Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biological material”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Storage and Diffusion of Carbon and Nitrogen in Crustal Materials

Nitrogen is a primary constituent of Earth’s atmosphere and an essential component of many biological processes. Recent developments in understanding N incorporation into silicate minerals suggest that the solid earth and lithosphere could provide a substantial reservoir for the planetary N budget. Furthermore, determining the concentration and distribution of low abundances of N in silicates presents a significant challenge in microanalysis. We tested capabilities for high spatial resolution quantification of low levels of N using EPMA with the goal of developing standards to be used in coupled N and noble gas analyses of silicate minerals. We investigated the concentration and distribution of N in a suite of ammonium-bearing silicate minerals that reflect the dominant N-bearing phases of the lithosphere: tobelite, buddingtonite, ammonioleucite, tsaregorodtsevite, and hyalophane. These minerals form during NH 4 -rich alteration of K-bearing silicate minerals, and the bonding environment of N in each mineral is likely to differ based on crystal structure. Using an optimized analytical routine for N quantification enables sensitivity approaching 0.02 weight% N and high-resolution quantitative mapping of sub-micron variations in N contents.

58 GEOSCIENCES↗
DOE OSTI2020

On Simulating the Formation of Structured, Crystalline Systems via Non-classical Pathways

Observations in crystal growth and assembly from recent in situ methods suggest alternative, non-classical crystallization pathways play an important role in the determination of the micro- and meso- structures in crystalline systems. These processes display parallels that cross-cut multiple disciplines investigating crystallization across four orders of magnitude in size scales and widely differing environments, hinting that alternative crystal growth pathways may be a fundamental scheme in natural crystal formation. Using a system of short-range attractive microbeads, we demonstrate that the addition of a small concentration of sub-species incommensurate with the lattice spacing of the dominant species results in a stark change in crystal size and morphology. These changes are attributed to the presence of fleeting, amorphous-like configurations of beads that ultimately change the melting and growth dynamics in preferred directions. From these real-time observations, we hypothesize the amorphous mineral precursors present in biological mineralized tissues undergo similar non-classical crystallization processes resulting in the complex structures found in biomineralization.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Storage-Induced Collapse of Lignin Macromolecular Structure and Its Impacts on the Biorefinery

Lignin plays a vital role in the economics of biorefineries, serving as a source of process energy and a feedstock for sustainable fuels and chemical production. While understanding lignin’s chemical composition is crucial, emerging evidence suggests that a more comprehensive understanding of its macromolecular structure is critical to explaining its complex behavior in the biorefinery. This study investigated the partial collapse of the lignin network in corn stover feedstock after harvest and storage as a result of the microbial digestion of hemicellulose. Fluorescence microscopy was used to detect the collapse of lignin in terms of lignin’s inter-molecular interaction and the re-orientation of lignin’s chromophores, by the changes in lignin’s fluorescence lifetime, anisotropy, and the number of effective emitters. With minimal sample perturbation, our in-situ microscopic results revealed lignin's coil-globule transition phenomena, which was only previously predicted by molecular dynamics modeling extracted lignin in solvent. This collapse of lignin macromolecular structure was confirmed by results from NMR, IR, Raman, and powder X-ray diffraction. We also investigated the impact of this storage-induced collapse on the downstream biorefinery processes. Our study revealed that the two major approaches for lignin valorization in the lignin-first biorefinery model, namely monomer extraction and milled wood lignin extraction, were negatively impacted by the lignin collapse. As changes during storage are a source of feedstock variability, our study highlights the importance of understanding the effect of feedstock handling on biorefinery operations and economics.

09 BIOMASS FUELS↗
NASA NTRS2004

Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions

In the robotic search for life on Mars, different proposed missions will analyze the chemical and biological signatures of life using different platforms. The analysis of samples via analytical instrumentation on the surface of Mars has thus far only been attempted by the two Viking missions. Robotic arms scooped relogith material into a pyrolysis oven attached to a GC/MS. No trace of organic material was found on any of the two different samples at either of the two different landing sites. This null result puts an upper limit on the amount of organics that might be present in Martian soil/rocks, although the level of detection for each individual molecular species is still debated. Determining the absolute limit of detection for each analytical instrument is essential so that null results can be understood. This includes investigating the trade off of using pyrolysis versus liquid solvent extraction to release organic materials (in terms of extraction efficiencies and the complexity of the sample extraction process.) Extraction of organics from field samples can be accomplished by a variety of methods such utilizing various solvents including HCl, pure water, supercritical fluid and Soxhelt extraction. Utilizing 6N HCl is one of the most commonly used method and frequently utilized for extraction of organics from meteorites but it is probably infeasible for robotic exploration due to difficulty of storage and transport. Extraction utilizing H2O is promising, but it could be less efficient than 6N HCl. Both supercritical fluid and Soxhelt extraction methods require bulky hardware and require complex steps, inappropriate for inclusion on rover spacecraft. This investigation reports the efficiencies of pyrolysis and solvent extraction methods for amino acids for different terrestrial samples. The samples studied here, initially created in aqueous environments, are sedimentary in nature. These particular samples were chosen because they possibly represent one of the best terrestrial analogs of Mars and they represent one of the absolute best case scenarios for finding organic molecules on the Martian surface.

