Johns Hopkins. The students pieced together short snippets of the synthetic DNA into stretches of 750 to 1,000 base pairs or more. These pieces were then assembled into larger ones, which were swapped for native yeast DNA, an effort led by Srinivasan Chandrasegaran, PhD, a professor at Johns Hopkins. Chandrasegaran is also the senior investigator of the team’s studies on synIII.


Student participation kicked off what has become an international effort, called Sc2.0 for short, in which several academic researchers have partnered to reconstruct the entire yeast genome, including collaborators at universities in China, Australia, Singapore, the United Kingdom, and elsewhere in the U.S.


Yeast chromosome III was selected for synthesis because it is among the smallest of the 16 yeast chromosomes and controls how yeast cells mate and undergo genetic change. DNA comprises four letter-designated base macromolecules strung together in matching sets, or base pairs, in a pattern of repeating letters. “A” stands for adenine, paired with “T” for thymine; and “C” represents cysteine, paired with “G” for guanine. When stacked, these base pairs form a helical structure of DNA resembling a twisted ladder.


Yeast shares roughly a third of its 6,000 genes—functional units of chromosomal DNA for encoding proteins — with humans. The team was able to manipulate large sections of yeast DNA without compromising chromosomal viability and function using a so-called scrambling technique that allowed the scientists to shuffle genes like a deck of cards, where each gene is a card. “We can pull together any group of cards, shuffle the order and make millions and millions of different decks, all in one small tube of yeast,” Dr. Boeke says. “Now that we can shuffle the genomic deck, it will allow us to ask, can we make a deck of cards with a better hand for making yeast survive under any of a multitude of conditions, such as tolerating higher alcohol levels.”


Using the scrambling technique, researchers say they will be able to more quickly develop synthetic strains of yeast that could be used in the manufacture of rare medicines, such as artemisinin for malaria, or in the production of certain vaccines, including the vaccine for hepatitis B, which is derived from yeast. Synthetic yeast, they say, could also be used to bolster development of more efficient biofuels, such as alcohol, butanol, and biodiesel.


The study will also likely spur laboratory investigations into specific gene function and interactions between genes, adds Dr. Boeke, in an effort to understand how whole networks of genes specify individual biological behaviors.


Their initial success rebuilding a functioning chromosome will likely lead to the construction of other yeast chromosomes (yeast has a total of 16 chromosomes, compared to humans’ 23 pairs), and move genetic research one step closer to constructing the organism’s entire functioning genome, says Dr. Boeke.


Dr. Boeke says the international team’s next steps involve synthesizing larger yeast chromosomes, faster and cheaper. His team, with further support from Build a Genome students, is already working on assembling base pairs in chunks of more than 10,000 base pairs. They also plan studies of synIII where they scramble the chromosome, removing, duplicating, or changing gene order.


Detailing the Landmark Research Process


Before testing the scrambling technique, researchers first assessed synIII’s reproductive fitness, comparing its growth and viability in its unscrambled from — from a single cell to a colony of many cells — with that of native yeast III. Yeast proliferation was gauged under 19 different environmental conditions, including changes in temperature, acidity, and hydrogen peroxide, a DNA-damaging chemical. Growth rates remained the same for all but one condition.


Further tests of unscrambled synIII, involving some 30 different colonies after 125 cell divisions, showed that its genetic structure remained intact as it reproduced. According to Dr. Boeke, individual chromosome loss of one in a million cell divisions is normal as cells divide. Chromosome loss rates for synIII were only marginally higher than for native yeast III.



To test the scrambling technique, researchers successfully converted a non-mating cell with synIII to a cell that could mate by eliminating the gene that prevented it from mating.


Story Source:


The above story is based on materials provided by New York University School of Medicine, David March.


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This brain implant may help people walk again

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Neural probe arrays are expected to significantly benefit the lives of amputees and people affected by spinal cord injuries or severe neuromotor diseases. By providing a direct route of communication between the brain and artificial limbs, these arrays record and stimulate neurons in the cerebral cortex.


This brain implant may help people walk again



The compact neural probe array consists of a three-dimensional probe array, a custom 100-channel neural recording chip and a flexible polyimide polymer cable. Credit: A*STAR Institute of Microelectronics



The need for neural probe arrays that are compact, reliable and deliver high performance has prompted researchers to use microfabrication techniques to manufacture probe arrays. Now, a team led by Ming-Yuan Cheng from the A*STAR Institute of Microelectronics, Singapore, has developed a three-dimensional probe array for chronic and long-term implantation in the brain. This array is compact enough to freely float along with the brain when implanted on the cortex.


The neural probe array needs to be implanted in the subarachnoid space of the brain, a narrow region of 1–2.5 millimeters in depth that lies between the pia mater and dura mater brain meninges. “A high-profile array may touch the skull and damage the tissue when relative micromotions occur between the brain and the probes,” explains Cheng. To avoid this problem, the array should be as thin as possible.

Existing approaches produce low-profile arrays using microscopic electrodes machined from a silicon substrate. These approaches, however, restrict the maximum probe length to the thickness of the substrate and the number of recording electrodes. Other methods generate three-dimensional arrays from silicon-supported two-dimensional probes. Complex and expensive to fabricate, these arrays are too bulky because the silicon support also incorporates the application-specific integrated circuit (ASIC) chip for neural recording.


Cheng and colleagues fabricated two-dimensional probes and inserted them into a thin slotted silicon platform for assembly (see image). To produce a three-dimensional probe array, they joined this assembly to the recording chip. Instead of being aligned, however, the team found that the contacts of the probe electrodes and recording chip were orthogonally arranged with respect to each other, resulting in mismatched planes.


