Posted on May 31, 2023 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
The U.S. Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) announced on May 15, 2023, that a new workflow developed by researchers at the Agile BioFoundry (ABF), a BETO-funded consortium of national laboratories and Agilent Research Laboratories (Agilent) addresses the need for faster analytical tools. According to BETO, the workflow “combines state-of-the-art analytical technologies with a machine learning-based algorithm, providing a faster and more powerful way to process data that could accelerate the Design-Build-Test-Learn framework, a bio-engineering cycle used to improve biomanufacturing research and processes.”
BETO notes that speeding up the bio-engineering cycle could ultimately speed up biomanufacturing research. According to BETO, one of the biggest barriers to accomplishing this is the ability to improve the Learn step of the cycle, which involves using data to improve future cycles. Improvements to the Learn step can happen only if large amounts of high-quality data are gathered in the Test step of the cycle, however.
BETO states that the consortium teams set out to create a workflow that could generate high-quality analytical Test data that could feed into the Learn step. The workflow they developed includes several components:
- A high-throughput analytical method developed in collaboration with Agilent that enables a threefold reduction in sample analysis time (compared to previous conventional approaches) by using optimized liquid chromatography conditions;
- The Automated Method Selection Software tool, which predicts the best liquid chromatography method to use for analyzing new molecules of interest; and
- PeakDecoder, a novel algorithm that processes multi-dimensional metabolite data and automatically calculates errors in metabolite identification.
To test the workflow’s effectiveness, the researchers used it to study metabolites of various strains of microorganisms engineered by ABF. The microorganisms they tested all have the capacity to make various bioproducts, such as polymer and diesel fuel precursors. According to BETO, using their workflow, the researchers were able to interpret 2,683 metabolite features across 116 microbial samples.
BETO states that the researchers see PeakDecoder “as a stepping stone towards creating an automated data-gathering pipeline.” According to BETO, the team is already working on leveraging state-of-the-art artificial intelligence methods like computer vision used in other fields. The next version of PeakDecoder is expected to have improved automation and identification performance and to be more applicable to other types of molecular profiling, including proteomics workflows.
Posted on April 24, 2023 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
The U.S. Government Accountability Office (GAO) published a “Science & Tech Spotlight” on synthetic biology on April 17, 2023. GAO defines synthetic biology as “a multidisciplinary field of biotechnology that involves engineering the genetic material of organisms -- such as viruses, bacteria, yeast, plants, or animals -- to have new characteristics.” According to GAO, scientists are currently exploring the use of synthetic biology to address environmental challenges by engineering organisms to use carbon dioxide, produce biofuels for vehicles, and transform methane into biodegradable plastics. GAO notes that the synthetic biology market could grow from about $10 billion in 2021 to between $37 billion and $100 billion dollars by 2030. Opportunities include:
- Widely adaptable. Synthetic biology holds the potential to help diagnose and treat diseases, improve industrial processes, and address some environmental challenges;
- More equitable access to biotechnology. Some of the tools needed for synthetic biology are low-cost and widely available, which could make access to beneficial applications more equitable; and
- Conservation efforts. Synthetic biology could support endangered species conservation, for example, by altering the genes of endangered plants to make them resilient to diseases.
GAO notes the following challenges:
- Safety and security concerns. Synthetic biology could pose a significant threat to national security if it were used for nefarious purposes, such as developing new biological or chemical weapons. Additionally, the computational tools used for synthetic biology could be vulnerable to cyberthreats such as automation hacking. For example, a bad actor could manipulate or steal information and use it to create drugs, weapons, or other harmful products.
- Environmental effects. Organisms made using synthetic biology and released into the environment could have unknown, unintended, and potentially irreversible effects on ecosystems. Such effects could be widespread if, for example, these organisms negatively affected food or water systems.
- Public acceptance and access. The public may hesitate to accept certain applications of synthetic biology due to concerns about interfering with nature and about unintended effects. In addition, some medical applications could be inaccessible for some patients due to cost or location of treatment centers.
GAO concludes the “Science & Tech Spotlight” with the following policy context and questions:
- Do policymakers have adequate access to expertise and resources to evaluate the societal effects and public policy implications of synthetic biology research and development?
- How effective is the coordination among 1) domestic and 2) global stakeholders for monitoring and assessing the risks associated with advances in synthetic biology research and applications?
- Is the current regulatory framework sufficient to address ongoing and future applications and their effects without unnecessarily hindering U.S. competitiveness in synthetic biology?
Posted on March 31, 2023 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
To celebrate its 125th anniversary, ASTM International invited case study submissions from committee members to highlight standards that have made a significant impact in society. One of the winning entries is on a set of standards for biodegradable plastic from Committee D20 on Plastics. According to ASTM International’s article, standard test methods for determining the biobased content of solid, liquid, and gaseous samples using radiocarbon analysis (D6866) allows industry, regulators, and government to determine experimentally the percent biobased carbon present in a product or fuel. The article notes that the U.S. Department of Agriculture’s (USDA) BioPreferred® program, mandated by Congress in the 2018 Farm Bill, authorizes the procurement of biobased products by the federal government. The article states that this standard is required to be used to report the percent biobased content of product for federal procurement, as well as for labeling a product with the BioPreferred logo showing biobased content.
