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Arcadia Bio, Partners to Produce Stress-Tolerant Soybeans

Soybean field

(Kevin Dooley, Flickr)

7 July 2015. Arcadia Biosciences, an agricultural biotechnology company, will develop a new variety of soybeans engineered for greater tolerance of environmental stresses, with partners in Brazil and Argentina, two major soybean growers. Financial details of the collaboration between the Davis, California company and Bioceres S.A. in Rosario, Argentina, and Tropical Melhoramento e Genética Ltda, in Cambé, Brazil were not disclosed.

Arcadia Bio and Bioceres are already collaborating in Verdeca LLC, a soybean technology joint venture, producing genetically-modified soybean traits with a greater tolerance for environmental stresses, particularly drought conditions. Bioceres is an agricultural biotech company owned by more than 250 growers in South America. Tropical Melhoramento e Genética is a soybean and cotton breeding company developing new varieties for growers in the region.

Soybeans are expected to play a more important role as a source of protein as the economies of India and China grow larger and develop middle-class diets. Soybean plants are processed mainly into animal feeds, edible oils, soy flour, and proteins.

Farmers worldwide in 2013, according to the U.N.’s Food and Agriculture Organization, produced 276.4 million metric tons (304.7 short tons) of soybeans. The U.S. accounts for 89.5 million metric tons, or about one-third (32%) of the total. But Argentina and Brazil — site of Arcadia’s two partner companies — together produced 131 metric tons, or 47.4 percent of the world’s soybean output.

The agreement calls for breeding of new soybean varieties incorporating Verdeca’s genetically-modified stress-tolerant traits, brand-named HB4, designed to produce stable and high yields in drought conditions and related environmental stresses. Verdeca says soybeans with HB4 traits were field tested for 6 growing seasons in Argentina and the U.S., and 2 years in regulatory field trials, with yields up to 14 percent higher under multiple stress conditions.

In April 2015, Argentina’s regulatory authorities —  its Ministry of Agriculture, Livestock and Fisheries, and National Advisory Commission on Agricultural Biotechnology that review safety of genetically-modified organisms — approved soybeans with HB4 traits for production in that country. Verdeca says the authorities concluded the HB4-modified soybeans would be as safe for the environment as conventional soybeans. It was the first regulatory approval for HB4 traits addressing abiotic stresses, those caused by non-living factors such as heat, drought, flooding, salinity, and nutrient availability.

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FDA Grants Orphan Status to Brain Cancer Surgery Aid

Emperor scorpion

Blaze Bioscience’s BLZ-100 is based on a peptide derived from scorpion venom. (Rosa Pineda, Wikimedia Commons)

7 July 2015. The U.S. Food and Drug Administration is granting orphan drug status to an engineered peptide that illuminates brain cancer cells making them easier to surgically remove. The treatment, code-named BLZ-100, is made by Blaze Bioscience, a biotechnology company in Seattle.

Blaze Bioscience is a spin-off enterprise from Fred Hutchinson Cancer Research Center, also in Seattle, to develop and commercialize drug candidates based on engineered peptides that better target tumor cells than conventional cancer drugs. The company is commercializing research begun at the Hutchinson center on optides — short for optimized peptides — engineered protein molecules that more precisely target cancer cells than most of today’s chemotherapy drugs. The better that cancer treatments can zero-in on and bind to tumor cells, the fewer the side-effects, often severe, that affect cancer patients undergoing chemotherapy.

BLZ-100 refines the optide technology into what the company calls tumor paint that combines optides with a fluorescent dye, emitting light in the near-infrared range. BLZ-100 is based on a peptide variant called chlorotoxin, originally derived from scorpion venom, which in its natural state has been shown to bind to some tumors. Blaze says treatments with BLZ-100 provide high-resolution visualization of cancer cells during surgery, making possible more precise and complete removal.

According to the company, FDA granted orphan drug status to BLZ-100 for its use in surgery on malignant brain tumors. Blaze is recruiting participants to test BLZ-100 in an early stage clinical trial of adults with glioma, a type of cancer affecting glial cells that surround and support the brain’s nerve cells. Cancers of this type can be aggressive and highly malignant, and account for about one-third of all brain cancers.

A second early-stage trial also to test BLZ-100 is recruiting children and young adults (up to age 30) with tumors in their central nervous systems. In both trials, investigators are looking primarily at safety of the treatments, but also concentrations of BLZ-100 in the blood up to 4 hours following injection, as well as the ability of BLZ-100 to illuminate cancerous brain tissue.

Orphan drug designation is granted by FDA to treatments being developed for diseases affecting fewer than 200,000 people in the U.S. Therapies, both drugs and biologics, designated as orphan drugs qualify for incentives such as tax credits for clinical trials and exemptions from marketing application fees.