“To solve this issue, the team manufactured a silicon-based connector, or interposer, that electrically linked these components,” says Cheng. “This innovative microassembly effectively controls the final height of the array to within 750 micrometers.”


Compared with commercial neural probes, the new array exhibited competitive electrical properties, including electrode impedance. Moreover, biocompatibility tests showed that the presence of array components did not rupture cell membranes or suppress cell growth. The team is currently refining their approach to integrate the array with a wireless recording chip and make the assembly fully implantable.


Story Source:


The above story is based on materials provided by A*STAR Institute of Microelectronics, Singapore.


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Logical circuits built using living slime molds

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A future computer might be a lot slimier than the solid silicon devices we have today. In a study published in the journal Materials Today, European researchers reveal details of logic units built using living slime molds, which might act as the building blocks for computing devices and sensors.


Logical circuits built using living slime molds



Credits: David C. Lam / Asian Garden



Andrew Adamatzky (University of the West of England, Bristol, UK) and Theresa Schubert (Bauhaus-University Weimar, Germany) have constructed logical circuits that exploit networks of interconnected slime mold tubes to process information.


One is more likely to find the slime mold Physarum polycephalum living somewhere dark and damp rather than in a computer science lab. In its “plasmodium” or vegetative state, the organism spans its environment with a network of tubes that absorb nutrients. The tubes also allow the organism to respond to light and changing environmental conditions that trigger the release of reproductive spores.


In earlier work, the team demonstrated that such a tube network could absorb and transport different colored dyes. They then fed it edible nutrients — oat flakes — to attract tube growth and common salt to repel them, so that they could grow a network with a particular structure. They then demonstrated how this system could mix two dyes to make a third color as an “output.” .


Using the dyes with magnetic nanoparticles and tiny fluorescent beads, allowed them to use the slime mold network as a biological “lab-on-a-chip” device. This represents a new way to build microfluidic devices for processing environmental or medical samples on the very small scale for testing and diagnostics, the work suggests. The extension to a much larger network of slime mold tubes could process nanoparticles and carry out sophisticated Boolean logic operations of the kind used by computer circuitry. The team has so far demonstrated that a slime mold network can carry out XOR or NOR Boolean operations. Chaining together arrays of such logic gates might allow a slime mold computer to carry out binary operations for computation.


“The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at the sites where protoplasmic tubes merge,” conclude Adamatzky and Schubert.

Are we entering the age of the biological computer? Stewart Bland, Editor of Materials Today, believes that “although more traditional electronic materials are here to stay, research such as this is helping to push and blur the boundaries of materials science, computer science and biology, and represents an exciting prospect for the future.”


The research was undertaken in a framework of EU FP7 Project “Physarum Chip” (Unconventional Computing program).


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Bioengineered bacteria produce biofuel alternative for high-energy rocket fuel

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Researchers at the Georgia Institute of Technology and the Joint BioEnergy Institute have engineered a bacterium to synthesize pinene, a hydrocarbon produced by trees that could potentially replace high-energy fuels, such as JP-10, in missiles and other aerospace applications. With improvements in process efficiency, the biofuel could supplement limited supplies of petroleum-based JP-10, and might also facilitate development of a new generation of more powerful engines.


Bioengineered bacteria produce biofuel alternative for high-energy rocket fuel



Georgia Tech researchers examine the production of the hydrocarbon pinene in a series of laboratory test tubes. Shown are (l-r) Pamela Peralta-Yahya, an assistant professor in the School of Chemistry and Biochemistry and the School of Chemical and Biomolecular Engineering, and Stephen Sarria, a graduate student in the School of Chemistry and Biochemistry. (Georgia Tech Photo: Rob Felt)



By inserting enzymes from trees into the bacterium, first author and Georgia Tech graduate student Stephen Sarria, working under the guidance of assistant professor Pamela Peralta-Yahya, boosted pinene production six-fold over earlier bioengineering efforts. Though a more dramatic improvement will be needed before pinene dimers can compete with petroleum-based JP-10, the scientists believe they have identified the major obstacles that must be overcome to reach that goal.


Funded by Georgia Tech startup funds awarded to Peralta-Yahya’s lab and by the U.S. Department of Energy’s Office of Science, the research was reported February 27, 2014, in the journal ACS Synthetic Biology.


“We have made a sustainable precursor to a tactical fuel with a high energy density,” said Peralta-Yahya, an assistant professor in the School of Chemistry and Biochemistry and the School of Chemical and Biomolecular Engineering at Georgia Tech. “We are concentrating on making a ‘drop-in’ fuel that looks just like what is being produced from petroleum and can fit into existing distribution systems.”


Fuels with high energy densities are important in applications where minimizing fuel weight is important. The gasoline used to power automobiles and the diesel used mainly in trucks both contain less energy per liter than the JP-10. The molecular arrangement of JP-10, which includes multiple strained rings of carbon atoms, accounts for its higher energy density.


The amount of JP-10 that can be extracted from each barrel of oil is limited, and sources of potentially comparable compounds such as trees can’t provide much help. The limited supply drives the price of JP-10 to around $25 per gallon. That price point gives researchers working on a biofuel alternative a real advantage over scientists working on replacing gasoline and diesel.


“If you are trying to make an alternative to gasoline, you are competing against $3 per gallon,” Peralta-Yahya noted. “That requires a long optimization process. Our process will be competitive with $25 per gallon in a much shorter time.”


While much research has gone into producing ethanol and bio-diesel fuels, comparatively little work has been done on replacements for the high-energy JP-10.


Peralta-Yahya and collaborators set out to improve on previous efforts by studying alternative enzymes that could be inserted into the E. coli bacterium. They settled on two classes of enzymes – three pinene synthases (PS) and three geranyl diphosphate synthases (GPPS) – and experimented to see which combinations produced the best results.


