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New material kills E. coli bacteria in 30 seconds

A microscopic image of the E. coli bacteria (credit: Institute of Bioengineering and Nanotechnology)

A new material that can kill E. coli bacteria within 30 seconds has been developed by researchers at the Institute of Bioengineering and Nanotechnology (IBN) of A*STAR in Singapore.

Triclosan, a common antibacterial ingredient found in many products such as toothpastes, soaps, and detergents to reduce or prevent bacterial infections, has been linked to making bacteria resistant to antibiotics, with adverse health effects. The European Union has restricted the use of triclosan in cosmetics, and the U.S. FDA is conducting an ongoing review of this ingredient.

Destroying the cell membrane to prevent resistance to antibiotics

To find a more suitable alternative, IBN Group Leader Yugen Zhang, PhD, and his team synthesized a chemical compound made up of molecules linked together in a chain (“imidazolium oligomers”), which they found can kill 99.7% of the E. coli bacteria within 30 seconds. The chain-like structure helps to penetrate the cell membrane and destroy the bacteria.

SEM image of E. coli before (left) and after treatment with IBN-C8 (right) (credit: S.N. Riduan et al./Small)

In contrast, current antibiotics only kill the bacteria but fail to destroy the cell membrane, allowing new antibiotic-resistant bacteria to grow.

“Our unique material can kill bacteria rapidly and inhibit the development of antibiotic-resistant bacteria. Computational chemistry studies supported our experimental findings that the chain-like compound works by attacking the cell membrane. This material is also safe for use because it carries a positive charge that targets the more negatively charged bacteria, without destroying red blood cells,” said Zhang.

The imidazolium oligomers come in the form of a white powder that is soluble in water. The researchers also found that once this was dissolved in alcohol, it formed gels spontaneously. So this material could be incorporated in alcohol-based sprays used for sterilization in hospitals or homes.

E. coli is a type of bacteria found in the intestines of humans and animals, and some strains can cause severe diarrhea, abdominal pain, and fever. Such infection is contagious and can spread through contaminated food or water, or from contact with people or animals.

Besides E. coli, IBN’s material was tested against other common strains of antibiotic-resistant bacteria and fungi such as Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans (which can cause conditions ranging from skin infections to pneumonia and toxic shock syndrome) and was able to kill 99.9% of these microbes within two minutes.

The finding was published in the peer-reviewed journal Small.

Abstract of Ultrafast Killing and Self-Gelling Antimicrobial Imidazolium Oligomers

Infectious diseases and the increasing threat of worldwide pandemics have underscored the importance of antibiotics and hygiene. Intensive efforts have been devoted to developing new antibiotics to meet the rapidly growing demand. In particular, advancing the knowledge of the structure–property–activity relationship is critical to expedite the design and development of novel antimicrobial with the needed potential and efficacy. Herein, a series of new antimicrobial imidazolium oligomers are developed with the rational manipulation of terminal group’s hydrophobicity. These materials exhibit superior activity, excellent selectivity, ultrafast killing (>99.7% killing within 30 s), and desirable self-gelling properties. Molecular dynamic simulations reveal the delicate effect of structural changes on the translocation motion across the microbial cell membrane. The energy barrier of the translocation process analyzed by free energy calculations provides clear kinetic information to suggest that the spontaneous penetration requires a very short timescale of seconds to minutes for the new imidazolium oligomers.

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Scientists plan to build human genome from scratch

Efficiency trends in DNA sequencing (green) and synthesis of double-stranded DNA (dsDNA, blue) and single-stranded DNA (ssDNA, red) over the past ~35 years. The disruptive improvement in sequencing and ssDNA (oligonucleotides) synthesis technologies has improved from multiplex and miniaturization technologies in high-throughput DNA sequencing and oligo microarray technologies, respectively. (credit: Jef D. Boeke et al./Science)

Leading genomics experts have announced Genome Project-write (HGP-write), which aims to synthesize entire genomes of humans and other species from chemical components and get them to function in living cells.

As explained in Science, the goal of HGP-write is to reduce the costs of engineering large genomes, including a human genome, and to develop an ethical framework for genome-scale engineering and transformative medical applications.

Impacts expected on human health, energy, agriculture, chemicals, and bioremediation

HGP-write will build on the knowledge gained by The Human Genome Project (HGP-read), especially in genomic-based discovery, diagnostics, and therapeutics. But while the Human Genome Project “read” DNA to understand its code, HGP-write will use the cellular machinery provided by nature to “write” code, constructing vast DNA chains.

The goal is to launch HGP-write in 2016 with $100 million in committed support from public, private, philanthropic, industry, and academic sources globally. Autodesk has already contributed a leadership gift of $250,000 to seed the planning and launch of HGP-write.

According to the authors of the Science commentary, although “…sequencing, analyzing and editing DNA continues to advance at breakneck pace, the capability to construct DNA sequences in cells is mostly limited to a small number of short segments, restricting the ability to manipulate and understand biological systems.”

Exponential improvements in genome engineering

The new effort is expected to lead to a massive amount of information connecting the sequence of nucleotide bases in DNA with their physiological properties and functions, and it promises to have a significant impact on human health and other critical areas such as energy, agriculture, chemicals, and bioremediation, according to the organizers.