Beegle, L. W.↗
DOE OSTI2020

Metamaterials for Mechanically Directing Cell Phenotype

Recently, abundant research has begun to reveal how microscale surface topography can influence a wide range of cell phenotypes in vitro, such as cell mobility, cell size and cell viability (Flemming et al. 1999, Nikkhah et al. 2012, Wang et al. 2016). However, while these studies shed some light on cell interactions with 2D surfaces of different length scales, cells in vivo experience their surroundings in 3D. Therefore, investigations into cell interactions with varying 3D microstructures are needed to gain biologically relevant insight into how microarchitecture and feature size influences cell behavior. Understanding this relationship between 3D microstructure and cell behavior will have a huge impact on tissue engineering and mechanobiology. Until now, the ability to fabricate complex 3D microstructures for cell behavior studies has been limited. This study harnessed LLNL’s Projection Micro-Stereolithography (PμSL) capability to probe the effects of micron-scale changes in 3D architecture on cell phenotype. Furthermore, our studies explored the application of external forces—such as cyclic loading and flow-induced shear stress—to cell-seeded 3D microstructures to further examine cell behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Near-Field Scanning Optical Microscopy of Soft, Biological, or Rough Objects in Aqueous Environment: Challenges and some Remedies to Circumvent

Near-field scanning optical microscopy is an established technique for sub-wavelength spatial resolution in imaging, spectroscopy, material science, surface chemistry, polarimetry, etc. A significant amount of confidence has been established for thin hard specimens in air. However when soft, biological, rough, in aqueous environment object, or a combination is involved, the progress has been slow. The tip-sample mechanical interaction, heat effects to sample, drag effects to the probe, difficulty in controlling tip-sample separation in case of rough objects, light scattering from sample thickness, etc. create problems. Although these problems are not even fully understood, there have been attempts to study them with the aim of performing reliable operations. In this review we describe these attempts. Starting with general problems encountered, various effects like polarization, thermal, and media are covered. The roles of independent tip-sample distance control tools in the relevant situations are then described. Finally progress in fluid cell aspect has been summarized.

Vikram, C. S.↗
DOE OSTI2023

Structural properties of optically clear bacterial cellulose produced by Komagataeibacter hansenii using arabitol

Here, bacterial cellulose (BC) exhibits beneficial properties for use in biomedical applications but is limited by its lack of tunable transparency capabilities. To overcome this deficiency, a novel method to synthesize transparent BC materials using an alternative carbon source, namely arabitol, was developed. Characterization of the BC pellicles was performed for yield, transparency, surface morphology, and molecular assembly. Transparent BC was produced using mixtures of glucose and arabitol. Zero percent arabitol pellicles exhibited 25% light transmittance, which increased with increasing arabitol concentration through to 75% light transmittance. While transparency increased, overall BC yield was maintained indicating that the altered transparency may be induced on a micro-scale rather than a macro-scale. Significant differences in fiber diameter and the presence of aromatic signatures were observed. Overall, this research outlines methods for producing BC with tunable optical transparency, while also bringing new insight to insoluble components of exopolymers produced by Komagataeibacter hansenii.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