Their results were much better than earlier efforts, but the researchers were puzzled because for a different hydrocarbon, similar enzymes produced more fuel per liter. So they tried an additional step to improve their efficiency. They placed the two enzymes adjacent to one another in the E. coli cells, ensuring that molecules produced by one enzyme would immediately contact the other. That boosted their production to 32 milligrams per liter – much better than earlier efforts, but still not competitive with petroleum-based JP-10.


Peralta-Yahya believes the problem now lies with built-in process inhibitions that will be more challenging to address.


“We found that the enzyme was being inhibited by the substrate, and that the inhibition was concentration-dependent,” she said. “Now we need either an enzyme that is not inhibited at high substrate concentrations, or we need a pathway that is able to maintain low substrate concentrations throughout the run. Both of these are difficult, but not insurmountable, problems.”


To be competitive, the researchers will have to boost their production of pinene 26-fold. Peralta-Yahya says that’s within the range of possibilities for bioengineering the E. coli.


“Even though we are still in the milligrams per liter level, because the product we are trying to make is so much more expensive than diesel or gasoline means that we are relatively closer,” she said.


Theoretically, it may be possible to produce pinene at a cost lower than that of petroleum-based sources. If that can be done – and if the resulting bio-fuel operates well in these applications – that could open the door for lighter and more powerful engines fueled by increased supplies of high-energy fuels. Pinene dimers, which result from the dimerization of pinene, have already been shown to have an energy density similar to that of JP-10.


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First comprehensive atlas of human gene activity

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A Large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.


First comprehensive atlas of human gene activity


“Now, for the first time, we are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles,” said Winston Hide, associate professor of bioinformatics and computational biology at Harvard School of Public Health (HSPH) and one of the core authors of the main paper in Nature. “This is a major advance that will greatly increase our ability to understand the causes of disease across the body.”


The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.


Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches”—called “promoters” and “enhancers”—are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.


“We now have the ability to narrow down the genes involved in particular diseases based on the tissue cell or organ in which they work,” said Hide. “This new atlas points us to the exact locations to look for the key genetic variants that might map to a disease.”


Funding for FANTOM 5 came from a research grant from RIKEN and from Innovative Cell Biology.


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Benchtop Human

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Significant progress toward creating “homo minutus” — a benchtop human — was reported at the Society of Toxicology meeting on Mar. 26 in Phoenix.


The advance — successful development and analysis of a liver human organ construct that responds to exposure to a toxic chemical much like a real liver — was described in a presentation by John Wikswo, the Gordon A. Cain University Professor and Director of the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE) at Vanderbilt University.


benchtop human



Photo Credits: Stefan Zimmerman



The achievement is the first result from a five-year, $19 million multi­ institutional effort led by Rashi Iyer, senior scientist at Los Alamos National Laboratory (LANL), and Wikswo. The project is developing four interconnected human organ constructs — liver, heart, lung and kidney — that are based on a highly miniaturized platform nicknamed ATHENA (Advanced Tissue-engineered Human Ectypal Network Analyzer). The project is supported by the Defense Threat Reduction Agency. Similar programs to create smaller, so-called organs-on-chips are underway at the Defense Advanced Research Projects Agency and the National Institutes of Health.


“The original impetus for this research comes from the problems we are having in developing new drugs,” said Wikswo. “A number of promising new drugs that looked good in conventional cell culture and animal trials have failed when they were tested in humans, many due to toxic effects. That represents more than $1 billion in effort down the drain. Our current process of testing first in cell lines on plastic and then in mice, rats and other animals simply isn’t working.”


In recent years, a cadre of scientists and clinicians around the world has begun to develop more relevant and advanced laboratory tests for drug efficacy and toxicity: small bioreactors that can form human organ structures and are equipped with sensors to monitor organ health.


Ultimately, the goal is to connect the individual organ modules chemically in a fashion that mimics the way the organs are connected in the body, via a blood surrogate. The ATHENA researchers hope that this ”homo minutus,” with its ability to simulate the spatial and functional complexity of human organs, will prove to be a more accurate way of screening new drugs for potency and potential side-effects than current methods.


Devices of this type could also be extremely useful in the field of toxicology. Of the tens of thousands of chemical compounds being used routinely in commerce today, only a small fraction has been tested for toxicity. And even those have been examined only for acute toxicity, not for sub-lethal or chronic effects, because of the expense and time required by such tests. Human organ construct/organ-on-a-chip technology could make this process substantially cheaper and faster.


The ATHENA project combines the skills and insights of some of the top researchers in this pioneering field of research. The liver construct is being developed by Katrin Zeilinger, head of the Bioreactor Group and her colleagues at the Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charite UniversiUitsmedizin, Berlin. Kevin Kit Parker, Tarr Family Professor of Bioengineering and Applied Physics at Harvard University, is leading the heart effort. Shuvo Roy, director of the Biomedical Microdevices Laboratory at the University of California, San Francisco (UCSF), and Associate Professor of Medicine William Fissell of Vanderbilt are developing the kidney construct. In addition to leading the project, Iyer is directing work on the lung organ at LANL. Wikswo and his VIIBRE group are building the hardware platform and a heart test system. Andrzej Przekwas, chief technology officer and senior vice president for research of CFD Research Corporation (CFDRC), a technology company in Huntsville, AL, and the LANL and Vanderbilt groups are creating a blood surrogate to sustain the four devices. CFDRC is also building a mathematical model of ATHENA to guide system design and data analysis.

One of the key questions for human organ construct developers is scale: What size should they make their artificial organs? Different groups have selected a variety of scales ranging from microhuman (one-millionth of size of human organs) to millihuman (one-thousandth the size).