The article states that there are two companion specification standards for compostable plastics and paper coatings, “redesigning plastic polymers for biodegradability in industrial composting for an environmentally responsible, managed end-of-life”:
- Standard specification for labeling of plastics designed to be aerobically composted in municipal or industrial facilities (D6400); and
- Standard specification for labeling of end items that incorporate plastics and polymers as coatings or additives with paper and other substrates designed to be aerobically composted in municipal or industrial facilities (D6868).
The standard specifications, which are “grounded in strong science and driven by consensus, provided much-needed clarity and credibility for acceptance in the marketplace and by regulatory bodies in states like California, Washington, Minnesota, Rhode Island, and Connecticut.” The article states that the BioPreferred program mandates D6866 as the only accepted standard for determining and reporting biobased content of products, and that the U.S. Environmental Protection Agency (EPA) requires the standard for reporting on biobased content in fuels. According to the article, industry uses D6400 and D6868 exclusively for making claims of biodegradability under industrial composting conditions. These standards are also the basis of certifications issued by U.S. and European organizations. The article notes that many stakeholders require that compostable products meet D6400 for plastics and D6868 for coatings on paper, and that industrial composters also require certification that the compostable products are certified to these standards.
Posted on December 05, 2022 by Lynn L Bergeson By Lynn L. Bergeson and Carla N. Hutton
On November 30, 2022, the U.S. Department of Agriculture’s (USDA) Agricultural Research Service (ARS) announced that its scientists have determined that plants could be used to produce nanobodies that quickly block emerging pathogens in human medicine and agriculture. The nanobodies are small antibody proteins naturally produced in specific animals like camels, alpacas, and llamas. ARS researchers evaluated nanobodies to prevent and treat citrus greening disease in citrus trees. The scientists are now using their newly developed and patented SymbiontTM technology to show that nanobodies can be easily produced in a plant system with broad agricultural and public health applications. According to ARS, as a proof-of-concept, researchers showed that nanobodies targeting the SARS-CoV-2 virus could be made in plant cells and remain functional in blocking the binding of the SARS-CoV-2 spike protein to its receptor protein: the process responsible for initiating viral infection in human cells.
AgroSource, Inc. collaborated with ARS to develop the plant-based production system. According to ARS, they are currently taking the necessary steps to see how they can move this advancement into the commercial sector. ARS notes that this research collaboration is in response to the White House’s Executive Order on advancing biotechnology and biomanufacturing innovation for a sustainable, safe, and secure American bioeconomy.
Posted on December 01, 2022 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
Research in the U.S. Environmental Protection Agency’s (EPA) Office of Research and Development (ORD) is organized around six highly integrated and transdisciplinary national research programs that are closely aligned with EPA’s strategic goals and cross-EPA strategies. Each program is guided by a Strategic Research Action Plan (StRAP) developed by EPA with input from its many internal and external partners and stakeholders. In October 2022, EPA published six StRAPs for fiscal years (FY) 2023-2026. EPA states that the StRAP for Chemical Safety for Sustainability (CSS) “is focused on addressing the pressing environmental and health challenge of a lack of sufficient information on chemicals needed to make informed, risk-based decisions.” The StRAP for CSS states that CSS will continue to:
- Develop the science needed to reduce, refine, and replace vertebrate animal testing consistent with EPA policies;
- Accelerate the pace of chemical assessment to enable our partners to make informed and timely decisions concerning the potential impacts of environmental chemicals on human health and the environment; and
- Provide leadership to transform chemical testing, screening, prioritization, and risk assessment practices.
Topic 1, Chemical Evaluation, includes three research areas, including emerging materials and technologies. The StRAP states that emerging materials and technologies often have unique physicochemical properties, warranting specialized approaches for evaluating hazard and exposure, and necessitating an evaluation of the environmental impacts of their use. In addition, investigation of novel products of synthetic biology, genome editing, and metabolic engineering is needed to support risk assessment of emerging biotechnology products. The emerging materials and technologies research area will develop, collate, mine, and apply information on emerging materials and technologies to support risk-based decisions, including potential impacts of disproportionately affected populations. It will address the additional data needed to characterize potential release of and exposure to these chemicals and materials, and subsequent environmental impacts of emerging materials on humans and ecological species. The research area will also address relevant cross-cutting priorities related to cumulative impacts and environmental justice potentially associated with incidental exposures.
Posted on September 01, 2022 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
Come learn about the 2023 Green Chemistry Challenge Awards program and the nomination process. This year the program will recognize winners in six categories, including: Greener Synthetic Pathways; Greener Reaction Conditions; The Design of Greener Chemicals; Specific Environmental Benefit: Climate Change; Small Business; and Academic.