The Athena Mars Rover Science Payload

The Mars Surveyor missions that will be launched in April of 2001 will include a highly capable rover that is a successor to the Mars Pathfinder mission's Sojourner rover. The design goals for this rover are a total traverse distance of at least 10 km and a total lifetime of at least one Earth year. The rover's job will be to explore a site in Mars' ancient terrain, searching for materials likely to preserve a record of ancient martian water, climate, and possibly biology. The rover will collect rock and soil samples, and will store them for return to Earth by a subsequent Mars Surveyor mission in 2005. The Athena Mars rover science payload is the suite of scientific instruments and sample collection tools that will be used to perform this job. The specific science objectives that NASA has identified for the '01 rover payload are to: (1) Provide color stereo imaging of martian surface environments, and remotely-sensed point discrimination of mineralogical composition. (2) Determine the elemental and mineralogical composition of martian surface materials. (3) Determine the fine-scale textural properties of these materials. (4) Collect and store samples. The Athena payload has been designed to meet these objectives. The focus of the design is on field operations: making sure the rover can locate, characterize, and collect scientifically important samples in a dusty, dirty, real-world environment. The topography, morphology, and mineralogy of the scene around the rover will be revealed by Pancam/Mini-TES, an integrated imager and IR spectrometer. Pancam views the surface around the rover in stereo and color. It uses two high-resolution cameras that are identical in most respects to the rover's navigation cameras. The detectors are low-power, low-mass active pixel sensors with on-chip 12-bit analog-to-digital conversion. Filters provide 8-12 color spectral bandpasses over the spectral region from 0.4 to 1.1 micron Narrow-angle optics provide an angular resolution of 0.28 mrad/pixel, nearly a factor of four higher than that of the Mars Pathfinder and Mars Surveyor '98 cameras. Image compression will be performed using a wavelet compression algorithm. The Mini-Thermal Emission Spectrometer (Mini-TES) is a point spectrometer operating in -the thermal IR. It produces high spectral resolution (5 /cm) image cubes with a wavelength range of 5-40 gm, a nominal signal/noise ratio of 500:1, and a maximum angular resolution of 7 mrad (7 cm at a distance of 10 in). The wavelength region over which it operates samples the diagnostic fundamental absorption features of rockforming minerals, and also provides some capability to see through dust coatings that could tend to obscure spectral features. The mineralogical information that Mini-TES provides will be used to select from a distance the rocks and soils that will be investigated in more detail and ultimately sampled. Mini-TES is derived from the MO/MGS TES instrument, but is significantly smaller and simpler. The instrument uses an 8-cm Cassegrain telescope, a Michelson interferometer, and uncooled pyroelectric detectors. Along with its mineralogical capabilities, Mini-TES can provide information on the thermophysical properties of rocks and soils. Viewing upward, it can also provide temperature profiles through the martian atmospheric boundary layer. Elemental and Mineralogical Composition: Once promising samples have been identified from a distance using Pancam/Mini-TES, they will be studied in detail using up to three compositional sensors that can be placed directly against them by an Instrument Arm. The two compositional sensors, presently on the payload are an Alpha-Proton-X-Ray Spectrometer (APXS), and a Mossbauer Spectrometer. The APXS is derived closely from the instrument that flew on Mars Pathfinder. Radioactive alpha sources and three detection modes (alpha, proton, and x-ray) provide elemental abundances of rocks and soils to complement and constrain mineralogical data. The Athena APXS will have a revised mechanical design that will cut down significantly on backscattering of alpha particles from martian atmospheric carbon. It will also include a target of known elemental composition that will be used for calibration purposes. The Athena Mossbauer Spectrometer is a diagnostic instrument for the mineralogy and oxidation state of Fe-bearing phases, which are particularly important on Mars. The instrument measures the resonant absorption of gamma rays produced by a Co-57 source to determine splitting of nuclear energy levels in Fe atoms that is related to the electronic environment surrounding them. It has been under development for space flight for many years at the Technical University of Darmstadt. The Mossbauer Spectrometer (and the other arm instruments) will be able to view a small permanent magnet array that will attract magnetic particles in the martian soil. The payload may also include a Raman Spectrometer. If included, the Raman Spectrometer will provide precise identification of major and minor mineral phases. It requires no sample preparation, and is also sensitive to organics. Fine-Scale Texture: The Instrument Arm a also carries a Microscopic Imager that will obtain high-resolution monochromatic images of the same materials for which compositional data will be obtained. Its spatial resolution is 20 micron/pixel over a 1 cm depth of field, and 40 micron/pixel over a 1-cm depth of field. Like Pancam, it uses the same active pixel sensor detectors and electronics as the rover's navigation cameras. The Instrument Arm is a three degree-of-freedom arm that uses designs and components from the Mars Pathfinder and Mars Surveyor '98 projects. Its primary function is instrument positioning. Along with the instruments noted above, it also carries a brush that can be used to remove dust and other loose coatings from rocks. Sample Collection and Storage: Martian rock and soil samples will be collected using a low-power rotary coring drill called the Mini-Corer. An important characteristic of this device is that it can obtain intact samples of rock from up to 5 cm within strong boulders and bedrock, Nominal core dimensions are 8xl7 mm. The Mini-Corer drills a core to the commanded depth in a rock, shears it off, retains it, and extracts it. It can also acquire samples of loose soil, using soil sample cups that are pressed downward into loose material. The Mini-Corer can drill at angles from vertical to 45' off vertical. It has six interchangeable bits for long life. Mechanical damage to the sample during drilling is minimal, and heating is negligible. After acquisition, the sample may be viewed by the arm instruments, and/or placed in one of 104 compartments in the Sample Container. A subset of the acquired samples may be replaced with other samples obtained later if desired. The Sample Container has no moving parts, and is mounted external to the rover for easy removal by the Mars Surveyor 2005 flight system. Operation of the rover will make extensive use of automated onboard navigation and hazard avoidance capabilities. Otherwise, use of onboard autonomy is minimal. Data downlink capability is about 40 Mbit/sol, and the use of the Mars Surveyor '01 orbiter for data relay imposes a limit of at most two command cycles per sol. Because of the significant amount of time available between command cycles, all payload elements will be operated sequentially, rather than in parallel.; this approach also significantly simplifies operations and minimizes peak power usage. The landing site for the '01 rover has not been selected yet. Site selection will make as full use as possible of Mars Global Surveyor data, and will involve substantial input from the broad Mars science community. Summary: The following table describes the mass, power, providers, and key scientific objectives of all the major elements of the Athena payload. Additional Athena payload information may be found at: http://astrosun.tn.cornell.edu/athena/index.html. Additional information contained in the original.