“Scale is extremely important,” said lyer. If the scale is too small, she pointed out, then it is difficult to recapture the physiology because you need a quorum of cells before they act as an organ and it is difficult to get enough effluent to analyze. If the scale is too large, the costs of fabrication and human cell acquisitiond make the devices prohibitively expensive.


The ATHENA team at Charite started with a patient-support liver bioreactor with the volume of a human liver and scaled it down to a four-layer, three-dimensional device with a volume of only one-tenth of a milliliter. Zeilinger noted that “the cell mass of the final design was optimized based on metabolic performance and enzyme release and cell structures now resemble native human liver tissue.”


Charite’s original organ perfusion system cost $80,000 and was the size of a small refrigerator. Using simple microfluidics, the VIIBRE team created a 5x4x3.5-inch perfusion device that costs about $2,000 to make, Wikswo reported. They have validated its basic characteristics and demonstrated that it can keep human liver cells healthy for an extended period of time — the goal is a month.


Scaling is also important to determine the relative sizes and function of each organ represented on the platform. So if one were to have a liver that represented one thousandth of a human with a lung that represented one millionth of a human, the outcome would be very skewed. It’s just like having the heart of a 10-pound infant pumping to a liver of a 300-pound adult — it’s a no-go.


“We have picked a scale that is between microhuman and millihuman — one-tenth of the millihuman,” Iyer said. “I think the success that we are having with our liver device means that we have hit the sweet spot.”


In addition to successfully shrinking the organ platform, researchers in the Vanderbilt lab of John McLean, Stevenson Associate Professor of Chemistry, have introduced another important innovation by connecting the organ platform to a powerful, highly specialized instrument called an ion mobility-mass spectrometer, which can simultaneously detect and identify minute quantities of thousands to tens of thousands of different biological molecules simultaneously.


Other human organ construct/organ-on-chip research projects have reported tracking the variations in concentrations of a few well-known chemical compounds that are expected to change, but this is the first to successfully monitor the fluctuations of the thousands of different molecules that living cells produce and consume.


The researchers have used this capability to monitor the liver cells’ response to different dosages of a well-known liver toxin, the drug acetaminophen.


“We could actually see what the acetaminophen is doing to the liver cells,” said Wikswo. “In the beginning we saw an increase in the drug and its metabolites. Then, over the next 24 hours, we recorded a steady increase in tryptophan as acetaminophen began to interfere with normal liver metabolism. After that we saw decreased production of bile acid, a clear indication that something was going very wrong with the liver, as expected when exposed to seriously high doses of acetaminophen, and a decreased ability to detoxify penicillin.”


According to Iyer, this rich level of detail confirms that the ATHENA organ platform coupled with mass spectrometry technology can provide a more sensitive and effective method for screening both new drugs and toxic agents than is available today.


The team plans on hooking up their liver device to the Harvard heart this winter. They expect to add the lung construct being developed at Los Alamos next year and the UCSF/Vanderbilt kidney the year after.


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26 Mart 2014 Çarşamba

Could a Robot Deliver Motivational Speeches?

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Imagine a day when a form of artificial intelligence could deliver a speech as compelling as one given by a human.


Could a Robot Deliver Motivational Speeches


A nonprofit organization called XPRIZE, which designs competitions to encourage the development of innovative technology for the benefit of humanity, announced it will award a prize to anyone who can develop an artificial intelligence, or “AI,” that could give an inspiring talk at the TED (Technology, Education, Design) conference without any human assistance.


“Advances in machine learning and artificial intelligence have made extraordinary progress over the past decade, but we’ve barely scratched the surface,” Peter Diamandis, chairman and CEO of XPRIZE, said in a statement. Diamandis and Chris Anderson, curator of TED, announced the prize Thursday (March 20) at the TED2014 Conference in Vancouver, British Columbia.


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Building heart tissue that beat

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When a heart gets damaged, such as during a major heart attack, there’s no easy fix. But scientists working on a way to repair the vital organ have now engineered tissue that closely mimics natural heart muscle that beats, not only in a lab dish but also when implanted into animals. They presented their latest results at the 247th National Meeting & Exposition of the American Chemical Society (ACS), the world’s largest scientific society.


Building heart tissue that beat


The talk was one of more than 10,000 being presented at the meeting, which continues here through Thursday.


“Repairing damaged hearts could help millions of people around the world live longer, healthier lives,” said Nasim Annabi, Ph.D. Right now, the best treatment option for patients with major heart damage — which can be caused by severe heart failure, for example — is an organ transplant. But there are far more patients on waitlists for a transplant than there are donated hearts. Even if a patient receives a new heart, complications can arise.


The ideal solution would be to somehow repair the tissue, which can get damaged over time when arteries are clogged and starve a part of the heart of oxygen. Scientists have been searching for years for the best fix. The quest has been confounded by a number of factors that come into play when designing a complex organ or tissue.


Simple applications, such as engineered skin, are already in use or in clinical trials. But building tissue for an organ as complicated as the heart requires a lot more research. To address this challenge and engineer complex 3-D tissues, researchers at the Brigham and Women’s Hospital and Harvard Medical School in Boston and the University of Sydney in Australia were able to combine a novel elastic hydrogel with microscale technologies to create an artificial cardiac tissue that mimics the mechanical and biological properties of the native heart.


“Our hearts are more than just a pile of cells,” said Ali Khademhosseini, Ph.D., who is at Harvard Medical School. “They’re very organized in their architecture.”


To tackle the challenge of engineering heart muscle, Khademhosseini and Annabi have been working with natural proteins that form gelatin-like materials called hydrogels.


“The reason we like these materials is because in many ways they mimic aspects of our own body’s matrix,” Khademhosseini said. They’re soft and contain a lot of water, like many human tissues.


