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At least 55 records · Page 3

Radiation-induced genomic instability: radiation quality and dose response

Genomic instability is a term used to describe a phenomenon that results in the accumulation of multiple changes required to convert a stable genome of a normal cell to an unstable genome characteristic of a tumor. There has been considerable recent debate concerning the importance of genomic instability in human cancer and its temporal occurrence in the carcinogenic process. Radiation is capable of inducing genomic instability in mammalian cells and instability is thought to be the driving force responsible for radiation carcinogenesis. Genomic instability is characterized by a large collection of diverse endpoints that include large-scale chromosomal rearrangements and aberrations, amplification of genetic material, aneuploidy, micronucleus formation, microsatellite instability, and gene mutation. The capacity of radiation to induce genomic instability depends to a large extent on radiation quality or linear energy transfer (LET) and dose. There appears to be a low dose threshold effect with low LET, beyond which no additional genomic instability is induced. Low doses of both high and low LET radiation are capable of inducing this phenomenon. This report reviews data concerning dose rate effects of high and low LET radiation and their capacity to induce genomic instability assayed by chromosomal aberrations, delayed lethal mutations, micronuclei and apoptosis.

Review↗

The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study

The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, for this work, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure–function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating charged defects at database scale

Point defects have a strong influence on the physical properties of materials, often dominating the electronic and optical behavior in semiconductors and insulators. The simulation and analysis of point defects is, therefore, crucial for understanding the growth and operation of materials, especially for optoelectronics applications. In this work, we present a general-purpose Python framework for the analysis of point defects in crystalline materials as well as a generalized workflow for their treatment with high-throughput simulations. The distinguishing feature of our approach is an emphasis on a unique, unit cell, structure-only, definition of point defects which decouples the defect definition, and the specific supercell representation used to simulate the defect. This allows the results of first-principles calculations to be aggregated into a database without extensive provenance information and is a crucial step in building a persistent database of point defects that can grow over time, a key component toward realizing the idea of a “defect genome” that can yield more complex relationships governing the behavior of defects in materials. We demonstrate several examples of the approach for three technologically relevant materials and highlight current pitfalls that must be considered when employing these methodologies as well as their potential solutions.

36 MATERIALS SCIENCE↗

A genomic analysis reveals the diversity of cellulosome displaying bacteria

Introduction Several species of cellulolytic bacteria display cellulosomes, massive multi-cellulase containing complexes that degrade lignocellulosic plant biomass (LCB). A greater understanding of cellulosome structure and enzyme content could facilitate the development of new microbial-based methods to produce renewable chemicals and materials. Methods To identify novel cellulosome-displaying microbes we searched 305,693 sequenced bacterial genomes for genes encoding cellulosome proteins; dockerin-fused glycohydrolases (DocGHs) and cohesin domain containing scaffoldins. Results and discussion This analysis identified 33 bacterial species with the genomic capacity to produce cellulosomes, including 10 species not previously reported to produce these complexes, such asAcetivibrio mesophilus. Cellulosome-producing bacteria primarily originate from theAcetivibrio, Ruminococcus, Ruminiclostridium, andClostridiumgenera. A rigorous analysis of their enzyme, scaffoldin, dockerin, and cohesin content reveals phylogenetically conserved features. Based on the presence of a high number of genes encoding both scaffoldins and dockerin-fused GHs, the cellulosomes inAcetivibrioandRuminococcusbacteria possess complex architectures that are populated with a large number of distinct LCB degrading GH enzymes. Their complex cellulosomes are distinguishable by their mechanism of attachment to the cell wall, the structures of their primary scaffoldins, and by how they are transcriptionally regulated. In contrast, bacteria in theRuminiclostridiumandClostridiumgenera produce ‘simple’ cellulosomes that are constructed from only a few types of scaffoldins that based on their distinct complement of GH enzymes are predicted to exhibit high and low cellulolytic activity, respectively. Collectively, the results of this study reveal conserved and divergent architectural features in bacterial cellulosomes that could be useful in guiding ongoing efforts to harness their cellulolytic activities for bio-based chemical and materials production.

