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At least 1,765 records · Page 98
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Krinos, Arianna I. (ORCID:0000000197678392)↗
DOE OSTI2022

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Automated Assembly Progress Monitoring in Modular Construction Factories Using Computer Vision-Based Instance Segmentation

Modular construction has recently gained interest as a transformative construction method. In this method, a large portion of the construction is performed inside factories, where processes are fast-paced and interdependent; therefore, any deviation from the schedule can delay the production. Such deviations are frequent in modular factories due to the labor-intensive nature of the tasks. This propagation of delays can be mitigated by continuously monitoring each process; however, current manual monitoring methods are laborious, and recently proposed contact sensor-based methods are intrusive to the work. In addition, recent computer vision-based monitoring methods inside factories are limited to detection algorithms that fail to provide the pixel-level accuracy required for assembly progress monitoring in highly occluded factory scenes, and they require a large number of manual annotations. Therefore, this paper proposes a method to monitor the installation of subassemblies in modular construction factories using mask R-CNN instance segmentation and improves the data efficiency of the model using a copy-paste augmentation method. This method was validated on the CCTV videos captured from a modular construction factory in the US, resulting in a 9% mAP improvement in segmentation.

computer vision↗
NASA NTRS2013

Materials Science Research Rack Onboard the International Space Station

The Materials Science Research Rack (MSRR) is a research facility developed under a cooperative research agreement between NASA and ESA for materials science investigations on the International Space Station (ISS). MSRR was launched on STS-128 in August 2009 and currently resides in the U.S. Destiny Laboratory Module. Since that time, MSRR has logged more than 1000 hours of operating time. The MSRR accommodates advanced investigations in the microgravity environment on the ISS for basic materials science research in areas such as solidification of metals and alloys. The purpose is to advance the scientific understanding of materials processing as affected by microgravity and to gain insight into the physical behavior of materials processing. MSRR allows for the study of a variety of materials, including metals, ceramics, semiconductor crystals, and glasses. Materials science research benefits from the microgravity environment of space, where the researcher can better isolate chemical and thermal properties of materials from the effects of gravity. With this knowledge, reliable predictions can be made about the conditions required on Earth to achieve improved materials. MSRR is a highly automated facility with a modular design capable of supporting multiple types of investigations. The NASA-provided Rack Support Subsystem provides services (power, thermal control, vacuum access, and command and data handling) to the ESA-developed Materials Science Laboratory (MSL) that accommodates interchangeable Furnace Inserts (FI). Two ESA-developed FIs are presently available on the ISS: the Low Gradient Furnace (LGF) and the Solidification and Quenching Furnace (SQF). Sample Cartridge Assemblies (SCAs), each containing one or more material samples, are installed in the FI by the crew and can be processed at temperatures up to 1400C. ESA continues to develop samples with 14 planned for launch and processing in the near future. Additionally NASA has begun developing SCAs to support US PIs and their partners. The first of these Flight SCAs are being developed for investigations to support research in the areas of crystal growth and liquid phase sintering. Subsequent investigations are in various stages of development. US investigations will include a ground test program in order to distinguish the particular effects of the absence of gravity.

Reagan, Shawn↗
NASA NTRS2013

Materials Science Research Rack Onboard the International Space Station

The Materials Science Research Rack (MSRR) is a research facility developed under a cooperative research agreement between NASA and ESA for materials science investigations on the International Space Station (ISS). MSRR was launched on STS-128 in August 2009 and currently resides in the U.S. Destiny Laboratory Module. Since that time, MSRR has logged more than 1000 hours of operating time. The MSRR accommodates advanced investigations in the microgravity environment on the ISS for basic materials science research in areas such as solidification of metals and alloys. The purpose is to advance the scientific understanding of materials processing as affected by microgravity and to gain insight into the physical behavior of materials processing. MSRR allows for the study of a variety of materials, including metals, ceramics, semiconductor crystals, and glasses. Materials science research benefits from the microgravity environment of space, where the researcher can better isolate chemical and thermal properties of materials from the effects of gravity. With this knowledge, reliable predictions can be made about the conditions required on Earth to achieve improved materials. MSRR is a highly automated facility with a modular design capable of supporting multiple types of investigations. The NASA-provided Rack Support Subsystem provides services (power, thermal control, vacuum access, and command and data handling) to the ESA-developed Materials Science Laboratory (MSL) that accommodates interchangeable Furnace Inserts (FI). Two ESA-developed FIs are presently available on the ISS: the Low Gradient Furnace (LGF) and the Solidification and Quenching Furnace (SQF). Sample Cartridge Assemblies (SCAs), each containing one or more material samples, are installed in the FI by the crew and can be processed at temperatures up to 1400C. ESA continues to develop samples with 14 planned for launch and processing in the near future. Additionally NASA has begun developing SCAs to support US PIs and their partners. The first of these Flight SCAs are being developed for investigations to support research in the areas of crystal growth and liquid phase sintering. Subsequent investigations are in various stages of development. US investigations will include a ground test program in order to distinguish the particular effects of the absence of gravity.