His group has found that they can tune these hydrogels to have the chemical, biological, mechanical and electrical properties they want for the regeneration of various tissues in the body. But there was one way in which the materials didn’t resemble human tissue. Like gelatin, early versions of the hydrogels would fall apart, whereas human hearts are elastic. The elasticity of the heart tissue plays a key role for the proper function of heart muscles such as contractile activity during beating. So, the researchers developed a new family of gels using a stretchy human protein aptly called tropoelastin. That did the trick, giving the materials much needed resilience and strength.


But building tissue is not just about developing the right materials. Making the right hydrogels is only the first step. They serve as the tissue scaffold. On it, the researchers grow actual heart cells. To make sure the cells form the right structure, Khademhosseini’s lab uses 3-D printing and microengineering techniques to create patterns in the gels. These patterns coax the cells to grow the way the researchers want them to. The result: small patches of heart muscle cells neatly lined up that beat in synchrony within the grooves formed on these elastic substrates. These micropatterned elastic hydrogels can one day be used as cardiac patches. Khademhosseini’s group is now moving into tests with large animals. They are also using these elastic natural hydrogels for the regeneration of other tissues such as blood vessels, skeletal muscle, heart valves and vascularized skin.


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Generator uses the human body as an electrode to power portable electronics

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It’s well-known that the human body is a good conductor of electricity, and now researchers have taken advantage of this fact to create a small generator that uses the body as an electrode to power portable devices without the need for batteries. The “body contact electrode” replaces a grounded electrode that was used in a previous version of the generator, which would have been impractical for portable devices.


Generator uses the human body as an electrode to power portable electronics



The energy harvesting mechanism and equivalent circuit of the STEG with the human body as an electrode. When a finger taps the friction surface, it has a tendency to donate electrons, causing an electric charge to move back and forth between the induction electrode and the charged skin. Credit: Meng, et al. ©2014 AIP Publishing LLC



The researchers, Bo Meng, et al., at Peking University in Beijing, China, have published a paper on the generator using a human body electrode in a recent issue of Applied Physics Letters.


“At present, the generator is more suitable for low-power devices,” coauthor Haixia Zhang, a professor at Peking University, told Phys.org. “In our future plans, we hope it can be used as a back-up power source for portable electronics.”


The device’s full name is a single-friction-surface triboelectric generator, or STEG. Due to the triboelectric effect, when certain materials rub against each other, they can become electrically charged. The most well-known example of the triboelectric effect is static electricity. Activities such as tapping a mobile phone with a STEG covering can also produce these electric charges. The STEG then harvests the electric charges, which can be used to power low-power electronics.


In their study, the researchers covered the front panel of a mobile phone with a flexible, transparent layer of STEG composite material. The body contact electrode—contacted with the palm of the hand or the fingers—was located on either the back side or the border of the phone to complete the electric connection.


The researchers demonstrated that patting the phone with the palm of the hand or tapping the phone with a finger causes electrons to be exchanged between human skin and the STEG material. After repeated patting/tapping, electric charge moves back and forth between the induction electrode and the charged skin.


Although researchers have a good understanding of how the triboelectric effect works, the difficulty lies in designing a generator that can achieve good performance. Somewhat surprisingly, when the researchers replaced the grounded electrode in the STEG with a human body electrode, the STEG achieved an increase in both the output current and the amount of charge transferred.


With these improvements, the STEG has potential applications for low-power portable electronics and wearable devices, which may include implanted medical devices and sensors. The researchers plan to further improve the STEG performance in the future.


“For the STEG devices, we are making efforts to improve the output of the STEG device, attempting to use new materials and fabrication methods,” Zhang said. “The advantage of the human body as a good conductor will be taken to develop several novel triboelectric generator devices as well.”


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Researchers reconstruct facial images locked in a viewer’s mind

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Using only data from an fMRI scan, researchers led by a Yale University undergraduate have accurately reconstructed images of human faces as viewed by other people.


Researchers reconstruct facial images locked in a viewer's mind



Credit: Alan Cowen



“It is a form of mind reading,” said Marvin Chun, professor of psychology, cognitive science and neurobiology and an author of the paper in the journal Neuroimage.


The increased level of sophistication of fMRI scans has already enabled scientists to use data from brain scans taken as individuals view scenes and predict whether a subject was, for instance, viewing a beach or city scene, an animal or a building.


“But they can only tell you they are viewing an animal or a building, not what animal or building,” Chun said. “This is a different level of sophistication.”


One of Chun’s students, Alan S. Cowen, then a Yale junior now pursing an advanced degree at the University of California at Berkeley, wanted to know whether it would be possible to reconstruct a human face from patterns of brain activity. The task was daunting, because faces are more similar to each other than buildings. Also large areas of the brain are recruited in the processing of human faces, a testament to its importance in survival.


“We perceive faces in a much greater level of detail than we perceive other things,” Cowen said.

Working with funding from the Yale Provost’s office, Cowen and post doctoral researcher Brice Kuhl, now an assistant professor at New York University, showed six subjects 300 different “training” faces while undergoing fMRI scans. They used the data to create a sort of statistical library of how those brains responded to individual faces. They then showed the six subjects new sets of faces while they were undergoing scans. Taking that fMRI data alone, researchers used their statistical library to reconstruct the faces their subjects were viewing.


Cowen said the accuracy of these facial reconstructions will increase with time and he envisions they can be used as a research tool, for instance in studying how autistic children respond to faces.

Chun said the study shows the value of funding research ambitions of Yale undergraduates.


“I would never have received external funding for this, it was too novel,” Chun said.


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25 Mart 2014 Salı

New technique brings us closer to HIV and hepatitis C vaccines

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Plans for a new type of DNA vaccine to protect against the deadly HIV and Hepatitis C viruses have taken an important step forward, with University of Adelaide researchers applying for a patent based on groundbreaking new research.