Microbiology↗

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗

Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline

Abstract As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.

36 MATERIALS SCIENCE↗

Siderophores and secondary metabolites produced by Ganoderma adspersum

Ganoderma adspersum is a white-rot wood-degrading basidiomycete of ecological, biotechnological and medicinal interest. In addition to its role in lignin degradation, it produces bioactive metabolites with reported antimicrobial and antioxidant activities. However, the mechanisms of iron acquisition, including siderophore-mediated pathways, remain poorly characterized in Ganoderma species. Improved understanding of these systems is essential to elucidate their contributions to fungal physiology, secondary metabolism and ecological adaptation. In this study, the genome of G. adspersum was sequenced for the first time and screened for genes that may be involved in the production of secondary metabolites. A gene cluster was identified as potentially involved in iron uptake. In particular, genes related to non-ribosomal peptide synthetases were detected next to a gene encoding a monooxygenase and indicated a potential hydroxamate-family siderophore. Liquid chromatography (LC)-ES-MS analysis of secondary metabolites secreted by G. adspersum into the growth medium under iron-limiting conditions revealed a group of previously undescribed siderophores. Genome and MS/MS analysis suggested that these structures might be related to the coprinoferrin family of siderophores. Aside from siderophores, the genome and LC-MS analysis revealed G. adspersum to be a prolific producer of a variety of triterpenoids and sesquiterpenoids, in agreement with previous findings. This is the first description of the genome sequence of G. adspersum and its siderophores.

Reyes, Carolina [Laboratory for Cellulose and Wood↗

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

Populations of resident, non-migratory Canada geese are rapidly increasing. Canada geese are known to transmit viral and bacterial diseases, posing a possible threat to human health. The most prevalent pathogens vectored by geese are Campylobacter species, yet the current understanding of the identity and virulence of these pathogens is limited. In our previous study, we observed a high prevalence of Campylobacter spp. in the Banklick Creek wetland—a constructed treatment wetland (CTW) located in northern KY (USA) used to understand sources of fecal contamination originating from humans and waterfowl frequenting the area. To identify the types of Campylobacter spp. found contaminating the CTW, we performed genetic analyses of Campylobacter 16s ribosomal RNA amplified from CTW water samples and collected fecal material from birds frequenting those areas. Our results showed a high occurrence of a Campylobacter canadensis-like clade from the sampling sites. Whole-genome sequence analyses of an isolate from Canada goose fecal material, called MG1, were used to confirm the identity of the CTW isolates. Further, we examined the phylogenomic position, virulence gene content, and antimicrobial resistance gene profile of MG1. Lastly, we developed an MG1-specific real-time PCR assay and confirmed the presence of MG1 in Canada goose fecal samples surrounding the CTW. Our findings reveal that the Canada goose-vectored Campylobacter sp. MG1 is a novel isolate compared to C. canadensis that possesses possible zoonotic potential, which may be of human health concern.

59 BASIC BIOLOGICAL SCIENCES↗

Perspectives for self-driving labs in synthetic biology

Self-driving labs (SDLs) combine fully automated experiments and data collection with artificial intelligence (AI) and control algorithms that decide not only the set of parameters for the next experiment, but also potentially which scientific hypotheses to test. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. Whereas there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single, easily accessible, target for affecting the incredibly wide repertoire of biological cell behavior. Since they can provide large amounts of high-quality data, SDLs can be a platform for AI to develop approaches to systematically convert data into scientific knowledge systems. These knowledge systems can be used both to understand the biological world and to design bioengineered systems to fit a desired specification (inverse design). However, the level of investment required for the creation of biological SDLs is only warranted if directed towards solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Final Technical Report for DE-SC0022206