HGP-write will be implemented through a new, independent nonprofit organization, the Center of Excellence for Engineering Biology as an open, international, multi-disciplinary research project.*

“This grand challenge is more ambitious and more focused on understanding the practical applications than the original Human Genome Project,” said George Church, Ph.D., Robert Winthrop Professor of Genetics at Harvard Medical School. “Exponential improvements in genome engineering technologies and functional testing provide an opportunity to deepen the understanding of our genetic blueprint and use this knowledge to address many of the global problems facing humanity.”

Another goal is development of new genomics analysis, design, synthesis, assembly and testing technologies, with the goal of making them more affordable and widely available. “Writing DNA code is the future of science and medicine, but our technical capabilities remain limited,” said Andrew Hessel, Distinguished Researcher, Bio/Nano Research Group, Autodesk, who will head a multidisciplinary team exploring computer-aided design and manufacturing for biotechnology and nanotechnology R&D.

“HGP-write will require research and development on a grand scale, and this effort will help to push our current technical limits by several orders of magnitude,” he said.

The HGP-write project developed from a series of meetings held over the last several years, including a closed-door meeting held May 10 in Boston, which brought together a diverse group of 130 participants from many different countries, including biologists, ethicists, engineers, plus representatives from industry, law and government.

* The Genome Project-write (HGP-write) will be an open, international research project led by a multi-disciplinary group of scientific leaders who plan to oversee a reduction in the costs of engineering and testing large genomes, including a human genome, in cell lines more than 1,000-fold within ten years. 

To ensure public engagement and transparency, HGP-write will include mechanisms to encourage public discourse around the emerging HGP-write capabilities. The Woodrow Wilson Center for International Scholars will help to lead such efforts for HGP-write.

Principals are:

  • Jef Boeke, Ph.D., Director, Institute for Systems Genetics, Professor, Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center. Dr. Boeke is a leader of the Synthetic Yeast Project (Sc2.0), which seeks to create living yeast cells with entirely redesigned chromosomes by 2017.
  • George Church, Ph.D., Robert Winthrop Professor of Genetics at Harvard Medical School, Core Faculty Member at the Wyss Institute for Biologically Inspired Engineering at Harvard University, Professor of Health Sciences and Technology at Harvard and the Massachusetts Institute of Technology (MIT), and Senior Associate Faculty member at the Broad Institute. Among the leaders of the original HGP-read, Dr. Church currently heads an effort to create a version of the bacteria E.coli with a redesigned genome.
  • Andrew Hessel, Distinguished Researcher, Bio/Nano Research Group, Autodesk. He spearheads a multidisciplinary team exploring computer-aided design and manufacturing for biotechnology and nanotechnology R&D.
  • Nancy J Kelley, J.D., M.P.P., President & CEO, Nancy J Kelley & Associates, formerly Founding Executive Director, New York Genome Center. She is lead executive of HGP-write and the related Center of Excellence for Engineering Biology.

Abstract of The Genome Project–Write

The Human Genome Project (“HGP-read”) nominally completed in 2004 aimed to sequence the human genome and improve technology, cost, and quality of DNA sequencing (1, 2). It was biology’s first genome-scale project, and at the time was considered controversial by some. Now it is recognized as one of the great feats of exploration, one that has revolutionized science and medicine.

Although sequencing, analyzing, and editing DNA continue to advance at breakneck pace, the capability to construct DNA sequences in cells is mostly limited to a small number of short segments, restricting the ability to manipulate and understand biological systems. Further understanding of genetic blueprints could come from construction of large, gigabase (Gb)–sized animal and plant genomes, including the human genome, which would in turn drive development of tools and methods to facilitate large-scale synthesis and editing of genomes. To this end, we propose the Human Genome Project–Write (HGP-write).

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Chronic stroke patients safely recover after injection of human stem cells


Injecting specially prepared human adult stem cells directly into the brains of chronic stroke patients proved safe and effective in restoring motor (muscle) function in a small clinical trial led by Stanford University School of Medicine investigators.

The 18 patients had suffered their first and only stroke between six months and three years before receiving the injections, which involved drilling a small hole through their skulls.

For most patients, at least a full year had passed since their stroke — well past the time when further recovery might be hoped for.  In each case, the stroke had taken place beneath the brain’s outermost layer, or cortex, and had severely affected motor function. “Some patients couldn’t walk,” Steinberg said. “Others couldn’t move their arm.”

Sonia Olea Coontz had a stroke in 2011 that affected the movement of her right arm and leg. After modified stem cells were injected into her brain as part of a clinical trial, she says her limbs “woke up.” (credit: Mark Rightmire/Stanford University School of Medicine)

One of those patients, Sonia Olea Coontz, of Long Beach, California, now 36, had a stroke in May 2011. “My right arm wasn’t working at all,” said Coontz. “It felt like it was almost dead. My right leg worked, but not well.” She walked with a noticeable limp. “I used a wheelchair a lot. After my surgery, they woke up,” she said of her limbs.

‘Clinically meaningful’ results

The promising results set the stage for an expanded trial of the procedure now getting underway. They also call for new thinking regarding the permanence of brain damage, said Gary Steinberg, MD, PhD, professor and chair of neurosurgery.

“This was just a single trial, and a small one,” cautioned Steinberg, who led the 18-patient trial and conducted 12 of the procedures himself. (The rest were performed at the University of Pittsburgh.) “It was designed primarily to test the procedure’s safety. But patients improved by several standard measures, and their improvement was not only statistically significant, but clinically meaningful. Their ability to move around has recovered visibly. That’s unprecedented. At six months out from a stroke, you don’t expect to see any further recovery.”