New technique brings us closer to HIV and hepatitis C vaccines



Credits: The Hospital Research Foundation



Professor Eric Gowans from the University’s Discipline of Surgery, based at the Basil Hetzel Institute at the Queen Elizabeth Hospital, has submitted a patent application for what he describes as a relatively simple but effective technique to stimulate the body’s immune system response, thereby helping to deliver the vaccine.


While pre-clinical research into this vaccination technique is still underway, he’s now searching for a commercial partner to help take it to the next stage.


Professor Gowans’ work has focused on utilizing the so-called “accessory” or “messenger” cells in the immune system, called dendritic cells, to activate an immune response. These are a type of white blood cell that play a key role during infection and vaccination.


“There’s been a lot of work done in the past to target the dendritic cells, but this has never been effective until now,” Professor Gowans says. “What we’ve done is incredibly simple, but often the simple things are the best approach. We’re not targeting the dendritic cells directly – instead, we’ve found an indirect way of getting them to do what we want.”


Professor Gowans and his team have achieved this by including a protein that causes a small amount of cell death at the point of vaccination.


“The dead cells are important because they set off danger signals to the body’s immune response. This results in inflammation, and the dendritic cells become activated. Those cells then create an environment in which the vaccination can be successful,” Professor Gowans says.


Using a micro-needle device provided by United States company FluGen Inc., the researchers can puncture the skin to a depth of 1.5mm, delivering the vaccination directly into the skin. “We chose the skin instead of the muscle tissue, which is more common for DNA vaccines, because the skin has a high concentration of dendritic cells,” Professor Gowans says.


Because the technique has the potential to translate to other, more common viruses in addition to the devastating HIV and Hepatitis C, the project attracted seed funding from The Hospital Research Foundation, and additional funding from the National Health and Medical Research Council (NHMRC).


The research is still in the pre-clinical phase, with a patient study due next year. “This technique has worked much better than I anticipated,” Professor Gowans says. “We’re now ready for a commercial partner to help us take this to the next phase, and we’re in discussions with some potential partners at the moment.”


Professor Gowans will present some of his work at the forthcoming 5th Australasian Vaccines & Immunotherapeutics Development Meeting (AVID2014), 7-9 May in Melbourne, Australia. Last month he was an invited speaker at the 23rd Australian Conference on Microscopy and Microanalysis (ACMM23) in Adelaide. A paper about this work has already been published recently in Immunology & Cell Biology.


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Zuckerberg, Musk and Kutcher Invest In Artificial Intelligence Firm

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Billionaire tech entrepreneurs Elon Musk and Mark Zuckerberg, along with actor Ashton Kutcher, have joined forces to make a $40 million investment in the artificial intelligence firm Vicarious FPC.


Zuckerberg, Musk and Kutcher Invest In Artificial Intelligence Firm


The firm hopes to build a system capable of replicating the functions of the neocortex of the human brain, the part that controls body movement, vision, understands language and does math, The Wall Street Journal reports. One day, the company hopes to build a “computer that thinks like a person,” Vicarious co-founder Scott Phoenix says. “except it doesn’t have to eat or sleep.”


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First stem cell study of bipolar disorder yields promising results

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Stem cell model shows nerve cells develop, behave and respond to lithium differently – opening doors to potential new treatments.


What makes a person bipolar, prone to manic highs and deep, depressed lows? Why does bipolar disorder run so strongly in families, even though no single gene is to blame? And why is it so hard to find new treatments for a condition that affects 200 million people worldwide?


First stem cell study of bipolar disorder yields promising results



These colorful neurons, seen forming connections to one another across synapses, were grown from induced pluripotent stem cells – Credit: University of Michigan



New stem cell research published by scientists from the University of Michigan Medical School, and fueled by the Heinz C. Prechter Bipolar Research Fund, may help scientists find answers to these questions.


The team used skin from people with bipolar disorder to derive the first-ever stem cell lines specific to the condition. In a new paper in Translational Psychiatry, they report how they transformed the stem cells into neurons, similar to those found in the brain – and compared them to cells derived from people without bipolar disorder.


The comparison revealed very specific differences in how these neurons behave and communicate with each other, and identified striking differences in how the neurons respond to lithium, the most common treatment for bipolar disorder.


It’s the first time scientists have directly measured differences in brain cell formation and function between people with bipolar disorder and those without.


The researchers are from the Medical School’s Department of Cell & Developmental Biology and Department of Psychiatry, and U-M’s Depression Center.


Stem cells as a window on bipolar disorder


The team used a type of stem cell called induced pluripotent stem cells, or iPSCs. By taking small samples of skin cells and exposing them to carefully controlled conditions, the team coaxed them to turn into stem cells that held the potential to become any type of cell. With further coaxing, the cells became neurons.


“This gives us a model that we can use to examine how cells behave as they develop into neurons. Already, we see that cells from people with bipolar disorder are different in how often they express certain genes, how they differentiate into neurons, how they communicate, and how they respond to lithium,” says Sue O’Shea, Ph.D., the experienced U-M stem cell specialist who co-led the work.


“We’re very excited about these findings. But we’re only just beginning to understand what we can do with these cells to help answer the many unanswered questions in bipolar disorder’s origins and treatment,” says Melvin McInnis, M.D., principal investigator of the Prechter Bipolar Research Fund and its programs.


“For instance, we can now envision being able to test new drug candidates in these cells, to screen possible medications proactively instead of having to discover them fortuitously.”


The research was supported by donations from the Heinz C. Prechter Bipolar Research Fund, the Steven M. Schwartzberg Memorial Fund, and the Joshua Judson Stern Foundation. The A. Alfred Taubman Medical Research Institute at the U-M Medical School also supported the work, which was reviewed and approved by the U-M Human Pluripotent Stem Cell Research Oversight committee and Institutional Review Board.