Reagan, Shawn↗
NASA NTRS2016

Materials Science Research Rack Onboard the International Space Station

The Materials Science Research Rack (MSRR) is a research facility developed under a cooperative research agreement between NASA and ESA for materials science investigations on the International Space Station (ISS). MSRR was launched on STS-128 in August 2009 and currently resides in the U.S. Destiny Laboratory Module. Since that time, MSRR has logged more than 1400 hours of operating time. The MSRR accommodates advanced investigations in the microgravity environment on the ISS for basic materials science research in areas such as solidification of metals and alloys. The purpose is to advance the scientific understanding of materials processing as affected by microgravity and to gain insight into the physical behavior of materials processing. MSRR allows for the study of a variety of materials, including metals, ceramics, semiconductor crystals, and glasses. Materials science research benefits from the microgravity environment of space, where the researcher can better isolate chemical and thermal properties of materials from the effects of gravity. With this knowledge, reliable predictions can be made about the conditions required on Earth to achieve improved materials. MSRR is a highly automated facility with a modular design capable of supporting multiple types of investigations. The NASA-provided Rack Support Subsystem provides services (power, thermal control, vacuum access, and command and data handling) to the ESA-developed Materials Science Laboratory (MSL) that accommodates interchangeable Furnace Inserts (FI). Two ESA-developed FIs are presently available on the ISS: the Low Gradient Furnace (LGF) and the Solidification and Quenching Furnace (SQF). Sample Cartridge Assemblies (SCAs), each containing one or more material samples, are installed in the FI by the crew and can be processed at temperatures up to 1400C. ESA continues to develop samples with 14 planned for launch and processing in the near future. Additionally NASA has begun developing SCAs to support US PIs and their partners. The first of these Flight SCAs are being developed for investigations to support research in the areas of crystal growth and liquid phase sintering. Subsequent investigations are in various stages of development. US investigations will include a ground test program in order to distinguish the particular effects of the absence of gravity.

Reagan, Shawn↗
NASA NTRS2016

Materials Science Research Rack Onboard the International Space Station

The Materials Science Research Rack (MSRR) is a research facility developed under a cooperative research agreement between NASA and ESA for materials science investigations on the International Space Station (ISS). MSRR was launched on STS-128 in August 2009 and currently resides in the U.S. Destiny Laboratory Module. Since that time, MSRR has logged more than 1400 hours of operating time. The MSRR accommodates advanced investigations in the microgravity environment on the ISS for basic materials science research in areas such as solidification of metals and alloys. The purpose is to advance the scientific understanding of materials processing as affected by microgravity and to gain insight into the physical behavior of materials processing. MSRR allows for the study of a variety of materials, including metals, ceramics, semiconductor crystals, and glasses. Materials science research benefits from the microgravity environment of space, where the researcher can better isolate chemical and thermal properties of materials from the effects of gravity. With this knowledge, reliable predictions can be made about the conditions required on Earth to achieve improved materials. MSRR is a highly automated facility with a modular design capable of supporting multiple types of investigations. The NASA-provided Rack Support Subsystem provides services (power, thermal control, vacuum access, and command and data handling) to the ESA-developed Materials Science Laboratory (MSL) that accommodates interchangeable Furnace Inserts (FI). Two ESA-developed FIs are presently available on the ISS: the Low Gradient Furnace (LGF) and the Solidification and Quenching Furnace (SQF). Sample Cartridge Assemblies (SCAs), each containing one or more material samples, are installed in the FI by the crew and can be processed at temperatures up to 1400degC. ESA continues to develop samples with 14 planned for launch and processing in the near future. Additionally NASA has begun developing SCAs to support US PIs and their partners. The first of these Flight SCAs are being developed for investigations to support research in the areas of crystal growth and liquid phase sintering. Subsequent investigations are in various stages of development. US investigations will include a ground test program in order to distinguish the particular effects of the absence of gravity.

