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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.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A polypeptide model for toxic aberrant proteins induced by aminoglycoside antibiotics

Aminoglycoside antibiotics interfere with the selection of cognate tRNAs during translation, resulting in the synthesis of aberrant proteins that are the ultimate cause of cell death. However, the toxic potential of aberrant proteins and how they avoid degradation by the cell’s protein quality control (QC) machinery are not understood. Here we report that levels of the heat shock (HS) transcription factor σ32 increased sharply following exposure of Escherichia coli to the aminoglycoside kanamycin (Kan), suggesting that at least some of the aberrant proteins synthesized in these cells were recognized as substrates by DnaK, a molecular chaperone that regulates the HS response, the major protein QC pathway in bacteria. To further investigate aberrant protein toxic potential and interaction with cell QC factors, we studied an acutely toxic 48-residue polypeptide (ARF48) that is encoded by an alternate reading frame in a plant cDNA. As occurred in cells exposed to Kan, σ32 levels were strongly elevated following ARF48 expression, suggesting that ARF48 was recognized as a substrate by DnaK. Paradoxically, an internal 10-residue region that was tightly bound by DnaK in vitro also was required for the ARF48 toxic effect. Despite the increased levels of σ32, levels of several HS proteins were unchanged following ARF48 expression, suggesting that the HS response had been aborted. Nucleoids were condensed and cell permeability increased rapidly following ARF48 expression, together suggesting that ARF48 disrupts DNA-membrane interactions that could be required for efficient gene expression. Our results are consistent with earlier studies showing that aberrant proteins induced by aminoglycoside antibiotics disrupt cell membrane integrity. Insights into the mechanism for this effect could be gained by further study of the ARF48 model system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Reversible domain closure modulates GlnBP ligand binding affinity

Glutamine binding protein (GlnBP) is an Escherichia Coli periplasmic binding protein, which binds and carries glutamine to the inner membrane ATP-binding cassette (ABC) transporter. GlnBP binds the ligand with affinity around 0.1μM measured by isothermal titration calorimetry (ITC) and ligand binding stabilizes protein structure shown by its increase in thermodynamic stability. However, the molecular determinant of GlnBP ligand binding is not known. Electrostatic and hydrophobic interaction between GlnBP and glutamine are critical factors. We propose that the freedome of closure movement is also vital for ligand binding. In order to approve this hypothesis, we generate a series of mutants with different linker length that has different magnitude of domain closure. Mutants show different ligand binding affinity, which indicates that the propensity of domain closure determines the ligand binding affinity. Ligand binding triggers gradual ensemble conformational change. Structural changes upon ligand binding are monitored by combination of small angle x-ray scattering (SAXS) and NMR spectroscopy. Detailed structure characterization of GlnBP contributes to a better understanding of ligand binding and provides the structural basis for biosensor design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis

Colonization factor CFA/I defines the major adhesive fimbriae of enterotoxigenic Escherichia coli and mediates bacterial attachment to host intestinal epithelial cells. The CFA/I fimbria consists of a tip-localized minor adhesive subunit, CfaE, and thousands of copies of the major subunit CfaB polymerized into an ordered helical rod. Biosynthesis of CFA/I fimbriae requires the assistance of the periplasmic chaperone CfaA and outer membrane usher CfaC. Although the CfaE subunit is proposed to initiate the assembly of CFA/I fimbriae, how it performs this function remains elusive. Here, we report the establishment of an in vitro assay for CFA/I fimbria assembly and show that stabilized CfaA-CfaB and CfaA-CfaE binary complexes together with CfaC are sufficient to drive fimbria formation. The presence of both CfaA-CfaE and CfaC accelerates fimbria formation, while the absence of either component leads to linearized CfaB polymers in vitro. We further report the crystal structure of the stabilized CfaA-CfaE complex, revealing features unique for biogenesis of Class 5 fimbriae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Abstract The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene‐protein‐reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high‐throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Digital Light Processing (DLP): 3D printing of polymer-based graphene oxide nanocomposites—Efficient antimicrobial material for biomedical devices