Squyes, S. W.↗
NASA NTRS1997

Materials for Shielding Astronauts from the Hazards of Space Radiations

One major obstacle to human space exploration is the possible limitations imposed by the adverse effects of long-term exposure to the space environment. Even before human spaceflight began, the potentially brief exposure of astronauts to the very intense random solar energetic particle (SEP) events was of great concern. A new challenge appears in deep space exploration from exposure to the low-intensity heavy-ion flux of the galactic cosmic rays (GCR) since the missions are of long duration and the accumulated exposures can be high. Because cancer induction rates increase behind low to rather large thickness of aluminum shielding according to available biological data on mammalian exposures to GCR like ions, the shield requirements for a Mars mission are prohibitively expensive in terms of mission launch costs. Preliminary studies indicate that materials with high hydrogen content and low atomic number constituents are most efficient in protecting the astronauts. This occurs for two reasons: the hydrogen is efficient in breaking up the heavy GCR ions into smaller less damaging fragments and the light constituents produce few secondary radiations (especially few biologically damaging neutrons). An overview of the materials related issues and their impact on human space exploration will be given.

Wilson, J. W.↗
DOE OSTI2026

Statistical Uncertainty of Inhalation Dose Coefficients: Impact of Particle Deposition in ICRP 66 Human Respiratory Tract Model

Inhaled radioactive materials can pose a long-term health concern, as the material can be incorporated into the body’s metabolic pathways and remain in organs and tissues for extended durations. During the retention period, the radioactive material may localize in a source organ and irradiate adjacent target organs and tissues. Distribution of these materials changes over time, requiring biokinetic modeling to evaluate their movement through various tissues and organs. The evolving distribution depends on multiple inputs characterizing the inhaled material, such as particle size and size distribution, particle density, aspect ratio, specific radionuclide, the chemical form, and solubility. In addition, biological parameters such as breathing rate, breathing type (nasal or nasal/oral), respiratory system morphometry, tidal volume, functional residual capacity, and anatomical dead space all influence material transport. These aerosol properties and physiological characteristics of the respiratory tract jointly define a range of initial conditions that influence the time-dependent distribution of radioactive material. To evaluate both uncertainty in the initial conditions of inhalation exposure and the final output (committed effective dose) from biokinetic models, a Python-based software tool, Radiological Exposure Dose Calculator (REDCAL), was developed to propagate uncertainty within the human respiratory tract model. Focusing on deposition fraction uncertainty, the primary objective was to characterize the initial activity distribution across respiratory regions as a function of anticipated particle sizes and distributions. The impact of the deposition fraction uncertainty was propagated to committed effective dose coefficients for selected radionuclides in a companion publication. For each particle size, a lognormal distribution, characterized by its geometric mean as defined within ICRP Publication 66, serves as the basis for introducing uncertainty into the physical processes governing deposition in various lung regions. Finally, this study addresses the deposition process and examines how uncertainty in deposition mechanisms affects activity distribution in the airways, ultimately presenting the expected range and standard deviation of deposited activity as a function of particle size.