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Compression Software for Genomic Analysis Being Designed

Genetic testing illustration

(National Institute of General Medical Sciences, NIH)

6 July 2015. Engineers at University of Illinois in Urbana and Stanford University in California are tackling the problem of massive data files generated by genomic analyses, an emerging issue as precision medicine harnessing genomics takes hold. A team led by engineering faculty Olgica Milenkovic at Illinois and Tsachy Weissman at Stanford is funded by a 3-year grant of $1.3 million from National Institutes of Health.

Precision medicine is the term given to the use of detailed information about human genomic variations to guide clinical decisions, particularly in identifying the best drugs or biologics for treatments. Cancer is considered a prime near-term candidate for precision medicine, given the high incidence of cancer, particularly as populations age. Precision medicine also offers the hope of finding treatments for cancer and other diseases that cause fewer adverse side effects than current chemo and radiation therapies.

Relying on genomic data to provide the detailed diagnostics guiding precision medical decisions means making use of massive biological databases and high-powered analytical tools. Files containing the raw 3 billion base pairs — the combinations of nucleotide bases in a genome labeled A, G, C, and T — can run as large as 200 gigabites for a single human. Adding in related protein and metabolite analyses can balloon an individual’s data files even further.

Milenkovic, Weissman and colleagues seek to apply tools from computer science that reduce the size of these files, while maintaining access to their fine-grain details. The researchers plan to study the nature of genomic data to find techniques for applying lossless compression, where each bit of data can be directly restored, combined with restricted forms of lossy compression that allow for tradeoffs in quality and file size. The team then plans to review current data compression algorithms applied to biological computing for meeting these requirements, and develop new algorithms as needed.

The researchers anticipate the project developing, as Milenkovic describes in a university statement, “a suite of software solutions for the next generation of biological data repositories and labs, which are currently facing enormous challenges with data storage, transfer, visualization, and wrangling.” The software would compress data from DNA sequencing, quality scores for sequences, and functional genomic analysis that describes gene and protein interactions from the transcripts revealing the molecular composition of cells and tissue.

The project is funded under NIH’s Big Data to Knowledge (BD2K) initiative that began in 2012. One objective of BD2K is to conduct research and develop the methods, software, and tools needed to analyze biomedical big data.

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Poll: Parents Consider Vaccines Safe, Beneficial

Infant being vaccinated

(Public Domain Images)

6 July 2015. A nationwide survey of parents in the U.S. shows the vast majority of parents believe vaccines for children are as safe and beneficial as a year ago, with sizable numbers — from a quarter to a third — saying vaccines’ safety and benefits are increasing. The results were published today by C.S. Mott Children’s Hospital, part of the University of Michigan Health System in Ann Arbor.

Despite the record of vaccines preventing millions of occurrences of diseases like polio and measles, increasing numbers of parents in the U.S. in recent years began opting out of having their children vaccinated. Despite voluminous evidence to the contrary, concerns among some parents persist over the safety of vaccines, particularly the link between the measles-mumps-rubella vaccine and autism.

A measles outbreak in the spring of 2015, traced to a single case at Disneyland in California, alerted health authorities and the public to pitfalls of of opting out from childhood vaccinations. Many of the 147 people getting measles, including 131 in California, were not vaccinated against the disease. By the end of June 2015, the California legislature passed, and governor signed, a bill removing most of the allowable exemptions, including religious and philosophical reasons, for opting out.

The poll, conducted in May 2015 with a nationwide panel, shows 2 in 3 parents in the U.S. (68%) believe vaccines are as safe as a year ago, with another quarter (25%) saying vaccines are getting safer. Only 7 percent believed vaccines are less safe. Six in 10 parents (61%) feel vaccines provide as many benefits as 1 year ago, while 1 in 3 parents indicate vaccines provide more benefits than a year ago. Only 5 percent say vaccines are less beneficial.

The poll shows as well a sizable concern about the risk of measles and whooping cough, two diseases once believed to be under control because of vaccines. Some 2 in 5 parents (40%) say the risk of measles is increasing in the U.S., while only a few more (45%) say the risk is about the same. Less than 2 in 10 (15%) believe the measles risk is lower.  Concerns about whooping cough among parents show a similar pattern, with 37 percent believing the risk is higher, about half (49%) saying the risk is about the same as a year ago, and 15 percent indicating the risk is lower.

In addition, the poll asked parents about their opinions of requiring children in school or day care to be vaccinated. About 1 in 3 parents (35%) say they are more supportive of these requirements than a year ago, while 6 percent are less supportive, and 6 in 10 (59%) say their level of support is unchanged.