Bacterial infections are one of the major causes of surgical implant inefficiency and failure. Herein, we present a Nanocomposite (NC) produced by the addition of Poly(N-vinyl carbazole)-Graphene Oxide dispersion (PVK-GO) as a nanofiller to a commercial photopolymer acrylate resin and 3D printed as coatings via the Digital Light Processing technique. Characterization and bioassay results against Escherichia coli and Staphylococcus aureus confirmed the elevated thermomechanical properties and efficient antibacterial activity of the printed NC-based coatings. In conclusion, the present study demonstrates the fabrication and optimization of a PVK-GO-based NC and its potential utilization as a 3D-printable material for biomedical applications.

2D materials↗
DOE OSTI2020

Annual Storm Water Report for the Y-12 National Security Complex Oak Ridge, Tennessee

This is the seventh annual storm water report prepared in accordance with the modified National Pollutant Discharge Elimination System permit issued to the Y-12 National Security Complex (Y-12) on April 1, 2014. This modified permit removed the authorization to augment flow in East Fork Poplar Creek (EFPC) and thus removed the requirement to sample this effluent in conjunction with other major outfalls on EFPC. The general condition of the site continues to improve. The concentrations of Escherichia Coli (Es. coli) at the major outfalls and instream monitoring locations on EFPC are no longer elevated as they were in 2018. Follow-up samples indicated normal levels. Monitoring for this parameter will continue into 2020. The repair of Outfall 014 is nearing completion and will be sampled for storm water in 2020. This repair was expected to occur in 2019 but was delayed until 2020. There are several construction and demolition activities currently in progress at Y-12. These include the construction of the Uranium Processing Facility (UPF), the Mercury Treatment Facility (MTF) on EFPC and the impending demolition of the Biology Complex. These projects will present challenges for the protection of storm water. Oversight of these activities will be a priority in 2020. Y-12 will continue to implement appropriate Best Management Practices and reduce outside material storage areas where possible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Efficiency of Room Air Cleaners for Removal of Bioaerosols From Ambient Air

The COVID-19 pandemic necessitated the evaluation of commercial air purification units to protect worker safety in indoor spaces. This project evaluated the efficacy of commercial off-the-shelf air purification systems that utilize electrostatic precipitation for the collection and removal of particulates (including bioaerosols) from ambient air. An aerosol mist containing Escherichia coli (E. coli) and bacteriophage surrogate virus, MS2, was produced using a nebulizer and delivered to the front intake of the commercial system with the ionizer ON and OFF. Removal efficiency was evaluated by colony/plaque formation assays using a small agar plate (60 X 15 mm) to passively collect E. coli and MS2 exhausting from the electrostatic precipitation cell. The system was determined to remove 98-99% of the microorganism introduced to the system. Testing was performed with all pre- and post-electrostatic cell filters removed so further removal is anticipated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Enhanced Filter Material for Pathogen Removal

It was determined that spherical silver (Ag) nanoparticles either bound to 316 stainless-steel filter material or as unbound nanomaterials in deionized water had anti-microbial activity on Escherichia coli K-12 (E. coli) cultures when aerosolized or waterborne. This effect however was attenuated when in the presence of the high-salt growth media. Nanoparticles are known to agglomerate in high salt solutions and this may have limited their ability to cross the cell membrane of the microorganisms and cause fatal damage.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗
DOE OSTI2024

High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology (Final Technical Report)

Fatty acids can be produced biosynthetically in microbes and these compounds can serve as precursors to biodiesels and other high value oleochemicals. However, progress on engineering fatty acid biosynthesis, and biofuel synthesis more generally, has been hindered by current quantification methods that are either indirect or not amenable to high-throughput or single-cell resolution screening. In this project, we assembled an interdisciplinary team with complimentary expertise in synthetic biology and microscopy, metabolic engineering, and chemical imaging to address these challenges. We used chemical imaging to directly measure lipid biosynthesis in Escherichia coli engineered to produce fatty acids, obtaining detailed single-cell resolution measurements. We deployed stimulated Raman scattering (SRS) microscopy in concert with multiplexed genome engineering and gene circuit design strategies from synthetic biology to optimize production of fatty acids. These results provided novel insight into cell-to-cell heterogeneity present in biofuel production strains. In addition, we introduced new chemical imaging methods which are label-free and do not require fluorescent reporters. These efforts were complemented by other studied developing foundational tools for regulation and control, which offer excellent potential for advancing researchers’ ability to rapidly design, build, and test strains for enhanced biofuel synthesis.

