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Datasheets relating to the article "Brachypodium SPEECHLESS2 promoter drives expression of a synthetic EPF to reduce stomatal density in sugarcane without pleiotropic effects" published in Plant Biotechnology Journal.
Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.
The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.
Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
Gas chromatography and mass spectrometry data obtained from monitoring atmospheric pollutants in Skylab spurred studies of indoor pollutants in terrestrial buildings. Subsequent studies of techniques for removing the pollutants from space habitats have led to building concepts which achieve the same purpose on earth. The Skylab data indicated that the synthesized organic materials used in many modern buildings, furnishings, personal clothing and aerosols add significant amounts of chemicals to the indoor atmosphere. Lowered circulation and ventilation rates to conserve energy have caused trapping of these substances in buildings. Studies of methods for space modules which will use plants and microbes to absorb airborne and wastewater pollutants have defined biotechnology designs which can be applied to remove pollutants from air and wastewater organically. Plant roots trap pollutants from wastewater and leaves readily absorb air pollutants, as well as improve the overall energy efficiency of buildings. Several designs which incorporate biotechnology to enhance both the aesthetics and efficiency of homes and office buildings are illustrated.
Four experiment systems which have fundamental significance in the field of biotechnology are developed for the Get Away Special (GAS). Unique considerations were necessary to develop the systems which carry out biotechnological experiments under GAS's restricted conditions: delicate thermal control, fluid handling and protection from contamination. All experimental processes are controlled by internal sequencers and results of the experiments are recorded as images and numerical data within the systems. The systems are standardized in order to enable repeated use with a variety of experiments by replacement of the experiment modules and modification of experiment sequencing programs.
The science and hardware programs laying the science and technology framework for experiments to be conducted aboard SSF are described. Six microgravity facilities planned for the Laboratory Module encompass the Fluid Physics/Dynamics Facility, investigating fundamental fluid behavior; the Advanced Protein Crystal Growth Facility, growing high-quality crystals for pharmaceutical, medical, chemical, and biotechnology applications; the Biotechnology Facility, investigating microgravity effects on biological processes and living organisms at the cellular level and on the purification and production of biological materials; the Space Station Furnace Facility, conducting metal and alloy solidification experiments; the Modular Containerless Processing Facility, supporting experiments through levitation techniques; and the Modular Combustion Facility, performing studies of fundumental combustion processes.
An objective of the US Department of Agriculture (USDA) Agriculture Research Service (ARS) is to develop technology leading to a broad portfolio of value-added marketable products. Modern scientific disciplines such as chemical engineering are brought into play to develop processes for converting bulk commodities into high-margin products. To accomplish this, the extremely sophisticated processing devices which form the basis of modern biotechnology, namely, genes and enzymes, can be tailored to perform the required functions. The USDA/ARS is a leader in the development of intelligent processing equipment (IPE) for agriculture in the broadest sense. Applications of IPE are found in the production, processing, grading, and marketing aspects of agriculture. Various biotechnology applications of IPE are discussed.
Microgravity Science in the U.S.A. involves research in fluids science, combustion science, materials science, biotechnology, and fundamental physics. The purpose is to achieve a thorough understanding of the effects of gravitational body forces on physical phenomena relevant to those disciplines. This includes the study of phenomena which are usually overwhelmed by the presence of gravitational body forces and, therefore, chiefly manifested when gravitational forces are weak. In the pragmatic sense, the research involves gravity level as an experimental parameter. Calendar year 1992 is a landmark year for research opportunities in low earth orbit for Microgravity Science. For the first time ever, three Spacelab flights will fly in a single year: IML-1 was launched on January 22; USML-1 was launched on June 25; and, in September, SL-J will be launched. A separate flight involving two cargo bay carriers, USMP-1, will be launched in October. From the beginning of 1993 up to and including the Space Station era (1997), nine flights involving either Spacelab or USMP carriers will be flown. This will be augmented by a number of middeck payloads and get away specials flying on various flights. All of this activity sets the stage for experimentation on Space Station Freedom. Beginning in 1997, experiments in Microgravity Science will be conducted on the Space Station. Facilities for doing experiments in protein crystal growth, solidification, and biotechnology will all be available. These will be joined by middeck-class payloads and the microgravity glove box for conducting additional experiments. In 1998, a new generation protein crystal growth facility and a facility for conducting combustion research will arrive. A fluids science facility and additional capability for conducting research in solidification, as well as an ability to handle small payloads on a quick response basis, will be added in 1999. The year 2000 will see upgrades in the protein crystal growth and fluids science facilities. From the beginning of 1997 to the fall of 1999 (the 'man-tended capability' era), there will be two or three utilization flights per year. Plans call for operations in Microgravity Science during utilization flights and between utilization flights. Experiments conducted during utilization flights will characteristically require crew interaction, short duration, and less sensitivity to perturbations in the acceleration environment. Operations between utilization flights will involve experiments that can be controlled remotely and/or can be automated. Typically, the experiments will require long times and a pristine environment. Beyond the fall of 1999 (the 'permanently-manned capability' era), some payloads will require crew interaction; others will be automated and will make use of telescience.