The polling company GfK Custom Research conducted the survey in May 2015 among a sample of parents with at least 1 child age 17 or younger. The sample of 1,416 participants was drawn from GfK’s KnowledgePanel, a collection of participants recruited over the Web that the company says is representative of the U.S. population. GfK says the survey had a completion rate of 55 percent, with a margin of error on responses of 2 to 3 percent.

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Science & Enterprise Featured in ACI Blog


3 July 2015. Because of the Independence Day holiday in the U.S., we’re taking today off. Blog posts will resume on Monday, 6 July.

We were looking for a suitable way to mark the 5th anniversary of Science & Enterprise — our first post while in stealth mode was 6 July 2010 — but the ACI Scholarly Blog Index took care of that. ACI Scholarly Blog Index compiles posts from 15,000 academic blogs, and since we’ve got “Science” in our name, they got us as well. Traci Hector of ACI talked to us this week and gave Science & Enterprise a nice write-up. Check it out.

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Engineered Mosquitoes Sharply Reduce Dengue Carriers

Mosquito biting a human

Aedes aegypti mosquito biting a human (U.S. Department of Agriculture)

2 July 2015. A variety of mosquito, engineered to produce offspring that die before maturity, was found to reduce the dengue mosquito population in a city in Brazil by 95 percent, well below the level needed to spread the disease. The team from the biotechnology company Oxitec Ltd. in Abingdon, U.K., with academic and business colleagues in the U.K. and Brazil, published its findings today in the journal PLoS Neglected Tropical Diseases.

Dengue is viral disease transmitted by infected mosquitoes (not person-to-person) that occurs most frequently in tropical urban regions of the world. World Health Organization estimates from 50 to 100 million dengue infections occur each year, with half of the world’s population at risk. WHO says the disease is now endemic in more than 100 countries, especially in Asia, Africa, the Americas, eastern Mediterranean, and Pacific islands.

The disease is a collection of four major types, but all types can cause high fever, severe headache, muscle and bone pain, and bleeding. Dengue hemorrhagic fever is a severe form of the disease that can cause respiratory problems, severe bleeding, and organ failure, and become fatal. There are no treatments for dengue other than caring for symptoms, and up to now, no vaccines to prevent its occurrence.

Dengue is spread by the Aedes aegypti mosquito. Oxitec uses genetic engineering techniques to insert a gene in males of the species that when released into the wild mate with females and produce offspring that die before becoming adults, and thus are prevented from having offspring. As a result the Aedes aegypti mosquito population in the area of the release is markedly reduced or eliminated.

Oxitec, a spin-off company from Oxford University, is currently testing its engineered mosquito, code-named OX513A, in field trials. The journal paper reported on one of those trials, in the Itaberaba suburb of Juazeiro city in Bahia State, Brazil, a region known to have a high incidence of dengue disease. The research team tested the engineered OX513A mosquito in an area of Itaberaba with 424 houses where 1,810 people reside. An adjacent area with 5,716 people living in 1,341 houses and a similar population density, but not exposed to the engineered mosquitoes, served as a comparison.

The team used ovitraps, devices that capture eggs from mosquitoes used for surveillance of the species, to track the number of mosquitoes in the test and comparison regions for a 1 year period, February 2011 to January 2012. The OX513A mosquitoes also had a fluorescent marker that appears in the eggs, which made it possible to follow the numbers engineered versus wild-type mosquitoes.

The results show the density of Aedes aegypti mosquitoes declined from 418 per hectare to 20 per hectare (1 hectare = 2.47 acres), a reduction of 95 percent, while densities in the adjacent region not receiving the engineered mosquitoes remained about the same over the period. A similar Oxitec study in Grand Cayman Island in 2010 found a similar, but not quite as dramatic reduction of 82 percent. The results of the later trial in Brazil, say the authors, suggest that the lower numbers of dengue-carrying mosquitoes could be below levels needed to spread the disease among human populations, according to accepted mathematical models of dengue transmission.

Other cities in Brazil are already beginning to use Oxitec’s engineered mosquitoes to control dengue. In May 2015, the Brazilian city of Piracicaba received approval from the nation’s biosafety authorities to begin a municipal dengue mosquito control program using Oxitec’s varieties.

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Commercial Space Launch Site Slated for New Zealand

Peter Beck with Electron rocket

Rocket Lab CEO Peter Beck with Electron rocket (Rocket Lab Ltd)

2 July 2015. Rocket Lab Ltd, a company aiming to make orbital space launches frequent and less costly, says it plans to build a launch site in New Zealand, with completion scheduled by the end of 2015. The company says test flights will begin soon after completing construction of the site, with commercial operations planned for later in 2016.

