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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WGCN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant (WNVE218A) virus infection. Sample data was obtained from mouse granule cell neurons for mRNA and miRNA expression analysis. See Experiment WGCN002 for corresponding independent biological replicate study. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WLN002

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for mRNA and miRNA expression analysis. See Experiment WLN003 for corresponding omics analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WLN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for proteomics, metabolomics, and lipidomics expression analysis. See Experiment WLN002 for corresponding transcriptome analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, and lipidomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations

Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6–9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3–5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Sex- and age-specific aspects of human peripheral T-cell dynamics

Background: The diversity of the antigenic T cell receptor (TCR) repertoire clonally expressed on T lymphocytes is a key element of the adaptive immune system protective functions. A decline in diversity in the older adults is associated with health deterioration. This diversity is generated by the rearrangement of TRB genes coding for TCR chains during lymphocyte differentiation in the thymus, but is essentially maintained by peripheral T lymphocytes proliferation for most of life. Deep sequencing of rearranged TRB genes from blood cells allows the monitoring of peripheral T cell repertoire dynamics. We analysed two aspects of rearranged TRB diversity, related to T lymphocyte proliferation and to the distribution of the T cell clone size, in a collection of repertoires obtained from 1 to 74 years-old donors. Results: Our results show that peripheral T lymphocytes expansion differs according to the recombination status of their TRB loci. Their proliferation rate changes with age, with different patterns in men and women. T cell clone size becomes more heterogeneous with time, and, in adults, is always more even in women. Importantly, a longitudinal analysis of TRB repertoires obtained at ten years intervals from individual men and women confirms the findings of this cross-sectional study. Conclusions: Peripheral T lymphocyte proliferation partially depends on their thymic developmental history. The rate of proliferation of T cells differing in their TRB rearrangement status is different in men and women before the age of 18 years old, but similar thereafter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes

Populus species are highly valued for bioenergy and bioproducts due to their rapid growth and productivity. Polyclonal plantings, or mixtures of Populus clones, have shown the potential to enhance resource utilization and productivity, likely due to phenotypic differences arising from niche differentiation. In this study, we investigated gene expression and productivity in monoclonal and polyclonal stands of P. deltoides . Phenotypic results showed that polyclonal plots exhibited higher leaf area index (LAI; p < 0.01, 2.96 ± 0.057 m 2 ) and total biomass (p < 0.01, 2.74 ± 0.06) compared to monoclonal plots, indicating superior productivity. RNA sequencing revealed upregulation of key genes such as exocyst subunit exo70 family protein H7 (EXO70H7), NDH-dependent cyclic electron flow 5 (NDF5) , and expansin-like A3 (EXLA3) . We also observed enrichment in phenylalanine metabolism and other secondary metabolic pathways in clone S7C8. Phenotypic results, upregulated genes and enriched biological pathways identified in this study may explain the enhanced productivity, increased nitrate content, and expanded canopy in polyclonal plantings. Overall, this study provides a foundation for future research to enhance forest productivity by linking molecular mechanisms to practical applications in field plantings.

differential gene expression↗
DOE OSTI2021

BETO 2021 Peer Review - Enzyme Engineering and Optimization (EEO)

The FY2020 SOT economic model for the DMR BDO process indicates that the production and use of biomass degrading enzymes represents ~10% of the MFSP of BDO. We are thus working to enhance the performance of the dominant cellulase enzyme, Cel7A. In Fy2018-19, we selected 100 promising genes from the "Cel7A wheel of life" and cloned them into T. reesei using a constitutive promotor. This natural diversity screening resulted in the discovery of several enzymes exhibiting improved characteristics relative to the industry standard Cel7A from T. reesei (Tr). Growth of the transformed host on glucose insured that the Cre1 induced cellulase expression cascade was suppressed, thus enabling purification of the target gene product. The first top performing enzyme found was from P. funiculosum (Pf). Other top performing enzymes were identified from T. aculeatus, T. terrestris, and A. oryzae. Computational modeling predicted the structural subsites responsible for the improvements, which were cloned into the sequence of PfCel7A. The recombinant enzymes were expressed in T. reesei, purified, and tested. Testing was not possible with SOT relevant substrates, so the best-case substrate was used; solids from the DMR process subjected to a novel dilute alkaline wash to remove the "lignin shield." Two chimeric Cel7A enzymes show improved performance (1.2 to 1.35x) relative to PfCel7A, which in turn showed considerable improvement (1.6x) relative to T. reesei Cel7A. These new enzymes have been provided to our industrial partner for evaluation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Development of a recombinant anti-VEGFR2-EPCAM bispecific antibody to improve antiangiogenic efficiency