Low gravity biotechnology experiments indicate a need to better understand and control a host of liquid-solid interfacial phenomena which reduce the efficiency of bioseparations methods on earth as well as in space. We have improved and utilized polymeric and silane derivatives, developed in association with MSFC, in order to control such phenomena. The objectives of the proposed research have been obtained. They were to improve NASA-patented coatings capable of controlling macromolecular adsorption, electroosmosis, and particle electrophoresis over a wide range of pH, and to further characterize the ability of polymeric coatings to control wall wetting interactions. To date this research has resulted in six publications and four abstracts. It has also aided researchers at MSFC with studies on the electrophoresis of large DNA molecules in free solution. It will continue to enhance NASA's efforts to exploit the space environment to enhance knowledge of phenomena relevant to biotechnology, and obtain bioseparations currently unobtainable on Earth. Abstracts from the 1994 ACS Meeting in Birmingham are attached.
On this fifth day of the STS-79 mission, the flight crew, Cmdr. William F. Readdy, Pilot Terrence W. Wilcutt, Mission Specialists, Thomas D. Akers, Shannon Lucid, Jay Apt, and Carl E. Walz, in the first full day of joint Shuttle/Mir operations begin in with the transfer of a biotechnology investigation and logistical supplies from Atlantis to Mir. The Biotechnology System, an investigation that will study the long-term development of cartilage cells in microgravity, was transported to Mir early this morning. During his planned four-month stay on Mir, John Blaha will take weekly samples of the culture which may provide researchers with information on engineering cartilage cells for possible use in transplantation. They also took time out of their schedules to talk with Good Morning America's Elizabeth Vargas in a brief interview. Prior to beginning the day's transfer activities, all nine astronauts and cosmonauts participated in a joint planning session to outline the day's schedule.
NASA's Microgravity Science and Applications Division (MSAD) sponsors a program that expands the use of space as a laboratory for the study of important physical, chemical, and biochemical processes. The primary objective of the program is to broaden the value and capabilities of human presence in space by exploiting the unique characteristics of the space environment for research. However, since flight opportunities are rare and flight research development is expensive, a vigorous ground-based research program, from which only the best experiments evolve, is critical to the continuing strength of the program. The microgravity environment affords unique characteristics that allow the investigation of phenomena and processes that are difficult or impossible to study an Earth. The ability to control gravitational effects such as buoyancy driven convection, sedimentation, and hydrostatic pressures make it possible to isolate phenomena and make measurements that have significantly greater accuracy than can be achieved in normal gravity. Space flight gives scientists the opportunity to study the fundamental states of physical matter-solids, liquids and gasses-and the forces that affect those states. Because the orbital environment allows the treatment of gravity as a variable, research in microgravity leads to a greater fundamental understanding of the influence of gravity on the world around us. With appropriate emphasis, the results of space experiments lead to both knowledge and technological advances that have direct applications on Earth. Microgravity research also provides the practical knowledge essential to the development of future space systems. The Office of Life and Microgravity Sciences and Applications (OLMSA) is responsible for planning and executing research stimulated by the Agency's broad scientific goals. OLMSA's Microgravity Science and Applications Division (MSAD) is responsible for guiding and focusing a comprehensive program, and currently manages its research and development tasks through five major scientific areas: biotechnology, combustion science, fluid physics, fundamental physics, and materials science. FY 1996 was an important year for MSAD. NASA continued to build a solid research community for the coming space station era. During FY 1996, the NASA Microgravity Research Program continued investigations selected from the 1994 combustion science, fluid physics, and materials science NRAS. MSAD also released a NASA Research Announcement in microgravity biotechnology, with more than 130 proposals received in response. Selection of research for funding is expected in early 1997. The principal investigators chosen from these NRAs will form the core of the MSAD research program at the beginning of the space station era. The third United States Microgravity Payload (USMP-3) and the Life and Microgravity Spacelab (LMS) missions yielded a wealth of microgravity data in FY 1996. The USMP-3 mission included a fluids facility and three solidification furnaces, each designed to examine a different type of crystal growth.