Reagan, S. E.↗
DOE OSTI2025

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

The Future of Bio-technology

Hosts of technologies, most notably in electronics, have been on the path of miniaturization for decades and in 2005 they have crossed the threshold of the nano-scale. Crossing the nano-scale threshold is a milestone in miniaturization, setting impressive new standards for component-packing densities. It also brings technology to a scale at which quantum effects and fault tolerance play significant roles and approaches the feasible physical limit form many conventional "top-down" manufacturing methods. I will suggest that the most formidable manufacturing problems in nanotechnology will be overcome and major breakthroughs will occur in a host of technologies, when nanotechnology converges with bio-technology; i.e. I will argue that the future of bio-technology is in nanotechnology. In 2005, methods in molecular biology, microscopy, bioinformatics, biochemistry, and genetic engineering have focused considerable attention on the nano-scale. On this scale, biology is a kind of recursive chemistry in which molecular recognition, self-assembly, self-organization and self-referencing context-control lead to the emergence of the complexity of structures and processes that are fundamental to all life forms. While we are still far from understanding this complexity, we are on the threshold of being able to use at least some of these biological properties for .technology. I will discuss the use of biomolecules, such as DNA, RNA, and proteins as "tools" for the bio-technologist of the future. More specifically, I will present in some detail an example of how we are using a genetically engineered 60-kDa protein (HSP60) from an organism living in near boiling sulfuric acid to build nano-scale templates for arranging metallic nanoparticles. These "extremophile" HSP60s self-assemble into robust double-ring structures called "chaperonins," which further assemble into filaments and arrays with nanometer accuracy. I will discuss our efforts to use chaperonins to organize quantum dots, electronic and magnetic nano-particles for electronic and photonic applications.

Trent, Jonathan↗
NASA NTRS2012

Materials Science Research Rack Onboard the International Space Station Hardware and Operations

The Materials Science Research Rack (MSRR) is a research facility developed under a cooperative research agreement between NASA and ESA for materials science investigations on the International Space Station (ISS). MSRR was launched on STS-128 in August 2009, and is currently installed in the U.S. Destiny Laboratory Module. Since that time, MSRR has performed virtually flawlessly, logging more than 620 hours of operating time. The MSRR accommodates advanced investigations in the microgravity environment on the ISS for basic materials science research in areas such as solidification of metals and alloys. The purpose is to advance the scientific understanding of materials processing as affected by microgravity and to gain insight into the physical behavior of materials processing. MSRR allows for the study of a variety of materials including metals, ceramics, semiconductor crystals, and glasses. Materials science research benefits from the microgravity environment of space, where the researcher can better isolate chemical and thermal properties of materials from the effects of gravity. With this knowledge, reliable predictions can be made about the conditions required on Earth to achieve improved materials. MSRR is a highly automated facility with a modular design capable of supporting multiple types of investigations. Currently the NASA-provided Rack Support Subsystem provides services (power, thermal control, vacuum access, and command and data handling) to the ESA developed Materials Science Laboratory (MSL) which accommodates interchangeable Furnace Inserts (FI). Two ESA-developed FIs are presently available on the ISS: the Low Gradient Furnace (LGF) and the Solidification and Quenching Furnace (SQF). Sample-Cartridge Assemblies (SCAs), each containing one or more material samples, are installed in the FI by the crew and can be processed at temperatures up to 1400 C. Once an SCA is installed, the experiment can be run by automatic command or science conducted via telemetry commands from the ground. Initially, 12 SCAs were processed in the first furnace insert for a team of European and US investigators. After these samples were processed the Furnaces Inserts were exchanged and an additional single sample was processed. The processed samples have been returned to Earth for evaluation and comparison of their properties to samples similarly processed on the ground. A preliminary examination of the samples indicates that the majority of the desired science objectives have been successfully met leading to significant improvements in the understanding of alloy solidification processes. Six SCAs were launched on Space Shuttle Mission STS-135 in July 2011 for processing during the Fall of 2011. Additional batches are planned for future processing. This facility is available to support additional materials science investigations through programs such as the US National Laboratory, Technology Development, NASA Research Announcements, and others.

Lehman, John R.↗
DOE OSTI2021

Engineering Graphene-Ceramic 3D Composite Foams by Freeze Drying

A 3D graphene foam produced by the chemical vapor deposition (CVD) technique is recognized as an effective nanofiller material, as it does not agglomerate in the matrix. Though CVD facilitates pristine graphene foam production, the method poses limitations in developing large-scale 3D graphene composite foams as advanced engineering materials. In this paper, a freeze-drying (FD) process is used to produce a composite 3D foam, which is a mixture of graphene nanoplatelet (GNP) and a low-temperature co-fired ceramic (LTCC). The freeze-dried GNP-LTCC reticulated 3D composite foam has an average pore size ranging from 70 to 100 μm. Pore size is varied by regulating the heat transfer rate during the freezing process using a thermally conductive aluminum (Al) mold and a thermally insulating acrylonitrile butadiene styrene (ABS) mold. Computational thermal modeling is used to visualize the heat transfer and its effect on foam pore size. Subsequently, a freeze-dried GNP-LTCC composite foam is embedded into the LTCC matrix to form a hierarchical assembly by a spark plasma technique without compromising the 3D structure of the FD foam. This study established that a simple, eco-friendly, and scalable processing methodology can produce advanced graphene-based 3D composite foams as the future tailorable nanofillers for designing multimatrix materials.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Chip Scale Package Integrity Assessment by Isothermal Aging