Rocket Lab, headquartered in Los Angeles but operating largely in New Zealand, plans to offer commercial launch services for small satellites in low earth orbit at less than $5 million a launch. Customers for its launch services are expected to be companies and organizations using satellites for weather reporting, crop monitoring, environmental tracking, maritime commerce, Internet transmissions, and GPS services.

The launch site will be located on the Kaitorete Spit, a strip of beach separating Lake Ellesmere (Te Waihora in Maori) from the Pacific Ocean on New Zealand’s south island. Rocket Lab says the site has minimal air and sea traffic nearby, which will help make possible more frequent launches, as many as 100 per year, one of the company’s key business objectives.

Rocket Lab is building two-stage launch rockets it calls Electron fueled by liquid oxygen and kerosene, with battery-powered electric motors for its pumping mechanisms. The engine, called Rutherford for the physicist Ernest Rutherford born in New Zealand, uses a propellent that is solid when stored, but becomes viscous under shear force. This capability, says the company, simplifies the design of the engine, offering the performance of solid fuels with the control of liquid fuels. In addition, all primary components in the Rutherford engine are produced with 3-D printing.

Electron is made with carbon composite materials that the company says provides for extra strength while reducing weight, compared to all-metal construction of conventional rockets. Fuel tanks on Electron are also made with carbon composites, which are compatible with the liquid oxygen. Rocket Lab claims the lower weight will make it possible to launch Electron with less fuel than used by a 737 flying between Los Angeles and San Francisco.

Rocket Lab was founded in 2007 by New Zealander Peter Beck. The company conducted some of its early research and development under contract to Defense Advanced Research Projects Agency (Darpa), and in partnership with NASA and DoD contractor L2 Aerospace. The company completed two venture funding rounds, securing early financing from Khosla Ventures, and joined in a second round in March 2015 by Bessemer Venture Partners and K1W1 investment fund. Aircraft manufacturer Lockheed Martin is also investing in the company.

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Drug Abusers, Smokers More Likely to Use Opioids Long-Term

Pills in blister packs

(PublicDomainPictures, Pixabay)

1 July 2015. A study by the Mayo Clinic finds people with a history of substance abuse and using tobacco are those most at risk for using opioid pain killers on a continuous basis. The team led by Michael Hooten, an anesthesiologist at Mayo Clinic in Rochester, Minnesota, published its findings in the July issue of the Mayo Clinic Proceedings.

Opioids work by reducing the intensity of pain signals to the brain, particularly regions of the brain controlling emotion, which reduces effects of the pain stimulus. Examples of leading opioid prescription pain medications are hydrocodone, oxycodon, morphine, and codeine.

Abuse of opioid pain killers is described by Centers for Disease Control and Prevention as a growing epidemic, fueled in part by growing numbers of prescriptions written for pain killing drugs. CDC reports that in 2012, physicians in the U.S. wrote 259 million prescriptions for pain killers, enough for one bottle of pills for every adult in the country. As of July 2014, according to the CDC, 46 people die each day in the U.S. from an overdose of prescription pain killers. The 10 states with the highest rates of prescriptions for pain killers, says CDC, are in the South.

Hooten and colleagues looked into the types of people receiving prescriptions for pain killers to identify patterns and characteristics of those most likely to end up using the drugs on a long-term basis. The Mayo Clinic team took advantage of a database of common electronic health records in its own region, the Rochester Epidemiology Project that compiles for researchers decades of medical records from tens of thousands of individuals in southeastern Minnesota.

The Mayo Clinic team drew a sample of 293 individuals who received a new prescription for opioid pain killers in 2009. The researchers then reviewed further use of opioids by people in the sample for 1 year, classifying their use of the drugs as short-term, episodic, or long-term.

The researchers found the 293 individuals received 515 prescription for pain killers in 2009, with about 1 in 5 (21%) showing a pattern of episodic use and 6 percent becoming long-term opioid users. The team also found people who use tobacco and those with a history of substance abuse were more highly correlated with episodic and long-term opioid prescribing pattern.

“From a patient perspective, it is important to recognize the potential risks associated with these medications,” says Hooten in a Mayo Clinic statement. “I encourage use of alternative methods to manage pain, including non-opioid analgesics or other non-medication approaches. That reduces or even eliminates the risk of these medications transitioning to another problem that was never intended.”

Hooten tells more about the study in the following video.