This project developed foundational genetic, genomic, and epigenetic tools for anaerobic fungi (Neocallimastigomycota), a group of microorganisms with exceptional natural abilities to deconstruct lignocellulosic biomass. Efficient biomass deconstruction remains a major barrier to economical production of renewable fuels, chemicals, and materials from agricultural and forestry residues. The project sought to enable mechanistic studies and future engineering of anaerobic fungi by improving genomic resources, establishing methods for gene expression, and investigating epigenetic regulation of biomass-degrading pathways. Major accomplishments included generation of the first chromosome-scale genome assemblies for multiple anaerobic fungal species, providing publicly available genomic resources that support both engineering and fundamental biological research. The project established the first reproducible system for heterologous gene expression in anaerobic fungi and identified genomic features and mobile genetic elements that may support future development of stable transformation technologies. In parallel, the project demonstrated direct conversion of untreated lignocellulosic biomass into fuels and specialty chemicals through a fungal-yeast bioprocess and identified anaerobic fungal enzymes with utility for metabolic engineering. The research also revealed that epigenetic regulation plays an important role in controlling fungal gene expression and enzyme production, identifying potential strategies for enhancing biomass degradation. Collectively, this work established anaerobic fungi as a tractable emerging platform for bioenergy and biomanufacturing research, generated valuable public resources, trained the next generation of researchers, and advanced DOE-BER goals related to predictive biology, sustainable bioprocessing, and the circular bioeconomy.

Solomon, Kevin [University of Delaware] (ORCID:000↗

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening (CRADA Final Report)

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗

An Integrated Design Tool for Tow-Steered Laminates of Composites in Abaqus and MSC.Patran/Nastran

Tow-steered composites can be tailored for optimal mechanical performance of lightweight structures. However, there are no commercial-grade design tools for tow-steered composite structures, which hinders the design innovation of tow-steered composites in realistic structures. The novelty of this paper is to develop an integrated design framework along with the development of graphical user interface (GUI) plug-ins in commercial finite element (FE) software Abaqus and MSC.Patran/Nastran. The GUI plug-ins take all the design setups and communicate with external codes for the material modeling and optimization, and hence provide a unified design environment within the FE codes. The mechanics of structure genome (MSG) plate model computes shell element properties based on user-defined fiber paths and layup, which are defined via the GUI plug-ins. The optimization is performed by an open-source code, Dakota, from Sandia National Laboratories (Sandia), which also coordinates the structural analysis, material modeling, and optimization in design iterations. Two examples are presented to demonstrate the user-friendliness and versatility of the developed GUI plug-ins. The developed tools will ease the design process and facilitate the application of tow-steered composites in realistic aerospace structures.

Xin Liu↗

An Integrated Design Tool for Tow-Steered Laminates of Composites in Abaqus and MSC.Patran/Nastran

Tow-steered composites can be tailored for optimal mechanical performance of lightweight structures. However, there are no commercial-grade design tools for tow-steered composite structures, which hinders the design innovation of tow-steered composites in realistic structures. The novelty of this paper is to develop an integrated design framework along with the development of graphical user interface (GUI) plug-ins in commercial finite element (FE) software Abaqus and MSC.Patran/Nastran. The GUI plug-ins take all the design setups and communicate with external codes for the material modeling and optimization, and hence provide a unified design environment within the FE codes. The mechanics of structure genome (MSG) plate model computes shell element properties based on user-defined fiber paths and layup, which are defined via the GUI plug-ins. The optimization is performed by an open-source code, Dakota, from Sandia National Laboratories (Sandia), which also coordinates the structural analysis, material modeling, and optimization in design iterations. Two examples are presented to demonstrate the user-friendliness and versatility of the developed GUI plug-ins. The developed tools will ease the design process and facilitate the application of tow-steered composites in realistic aerospace structures.