Many aspects of chip scale package (CSP) technology, with focus on assembly reliability characteristics, are being investigated by the JPL-led consortia. Three types of test vehicles were considered for evaluation and currently two configurations have been built to optimize attachment processes. These test vehicles use numerous package types. To understand potential failure mechanisms of the packages, particularly solder ball attachment, the grid CSPs were subjected to environmental exposure. Package I/Os ranged from 40 to nearly 300. This paper presents both as assembled, up to 1, 000 hours of isothermal aging shear test results and photo micrographs, and tensile test results before and after 1,500 cycles in the range of -30/100 C for CSPs. Results will be compared to BGAs with the same the same isothermal aging environmental exposures.

Ghaffarian, Reza↗
NASA NTRS1997

The first living systems: a bioenergetic perspective

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

Review↗
NASA NTRS2005

[Microfabricated X-ray Optics Technology Development for the Constellation X-Mission]

MIT has previously developed advanced methods for the application of silicon microstructures (so-called microcombs) in the precision assembly of foil x-ray optics in support of the Constellation-X Spectroscopy X-ray Telescope (SXT) technology development at the NASA Goddard Space Flight Center (GSFC). During the first year of the above Cooperative Agreement, MIT has developed a new, mature, potentially high- yield process for the manufacturing of microcombs that can be applied to a range of substrates independent of thickness. MIT also developed techniques to extract microcomb accuracy from an assembly truss metrology test stand and to extend the dynamic range of its Shack-Hartmann foil metrology tool. The placement repeatability of foil optics with microcombs in the assembly truss has been improved by a factor of two to approximately 0.15 micron. This was achieved by electric contact determination in favor of determining contact through force measurements. Development work on a stress-free thin foil holder was also supported by this agreement and successfully continued under a different grant.

Schattenburg, Mark L.↗
DOE OSTI2024

Vortex fluidic regulated phospholipid equilibria involving liposomes down to sub-micelle size assemblies

Conventional channel-based microfluidic platforms have gained prominence in controlling the bottom-up formation of phospholipid based nanostructures including liposomes. However, there are challenges in the production of liposomes from rapidly scalable processes. These have been overcome using a vortex fluidic device (VFD), which is a thin film microfluidic platform rather than channel-based, affording ~110 nm diameter liposomes. The high yielding and high throughput continuous flow process has a 45° tilted rapidly rotating glass tube with an inner hydrophobic surface. Processing is also possible in the confined mode of operation which is effective for labelling pre-VFD-prepared liposomes with fluorophore tags for subsequent mechanistic studies on the fate of liposomes under shear stress in the VFD. In situ small-angle neutron scattering (SANS) established the co-existence of liposomes ~110 nm with small rafts, micelles, distorted micelles, or sub-micelle size assemblies of phospholipid, for increasing rotation speeds. The equilibria between these smaller entities and ~110 nm liposomes for a specific rotational speed of the tube is consistent with the spatial arrangement and dimensionality of topological fluid flow regimes in the VFD. The prevalence for the formation of ~110 nm diameter liposomes establishes that this is typically the most stable structure from the bottom-up self-assembly of the phospholipid and is in accord with dimensions of exosomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Application of lipid-stabilized liquid-liquid interfaces in 3D printing of biomaterials

Developing strategies to stabilize liquid-liquid interfaces is essential for advancing applications in various biomedical systems. This study introduces a novel biocompatible in situ-forming material in which lipid self-assembly stabilizes water–oil interfaces, enabling controlled structuring of liquids through liquid-in-liquid 3D printing. The stabilization process, driven by the formation of nanostructures at the interface, is thoroughly analyzed through small-angle X-ray scattering (SAXS), rheometry, and microscopy techniques. This material system enables the fabrication of complex 3D constructs, including fibers, substrates, and microneedle patches, which exhibit outstanding mechanical properties and biocompatibility, as confirmed by tensile testing and cell viability tests. Here, by leveraging the unique properties of lipid-stabilized interfaces, this work demonstrates the potential of this approach for diverse biomedical applications such as drug delivery and tissue engineering while establishing a foundation for future advancements in liquid-in-liquid 3D printing technology.

36 MATERIALS SCIENCE↗