Registration is open.
Posted on September 01, 2022 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
On September 1, 2022, the U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS) announced the availability of two new resources to answer stakeholder questions regarding the revised biotechnology regulations under 7 C.F.R. Part 340:
These resources, along with other information on the revised biotechnology regulations, are available on the APHIS website. For additional questions regarding the regulation of modified microorganisms, contact APHIS at .(JavaScript must be enabled to view this email address). For questions regarding confirmation requests, contact APHIS at .(JavaScript must be enabled to view this email address).
Posted on August 29, 2022 by Lynn L BergesonBy Lynn L. Bergeson and Carla N. Hutton
On August 25, 2022, the U.S. Environmental Protection Agency (EPA) announced that registration was open for the 2022 Conference on the State of the Science on Development and Use of New Approach Methods (NAM) for Chemical Safety Testing. EPA notes that there will be limited availability in person at EPA headquarters in Washington, DC, on October 12-13, 2022, and a virtual option will also be available. Conference topics include:
- Variability and Relevance of Traditional Toxicity Tests;
- Evolution of Validation and Scientific Confidence Frameworks to Incorporate 21st Century Science; and
- Breakout groups discussing Variability of Traditional Toxicity Tests, Relevance of Traditional Toxicity Tests, and Feedback on EPA Scientific Confidence Framework.
EPA asks that attendees register for the NAMs conference before October 7, 2022.
On October 18, 2022, EPA will provide training on the Computational Toxicology (CompTox) Chemicals Dashboard, which is part of a suite of databases and web applications developed by EPA to support the development of innovative methods to evaluate chemicals for potential health risks. The computational toxicology tools and data in the Dashboard help prioritize chemicals based on potential health risks. Specifically targeted for decision-makers, the training will provide:
- An overview of the Dashboard content and function;
- Application-oriented use-case demonstrations in the areas of general use, hazard/bioactivity, exposure/absorption, distribution, metabolism, and excretion (ADME)-in vitro to in vivo extrapolation (IVIVE), and chemistry; and
- Opportunities for participatory learning and engagement.
The training will offer information about the latest release of the Dashboard and how it can be used to gather actionable information about chemical properties and risks through case examples, demonstrations, and hands-on exercises. Registration is now open (attendees must register for the training portions individually):
Posted on August 23, 2022 by Lynn L Bergeson By Lynn L. Bergeson and Carla N. Hutton
The U.S. Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) announced on August 11, 2022, that a research team from Pacific Northwest National Laboratory investigated how potassium in biomass feedstocks poisons a catalyst. The researchers focused their study on potassium, a common alkali metal found in biomass feedstocks, since previous analysis of deactivated catalysts after catalytic fast pyrolysis (CFP) of woody biomass feedstock revealed potassium accumulation on the catalysts’ surface.
The research team simulated catalyst poisoning at different potassium levels to trigger deactivation during industrial operations. They then analyzed the catalysts and conducted kinetic measurements to determine how the catalysts’ ability to catalyze chemical reaction changed with the introduction of potassium. According to BETO, the team found potassium poisoning could be substantially mitigated with a developed regeneration method -- a water washing process -- that can successfully remove most of the loaded potassium, restoring more than 90 percent of the catalytic activities.
BETO states that the results of these studies provide new insights for the bioenergy industry that will foster improved catalyst design and regeneration for longer lasting catalysts. The studies also created “a solid knowledge base for developers of biomass conversion technologies to continue to build upon, making new and innovative conversion technologies less risky to research and develop.” According to BETO, the work “also supports accelerated process development that can help industry convert biomass feedstocks commercially, leading to more effective and inexpensive production of biofuels.”
Posted on April 12, 2022 by Lynn L BergesonBy Lynn L. Bergeson and Ligia Duarte Botelho, M.A.
On March 22, 2022, DOE announced a $34.5 million funding opportunity to improve the science and infrastructure for converting waste streams into bioproducts and biofuels that can benefit the local energy economy. DOE Principal Deputy Assistant Secretary for Energy Efficiency and Renewable Energy (EERE), Kelly Speakes-Backman, stated that “through this investment, we see an opportunity to support the bioeconomy and the equitable transition to a clean energy economy.” The FY22 Waste Feedstock and Conversion R&D Funding Opportunity Announcement (FOA) encourages the development of improved organisms and inorganic catalysts to support the next generation of low-carbon biofuels and bioproducts. This FOA has four topic areas:
- Community Scale Resource and Energy Recovery from Organic Wastes;
- Municipal Solid Waste Feedstock Technologies;
- Robust Catalytic Processes; and
- Robust Microbial Cells.
DOE will accept concept papers for this FOA until 5:00 p.m. (EDT) on April 18, 2022. Applications are due by 5:00 p.m. (EDT) on June 7, 2022. Additional information on this FOA is available here.
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