The trial’s results are detailed in a paper published online June 2 in Stroke. Steinberg, who has more than 15 years’ worth of experience in work with stem cell therapies for neurological indications, is the paper’s lead and senior author.

The procedure involved injecting SB623 mesenchymal stem cells, derived from the bone marrow of two donors and then modified to beneficially alter the cells’ ability to restore neurologic function.*

Motor-function improvements

Substantial improvements were seen in patients’ scores on several widely accepted metrics of stroke recovery. Perhaps most notably, there was an overall 11.4-point improvement on the motor-function component of the Fugl-Meyer test, which specifically gauges patients’ movement deficits. “Patients who were in wheelchairs are walking now,” said Steinberg, who is the Bernard and Ronni Lacroute-William Randolph Hearst Professor in Neurosurgery and Neurosciences.

“We know these cells don’t survive for more than a month or so in the brain,” he added. “Yet we see that patients’ recovery is sustained for greater than one year and, in some cases now, more than two years.”

Importantly, the stroke patients’ postoperative improvement was independent of their age or their condition’s severity at the onset of the trial. “Older people tend not to respond to treatment as well, but here we see 70-year-olds recovering substantially,” Steinberg said. “This could revolutionize our concept of what happens after not only stroke, but traumatic brain injury and even neurodegenerative disorders. The notion was that once the brain is injured, it doesn’t recover — you’re stuck with it. But if we can figure out how to jump-start these damaged brain circuits, we can change the whole effect.

“We thought those brain circuits were dead. And we’ve learned that they’re not.”

New trial now recruiting 156 patients

A new randomized, double-blinded multicenter phase-2b trial aiming to enroll 156 chronic stroke patients is now actively recruiting patients. Steinberg is the principal investigator of that trial. For more information, you can e-mail stemcellstudy@stanford.edu. “There are close to 7 million chronic stroke patients in the United States,” Steinberg said. “If this treatment really works for that huge population, it has great potential.”

Some 800,000 people suffer a stroke each year in the United States alone. About 85 percent of all strokes are ischemic: They occur when a clot forms in a blood vessel supplying blood to part of the brain, with subsequent intensive damage to the affected area. The specific loss of function incurred depends on exactly where within the brain the stroke occurs, and on its magnitude.

Although approved therapies for ischemic stroke exist, to be effective they must be applied within a few hours of the event — a time frame that often is exceeded by the amount of time it takes for a stroke patient to arrive at a treatment center.

Consequently, only a small fraction of patients benefit from treatment during the stroke’s acute phase. The great majority of survivors end up with enduring disabilities. Some lost functionality often returns, but it’s typically limited. And the prevailing consensus among neurologists is that virtually all recovery that’s going to occur comes within the first six months after the stroke.

* Mesenchymal stem cells are the naturally occurring precursors of muscle, fat, bone and tendon tissues. In preclinical studies, though, they’ve not been found to cause problems by differentiating into unwanted tissues or forming tumors. Easily harvested from bone marrow, they appear to trigger no strong immune reaction in recipients even when they come from an unrelated donor. In fact, they may actively suppress the immune system. For this trial, unlike the great majority of transplantation procedures, the stem cell recipients received no immunosuppressant drugs.

During the procedure, patients’ heads were held in fixed positions while a hole was drilled through their skulls to allow for the injection of SB623 cells, accomplished with a syringe, into a number of spots at the periphery of the stroke-damaged area, which varied from patient to patient.

Afterward, patients were monitored via blood tests, clinical evaluations and brain imaging. Interestingly, the implanted stem cells themselves do not appear to survive very long in the brain. Preclinical studies have shown that these cells begin to disappear about one month after the procedure and are gone by two months. Yet, patients showed significant recovery by a number of measures within a month’s time, and they continued improving for several months afterward, sustaining these improvements at six and 12 months after surgery. Steinberg said it’s likely that factors secreted by the mesenchymal cells during their early postoperative presence near the stroke site stimulates lasting regeneration or reactivation of nearby nervous tissue.

No relevant blood abnormalities were observed. Some patients experienced transient nausea and vomiting, and 78 percent had temporary headaches related to the transplant procedure.

Abstract of Clinical Outcomes of Transplanted Modified Bone Marrow–Derived Mesenchymal Stem Cells in Stroke: A Phase 1/2a Study

Background and Purpose—Preclinical data suggest that cell-based therapies have the potential to improve stroke outcomes.

Methods—Eighteen patients with stable, chronic stroke were enrolled in a 2-year, open-label, single-arm study to evaluate the safety and clinical outcomes of surgical transplantation of modified bone marrow–derived mesenchymal stem cells (SB623).

Results—All patients in the safety population (N=18) experienced at least 1 treatment-emergent adverse event. Six patients experienced 6 serious treatment-emergent adverse events; 2 were probably or definitely related to surgical procedure; none were related to cell treatment. All serious treatment-emergent adverse events resolved without sequelae. There were no dose-limiting toxicities or deaths. Sixteen patients completed 12 months of follow-up at the time of this analysis. Significant improvement from baseline (mean) was reported for: (1) European Stroke Scale: mean increase 6.88 (95% confidence interval, 3.5–10.3;P<0.001), (2) National Institutes of Health Stroke Scale: mean decrease 2.00 (95% confidence interval, −2.7 to −1.3; P<0.001), (3) Fugl-Meyer total score: mean increase 19.20 (95% confidence interval, 11.4–27.0; P<0.001), and (4) Fugl-Meyer motor function total score: mean increase 11.40 (95% confidence interval, 4.6–18.2;P<0.001). No changes were observed in modified Rankin Scale. The area of magnetic resonance T2 fluid-attenuated inversion recovery signal change in the ipsilateral cortex 1 week after implantation significantly correlated with clinical improvement at 12 months (P<0.001 for European Stroke Scale).

