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Biotech, McGill Univ Partner on Soil Enhancement Microbes

Soybean field (ARS/USDA)

Soybean field (Agricultural Research Service/USDA)

23 October 2014. Inocucor Technologies Inc. and McGill University are collaborating on development of new types of microbes that improve soil for greater yields of large-scale crops such as corn and soybeans. Financial details of the research and licensing agreement between the company and university, both in Montreal, Quebec, Canada, were not disclosed.

Inocucor Technologies produces soil enhancement products based on microbial consortia, communities of engineered microbes, similar to bacteria or yeast, designed to produce desired outcomes in their environments. The company’s technology, invented by its founders Maggie Bywater-Ekegärd and Ananda Fitzsimmons, produces microbes with a fermentation process that boost the soil’s ability to stimulate the crop’s seed, plant, and root system. The engineered microbes send and receive biochemical signals with plant cells to achieve these results.

Bywater-Ekegärd and Fitzsimmons continue as vice presidents of Inocucor.

In the deal with McGill University, Inocucor engages the lab of plant biologist Donald Smith who earlier carried out sponsored field trials of the company’s current Garden Solution soil enhancement product. Smith’s research interests include studies of rhizobacteria that increase the growth and yield of many crops.

Garden Solution is designed to accelerate maturation and increase yields of vegetable and fruit crops. The collaboration with McGill aims to produce a new type of microbial product more applicable to large-scale agricultural crops including wheat, corn, canola, and soybeans. Trials conducted by Smith at McGill include tests of the company’s current formulation with soybeans and corn.

“Inocucor’s microbial innovations have huge implications for agriculture,” says Smith in an Inocucor statement. “The McGill team will study these active microbials with the intention of creating products for conventional farmers that give them a sustainable way to enhance yields and improve long-term health of soils.”

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IBM, Health Tech, Univ Designing Critical Care Mobile System



23 October 2014. IBM, University of Michigan, and mobile health technology company AirStrip are developing a system to provide real time monitoring and analytics for patients with chronic or critical disorders. The system is being designed to collect data directly from patients and provide early warning initially for hemodynamic decompensation, a type of heart failure and potentially lethal complication for critically ill and injured people. Financial and intellectual property aspects of the collaboration were not disclosed.

Hemodynamic decompensation results in a sudden worsening of heart functions. The ensuing reduction in heart output is marked by hypertension, malfunctions in heart muscles, and restriction of blood supply to tissues. Attempts by the heart to compensate for these deteriorating conditions only increases the damage, leading to a downward spiral for the patient.

Data in this early warning system for hemodynamic decompensation will come from sensors worn by patients, while in the hospital and at home, linked to their electronic health records. University of Michigan’s Center for Integrative Research in Critical Care in Ann Arbor will design algorithms to process these data and identify predictive risk factors that can alert clinicians of impending deterioration in the patient’s condition.

IBM will adapt its InfoSphere Streams analytics platform to integrate the real-time patient monitoring data with health records information and the algorithms from Michigan. IBM says InfoSphere Streams is designed to combine structured and unstructured data, like those often found in health IT records.

AirStrip, in San Antonio, Texas, develops mobile systems for clinicians that combine real time patient monitoring with data from electronic health records. AirStrip will adapt its AirStrip One platform designed for reporting patient data for clinicians on smartphones and tablets, which will receive the stream of integrated real-time data and analytics, for display and interaction on clinicians’ Apple, Android and Windows devices.

Early intervention in these cases is expected to improve care of critically ill patients and help reduce admission to intensive care units. The partners in the project say if this first application is a success, the system could be expanded to to detect deterioration in other chronic conditions, such as diabetes, chronic obstructive pulmonary disease (COPD), and congestive heart failure. The system can also be part of a more comprehensive model of continuous hospital-to-home patient monitoring.

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Hat tip: MedCity News

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Clinical Trial Proposals Sought for ALS Treatments

3-D brain wiring illustration

3-D brain wiring illustration (NIH)

22 October 2014. A group of U.S. organizations promoting research on therapies for amyotrophic lateral sclerosis or ALS are seeking proposals from academic-industry research teams for intermediate stage clinical trials to test treatment candidates for the disease. The organizations — ALS Association, ALS Accelerated Therapeutics or ALS ACT, and Northeast ALS Consortium — plan to award up to $1.5 million in research support, with letters of intent due by 9 January 2015.

Amyotrophic lateral sclerosis, also known as Lou Gehrig’s disease, is a progressive disorder that attacks nerve cells or neurons controlling voluntary muscle movements. In ALS, motor neurons in the brain stop sending signals to motor neurons in the spinal cord, and thus stop sending signals to muscles. Muscles begin to weaken and atrophy, eventually losing control over voluntary muscle movement. The result is disability and paralysis, including respiratory functions, leading to death. ALS affects 1 in about 30,000 people in the U.S., with 5,000 new cases each year.