O’Shea, a professor in the Department of Cell & Developmental Biology and director of the U-M Pluripotent Stem Cell Research Lab, and McInnis, the Upjohn Woodworth Professor of Bipolar Disorder and Depression in the Department of Psychiatry, are co-senior authors of the new paper.


McInnis, who sees firsthand the impact that bipolar disorder has on patients and the frustration they and their families feel about the lack of treatment options, says the new research could take treatment of bipolar disorder into the era of personalized medicine.


Not only could stem cell research help find new treatments, it may also lead to a way to target treatment to each patient based on their specific profile – and avoid the trial-and-error approach to treatment that leaves many patients with uncontrolled symptoms.


More about the findings:


The skin samples were used to derive the 42 iPSC lines. When the team measured gene expression first in the stem cells, and then re-evaluated the cells once they had become neurons, very specific differences emerged between the cells derived from bipolar disorder patients and those without the condition.


Specifically, the bipolar neurons expressed more genes for membrane receptors and ion channels than non-bipolar cells, particularly those receptors and channels involved in the sending and receiving of calcium signals between cells.


Calcium signals are already known to be crucial to neuron development and function. So, the new findings support the idea that genetic differences expressed early during brain development may have a lot to do with the development of bipolar disorder symptoms – and other mental health conditions that arise later in life, especially in the teen and young adult years.


Meanwhile, the cells’ signaling patterns changed in different ways when the researchers introduced lithium, which many bipolar patients take to regulate their moods, but which causes side effects. In general, lithium alters the way calcium signals are sent and received – and the new cell lines will make it possible to study this effect specifically in bipolar disorder-specific cells.


Like misdirected letters and packages at the post office, the neurons made from bipolar disorder patients also differed in how they were ‘addressed’ during development for delivery to certain areas of the brain. This may have an impact on brain development, too.


The researchers also found differences in microRNA expression in bipolar cells – tiny fragments of RNA that play key roles in the “reading” of genes. This supports the emerging concept that bipolar disorder arises from a combination of genetic vulnerabilities.


The researchers are already developing stem cell lines from other trial participants with bipolar disorder, though it takes months to derive each line and obtain mature neurons that can be studied. They will share their cell lines with other researchers via the Prechter Repository at U-M. They also hope to develop a way to use the cells to screen drugs rapidly, called an assay.


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The above story is based on materials provided by University of Michigan Health System, Ann ARBOR.


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Lab-on-fiber could shine light on disease

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“Imagine turning on your home lab kit, pricking your finger, and blotting the blood on an array of fiber probes. In just a few minutes, the machine would automatically e-mail the results to your doctor, who could get back to you within hours if there was a problem. Meanwhile, you could get on with the rest of your day.” This is the scenario painted in a detailed essay in IEEE Spectrum of what the future might hold, according to Jacques Albert, who heads the Advanced Photonic Components group at Carleton University in Ottawa, Canada.


Lab-on-fiber could shine light on disease



Credit: James Archer/anatomyblue, via IEEE



Albert’s team together with collaborating groups around the globe, including the Université de Mons in Belgium and Jinan University in China, are working on the lab-on-fiber, that is, the use of optical glass fibers as platforms for chemical sensors. This is an approach to bringing on a more affordable mobile labs system in which chemical sensors do the monitoring. Optical glass fibers hold the key to labs on fiber with their tiny diameter yet huge information-carrying capacity and dirt-cheap cost, said Albert.


Attempts to develop labs with components that are cheap and portable have been evident for many years. Lab-on-a-chip sensors have looked promising, he wrote, but obstacles have stood in the way of progress; he gave examples such as a chip’s metal conductors that may corrode or short, or the chip having arsenic, toxic to humans. Another drawback he said has been size. Albert also said some researchers seek to replace a chip’s electronic circuits with optical ones.


“By using light rather than current to read chemical reactions, a photonic chip works reliably in aqueous solutions, is immune to electromagnetic radiation, tolerates a wide range of temperatures, and poses fewer risks to biological tissues.” A photonic lab on a chip, however, has not been any magic bullet either, he said, because of size and expense.


Instead, Albert made a case for what his team and colleagues are developing, a lab on fiber. He said, “We coat this probe with a chemical compound, called a reagent, that will interact with whatever target molecules we want to measure, such as blood enzymes or food additives.”


Ultimately, they aim to develop a lab on fiber that can be inserted directly into humans to monitor biological changes realtime.


“We are currently planning experiments—first in test tubes and eventually in animals—to see if a fiber probe can detect metastasized cancer cells in the bloodstream. We hope to shed light (literally) on the process by which these cells invade other organs.”


The team also hopes their work leads to developments in scanner screening technologies less invasive than tools such as biopsies. He posed an example where a doctor may insert a fiber probe into a blood vessel using a hypodermic needle. “no more painful than a flu shot.”


Nonetheless, further developments will be necessary before such ideas materialize. He said it likely will be at least five years before lab-on-fiber instruments are ready for commercial use. One challenge is to figure out how to toughen the probes’ surface coating so they can be stored for several months without becoming unstable and losing their ability to bind with target molecules.


Story Source:


The above story is based on materials provided by IEEE, Nancy Owano.


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A first dance, on a next-generation bionic limb

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Hugh Herr, director of the Biomechatronics Group at The MIT Media Lab, strolls onto the TED2014 stage in a pair of long, black shorts. Normally, what he’s wearing wouldn’t be of note—except that he’s chosen his ensemble today to show us something. Below the hem of his shorts, we see that he has two prosthetic legs. His lab not only creates bionic limbs; he wears them himself.