Conclusions—In this interim report, SB623 cells were safe and associated with improvement in clinical outcome end points at 12 months.

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Dietary fiber has biggest influence on successful aging, research reveals

(credit: iStock)

Eating the right amount of dietary fiber from breads, cereals, and fruits can help us avoid disease and disability into old age, according to an open-access paper published in The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences by scientists from The Westmead Institute for Medical Research in Australia.

Using data compiled from the Blue Mountains Eye Study, a benchmark population-based study that examined a cohort of more than 1,600 adults aged 50 years and older for long-term sensory loss risk factors and systemic diseases, the researchers found that out of all the factors they examined — including a person’s total carbohydrate intake, total fiber intake, glycemic index, glycemic load, and sugar intake — it was, surprisingly, fiber that made the biggest difference to what the researchers termed “successful aging.”

Successful aging was defined as including an absence of disability, depressive symptoms, cognitive impairment, respiratory symptoms, and chronic diseases including cancer, coronary artery disease, and stroke.

Fiber, or roughage, is the indigestible part of plant foods that pushes through the digestive system, absorbing water along the way and easing bowel movements.

According to lead author of the paper, Associate Professor Bamini Gopinath, PhD, from the Institute’s Centre for Vision Research, “Out of all the variables that we looked at, fiber intake —- which is a type of carbohydrate that the body can’t digest — had the strongest influence,” she said. “Essentially, we found that those who had the highest intake of fiber or total fiber actually had an almost 80 percent greater likelihood of living a long and healthy life over a 10-year follow-up. That is, they were less likely to suffer from hypertension, diabetes, dementia, depression, and functional disability.”

While it might have been expected that the level of sugar intake would make the biggest impact on successful aging, Gopinath pointed out that the particular group they examined were older adults whose intake of carbonated and sugary drinks was quite low.

Although it is too early to use the study results as a basis for dietary advice, Gopinath said the research has opened up a new avenue for exploration. “There are a lot of other large cohort studies that could pursue this further and see if they can find similar associations. And it would also be interesting to tease out the mechanisms that are actually linking these variables,” she said.

This study backs up similar recent findings by the researchers, which highlight the importance of the overall diet and healthy aging.

In another study published last year in The Journals of Gerontology, Westmead Institute researchers found that, in general, adults who closely adhered to recommended national dietary guidelines reached old age with an absence of chronic diseases and disability, and had good functional and mental health status.

Abstract of Association Between Carbohydrate Nutrition and Successful Aging Over 10 Years

Background: We prospectively examined the relationship between dietary glycemic index (GI) and glycemic load (GL), carbohydrate, sugars, and fiber intake (including fruits, vegetable of breads/cereals fiber) with successful aging (determined through a multidomain approach).

Methods: A total of 1,609 adults aged 49 years and older who were free of cancer, coronary artery disease, and stroke at baseline were followed for 10 years. Dietary data were collected using a semiquantitative Food Frequency Questionnaire. Successful aging status was determined through interviewer-administered questionnaire at each visit and was defined as the absence of disability, depressive symptoms, cognitive impairment, respiratory symptoms, and chronic diseases (eg, cancer and coronary artery disease).

Results: In all, 249 (15.5%) participants had aged successfully 10 years later. Dietary GI, GL, and carbohydrate intake were not significantly associated with successful aging. However, participants in the highest versus lowest (reference group) quartile of total fiber intake had greater odds of aging successfully than suboptimal aging, multivariable-adjusted odds ratio (OR), 1.79 (95% confidence interval [CI] 1.13–2.84). Those who remained consistently below the median in consumption of fiber from breads/cereal and fruit compared with the rest of cohort were less likely to age successfully, OR 0.53 (95% CI 0.34–0.84) and OR 0.64 (95% CI 0.44–0.95), respectively.

Conclusions: Consumption of dietary fiber from breads/cereals and fruits independently influenced the likelihood of aging successfully over 10 years. These findings suggest that increasing intake of fiber-rich foods could be a successful strategy in reaching old age disease free and fully functional.

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Soft, safe robot actuators inspired by human bicep muscles

VAMPs are functionally modeled after the human bicep, similar to the biological muscle in terms of response time and efficiency. (credit: Wyss Institute at Harvard University)

If robots are going work around humans, they will have to be softer and safer. A Harvard team has designed a new actuator with that in mind. Its movements are similar to those of a human bicep muscle, using vacuum power to automate soft rubber beams. Like real muscles, the actuators are soft, shock-absorbing, and pose no danger, according to the researchers.

The work is led by George Whitesides, Ph.D., a Core Faculty member at Harvard’s Wyss Institute for Biologically Inspired Engineering, the Woodford L. and Ann A. Flowers University Professor of Chemistry and Chemical Biology in Harvard University’s Faculty of Arts and Sciences (FAS), and a Director of the Kavli Institute for Bionano Science and Technology at Harvard University.