At present there is no cure for ALS and only one approved drug — Riluzole, marketed as Rilutek by Sanofi — that slows the progress of the disease. The organizations say the research funded in this initiative can fill an urgent need for more treatments, particularly those beyond preclinical and early safety studies on humans.

Proposals should outline intermediate-stage studies of interventions that include markers to measure the therapy’s affect on the body, as well as a plan to collect samples for studies involving biomarkers. Intermediate-stage trials, sometimes called phase 2 trials, are studies involving larger numbers of patients than the small samples used in earlier safety studies, and test the effectiveness of the drug, as well as watch for safety or side-effects issues.

The organizations encourage teams comprised of academic and industry researchers, including those from pharmaceutical and biotechnology companies, to submit proposals. Letters of intent are due by 9 January 2015, with invitations to send in full proposals issued on 23 January. Full proposals are due by 2 March 2015, with evaluations conducted by a review panel from ALS ACT.

The winning proposal will be announced in May 2015. The successful bidder, say the organizations, will retain control of the study as well as intellectual property of the therapy being tested.

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Graphene Sensor Offers Clear Optical Access to Brain Cells

Blue light shines through brain sensor

Blue light shines through a clear sensor implanted in the brain of a lab animal. (Williams research group, Univ of Wisconsin – Madison)

22 October 2014. Engineers at University of Wisconsin in Madison developed an implanted transparent sensor made with graphene that allows for imaging and diagnostics in the brain requiring line-of-sight access. The team led by electrical engineering professor Zhenqiang Ma and biomedical engineering faculty Justin Williams published its findings this week in the journal Nature Communications.

A continuing problem with current implanted sensors to measure neural activity in the brain, say the researchers, is the composition of the devices, which blocks viewing by imaging and diagnostic technologies. “A traditional implant looks like a square of dots, and you can’t see anything under it,” says Williams in a university statement. “We wanted to make a transparent electronic device.”

Ma, Williams, and colleagues chose graphene as the main material for the electronics in their sensor. Graphene is a carbon material closely related to graphite like that used in pencils, but consists of only a single layer of atoms arrayed in a hexagonal mesh pattern. The material is very light, strong, chemically stable, and can conduct both heat and electricity, with applications in fields such as electronics, energy, and health care.

The Wisconsin device consists of 4 graphene circuits, each fabricated in a wafer, coated with Parylene C, a transparent and biocompatible polymer compound, using chemical vapor deposition. Graphene allows the device to remain extremely thin, even with 4 layers. “It’s got to be very thin and robust to survive in the body,” notes Ma.

The researchers tested the device, called carbon-layered electrode array, or Clear, for optical transparency over the spectrum from infrared to ultraviolet frequencies and found the sensor allows for transmission rates of 90 percent or more. The team also implanted devices in lab rats and mice, and found the devices allow for fluorescent microscope images and three-dimensional optical coherence tomography of the blood vessels in the brain immediately under the sensor. Optical coherence tomography is an imaging technology analogous to ultrasound, but using light rather than sound waves.

The researchers also conducted optogenetics tests in the focal cortical areas of the lab animals where the sensors were implanted. Optogenetics uses light to influence activities of genes sensitive to light. Focal cortical areas are parts of the cerebral cortex often causing seizures in children with epilepsy.

Lab mice with brain cells expressing a channelrhodopsin protein were fitted with Clear sensors in their brains and exposed to blue light, known to stimulate that protein. The results showed at some light intensity levels, nerve cells respond to the blue light exposure.

University of Wisconsin is in the process of patenting the technology. The team believes the Clear device can be a significant help to neuromodulation therapies involving electrical stimulation of brain cells, to treat disorders such as hypertension, epilepsy, and Parkinson’s disease. The device can assist in understanding precise effects of the stimulation, which at present are considered rudimentary.

The researchers are also working with colleagues at University of Illinois-Chicago developing contact lenses with built-in transparent sensors to detect damage to the retina and early stages of disorders such as glaucoma.

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Project Developing DNA Antibodies for Infectious Diseases

3-D image of MRSA bacteria

3-D image of MRSA bacteria (Melissa Brower, CDC)

21 October 2014. The biotechnology company Inovio Pharmaceuticals Inc. and partners are developing synthetic antibodies based on DNA that generate an immune reaction to prevent infectious diseases, a project funded by Department of Defense Advanced Research Projects Agency or DARPA. The $12.2 million DARPA grant is supporting the work of Inovia, in Plymouth Meeting, Pennsylvania, with the MedImmune division of pharmaceutical company AstraZeneca, and University of Pennsylvania medical school.