A first dance, on a next-generation bionic limb



Adrianne Haslet-Davis thanks Hugh Herr on the TED stage. Photo: James Duncan Davidson



“Bionics explores the interplay between biology and design,” says Herr. “Today, I will tell human stories of bionic integration. Of how electromechanics attached to the body and implanted inside the body are beginning to bridge the gap between disability and ability, between human limitation and potential.”


Herr begins by telling his story—his legs were amputated after he got frostbite during a rock climbing accident in 1982. “At the time, I didn’t view my body as broken. I reasoned that a human being can never be broken,” he says. “I thought: Technology is broken. Technology is inadequate. This simple but powerful idea was a call to arms to advance technology to the elimination of my own disability, and ultimately the disabilities of others.”


Herr began in the field of prosthetics with the idea that the body is malleable, a blank slate that could be improved. He created special limbs to help him return to rock climbing—and to be better than he had been before. His thin prosthetic feet allowed him to wedge into spaces where a foot couldn’t fit and to don special spiked feet in order to climb vertical ice. He adjusted his height as he chose — and jokes,”When I was feeling badly about myself and insecure, I would jack myself up a few inches,” he says. “When feeling sauve, I’d knock down my height down just to give my competition a chance.”


Throughout his career, a simple idea guided Herr’s work. “I imagine a future so advanced that we could rid the world of disability—in which neuroimplants allowed the blind to see, in which the paralyzed could walk with exoskeletons,” he says. “We need to do a better job in bionics to allow full rehabilitation.”


At the Center for Extreme Bionics at the MIT Media Lab, Hugh and his team work on the science and technology to allow repair of humans across a broad range of brain and body issues. A focus is bionic limbs. For these limbs, there are three areas of improvement involved: the mechnical, the dynamic and the electric.


The mechanical has to do with how prosthetics are attached to the body. And this is a true challenge, says Herr. “One of the oldest technologies in the human timeline—the shoe—still gives us blisters. We have no idea how to attach things to our body,” he says. Prosthetics, he explains, are attached via synthetic skins. To create this, his lab uses an round rig of actuators that measure the shape of the remaining limb and the tissue compliance at each anatomical point. They use fMRI to figure out precise geometry. The rule is: where the body is stiff, the skin should be soft and vice versa. “We produce the most comfortable limbs I have ever worn,” says Herr.


Next, come the dynamic challenges. To make prosthetics that “move like flesh and bone,” Hugh’s team uses a smart material which is floppy like paper but becomes stiff like a board when voltage is applied. They attach this to the synthetic skin. “When I walk, there’s no voltage, and my interface is soft compliant,” he says. “But when voltage is applied, it stiffens, creating greater maneuverability of limb.”


The lab studies how people with disabilities walk and run, to understand exactly what happens in the body when these deceptively easy things are done. They use this information, on which muscles are doing what and how they’re being controlled by the brain, to create limbs that work like natural ones. On heel strike, the system modulates stiffness and then lifts the person into walking stride just like the muscles in the calf region. These bionics allow wearers to walk up stairs easily, even run up steep inclines.


The lab is also working on exoskeleton-like devices, which Herr predicts everyone will wear in the future to protect their limbs during activities like running. In a version made for people who aren’t missing limbs at all, the exoskeleton actually augments walking, applying torque and power as needed. ”We’re beginning the age in which machines attached to our bodies will make us stronger and more efficient,” says Herr.


And finally, Herr explains the electric challenges, which determine how a prosthetic “connects with my nervous system.” For this, the lab measures electrical pulses of muscles and what happens when a person thinks about moving their limb. They embed this capability in the chips of bionic limbs. To demonstrate how this works, Herr begins to run. “That was the first demonstration of a running gait under neural command,” he says. “The more I fire my muscles, the more torque I get.”


But really, Herr says there is much more to be done from here. “We want to close the loop between the human and the bionic limb,” he says. “We’re doing experiments where we’re growing nerves … When this is fully developed, persons like myself will not only have synthetic limbs that move like flesh and bone, but that feel like flesh and bone.”


Herr hopes to work to make these next-generation prosthetics both available and affordable. “The basic levels of physiological function should be part of basic human rights,” says Herr. “It’s not well appreciated, but over half the world’s population suffers from some kind of cognitive, emotional, sensory or motor condition. Every person should have the right to live without disability, if they choose to.”


Herr brings it back to the personal, telling the story of Adrianne Haslet-Davis, a professional ballroom dancer whose left leg was partially amputated after the Boston Marathon bombing. Herr had the honor of meeting her at a rehabilitation hospital in Boston and, after hearing her story, decided, “Let’s build her a bionic limb.”


Herr’s lab launched a 200-day research period to study the dynamics of dance — to look at how dancers move and what forces they apply while they go. They embedded the fundamentals of dance into a limb for Haslet-Davis.


“In 3.5 seconds, the criminals and cowards took Adrianne off the dance floor,” he says. “In 200 days, we put her back.”


With that, Herr calls Haslet-Davis out for what will be her first dance since the bombing, just a little under a year ago.


Haslet-Davis steps on stage with her partner, professional dancer Christian Lightner. The two begin to dance a rumba, Haslet-Davis performing intricate back-and-forth footwork. To Enrique Iglesias’ “Ring My Bells,” she twirls around her partner as the white fringe of her skirt flaps in the air. Her body looks lithe and unimpaired. Her bionic foot is encased in a white dancing slipper, just like her right foot.


It’s a stunning moment. One that underscores Herr’s ultimate point.


“Bionics are not only about making people stronger and faster,” he says. “Our expression, our humanity can be embedded into our electromechanics.”


Story Source:


The above story is based on materials provided by TED BLOG, Kate Torgovnick May.


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