Whitesides’ team took an unconventional approach to its design, relying on vacuum to decrease the actuator’s volume and cause it to buckle. While conventional engineering would consider bucking to be a mechanical instability and a point of failure, in this case the team leveraged this instability to develop VAMPs (vacuum-actuated muscle-inspired pneumatic structures). Previous soft actuators rely on pressurized systems that expand in volume, but VAMPs mimic true muscle because they contract, which makes them useful in confined spaces and for a variety of purposes.

In this image, VAMPs are shown actuated and cut open in cross section. The honeycomb cross section shows the inner chambers that collapse when vacuum is applied. (credit: Wyss Institute at Harvard University)

The actuator has soft elastomeric rubber beams filled with small, hollow chambers of air like a honeycomb. By applying vacuum, the chambers collapse and the entire actuator contracts, generating movement. The internal honeycomb structure can be custom tailored to enable linear, twisting, bending, or combinatorial motions.

The team envisions that robots built with VAMPs could be used to assist the disabled or elderly, to serve food, deliver goods, and perform other tasks related to the service industry. Soft robots could also make industrial production lines safer and faster, and quality control easier to manage by enabling human operators to work in the same space.

Fail-safe design

VAMPs are designed to prevent failure — even when damaged with a 2mm hole, the team showed that VAMPs will still function. In the event that major damage is caused to the system, it fails safely. “It can’t explode, so it’s intrinsically safe,” said Whitesides. Whereas other actuators powered by electricity or combustion could cause damage to humans or their surroundings, loss of vacuum pressure in VAMPs would simply render the actuator motionless.

“These self-healing, bioinspired actuators bring us another step closer to being able to build entirely soft-bodied robots, which may help to bridge the gap between humans and robots and open entirely new application areas in medicine and beyond,” said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Boston Children’s Hospital Vascular Biology Program, as well as Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS).

The work was reported June 1 in the journal Advanced Materials Technologies.

Harvard’s Office of Technology Development has filed patents on this and related inventions, and the soft actuator technology has been licensed to Soft Robotics, Inc., a startup launched in 2013 and cofounded by Whitesides. The company is developing robotic grasping systems toward initial applications including picking and packing in unstructured environments — for example, handling fruits and vegetables in produce distribution warehouses. Longer term, this technology can be leveraged to develop products for biomedical applications.

Abstract of Buckling Pneumatic Linear Actuators Inspired by Muscle

The mechanical features of biological muscles are difficult to reproduce completely in synthetic systems. A new class of soft pneumatic structures (vacuum-actuated muscle-inspired pneumatic structures) is described that combines actuation by negative pressure (vacuum), with cooperative buckling of beams fabricated in a slab of elastomer, to achieve motion and demonstrate many features that are similar to that of mammalian muscle.

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Ancient anti-inflammatory drug salicylic acid has cancer-fighting properties

White willow (Salix alba) is a natural source of salicylic acid (credit: Otto Wilhelm Thomé (1885)/public domain)

Scientists from the Gladstone Institutes have identified a new pathway by which salicylic acid — a key compound in aspirin (acetylsalicylic acid) — stops inflammation and cancer.

In a study published in eLife, the researchers found that both salicylic acid — and also diflunisal, a cousin of aspirin — suppress two key proteins (p300 and CREB-binding protein or CBP) that help control gene expression throughout the body.

These proteins are epigenetic regulators that control the levels of proteins that cause inflammation or are involved in cell growth.

So by suppressing these proteins, these compounds can prevent cellular damage caused by inflammation. This study provides the first concrete demonstration that both p300 and CBP can be targeted by drugs and may have important clinical implications.

“Salicylic acid is one of the oldest drugs on the planet, dating back to the Egyptians and the Greeks, but we’re still discovering new things about it,” said senior author Eric Verdin, MD, associate director of the Gladstone Institute of Virology and Immunology. “Uncovering this pathway of inflammation that salicylic acid acts upon opens up a host of new clinical possibilities for these drugs.”

Shrinking tumors

Scientists at Gladstone and Sylvester Comprehensive Cancer Center, at the University of Miami Miller School of Medicine, worked together to test whether suppressing p300 with diflunisal would suppress leukemia growth in mice. As predicted, diflunisal stopped cancer progression and shrunk the tumors in the mouse model of leukemia.

“We have conducted a clinical trial of salicylic acid in patients with hematologic cancers and found it to be safe,” said Sylvester director and co-author Stephen D. Nimer, MD. “Thus, this collaborative effort to develop novel epigenetic therapies is an important next step in our journey to find more effective treatment for leukemia patients.”

The scientists are now pursuing a clinical trial that will test the ability of salicylic acid to treat patients with leukemia as part of novel combination therapies. Other possible clinical applications for salicylic acid include other forms of cancer, type 2 diabetes, inflammatory diseases, and even neurodegenerative disorders, such as Alzheimer’s disease.

Prior Gladstone research showed that another drug containing salicylic acid prevented the accumulation of tau in neurons and protected against cognitive decline in a mouse model of dementia.

Researchers from the University of Miami, University of Pennsylvania, and the National Cancer Institute also took part in the study.

Funding was provided by the University of California, San Francisco-Gladstone Institute of Virology and Immunology Center for AIDS Research (CFAR), the University of California, Berkeley Fogarty International AIDS Training Program, the American Cancer Society, the Larry L. Hillblom Foundation, the John A. Hartford Foundation, the National Cancer Institute, and the UCSF Geriatric Research Training Program.