The study aims to design and test monoclonal antibodies, proteins created to bind to the surface of specific antigen cells, lymphocytes or white blood cells in the immune system that generate an immune response attacking pathogen invaders, such as bacteria or viruses. The pathogens targeted in this project are Pseudomonas aeruginosa, Staphylococcus aureus, and influenza viruses.

Pseudomonas aeruginosa is a bacterium that can cause ear infections and skin rashes in healthy people, but poses a more serious risk to hospitalized patients and those with weakened immune systems, resulting in blood infections or pneumonia, often in health care settings. Staphylococcus aureus is bacterium responsible for staph infections on the skin, food poisoning, and serious disorders including toxic shock syndrome. One form of staph infection, Methicillin-resistant Staphylococcus aureus or MRSA is resistant to methicillin and other antibiotics, making it difficult to treat.

MedImmune, in Gaithersburg, Maryland, is a pioneer in the development of monoclonal antibodies, while Inovia is designing DNA-based monoclonal antibodies and vaccines, as well as a delivery system for these biologics. The delivery system, known as electroporation, sends millisecond-timed electrical impulses to create temporary pores in cell membranes, allowing for faster uptake of the payload.

While monoclonal antibodies are gaining more interest for their therapeutic potential, they remain time-consuming and expensive to produce, as well as having limited duration of potency in the body, requiring frequent repeated doses. In this project, the team plans to advance the technology, making it possible for monoclonal antibodies to be generated inside the body, thus simplifying their design.

The researchers aims to adapt a technology harnessing DNA, developed in the lab of David Weiner, a professor of pathology and immunology at Penn’s Perelman School of Medicine, and licensed by Inovio. Weiner and colleagues created some of the earliest DNA-based vaccines for HIV and cancer, and advanced them into clinical stages.

The companies and university plan to test encoding DNA sequences for monoclonal antibodies in DNA plasmids, circular DNA molecules found in nature, but can be used to transfer or manipulate genes. The plasmids then are delivered via electroporation directly into the target cells, where the DNA sequences produce the desired monoclonal antibodies inside the cells. Inovio says preclinical studies show monoclonal antibodies based on DNA generated immune responses against HIV in lab mice.

In this project, the team will demonstrate the ability of DNA plasmids with DNA sequences to generate monoclonal antibodies specific to the two targeted bacteria and influenza viruses, and in sufficient quantities to protect against those pathogens. While the grant funds preclinical studies, the researchers expect successful results will lead to commercial product candidates and clinical trials.

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Genomic Data Analysis Service Launches, Hosts Autism Data

DNA fragment (Wikimedia Commons)

(Wikimedia Commons)

20 October 2014. NextCode Health, a start-up informatics company in Cambridge, Massachusetts, unveiled its NextCode Exchange, a shared online genomics database and analysis service for diagnostics and research with sequencing data. The 1 year-old company also is hosting a genomics database of people with autism for online access to researchers.

NextCode Health says its databases have data from 350,000 whole genomes representing some 40 million known variants, which can be accessed from ordinary Web browsers. The company, begun in October 2013 as a spin-off from deCode Genetics in Iceland, licenses deCode’s genomics analysis platform, including IT infrastructure, for clinical diagnostics based on sequencing data. Hannes Smarason and Jeff Gulcher, CEO and chief scientist respectively of NextCode, are former executives of deCode Genetics, now a division of the U.S. biotechnology company Amgen.

The company says computational and analytical services in NextCode Exchange improve the ability of physicians and geneticists to diagnose diseases of unknown origin by identifying suspect genes and mutations faster and with greater accuracy. These services, says NextCode, can also be shared in real time with collaborators, or accessed privately and anonymously to validate findings relating genomic analysis to specific physical traits or conditions. The company also offers its own sequencing services, including for whole genomes, for clients lacking their own sequencing capability.

In addition, NextCode can host genomic databases for clients. In a partnership announced yesterday, NextCode is hosting the Simons Simplex Collection, a database of detailed genomics and related physical traits that aims to discover rare genetic events increasing the risk of developing autism spectrum disorders. Simons Simplex Collection consists of data from 2,600 so-called simplex families — those with one child diagnosed with autism, unaffected parents, and at least one unaffected sibling.

The collection is supported by the Simons Foundation Autism Research Initiative, and partners with 12 university-affiliated autism research clinics. Data in the collection were drawn from blood samples where DNA was extracted and analyzed by Rutgers University. Sequencing of Simons Simplex Collection data, says the foundation, has already yielded some 100 gene candidates for autism.

