NIST Announces New Scaffold Reference Material for Tissue Engineering Research

ORIGINAL: NIST
Contact: Michael Baum
June 25, 2013

The National Institute of Standards and Technology (NIST) has issued a new reference material—a sort of standardized sample—of cellular scaffolds for use in tissue engineering research.

Fluorescense micrographs of a test culture of bone cells after one day shows the cells proliferating on the struts of new NIST reference scaffold for tissue engineering. Credit: NIST View hi-resolution image

Growing custom replacement tissue—cartilage, bone, blood vessels, possibly even whole organs—is one of the hot research fields in modern medicine. If the techniques could be perfected, it might become possible to grow transplant materials for patients based on their own cells, avoiding problems with compatibility, immune response and tissue rejection.

Scaffolds—biologically innocuous materials that give developing cells a three-dimensional structural template on which to grow—are important to this process. Considerable research centers on determining the best scaffold materials and designs to encourage the growth of various sorts of tissue. The new NIST reference material is designed as a common ground for research labs, a well-understood, uniform scaffold that can be used as a baseline or control in experiments that measure factors such as cell adhesion and proliferation.

Each unit of NIST Reference Material 8394, “Tissue Engineering Reference Scaffolds for Cell Culture,” includes 24 “free-form” scaffolds made of PCL* in a standard 96-well plate. Each scaffold has six layers of PCL struts laid down in a crisscross pattern. NIST provides reference values for the diameter, spacing and porosity of the struts, as well as adhesion and proliferation of osteoblasts (bone cells).

For more information on RM 8394, go to https://www-s.nist.gov/srmors/view_detail.cfm?srm=8394.

Standard reference materials are among the most widely distributed and used products from NIST. The agency prepares, analyzes and distributes about 1,300 different materials that are used throughout the world to check the accuracy of instruments, validate test procedures and serve as the basis for quality assurance worldwide. NIST reference materials are considered by NIST to be sufficiently homogeneous and stable with respect to one or more properties to be useful for measurement purposes, though they do not meet the more stringent requirements for a standard reference material.**
*poly(e-caprolactone).
**For more on the distinctions between “reference materials” and “standard reference materials,” see www.nist.gov/srm/definitions.cfm.

Training Your Robot the PaR-PaR Way - Berkeley Lab and JBEI Researchers Develop a Biology-Friendly Robot Programming Language

ORIGINAL: Lawrence Berkeley Lab

Berkeley Lab and JBEI Researchers Develop a Biology-Friendly Robot Programming Language

OCTOBER 23, 2012

Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

Feature

Teaching a robot a new trick is a challenge. You can’t reward it with treats and it doesn’t respond to approval or disappointment in your voice. For researchers in the biological sciences, however, the future training of robots has been made much easier thanks to a new program called “PaR-PaR.”

Nathan Hillson, a biochemist at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), led the development of PaR-PaR, which stands for Programming a Robot. PaR-PaR is a simple high-level, biology-friendly, robot-programming language that allows researchers to make better use of liquid-handling robots and thereby make possible experiments that otherwise might not have been considered.

“The syntax and compiler for PaR-PaR are based on computer science principles and a deep understanding of biological workflows,” Hillson says. “After minimal training, a biologist should be able to independently write complicated protocols for a robot within an hour. With the adoption of PaR-PaR as a standard cross-platform language, hand-written or software-generated robotic protocols could easily be shared across laboratories.”

Hillson, who directs JBEI’s Synthetic Biology program and also holds an appointment with the Lawrence Berkeley National Laboratory (Berkeley Lab)’s Physical Biosciences Division, is the corresponding author of a paper describing PaR-PaR that appears in the American Chemical Society journal Synthetic Biology. The paper is titled “PaR-PaR Laboratory Automation Platform.” Co-authors are Gregory Linshiz, Nina Stawski, Sean Poust, Changhao Bi and Jay Keasling.

Using robots to perform labor-intensive multi-step biological tasks, such as the construction and cloning of DNA molecules, can increase research productivity and lower costs by reducing experimental error rates and providing more reliable and reproducible experimental data. 

To date, however, automation companies have targeted the highly-repetitive industrial laboratory operations market while largely ignoring the development of flexible easy-to-use programming tools for dynamic non-repetitive research environments. As a consequence, researchers in the biological sciences have had to depend upon professional programmers or vendor-supplied graphical user interfaces with limited capabilities.

The PaR-PaR development team included (from left) Nina Stawski, Changhao Bi, Nathan Hillson, Sean Poust and Gregory Linshiz. (Photo by Roy Kaltschmidt)

“Our vision was for a single protocol to be executable across different robotic platforms in different laboratories, just as a single computer software program is executable across multiple brands of computer hardware,” Hillson says. “We also wanted robotics to be accessible to biologists, not just to robot specialist programmers, and for a laboratory that has a particular brand of robot to benefit from a wide variety of software and protocols.”