Highlights: • Targeted therapy can be a useful therapeutic method along with traditional methods for breast cancer treatment. • Decreasing Akt/Nf-Kβ signaling pathway is crucial target in order to decreasing angiogenesis in TNBC. • The recombinant antibody can have inhibitory effects on production IL6,8, MMP2, and MMP9. Tumor progression and metastasis, especially in invasive cancers (such as triple-negative breast cancer [TNBC]), depend on angiogenesis, in which vascular epithelial growth factor (VEGF)/vascular epithelial growth factor receptor [1] has a decisive role, followed by the metastatic spread of cancer cells. Although some studies have shown that anti-VEGFR2/VEGF monoclonal antibodies demonstrated favorable results in the clinic, this approach is not efficient, and further investigations are needed to improve the quality of cancer treatment. Besides, the increased expression of epithelial cell adhesion molecule (EpCAM) in various cancers, for instance, invasive breast cancer, contributes to angiogenesis, facilitating the migration of tumor cells to other parts of the body. Thus, the main goal of our study was to target either VEGFR2 or EpCAM as pivotal players in the progression of angiogenesis in breast cancer. Regarding cancer therapy, the production of bispecific antibodies is easier and more cost-effective compared to monoclonal antibodies, targeting more than one antigen or receptor; for this reason, we produced a recombinant antibody to target cells expressing EpCAM and VEGFR2 via a bispecific antibody to decrease the proliferation and metastasis of tumor cells. Following the cloning and expression of our desired anti-VEGFR2/EPCAM sequence in E. coli, the accuracy of the expression was confirmed by Western blot analysis, and its binding activities to VEGFR2 and EPCAM on MDA-MB-231 and MCF-7 cell lines were respectively indicated by flow cytometry. Then, its anti-proliferative potential was indicated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and apoptosis assay to evaluate inhibitory effects of the antibody on tumor cells. Subsequently, the data indicated that migration, invasion, and angiogenesis were inhibited in breast cancer cell lines via the bispecific antibody. Furthermore, cytokine analysis indicated that the bispecific antibody could moderate interleukin 8 (IL-8) and IL-6 as key mediators in angiogenesis progression in breast cancer. Thus, our bispecific antibody could be considered as a promising candidate tool to decrease angiogenesis in TNBC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Comparative productivity of six bioenergy cropping systems on marginal lands in the Great Lakes Region, United States

Abstract Growing lignocellulosic crops on marginal lands is a promising solution for sustainable biofuel production. We evaluated the productivity of bioenergy cropping systems (switchgrass [ Panicum virgatum L., var. Cave‐In‐Rock], miscanthus [ Miscanthus × giganteus , ‘Illinois clone’], hybrid poplar [ Populus nigra × P. maximowiczii A. Henry ‘NM6’], native grasses [five species], early successional vegetation, and restored prairie vs. historical vegetation [as reference control]) with and without nitrogen fertilization on low‐fertility former cropland at five sites in the Great Lakes Region, United States. We reported biomass yields for the first 7 years after establishment. Switchgrass was most consistently productive across all sites but miscanthus was more productive at three of the five sites. When averaged across sites, years, and nitrogen (N) treatments, biomass yields followed the order miscanthus > switchgrass > hybrid poplar ≈ native grasses > restored prairie > early successional vegetation ≈ historical vegetation, but varied substantially by crop and site, with a significant crop by site interaction. Yields of miscanthus and switchgrass peaked after four–five growing seasons and declined thereafter, while yields of both native grasses and restored prairie increased throughout 6 years with no sign of follow‐on decline, suggesting that polycultures may outperform monocultures over the long term. Yields of early successional vegetation—similar in composition to historical vegetation at each site—did not improve with time. Nitrogen fertilization increased the yields of all cropping systems at all sites. Our results demonstrate the viability of low‐productivity former cropland for long‐term bioenergy production and suggest there is no single crop best suited for all low fertility soils.