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Foundation Supporting ALS Pilot Clinical Trials

Brain illustration


1 July 2015. ALS Association is funding pilot studies with patients having amyotrophic lateral sclerosis to confirm biomarkers, or biochemical indicators, that improve responsiveness to therapies. The studies are being conducted by Neuraltus Pharmaceuticals Inc., a biopharmaceutical developer in Palo Alto, California, and University of Washington Medical Center in Seattle.

ALS, also known as Lou Gehrig’s disease, is a progressive neurological disease that attacks the nerve cells controlling voluntary muscles, such as those in the arms, legs, and face. In ALS, muscles gradually weaken and waste away, leading to individuals losing their strength and their ability to move their arms, legs, and body. When diaphragm and chest wall muscles fail, people lose the ability to breathe without ventilatory support, often leading to death from respiratory failure.

Neuraltus Pharmaceuticals develops treatments for neurodegenerative disorders, with its lead product code-named NP001 designed to regulate the inflammation of macrophages, white blood cells in the immune system that ingest dead or damaged cells. People with ALS are believed to have higher levels of inflamed macrophage activity that release factors in the central nervous system that damage motor neurons.

The new clinical trial aims to confirm the mechanism of NP001 in reducing biomarkers associated with inflammation: interleukin-18 and lipopolysaccharide. In an earlier trial, individuals with ALS taking higher doses of NP001 reported no progression of their symptoms during the 6 months they were taking the drug. People responding to NP001 had higher levels of interleukin-18 and lipopolysaccharide before the treatments that decreased after the treatments.

The new study is led by Robert Miller, director of Forbes Norris MDA/ALS Research Center at California Pacific Medical Center in San Francisco., who led the earlier trial. ALS Association is providing a grant of $1.5 million for the study, in addition to about $1.2 million from Neuraltus.

ALS Association with other funders are also supporting an 8-week study of the drug mexiletine, designed to treat irregular heart rhythms that acts by reducing hyperexcitability of motor neurons. The study, led by neuromuscular specialist Michael Weiss at University of Washington, will investigate the effect of mexiletine on hyperexcitability in the brain’s motor cortex, which controls movements. The trial is expected to measure markers of hyperexcitability with transcranial magnetic stimulation, a non-invasive way to determine hyperexcitability in the brain.

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Environmental Sensor Developer Reveals Collaborations

Industrial air pollution

(National Park Service, Wikimedia Commons)

30 June 2015. Aclima Inc., a designer of environmental monitoring sensors and networks, unveiled today collaborations with Google Inc., U.S. Environmental Protection Agency, and Lawrence Berkeley National Lab, among others. The San Francisco company, operating with little publicity for long as 5 years, did not disclose financial details from any of these partnerships.

Aclima Inc. develops sensor-based systems for measuring health and environmental air quality. The systems are designed to capture data from large numbers of air quality sensors inside buildings or for fine-grained local conditions in cities or regions. In addition, says Aclima, sensors can be deployed on vehicles running regular routes, such as buses or delivery vans, to capture air quality data in snapshots at various times of the day. The company then integrates the data collected in a cloud-based platform, with big-data analytical tools for users in business, public health, traffic management, and urban planning.

The collaboration with Google, operating for “several years,” according to an Aclima statement, monitors indoor air quality at 21 Google offices worldwide. Aclima says some 500 devices currently track temperature, humidity, noise, and light, as well as carbon dioxide and particulate matter in the office air, to help make decisions on workplace design for employee health and productivity.

Aclima is also partnering with EPA and Lawrence Berkeley National Lab on design of a miniaturized sensor to measure particulate matter in the air, of special concern for people with asthma and other respiratory problems. The sensors produced by the project, which includes participants at University of California in Berkeley and University of Illinois in Chicago, are expected to be small and inexpensive so they can be deployed in large numbers to capture outdoor air quality data.

A preview of the device can be found in an October 2013 paper published in the journal Sensors and Actuators A: Physical that outlines design of a sensor to measure airborne particulate matter. The paper, which says representatives from Aclima Inc. made contributions, has a micro electro mechanical system (MEMS) circuit that combines air and microfluidic components, which the authors — including those from EPA and Berkeley Lab — demonstrated with diesel exhaust and tobacco smoke.

In addition, EPA and Aclima in April 2013 entered into a 5-year research and development agreement to develop and integrate low-cost sensors into systems and networks deployed indoors and outdoors at stationary sites, and on mobile platforms. The sensors aim to detect the chemical composition of pollutants, including black carbon and particulate matter.

“Aclima has spent years in stealth creating a complete system to map environmental quality in an entirely new way,” says CEO Davida Herzyl in a company statement, “enabling us to see how our buildings, communities, and cities live and breathe.” According to Herzyl’s LinkedIn page, she co-founded the company in 2010.

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