Xin Liu↗

Thermoviscoelastic modelling of high strain thin-ply composites by means of multiscale plate and beam model

High strain thin-ply (HS-TPC) technology is being increasingly adopted for high-performanceaerospace applications. Albeit many of these structures such as deployable booms can bemodeled as one-dimensional beam problems, there is a lack of themoviscoelastic beam mod-els to efficiently and accurately simulate HS-TPC. This work will use mechanics of struc-ture genome (MSG) to construct linear thermoviscoelastic beam models that can homogenizethree-dimensional heterogeneous materials made of constituents with time- and temperature-dependent behavior. The formulation derives the transient strain energy based on integralformulation for thermorheologically simple materials subject to finite temperature changeswith the restriction that the strain is small. A lenticular boom is used as a numerical exampleto verify the MSG-based linear thermoviscoelastic beam model against MSG-based shell/platemodel, which has already been validated against experimental data provided by NASA, anddirect numerical simulations performed in a finite element commercial package.

Orzuri Rique Garaizar↗

Computed entropy spectra for grain boundary segregation in polycrystals

Abstract Grain boundary solute segregation influences most bulk material properties, and understanding solute thermodynamics at grain boundaries is critical for engineering them. However, the vast grain boundary space in polycrystals is challenging to evaluate due to its size, especially for the intrinsically hard-to-compute segregation excess entropy. Here data science methods are used to generate a database of site-wise grain boundary segregation entropy spectra for 155 dilute binary alloys within the harmonic approximation. The spectral framework allows scale bridging between the calculated atomistic site-wise energy-entropy spectra and macroscopic segregation entropy estimates. The results affirm that macroscopic averaging is not sufficient: a spectral treatment of grain boundary segregation is needed to accurately model bulk temperature dependence of grain boundary solute segregation. The calculated spectral entropy database and thermodynamic framework can be applied for both understanding segregation experiments and alloy design exercises, paving the way to a finite-temperature grain boundary genome.

Chemistry↗

Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a

In forensic DNA casework, a highly accurate real-time quantitative polymerase chain reaction (qPCR) assay is recommended per the Scientific Working Group on DNA Analysis Methods (SWGDAM) (SWGDAM Validation Guidelines for DNA Analysis Methods [1]) to determine whether a DNA sample is of sufficient quantity and robust quality to move forward with downstream short tandem repeats (STR) or sequencing analyses. Most of these assays rely on a standard curve, referred to herein and traditionally as absolute qPCR, in which an unknown is compared, relative to that curve. However, one fundamental issue with absolute qPCR is the quantifiable concentration of commercial assay standards can vary depending on (1) origin, i.e., whether from a cell line or a human subject, (2) supplier, (3) lot number, (4) shipping method, etc. In 2018, the National Institute for Standards and Technology (NIST) released a human DNA standard reference material for evaluating qPCR quantification standards, Standard Reference Material (SRM) 2372a, Romsos et al. (2018) [2] which contains three well-characterized human genomic DNA samples: Component A) a single male1 donor, Component B) a single female 1 donor, and Component C) a 1:3 male 2 :female 2 donor, each with certification data for nDNA and informational mitochondrial DNA(mtDNA)/nuclear DNA (nDNA) ratio data. The SRM 2372a was used to assess four qPCR assays: (1) Quantifiler Trio (Thermo Fisher Scientific, Waltham, MA) for nDNA quantification, (2) NovaQUANT (EMD Millipore Corporation, San Diego, CA) for nDNA and mtDNA quantification, (3) a custom duplex mtDNA assay, and (4) a custom triplex mtDNA assay. Additionally, extracts from eighteen (18) skeletal remains were tested with the latter three assays for concordance of DNA concentration and with assays (2) and (3), for the degradation state. Our assessment revealed that an accurate, efficient, and reproducible qPCR assay is dependent on (1) the quality and reliability of the DNA standard, (2) the qPCR chemistry, and (3) the specific primers, and probes (if applicable), used in an assay. Finally, our findings indicate qPCR assays may not always quantify as expected and that performance of each lot should be verified using a well-characterized DNA standard such as the NIST SRM 2372a and adjusted if warranted.

59 BASIC BIOLOGICAL SCIENCES↗

Halophytes and heavy metals: A multi‐omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima

Abstract Premise The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we usedCakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. Methods Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response inC. maritimaand identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. Results Cakile maritimais tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool inC. maritimaand likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved inC. maritimaabiotic stress tolerance. Conclusions These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

Plant Sciences↗