The Microgravity Research Program Office (MRPO) participated aggressively in Phase I of the International Space Station Program using the Russian Mir Space Station. The Mir Station offered an otherwise unavailable opportunity to explore the advantages and challenges to long duration microgravity space research. Payloads with both NASA and commercial backing were included as well as cooperative research with the Canadian Space Agency (CSA). From this experience, much was learned about dealing with long duration on orbit science utilization and developing new working relationships with our Russian partner to promote efficient planning, operations, and integration to solve complexities associated with a multiple partner program. Microgravity participation in the NASA Mir Program began with the first joint NASA Mir flight to the Mir Space Station. The earliest participation setup acceleration measurement capabilities that were used throughout the Program. Research, conducted by all Microgravity science disciplines, continued on each subsequent increment for the entire three-year duration of the Program. The Phase I Program included the Microgravity participation of over 30 Fluids, Combustion, Materials, and Biotechnology Sciences and numerous commercially sponsored research payloads. In addition to the research gained from Microgravity investigations, long duration operation of facility hardware was tested. Microgravity facilities operated on Mir included the Space Acceleration Measurement System (SAMS), the Microgravity Glovebox (MGBX), the Biotechnology System (BTS) and the Canadian Space Agency sponsored Microgravity Isolation Mount (MIM). The Russian OPTIZONE Furnace was also incorporated into our material science research. All of these efforts yielded significant and useful scientific research data. This paper focuses on the microgravity research conducted onboard the Mir space station. It includes the Program preparation and planning necessary to support this type of cross increment research experience; the payloads which were flown; and summaries of significant microgravity science findings. Most importantly this paper highlights the various disciplines of microgravity research conducted during the International Space Station, Phase 1 Program onboard the Mir Station. A capsulation of significant research and the applicability of our findings are provided. In addition, a brief discussion of how future microgravity science gathering capabilities, hardware development and payload operations techniques have enhanced our ability to conduct long duration microgravity research.
The ability to manipulate matter at the atomic and molecular levels is likely to change the way almost everything is designed and made, from computers to engineering systems to objects not yet imagined. For nanometer-scale objects, biological systems provide a rich storehouse of interesting ideas and strategies, and this is why there has been synergistic coupling between nanotechnology and biotechnology. The field of nanobiotechnology is garnering much interest around the world. In January 2000, the President announced the establishment of the National Nanotechnology Initiative and has made it a top priority. An attempt is made in this overview to define some of the buzzwords and set the stage for the succeeding presentations. This presentation is divided into four parts. The first part identifies the major characteristics of future aerospace systems that distinguish them from the current systems. The second and third parts describe the revolutionary and key technologies and future research and learning environments required for the realization of future systems. The fourth part lists the objectives of the workshop and the sources of information about nano and biotechnologies. This document consists of viewgraphs with an explanation for each slide.
As part of NASA's mission of furthering the commercial development of space, the Space Product Development Office has sponsored the flight of seven commercial payloads to the International Space Station (ISS) during calendar year 2001. Most of these payloads, which are among the first users of this new laboratory, build upon successful commercial investigations that previously were restricted to the limited flight duration of the Space Shuttle. These commercial operations range from multi-media, in the form of Dreamtime, to biotechnology such as in Advanced Astroculture, to advanced materials such as Zeolite Crystal Growth. Industry investment in the commercial program has continued to remain high, while awaiting long term access to space, which the ISS provides. While the majority of early commercial use of the ISS is in the area of biotechnology, there is a significant shift towards commercial materials research over the next two years. In order to take fall advantage of the ISS, much of the commercial hardware is designed to be left on Station, while the Shuttle brings samples up and down. This not only makes good use of this valuable space resource, it has the added benefit of having commercial hardware available on the ISS for scientific users. In order to provide benefit to the entire NASA microgravity program, the scientific community on a space available basis can use a variety of commercial apparatus at very low cost. In addition to the solution crystal growth capability of Creosote Crystal Growth, in 2002 containerless processing will be available in the form of Space-DRUMS, and in 2003, thermophysical properties research can be performed in the Vulcan furnace. The first commercial operations on the ISS provides not only a much needed capability to the commercial development of space program, it also has the potential to augment the science program as well.
The science program at Marshall Space Flight Center will be reviewed in the context of the overall NASA science program. An overview will be given on how Marshall science supports the International Space Station research program. The Microgravity research capabilities at Marshall's Biological and Physical Space Research Laboratory will be reviewed. The environment in orbit provides a unique opportunity to study Materials Science and Biotechnology in the absence of sedimentation and convection. There are a number of peer-selected investigations that have been selected to fly on the Space Station that have been conceived and are led by Marshall civil service and contractor scientists. In addition to Microgravity research the Station will enable research in New Initiative Research Areas that focus on enabling humans to live, work, and explore the solar system safely. The specific scientific instruments that have been developed for Materials Science and Biotechnology Research on the International Space Station will be discussed.
The challenge of human space exploration places demands on technology that push concepts and development to the leading edge. In biotechnology and biomedical equipment development, NASA science has been the seed for numerous innovations, many of which are in the commercial arena. The biotechnology effort has led to rational drug design, analytical equipment, and cell culture and tissue engineering strategies. Biomedical research and development has resulted in medical devices that enable diagnosis and treatment advances. NASA Biomedical developments are exemplified in the new laser light scattering analysis for cataracts, the axial flow left ventricular-assist device, non contact electrocardiography, and the guidance system for LASIK surgery. Many more developments are in progress. NASA will continue to advance technologies, incorporating new approaches from basic and applied research, nanotechnology, computational modeling, and database analyses.