Abstract of Salicylate, diflunisal and their metabolites inhibit CBP/p300 and exhibit anticancer activity

Salicylate and acetylsalicylic acid are potent and widely used anti-inflammatory drugs. They are thought to exert their therapeutic effects through multiple mechanisms, including the inhibition of cyclo-oxygenases, modulation of NF-κB activity, and direct activation of AMPK. However, the full spectrum of their activities is incompletely understood. Here we show that salicylate specifically inhibits CBP and p300 lysine acetyltransferase activity in vitro by direct competition with acetyl-Coenzyme A at the catalytic site. We used a chemical structure-similarity search to identify another anti-inflammatory drug, diflunisal, that inhibits p300 more potently than salicylate. At concentrations attainable in human plasma after oral administration, both salicylate and diflunisal blocked the acetylation of lysine residues on histone and non-histone proteins in cells. Finally, we found that diflunisal suppressed the growth of p300-dependent leukemia cell lines expressing AML1-ETO fusion protein in vitro and in vivo. These results highlight a novel epigenetic regulatory mechanism of action for salicylate and derivative drugs.

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Implanted neuroprosthesis improves walking ability in stroke patient

Left: multichannel implantable gait-assist system. Right: participant walking with the system. (credit: N.S. Makowski et al./Am. J. Phys. Med. Rehabil.)

A surgically implanted neuroprosthesis has led to substantial improvement in walking speed and distance in a patient with limited mobility after a stroke, according to a single-patient study in the American Journal of Physical Medicine & Rehabilitation.

The system, programmed to stimulate coordinated activity of hip, knee, and ankle muscles, “is a promising intervention to provide assistance to stroke survivors during daily walking,” write Nathaniel S. Makowski, PhD, and colleagues of the Louis Stokes Cleveland Veterans Affairs Medical Center.

With technical refinements and further research, such implanted neuroprosthesis systems might help to promote walking ability for at least some patients with post-stroke disability.

Clinically relevant gait improvements

The researchers report their experience with an implanted neuroprosthesis in a 64-year-old man with impaired motion and sensation of his left leg and foot after a hemorrhagic (bleeding) stroke. After thorough evaluation, he underwent surgery to place an implanted pulse generator and intramuscular stimulating electrodes in seven muscles of the hip, knee, and ankle.*

Makowski and colleagues then created a customized electrical stimulation program to activate the muscles, with the goal of restoring a more natural gait pattern. The patient went through extensive training in the researchers’ laboratory for several months after neuroprosthesis placement.

With training without muscle stimulation, gait speed only increased from 0.29 meters per second (m/s) before surgery, to 0.35 m/s after training, a non-significant improvement. But when muscle stimulation was turned on, gait speed increased dramatically: to 0.72 m/s, with “more symmetrical and dynamic gait.”

In addition, the patient was able to walk much farther. When first evaluated, he could walk only 76 meters before becoming fatigued. After training but without stimulation, he could walk about 300 meters (in 16 minutes). With stimulation, the patient’s maximum walking distance increased to more than 1,400 meters (in 41 minutes) with stimulation.

Even though the patient wasn’t walking with stimulation outside the laboratory, his walking ability in daily life improved significantly. He went from “household-only” ambulation to increased walking outside in the neighborhood.

“The therapeutic effect is likely a result of muscle conditioning during stimulated exercise and gait training,” according to the authors. “Persistent use of the device during walking may provide ongoing training that maintains both muscle conditioning and cardiovascular health.”

While the results of this initial experience in a single patient are encouraging, the researchers emphasize that large-scale studies will be needed to demonstrate the wider applicability of a neuroprosthesis for multi-joint control. If the benefits are confirmed, Makowski and colleagues conclude, “daily use of an implanted system could have significant clinical relevance to a portion of the stroke population.”

* Tensor fasciae latae (hip flexor), sartorius (hip and knee flexor), gluteus maximus (hip extensor), short head of biceps femoris (knee flexor), quadriceps (knee extensor), tibialis anterior/peroneus longus (ankle dorsiflexors), and gastrocnemius.

Abstract of Improving Walking with an Implanted Neuroprosthesis for Hip, Knee, and Ankle Control After Stroke.

Objective: The objective of this work was to quantify the effects of a fully implanted pulse generator to activate or augment actions of hip, knee, and ankle muscles after stroke.

Design: The subject was a 64-year-old man with left hemiparesis resulting from hemorrhagic stroke 21 months before participation. He received an 8-channel implanted pulse generator and intramuscular stimulating electrodes targeting unilateral hip, knee, and ankle muscles on the paretic side. After implantation, a stimulation pattern was customized to assist with hip, knee, and ankle movement during gait.

The subject served as his own concurrent and longitudinal control with and without stimulation. Outcome measures included 10-m walk and 6-minute timed walk to assess gait speed, maximum walk time, and distance to measure endurance, and quantitative motion analysis to evaluate spatial-temporal characteristics. Assessments were repeated under 3 conditions: (1) volitional walking at baseline, (2) volitional walking after training, and (3) walking with stimulation after training.

Results: Volitional gait speed improved with training from 0.29 m/s to 0.35 m/s and further increased to 0.72 m/s with stimulation. Most spatial-temporal characteristics improved and represented more symmetrical and dynamic gait.

Conclusions: These data suggest that a multijoint approach to implanted neuroprostheses can provide clinically relevant improvements in gait after stroke.

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‘On-the-fly’ 3-D printing system prints what you design, as you design it

This wire frame prototype of a toy aircraft was printed in just 10 minutes, including testing for correct fit, and modified during printing to create the cockpit. The file was updated in the process, and could be used to print a finished model. (credit: Cornell University)

Cornell researchers have developed an interactive prototyping system that prints a wire frame of your design as you design it. You can pause anywhere in the process to test or measure and make needed changes, which will be added to the physical model still in the printer.