International Commission on Radiological Protectio↗
DOE OSTI2022

Mixed Plastics Waste Valorization through Tandem Chemical Oxidation and Biological Funneling

Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of these materials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium, Pseudomonas putida, to funnel these oxygenated compounds into a single exemplary chemical product, either ..beta..-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Using Methyl Bromide for Interspecies Cell–Cell Signaling and As a Reporter in a Model Soil Consortium

Synthetic microbial communities are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five member MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that Variovorax beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally-relevant hydration conditions. We find that methyl halide production can report on a MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. Finally, these tools will be useful for future studies that investigate how MSC respond to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High-Resolution Imaging of Cellulose Organization in Cell Walls by Field Emission Scanning Electron Microscopy

Field emission scanning electron microscopy (FESEM) is a powerful tool for analyzing surface structures of biological and nonbiological samples. However, when it is used to study fine structures of nanometer-sized microfibrils of epidermal cell walls, one often encounters tremendous challenges to acquire clear and undistorted images because of two major issues: (1) Preparation of samples suitable for high resolution imaging; due to the delicateness of some plant materials, such as onion epidermal cell walls, many things can happen during sample processing, which subsequently result in damaged samples or introduce artifacts. (2) Difficulties to acquire clear images of samples which are electron-beam sensitive and prone to charging artifacts at magnifications over 100,000×. In this chapter we described detailed procedures for sample preparation and conditions for high-resolution FESEM imaging of onion epidermal cell walls. Lastly, the methods can be readily adapted for other wall materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Mesoporous peptide frameworks engineered from crystallizable collagen-mimetic peptide amphiphiles

The rational design of porous frameworks with tunable pore dimensions and chemical functionalities is a critical step toward their implementation in diverse applications. While traditional porous materials are typically constructed from abiotic components, there is increasing interest in employing biologically derived building blocks (e.g., peptides and proteins) that offer unmatched structural and functional diversity. Here, we report the construction of crystalline mesoporous frameworks that are self-assembled from amphiphilic collagen-mimetic peptides. Comprehensive structural characterization via microscopy, spectroscopy, and computational techniques provides insights into the assembly packing model, in which hexagonally packed channels are interconnected by antiparallel-aligned collagen triple helices via hydrophobic and electrostatic interactions. Lastly, we demonstrate the functional potential of aCMP frameworks through the encapsulation of various molecular guests, including doxorubicin, an anti-cancer drug. Overall, this work establishes a class of mesoporous frameworks, derived from synthetically engineerable peptide conjugates, marking a significant step forward in broadening the architectural scope and application potential of peptide-based materials.

Perez, Anthony R↗
DOE OSTI2024

Rapid biodegradation of microplastics generated from bio-based thermoplastic polyurethane

The accumulation of microplastics in various ecosystems has now been well documented and recent evidence suggests detrimental effects on various biological processes due to this pollution. Accumulation of microplastics in the natural environment is ultimately due to the chemical nature of widely used petroleum-based plastic polymers, which typically are inaccessible to biological processing. One way to mitigate this crisis is adoption of plastics that biodegrade if released into natural environments. In this work, we generated microplastic particles from a bio-based, biodegradable thermoplastic polyurethane (TPU-FC1) and demonstrated their rapid biodegradation via direct visualization and respirometry. Furthermore, we isolated multiple bacterial strains capable of using TPU-FC1 as a sole carbon source and characterized their depolymerization products. Finally, to visualize biodegradation of TPU materials as real-world products, we generated TPU-coated cotton fabric and an injection molded phone case and documented biodegradation by direct visualization and scanning electron microscopy (SEM), both of which indicated clear structural degradation of these materials and significant biofilm formation.

09 BIOMASS FUELS↗
DOE OSTI2021

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

Biology has changed radically in the past two decades, growing from a purely descriptive science into also a design science. The availability of tools that enable the precise modification of cells, as well as the ability to collect large amounts of multimodal data, open the possibility of sophisticated bioengineering to produce fuels, specialty and commodity chemicals, materials, and other renewable bioproducts. However, despite new tools and exponentially increasing data volumes, synthetic biology cannot yet fulfill its true potential due to our inability to predict the behavior of biological systems. Here, we showcase a set of computational tools that, combined, provide the ability to store, visualize, and leverage multiomics data to predict the outcome of bioengineering efforts. We show how to upload, visualize, and output multiomics data, as well as strain information, into online repositories for several isoprenol-producing strain designs. We then use these data to train machine learning algorithms that recommend new strain designs that are correctly predicted to improve isoprenol production by 23%. This demonstration is done by using synthetic data, as provided by a novel library, that can produce credible multiomics data for testing algorithms and computational tools. In short, this paper provides a step-by-step tutorial to leverage these computational tools to improve production in bioengineered strains.

09 BIOMASS FUELS↗
DOE OSTI2020

Cu Homeostasis in Bacteria: The Ins and Outs

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.

36 MATERIALS SCIENCE↗