09 BIOMASS FUELS↗
DOE OSTI2025

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗
DOE OSTI2025

Development of emerging model microorganisms: Megasphaera elsdenii for biomass and organic acid upgrading to fuels and chemicals

The metabolic diversity of microorganisms in nature represents a largely untapped source of valuable compounds that are difficult or impossible to produce in the limited number of available model systems. Efforts to produce longer-chain alcohols, such as hexanol, in organisms like Escherichia coli have met with limited success; production of C6 and larger products remains low, highlighting the challenges of extending chain elongation pathways beyond a single cycle. Megasphaera elsdenii naturally condenses acetyl-CoA to efficiently generate C4–C8 organic acids, making it a promising candidate for producing fuels and chemicals from lactate and plant-derived carbohydrates. This high native flux through the chain elongation pathway offers the potential for higher yields and titers of medium-chain products, such as hexanol, compared to conventional hosts. Recent advances—most notably the development of a transformation method for M. elsdenii—have further opened the organism to detailed physiological studies and bioengineering. While full development of M. elsdenii as a hexanol-producing platform was not achieved, significant progress was made in understanding its metabolism and building foundational genetic tools for future engineering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Digital Droplet PCR and Mesocosm-Based Methods to Evaluate Biocontainment Strategies in a Native Soil Ecosystem

Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect the complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees within a complex soil microbiome and differentiation between closely related strains. To this end, we have developed an approach that utilizes soil mesocosms and integrated digital droplet PCR (ddPCR) system to evaluate the efficacy of novel biocontainment strategies. We demonstrate the utility of this approach by modeling contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, strains of Synechocystis sp. PCC 6803 contained via gene knockout or toxin anti-toxin system, and strains of Escherichia coli that are contained via genomic recoding. We also show that ddPCR can be used to detect gene copies from E. coli equal to those counted by traditional spot plating assays. The resultant data demonstrates that this system has broad utility across diverse microbial chassis and biocontainment strategies and enables researchers to track the fate of our contaminating microbe with high sensitivity in the soil. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Development of high throughput and in vitro assays for analyzing RNA modifications

Modifications on RNAs play major roles in their stability, translation, and enzymatic activity. Despite its importance, the current techniques are insufficient to study the structure and function of RNA modifications. Indeed, the National Academies of Science, Engineering and Medicine indicate that developing new tools and further study the function of RNA modifications is strategically a high priority for advancing science in the coming years (https://www.nationalacademies.org/our-work/toward-sequencing-and-mapping-of-rna-modifications). RNA modifications occur in all domains of life controlling processes such as RNA turnover, translation regulation, cellular defenses and bioproduction. Our preliminary data indicated that the insulin mRNA might get ADP-ribosylated by the ADP-ribosyltransferase PARP12. RNA ADP-ribosylation has been described in Escherichia coli. Combined to the fact that ADP-ribosyltransferase (PARP) genes are conserved throughout evolution we hypothesize that this modification might play essential roles in cells. Therefore, we proposed to develop sequencing techniques and in vitro enzymatic assays to identify and validate ADP-ribosylation motifs and sites. Here we report the development of RNA-seq and qPCR assays to identify ADP-ribosylated RNAs, in addition to a nicotinamide adenosine dinucleotide (NAD – ADP-ribosylation donor) consumption assay and an enzyme-linked immunosorbent assay (ELISA) to measure ADP-ribosyltransferase activity. Testing these assays with the insulin mRNA confirmed that this transcript is ADP-ribosylated. These assays will not only enable studying the function of ADP-ribosylation but can be easily adapted for studying other RNA modifications. This will open opportunities to study RNA modifications in different model systems from bacteria to viruses to plants, bringing insights into their cellular functions and the possibility of targeting them for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Harnessing Heterologous Bacterial Two-Component Systems as Biosensors to Address Challenges in Fermentation Scale-Up