In conventional 3-D printing, a nozzle scans across a stage depositing drops of plastic, rising slightly after each pass to build an object in a series of layers. With the On-the-Fly-Print system, the nozzle instead extrudes a rope of quick-hardening plastic to create a wire frame that represents the surface of the solid object described in a computer-aided design (CAD) file and allows the designer to make refinements while printing is in progress.

Wireframe test models printed with On-The-Fly Print system (credit: Cornell University)

The printer’s stage can be rotated to present any face of the model facing up; so an airplane fuselage, for example, can be turned on its side to add a wing. There is also a cutter to remove parts of the model, say, to give the airplane a cockpit, and the nozzle can reach through the wire mesh to make changes inside. The system also adds yaw and pitch for five degrees of freedom.

The researchers described the On-the-Fly-Print system in a paper presented at the 2016 ACM Conference for Human Computer Interaction. The work was supported in part by the National Science Foundation and by Autodesk Corp.


Huaishu Peng | On-the-Fly Print: Incremental Printing While Modelling

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How to make opaque AI decisionmaking accountable

Machine-learning algorithms are increasingly used in making important decisions about our lives — such as credit approval, medical diagnoses, and in job applications — but exactly how they work usually remains a mystery. Now Carnegie Mellon University researchers may devised an effective way to improve transparency and head off confusion or possibly legal issues.

CMU’s new Quantitative Input Influence (QII) testing tools can generate “transparency reports” that provide the relative weight of each factor in the final decision, claims Anupam Datta, associate professor of computer science and electrical and computer engineering.

Testing for discrimination

These reports could also be used proactively by an organization to see if an artificial intelligence system is working as desired, or by a regulatory agency to determine whether a decision-making system inappropriately discriminated, based on factors like race and gender.

To achieve that, the QII measures considers correlated inputs while measuring influence. For example, consider a system that assists in hiring decisions for a moving company, in which two inputs, gender and the ability to lift heavy weights, are positively correlated with each other and with hiring decisions.

Yet transparency into whether the system actually uses weightlifting ability or gender in making its decisions has substantive implications for determining if it is engaging in discrimination. In this example, the company could keep the weightlifting ability fixed, vary gender, and check whether there is a difference in the decision.

CMU researchers are careful to state in an open-access report on QII (presented at the IEEE Symposium on Security and Privacy, May 23–25, in San Jose, Calif.), that “QII does not suggest any normative definition of fairness. Instead, we view QII as a diagnostic tool to aid fine-grained fairness determinations.”

Is your AI biased?

The Ford Foundation published a controversial blog post last November stating that “while we’re lead to believe that data doesn’t lie — and therefore, that algorithms that analyze the data can’t be prejudiced — that isn’t always true. The origin of the prejudice is not necessarily embedded in the algorithm itself. Rather, it is in the models used to process massive amounts of available data and the adaptive nature of the algorithm. As an adaptive algorithm is used, it can learn societal biases it observes.

“As Professor Alvaro Bedoya, executive director of the Center on Privacy and Technology at Georgetown University, explains, ‘any algorithm worth its salt’ will learn from the external process of bias or discriminatory behavior. To illustrate this, Professor Bedoya points to a hypothetical recruitment program that uses an algorithm written to help companies screen potential hires. If the hiring managers using the program only select younger applicants, the algorithm will learn to screen out older applicants the next time around.”

Influence variables

The QII measures also quantify the joint influence of a set of inputs (such as age and income) on outcomes, and the marginal influence of each input within the set. Since a single input may be part of multiple influential sets, the average marginal influence of the input is computed using “principled game-theoretic aggregation” measures that were previously applied to measure influence in revenue division and voting.

Examples of outcomes from transparency reports for two job applicants. Left: “Mr. X” is deemed to be a low income individual, an income classifier learned from the data. This result may be surprising to him: he reports high capital gains ($14k), and only 2.1% of people with capital gains higher than $10k are reported as low income. In fact, he might be led to believe that his classification may be a result of his ethnicity or country of origin. Examining his transparency report in the figure, however, we find that the most influential features that led to his negative classification were Marital Status, Relationship and Education. Right: “Mr. Y” has even higher capital gains than Mr. X. Mr. Y is a 27-year-old, with only Preschool education, and is engaged in fishing. Examination of the transparency report reveals that the most influential factor for negative classification for Mr. Y is his Occupation. Interestingly, his low level of education is not considered very important by this classifier. (credit: Anupam Datta et al./2016 P IEEE S SECUR PRIV)

“To get a sense of these influence measures, consider the U.S. presidential election,” said Yair Zick, a post-doctoral researcher in the CMU Computer Science Department. “California and Texas have influence because they have many voters, whereas Pennsylvania and Ohio have power because they are often swing states. The influence aggregation measures we employ account for both kinds of power.”

The researchers tested their approach against some standard machine-learning algorithms that they used to train decision-making systems on real data sets. They found that the QII provided better explanations than standard associative measures for a host of scenarios they considered, including sample applications for predictive policing and income prediction.

Privacy concerns

But transparency reports could also potentially compromise privacy, so in the paper, the researchers also explore the transparency-privacy tradeoff and prove that a number of useful transparency reports can be made differentially private with very little addition of noise.