Hillson, who earlier led the development of a unique software program called “j5” for identifying cost-effective DNA construction strategies, says that beyond enabling biologists to manually instruct robots in a time-effective manner, PaR-PaR can also amplify the utility of biological design automation software tools such as j5.

“Before PaR-PaR, j5 only outputted protocols for one single robot platform,” Hillson says. “After PaR-PaR, the same protocol can now be executed on many different robot platforms.”

The PaR-PaR language uses an object-oriented approach that represents physical laboratory objects – including reagents, plastic consumables and laboratory devices – as virtual objects. Each object has associated properties, such as a name and a physical location, and multiple objects can be grouped together to create a new composite object with its own properties.

PaR-PaR makes it much easier to train robots to perform labor-intensive multi-step biological tasks. (Photo by Roy Kaltschmidt)

Actions can be performed on objects and sequences of actions can be consolidated into procedures that in turn are issued as PaR-PaR commands. Collections of procedural definitions can be imported into PaR-PaR via external modules.

“A researcher, perhaps in conjunction with biological design automation software such as j5, composes a PaR-PaR script that is parsed and sent to a database,” Hillson says. “The operational flow of the commands are optimized and adapted to the configuration of a specific robotic platform. Commands are then translated from the PaR-PaR meta-language into the robotic scripting language for execution.”

Hillson and his colleagues have developed PaR-PaR as open-source software freely available through its web interface on the public PaR-PaR webserver http://parpar.jbei.org.

“Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work,” Hillson says. “PaR-PaR accomplishes all of these objectives and is intended to benefit a broad segment of the biological research community, including non-profits, government agencies and commercial companies.”

This work was primarily supported by the DOE Office of Science.

# # #

JBEI is one of three Bioenergy Research Centers established by the DOE’s Office of Science in 2007. It is a scientific partnership led by Berkeley Lab and includes the Sandia National Laboratories, the University of California campuses of Berkeley and Davis, the Carnegie Institution for Science, and the Lawrence Livermore National Laboratory. DOE’s Bioenergy Research Centers support multidisciplinary, multi-institutional research teams pursuing the fundamental scientific breakthroughs needed to make production of cellulosic biofuels, or biofuels from nonfood plant fiber, cost-effective on a national scale. For more, visit www.jbei.org

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit the Office of Science website atscience.energy.gov/.

Additional Information

The ACS Synthetic Biology paper “PaR-PaR Laboratory Automation Platform,” by Hillson, et. al., can be viewed and downloaded here

The PaR-PaR software is also available at https://github.com/jbei/parpar

To learn more about the j5 DNA construction software visit the j5 Website athttp://j5.jbei.org/

TAGS: biochemistry, biofuels, biology, energy, Joint Bioenergy Institute, synthetic biology

Greenpeace calls for global REDD standards to reduce negative impacts of forest carbon projects

ORIGINAL: Mongabay

mongabay.com

June 26, 2012

Rainforest in Malaysia.

Greenpeace has launched a consultation process to establish global standards for Reducing Emissions from Deforestation and Degradation (REDD+) projects.

Today the environmental group released a set of international safeguards to reduce the likelihood REDD+ projects result in social conflict, have adverse impacts on wildlife and forest biodiversity, fuel corruption, subsidize industrial logging of primary forests, or disenfranchise local communities. Greenpeace is seeking comment on the standards through September 2, 2012.

"Forest protection and emission reductions schemes are not going to work without guarantees that local people's rights are fully respected and that biodiversity is protected," said Susanne Breitkopf, Greenpeace International Senior Political Advisor for Forest Finance, in a press release.

"Without strong binding safeguards, we can end up with monoculture plantations instead of natural forests, or even see local communities evicted from project sites taken over by foreigners."

As a concept, REDD+ aims to cut greenhouse gas emissions by paying tropical countries to protect their forests. While many of the details — including sources of finance, safeguards, and implementation protocols — are still being hammered out, a number of REDD+ projects are underway in countries ranging from Brazil to Cambodia. Some dodgy REDD+ projects, which have cheated local landowners or failed to seek approval from stakeholders, have shown that without standards, the sector could fail to move forward.

"Supporting strong, coherent safeguards really is in the interest of everyone involved, it's common sense," Breitkopf added. "We invite everyone to contribute to this effort and hope that governments and institutions who have been promoting and supporting REDD+ will adopt the final recommendations."

The Greenpeace report, titled Forests & People First [PDF] includes a comparative matrix showing the various standards that presently apply to REDD+ projects as well as the certifying bodies.

Read more: http://news.mongabay.com/2012/0626-forests-and-people-first.html#ixzz1yxeoigri