Scaling up bacterial fermentation from bench to industrial scale often results in unpredictable performance losses, possibly in part due to changes in microenvironmental conditions such as pH. To investigate this, we developed a suite of pH-sensitive biosensors from bacterial two-component systems (TCSs) that provide a dynamic, fluorescent readout in response to extracellular pH changes. TCSs consist of a periplasmic sensor histidine kinase (HK) that, in response to an extracellular stimulus, autophosphorylates intracellularly and subsequently transfers the phosphate to a cognate response regulator (RR) that modulates transcription of target genes. We utilized three pH-responsive TCSs (referred to here as CVJ1, CVJ30, and CVJ79) and linked their output to GFP. This was achieved by placing the RR promoter upstream of GFP or by constructing a chimeric RR composed of the native receiver domain and the DNA-binding domain of another well-characterized RR with a defined promoter. All components - HK, RR (native or chimeric), and GFP under its corresponding promoter - were cloned into a broad-host-range plasmid. Sensors were validated in Escherichia coli and Pseudomonas putida, including the muconic acid-producing strain P. putida TL207. All three biosensors successfully reported pH, with fluorescence (normalized to optical density) correlating strongly with media pH. Among the native sensors, CVJ79 showed the most robust performance while CVJ1 also performed best in its native form; CVJ30 exhibited improved functionality as a chimera, suggesting that modular RR design can enhance compatibility in some heterologous hosts. Further, CVJ79 was activated by alkaline conditions, while CVJ30 responded to acidic environments. Notably, CVJ1 was induced by high pH in wild-type E. coli and P. putida, but low pH in TL207. The observed differences in sensor activation between strains - particularly the divergent response of CVJ1 - suggest that host-specific regulatory pathways may influence how cells perceive and adapt to pH stress. Moving forward, these biosensors can be used to guide the rational design of more robust strains, optimize process conditions in real time, and inform strategies to minimize physiological heterogeneity during scale-up. Integrating these tools into high-throughput screening and bioreactors will be a key step toward improving predictability and performance in industrial bioprocesses.

09 BIOMASS FUELS↗
DOE OSTI2025

Quantifying Growth of Three Common Bacterium on Phytic Acid: Investigating Effects of Media Composition

Microbes can produce a plethora of metabolites and enzymes that allow mobilization of various elements and nutrients in the soil, including phosphorus. Phosphorus is essential to plant growth; however, only a limited amount of it is in a bio-accessible inorganic form that can be utilized by most plants. Microbes can produce enzymes called phosphatase, which break down phytic acid (organic phosphorus) into bioavailable inorganic phosphate. My work aimed to understand how inorganic phosphate, phytic acid, and calcium in media affect the growth of Bacillus subtilis168 (B. subtilis), Escherichia coli K12 BW25113 (E. coli), Pseudomonas putida KT2440 (P. putida), and a strain of Pseudomonas putida AG5577_MS238 engineered to produce a phytase. Eight media were made to test how these components affect growth, and an additional two to understand the effects of multiple carbon sources versus one. It was observed that P. putida’s growth increased in the presence of phytic acid and was strongly driven by nitrate availability. Furthermore, it was able to initiate faster growth when multiple carbon sources were available rather than just one. E. coli’s growth seemed to be limited when inorganic phosphate was unavailable and little to no growth occurred when phytic acid, calcium, and inorganic phosphate were absent. B. subtilis was unable to substantially grow within 28 hrs in any of the mediums tested. The results of this research aid in understanding the growth responses of P. putida, E. coli, and B. subtilis on less accessible and bioavailable forms of phosphorus.

Black, Grace S.↗
DOE OSTI2023

KBase Narrative - SOMATA - Motivating Example

A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.

Cashman, Mikaela↗