QII is not yet available, but the CMU researchers are seeking collaboration with industrial partners so that they can employ QII at scale on operational machine-learning systems.

Abstract of Algorithmic Transparency via Quantitative Input Influence: Theory and Experiments with Learning Systems

Algorithmic systems that employ machine learning play an increasing role in making substantive decisions in modern society, ranging from online personalization to insurance and credit decisions to predictive policing. But their decision-making processes are often opaque—it is difficult to explain why a certain decision was made. We develop a formal foundation to improve the transparency of such decision-making systems. Specifically, we introduce a family of Quantitative Input Influence (QII) measures that capture the degree of influence of inputs on outputs of systems. These measures provide a foundation for the design of transparency reports that accompany system decisions (e.g., explaining a specific credit decision) and for testing tools useful for internal and external oversight (e.g., to detect algorithmic discrimination). Distinctively, our causal QII measures carefully account for correlated inputs while measuring influence. They support a general class of transparency queries and can, in particular, explain decisions about individuals (e.g., a loan decision) and groups (e.g., disparate impact based on gender). Finally, since single inputs may not always have high influence, the QII measures also quantify the joint influence of a set of inputs (e.g., age and income) on outcomes (e.g. loan decisions) and the marginal influence of individual inputs within such a set (e.g., income). Since a single input may be part of multiple influential sets, the average marginal influence of the input is computed using principled aggregation measures, such as the Shapley value, previously applied to measure influence in voting. Further, since transparency reports could compromise privacy, we explore the transparency-privacy tradeoff and prove that a number of useful transparency reports can be made differentially private with very little addition of noise. Our empirical validation with standard machine learning algorithms demonstrates that QII measures are a useful transparency mechanism when black box access to the learning system is available. In particular, they provide better explanations than standard associative measures for a host of scenarios that we consider. Further, we show that in the situations we consider, QII is efficiently approximable and can be made differentially private while preserving accuracy.

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How to erase bad memories and enhance good ones

Mice normally freeze in position as a response to fear, as shown here under control condition (center row): fear conditioning induces freezing behavior in response (recall) to exposure to the conditioned stimulus (tone), but the freezing response normally decreases (extinction) following several days of multiple tone exposures (the mice get used to it). However, enhancing release of acetylcholine (blue light) to the amygdala during conditioned fear training resulted in continued freezing behavior 24 hours later and persisted over long periods of time (extinction). In contrast, reducing acetylcholine (yellow light) during the initial training period reduced the freezing behavior (during recall) and led to greater retention of the extinction learning (reduced freezing). (credit: Li Jiang et al./Neuron)

Imagine if people with dementia could enhance good memories or those with post-traumatic stress disorder could wipe out bad memories. A Stony Brook University research team has now taken a step toward that goal by manipulating one of the brain’s natural mechanisms for signaling involved in emotional memory: a neurotransmitter called acetylcholine.

The region of the brain most involved in emotional memory is thought to be the amygdala. Cholinergic neurons that reside in the base of the brain — the same neurons that appear to be affected early in cognitive decline — stimulate release of acetylcholine by neurons in the amygdala, which strengthens emotional memories.

Because fear is a strong and emotionally charged experience, Lorna Role, PhD, Professor and Chair of the Department of Neurobiology and Behavior, and colleagues used a fear-based memory model in mice to test the underlying mechanism of memory and the specific role of acetylcholine in the amygdala.

A step toward reversing post-traumatic stress disorder

Be afraid. Be very afraid. Optogenetic stimulation with blue light. (credit: Deisseroth Laboratory)

To achieve precise control, the team used optogenetics, a research method using light, to stimulate specific populations of cholinergic neurons in the amygdala during the experiments to release acetylcholine. As noted in previous studies reported on KurzweilAI, shining blue (or green) light on neurons treated with light-sensitive membrane proteins stimulates the neurons while shining yellow (or red) light inhibits (blocks) them.

So when the researchers used optogenetics with blue light to increase the amount of acetylcholine released in the amygdala during the formation of a traumatic memory, they found it greatly strengthened fear memory, making the memory last more than twice as long as normal.

But when they decreased acetylcholine signaling (using yellow light) in the amygdala from a traumatic experience — one that normally produces a fear response — they could actually extinguish (wipe out) the memory.

Role said the long-term goal of their research is to find ways — potentially independent of acetylcholine (or drug administration) — to enhance or diminish the strength of good memories and diminish the bad ones.

Their findings are published in the journal Neuron. The research was supported in part by the National Institutes of Health.

Abstract of Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits

We examined the contribution of endogenous cholinergic signaling to the acquisition and extinction of fear- related memory by optogenetic regulation of cholinergic input to the basal lateral amygdala (BLA). Stimulation of cholinergic terminal fields within the BLA in awake-behaving mice during training in a cued fear-conditioning paradigm slowed the extinction of learned fear as assayed by multi-day retention of extinction learning. Inhibition of cholinergic activity during training reduced the acquisition of learned fear behaviors. Circuit mechanisms underlying the behavioral effects of cholinergic signaling in the BLA were assessed by in vivo and ex vivo electrophysiological recording. Photostimulation of endogenous cholinergic input (1) enhances firing of putative BLA principal neurons through activation of acetylcholine receptors (AChRs), (2) enhances glutamatergic synaptic transmission in the BLA, and (3) induces LTP of cortical-amygdala circuits. These studies support an essential role of cholinergic modulation of BLA circuits in the inscription and retention of fear memories.