Jayawardena, Dileepa M.↗
DOE OSTI2023

Mammalian Chromosome Analysis and Sorting by Flow Cytometry

The analysis of chromosomes by flow cytometry is termed flow cytogenetics, and it involves the analysis and sorting of single mitotic chromosomes in suspension. The study of flow karyograms provides insight into chromosome number and structure to provide information on chromosomal DNA content and can enable the detection of deletions, translocations, or any forms of aneuploidy. Beyond its clinical applications, flow cytogenetics greatly contributed to the Human Genome Project through the ability to sort pure populations of chromosomes for gene mapping, cloning, and the construction of DNA libraries. Maximizing the potential of these important applications of flow cytogenetics relies on precise instrument setup and optimal sample processing, both of which impact the accuracy and quality of the data that are generated. This article is a compilation of the existing protocols that describe the stepwise methodology of accumulating, isolating, and staining metaphase chromosomes to prepare single-chromosome suspensions for flow cytometric analysis and sorting. Although the chromosome preparation protocols have remained largely unchanged, cytometer technology has advanced dramatically since these protocols were originally developed. Advances in cytometry technologies offer new and exciting approaches for understanding and monitoring chromosomal aberrations, but the hallmark of these protocols remains their simplicity in methodologies and reagent requirements and the accuracy of data resolvable to every chromosome of the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring novel HIV ‐1 reverse transcriptase inhibitors with drug‐resistant mutants: A double mutant surprise

Abstract HIV‐1 reverse transcriptase (RT) remains a key target for HIV drug development. As successful management of the disease requires lifelong treatment, the emergence of resistance mutations is inevitable, making development of new RT inhibitors, which remain effective against resistant variants crucial. To this end, previous computationally guided drug design efforts have resulted in catechol diether compounds, which inhibit wildtype RT with picomolar affinities and appear to be promising preclinical candidates. To confirm that these compounds remain potent against Y181C, a widespread mutation conferring resistance to first generation inhibitors, they were screened against the HIV‐1 N119 clinical isolate, reported as a Y181C single mutant. In comparison to a molecular clone with the same mutation, N119 appears less susceptible to inhibition by our preclinical candidate compounds. A more detailed sequencing effort determined that N119 was misidentified and carries V106A in combination with Y181C. While both indolizine and naphthalene substituted catechol diethers are potent against the classical Y181C single mutant, the addition of V106A confers more resistance against the indolizine derivatives than the naphthalene derivatives. Crystal structures presented in this study highlight key features of the naphthyl group, which allow these compounds to remain potent in the double mutant, including stronger interactions with F227 and less reliance on V106 for stabilization of the ethoxy‐uracil ring, which makes critical hydrogen bonds with other residues in the binding pocket.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5.

Modern DNA assembly techniques are known for their potential to link multiple large DNA fragments together into even larger constructs in single pot reactions that are easier to automate and work more reliably than traditional cloning methods. The simplicity of the chemistry is in contrast to the increased work needed to design optimal reactions that maximize DNA fragment reuse, minimize cost, and organize thousands of potential chemical reactions. Here we examine available DNA assembly methods and describe through example, the construction of a complex but not atypical combinatorial and hierarchical library using protocols that are generated automatically with the assistance of modern synthetic biology software.

Fero, Michael J↗
DOE OSTI2023

Encoding beyond cosmological horizons in de Sitter JT gravity

Black hole event horizons and cosmological event horizons share many properties, making it natural to ask whether our recent advances in understanding black holes generalize to cosmology. To this end, we discuss a paradox that occurs if observers can access what lies beyond their cosmological horizon in the same way that they can access what lies beyond a black hole horizon. In particular, distinct observers with distinct horizons may encode the same portion of spacetime, violating the no-cloning theorem of quantum mechanics. This paradox is due precisely to the observer-dependence of the cosmological horizon — the sharpest difference from a black hole horizon — although we will argue that the gravity path integral avoids the paradox in controlled examples.