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FDA Exemption Sought for Ebola Blood Plasma Device

Scanning electron micrograph of Ebola virus

Scanning electron micrograph of Ebola virus (National Institute of Allergy and Infectious Diseases)

20 October 2014. Cerus Corp., a developer of blood safety devices, is asking the U.S. Food and Drug Administration to allow its system for removing pathogens from blood plasma be used to treat patients in the U.S. with Ebola, while the device is under review. The provision, called a Compassionate Use Investigational Device Exemption, allows physicians to allow the use of medical devices still under review in cases of serious or life-threatening conditions, and where no other alternatives are available.

Plasma is the part of blood containing proteins for blood clotting and antibodies to fight infections. Processes for donating plasma separate the plasma from blood, then return the remaining red blood cells to the donor’s blood stream. Plasma can be frozen and kept for up to a year.

The Concord, California company’s Intercept system for plasma synthesizes psoralen, a natural substance, into a compound known as amotosalen that penetrates DNA and RNA of targeted pathogens in plasma. When exposed to ultraviolet light, amotosalen forms a chemical cross-link with the genetic material, preventing it from replicating, thus deactivating the pathogen and preventing disease. Another Cerus system works the same way with blood platelets.

Because blood from Ebola victims contains antibodies against the disease, public health authorities are considering transfusions from Ebola patients who survived — now about half of those who contract the disease — as a therapy. Anecdotal evidence from previous Ebola outbreaks in Africa going back to 1976 show transfusions of whole blood or plasma help some patients recover. Kent Brantly, an American physician who contracted Ebola in Liberia and survived, received a whole-blood transfusion from another survivor, and in turn provided his plasma to three other patients.

One risk of blood or plasma transfusions is the presence of other pathogens that can cause other serious conditions, such as HIV or malaria, for Ebola patients. Cerus says its Intercept system can remove those pathogens, thus ensuring a safer supply of plasma for therapeutic transfusions.

The Intercept system is already approved for use in Europe and now under review by FDA. The company says a decision by FDA is expected in 2015.

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Better DNA Sample Prep Methods Sought in Challenge

DNA strand (NSF)

(James. J. Caras, National Science Foundation)

17 October 2014. A new challenge on InnoCentive is seeking methods that make it possible to prepare DNA samples in the field for sequencing, based on smaller quantities of microbial evidence. The challenge has an award of $25,000 and a deadline of 7 December 2014.

InnoCentive in Waltham, Massachusetts conducts open-innovation, crowdsourcing competitions for corporate and organization sponsors. The sponsor, in this case, is not disclosed. Innocentive calls this type of competition a theoretical challenge that requires a written proposal.

The sponsor of this challenge is seeking better ways of preparing DNA samples in the field — on-site, where samples are collected — for sequencing, which can be of considerable benefit to environmental and energy companies, as well as in forensic investigations. These methods would prepare samples for a type of DNA analysis called metagenomic sequencing that reveals genetic signatures of complex microbial communities.

DNA extraction kits today use technologies such as magnetic particles, known as functionalized magnetic beads, for isolation of nucleic acids, as well as purification and concentration of the samples for further analysis. With metagenomic sequencing, however, the amount of usable specimen material isolated for analysis can be extremely limited, , sometimes as little as 1 picogram, since only trace amounts of the total specimen material are often collected.

Today’s sequencing technologies require 50 nanograms of DNA to return high-quality and reproducible sequencing results. The challenge sponsor is looking for techniques with the sensitivity to process DNA samples as small as 1 to 10 nanograms, and return results of the analysis faster.

Participants in the competition will need to prepare and submit a written proposal with their solutions. To receive the full award, the winning entry will be required to transfer exclusive intellectual property rights to the sponsor. However, the sponsor will consider a partial award in cases where full intellectual property rights cannot be transferred.

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Simple 3-D Graphene Construction Process Devised

Porous graphene-based structure

Electron microscope image of porous graphene-based structure created by diffusion driven layer-by-layer assembly (Kyoto University)

17 October 2014. Materials scientists at Kyoto University in Japan developed a new process that simplifies the building of three-dimension structures with graphene, a light, strong, conductive material with many industrial and commercial applications. Franklin Kim and Jianli Zou from Kyoto’s Institute for Integrated Cell-Material Sciences  published their findings yesterday in the journal Nature Communications (paid subscription required).

Graphene is a material closely related to graphite like that used in pencils, but consists of only a single layer of carbon atoms arrayed in a hexagonal mesh pattern. The material is very light, strong, chemically stable, and can conduct both heat and electricity, with applications in fields such as electronics, energy, and health care.