2D gravity↗
DOE OSTI2024

Interacting chiral form field theories and $$ T\overline{T} $$-like flows in six and higher dimensions

Abstract In this paper we initiate the study of six-dimensional non-linear chiral two-form gauge theories as deformations of free chiral two-form gauge theories driven by stress-tensor$$ T\overline{T} $$ T T ¯ -like flows. To lay the background for this study, we elaborate on the relationship between different Lagrangian formulations of duality-invariantp-form theories and corresponding$$ T\overline{T} $$ T T ¯ -like flows in various dimensions. To this end we propose a new formulation which (i) is a generalization of the four-dimensional construction by Ivanov, Nurmagambetov and Zupnik (INZ) and (ii) turns into the PST formulation upon integrating out an auxiliary self-dual field. We elucidate space-time covariant properties of the PST formulation by clarifying and making use of its relation to the INZ-type formulation and to a so-called “clone” construction.

Physics↗
DOE OSTI2021

Shocks and information exchange in de Sitter space

We discuss some implications of recent progress in understanding the black hole information paradox for complementarity in de Sitter space. Extending recent work by two of the authors, we describe a bulk procedure that allows information expelled through the cosmological horizon to be received by an antipodal observer. Generically, this information transfer takes a scrambling time t=H- 1 (S ds ). We emphasize that this procedure relies crucially on selection of the Bunch-Davies vacuum state, interpreted as the thermofield double state that maximally entangles two antipodal static patches. The procedure also requires the presence of an (entangled) energy reservoir, created by the collection of Hawking modes from the cosmological horizon. We show how this procedure avoids a cloning paradox and comment on its implications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359

The filamentous fungus Aspergillus terreus has been successfully used for industrial production of itaconic acid (IA) for many years. The IA biosynthesis pathway has recently been characterized at a molecular genetic level as an IA gene cluster (IA cluster) by a clone-based transcriptomic approach. The cluster consists of four genes, including genes for cis-aconitic acid decarboxylase (cadA), a predicted transcription factor (tf), mitochondrial organic acid transporter (mttA), and MFS (Major Facilitator Superfamily) type transporter (mfsA). In this research, we performed EST (Expressed Sequence Tag) analysis and systematic gene deletions to investigate the role of those genes in IA biosynthesis in A. pseudoterreus ATCC32359. EST analysis showed a similar expression pattern among those four genes that was distinct from neighbouring genes and further confirmed that they belong to the same biosynthesis cluster. Systematic gene deletion analysis demonstrated that tf, cadA, mttA, and mfsA genes in the cluster are essential for IA production. Deletion of any of them will either completely abolish the IA production or dramatically decrease amount of IA produced. More importantly, a significant amount of aconitic acid was detected in the cadA deletion strain but not in the other deletion strains. Therefore, the cadA deletion strain is a novel microorganism host for production of aconitic acid and other value-added chemicals from lignocellulosic biomass.

Deng, Shuang↗
DOE OSTI2022

Improved high-throughput screening technique to rapidly isolate Chlamydomonas transformants expressing recombinant proteins

Abstract The single-celled eukaryotic green alga Chlamydomonas reinhardtii has long been a model system for developing genetic tools for algae, and is also considered a potential platform for the production of high-value recombinant proteins. Identifying transformants with high levels of recombinant protein expression has been a challenge in this organism, as random integration of transgenes into the nuclear genome leads to low frequency of cell lines with high gene expression. Here, we describe the design of an optimized vector for the expression of recombinant proteins in Chlamydomonas , that when transformed and screened using a dual antibiotic selection, followed by screening using fluorescence activated cell sorting (FACS), permits rapid identification and isolation of microalgal transformants with high expression of a recombinant protein. This process greatly reduces the time required for the screening process, and can produce large populations of recombinant algae transformants with between 60 and 100% of cells producing the recombinant protein of interest, in as little as 3 weeks, that can then be used for whole population sequencing or individual clone analysis. Utilizing this new vector and high-throughput screening (HTS) process resulted in an order of magnitude improvement over existing methods, which normally produced under 1% of algae transformants expressing the protein of interest. This process can be applied to other algal strains and recombinant proteins to enhance screening efficiency, thereby speeding up the discovery and development of algal-derived recombinant protein products. Key points • A protein expression vector using double-antibiotic resistance genes was designed • Double antibiotic selection causes fewer colonies with more positive for phenotype • Coupling the new vector with FACS improves microalgal screening efficiency > 60%

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