The thin, single-atomic structure that makes graphene a desirable material also makes it difficult to piece together into 3-D structures needed for practical use, which hampers the advance of graphene into commercial applications. Stacking graphene layers, for example, causes the nanoscale sheets to lose their unique individual properties. Current methods for addressing this problem, say the authors, are costly and time consuming.

Kim and Zou sought a simple and scalable method for assembling graphene sheets that can be adapted to commercial and industrial enterprises. The researchers applied a chemical process known as interfacial complexation, where layers of negatively-charged graphene oxide sheets are interspersed with a positively-charged polymer. The polymer in this case is polyethylenimine, a compound used in detergents, adhesives, inks, dyes, and cosmetics, as well as a number of industrial processes.

Putting the opposite-charged layers of graphene oxide and polyethylenimine into contact forms a stable composite layer.  “Interestingly, the polymer could continuously diffuse through the interface, and induce additional reactions” says Zou in a university statement, “which allowed the graphene-based composite to develop into thick multi-layered structures.”

The multi-layered structures, say the authors are robust and can be designed with various porosity, from ultra-light to extremely dense, by adjusting the input properties and conditions. The process can be scaled easily for producing large-area films with patterns, or into free-standing shapes for energy generation or storage, such as in batteries or supercapacitors.

Kim adds that the process can be applied to more than just graphene, noting “we strongly believe that the new technique will be able to serve as a general method for the assembly of a much wider range of nanomaterials.”

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Personalized Leukemia Immunotherapy Gets 90 Pct Remission


T-cell (NIAID/NIH)

16 October 2014. Nine in 10 children and adults in early-stage clinical trials of a personalized therapy harnessing the patients’ immune systems achieved full remission of their acute lymphoblastic leukemia. The findings of the team from University of Pennsylvania and Children’s Hospital of Philadelphia are reported today in New England Journal of Medicine (paid subscription required).

The trials tested a personalized therapy code-named CTL019 with 30 patients having relapsed or unresponsive cases of acute lymphoblastic leukemia, a cancer of blood and bone marrow. The disease progresses quickly, making an overabundance of immature lymphocytes, a type of white blood cell. It is also the most common type of cancer among children, although it can also affect adults.

The process to make CTL019 starts with an individual’s blood cells and separates out T cells, white blood cells used by the immune system to fight invading pathogens, then reprograms the T cells with genetic engineering to find and kill cancer cells. The engineered T cells then become hunter cells, containing a protein known as chimeric antigen receptor that acts like an antibody. These hunter cells are infused back into the patient, seeking out and binding to a protein called CD19 found on the surface of B cells — another type of white blood cell — associated with several types of leukemia.

Among the properties programmed into CTL019 is the ability of hunter cells to quickly multiply and accumulate to battle the cancerous cells. The authors, led by pediatrics professor Stephan Grupp of Children’s Hospital, say their tests show some 10,000 hunter cells are produced for each engineered T cell received by patients.

The trials enrolled 25 patients, ages 5 to 22, at Children’s Hospital and 5 adult patients, ages 26 to 60, at University of Pennsylvania. “The patients who participated in these trials had relapsed as many as four times, including 60 percent whose cancers came back even after stem cell transplants,” says Grupp in a hospital statement. “Their cancers were so aggressive they had no treatment options left.”

The researchers began giving the CTL019 infusions two years ago. Of the 30 patients receiving these personalized infusions, 27 or 90 percent, achieved complete remission. Some 78 percent of the patients survived at least 6 months after the treatments. Of the original patients, 19 remain in remission, 15 of whom received only the CTL019 therapy, while 5 others sought out other therapies, including stem cell transplants. Also of the original patients, 7 relapsed between 6 weeks and 8.5 months after the infusions, although 3 of the relapsed patients developed a different form of leukemia, one where the CD19 protein is not expressed, thus it would not have been helped by the CTL019 therapy.

All of the patients receiving CTL019 experienced an adverse reaction a few days after the infusions called a cytokine release syndrome. While these reactions cause flu-like symptoms, they’re considered an indicator of hunter cells’ progress in fighting the cancer cells. However, nine patients developed severe cytokine release syndrome reactions requiring treatment with immunosuppressant drugs and steroids. All of the patients fully recovered from these reactions.

The pharmaceutical company Novartis is licensing the immunotherapy technology, under an agreement reached two years ago with University of Pennsylvania. In July 2014, CTL019 received breakthrough therapy status from the U.S. Food and Drug Administration, which provides expedited review for new therapies treating serious conditions and where the treatments are shown to be an improvement over current methods.

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