SEARCH · Search NASA

Results for “Selectable marker”

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.

SourceResearch connectionFrom yearThrough year

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

At least 379 records · Page 21

All sources NASA NTRS DOE OSTI

NASA NTRS2017

Prediction of Cognitive States During Flight Simulation Using Multimodal Psychophysiological Sensing

The Commercial Aviation Safety Team found the majority of recent international commercial aviation accidents attributable to loss of control inflight involved flight crew loss of airplane state awareness (ASA), and distraction was involved in all of them. Research on attention-related human performance limiting states (AHPLS) such as channelized attention, diverted attention, startle/surprise, and confirmation bias, has been recommended in a Safety Enhancement (SE) entitled "Training for Attention Management." To accomplish the detection of such cognitive and psychophysiological states, a broad suite of sensors was implemented to simultaneously measure their physiological markers during a high fidelity flight simulation human subject study. Twenty-four pilot participants were asked to wear the sensors while they performed benchmark tasks and motion-based flight scenarios designed to induce AHPLS. Pattern classification was employed to predict the occurrence of AHPLS during flight simulation also designed to induce those states. Classifier training data were collected during performance of the benchmark tasks. Multimodal classification was performed, using pre-processed electroencephalography, galvanic skin response, electrocardiogram, and respiration signals as input features. A combination of one, some or all modalities were used. Extreme gradient boosting, random forest and two support vector machine classifiers were implemented. The best accuracy for each modality-classifier combination is reported. Results using a select set of features and using the full set of available features are presented. Further, results are presented for training one classifier with the combined features and for training multiple classifiers with features from each modality separately. Using the select set of features and combined training, multistate prediction accuracy averaged 0.64 +/- 0.14 across thirteen participants and was significantly higher than that for the separate training case. These results support the goal of demonstrating simultaneous real-time classification of multiple states using multiple sensing modalities in high fidelity flight simulators. This detection is intended to support and inform training methods under development to mitigate the loss of ASA and thus reduce accidents and incidents.

Harrivel, Angela R.↗

DOE OSTI2026

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗

DOE OSTI2021

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Electromagnetic guided couch and multileaf collimator tracking on a TrueBeam accelerator

Purpose: Couch and MLC tracking are two promising methods for real-time motion compensation during radiation therapy. So far, couch and MLC tracking experiments have mainly been performed by different research groups, and no direct comparison of couch and MLC tracking of volumetric modulated arc therapy (VMAT) plans has been published. The Varian TrueBeam 2.0 accelerator includes a prototype tracking system with selectable couch or MLC compensation. This study provides a direct comparison of the two tracking types with an otherwise identical setup. Methods: Several experiments were performed to characterize the geometric and dosimetric performance of electromagnetic guided couch and MLC tracking on a TrueBeam accelerator equipped with a Millennium MLC. The tracking system latency was determined without motion prediction as the time lag between sinusoidal target motion and the compensating motion of the couch or MLC as recorded by continuous MV portal imaging. The geometric and dosimetric tracking accuracies were measured in tracking experiments with motion phantoms that reproduced four prostate and four lung tumor trajectories. The geometric tracking error in beam’s eye view was determined as the distance between an embedded gold marker and a circular MLC aperture in continuous MV images. The dosimetric tracking error was quantified as the measured 2%/2 mm gamma failure rate of a low and a high modulation VMAT plan delivered with the eight motion trajectories using a static dose distribution as reference. Results: The MLC tracking latency was approximately 146 ms for all sinusoidal period lengths while the couch tracking latency increased from 187 to 246 ms with decreasing period length due to limitations in the couch acceleration. The mean root-mean-square geometric error was 0.80 mm (couch tracking), 0.52 mm (MLC tracking), and 2.75 mm (no tracking) parallel to the MLC leaves and 0.66 mm (couch), 1.14 mm (MLC), and 2.41 mm (no tracking) perpendicular to the leaves. The motion-induced gamma failure rate was in mean 0.1% (couch tracking), 8.1% (MLC tracking), and 30.4% (no tracking) for prostate motion and 2.9% (couch), 2.4% (MLC), and 41.2% (no tracking) for lung tumor motion. The residual tracking errors were mainly caused by inadequate adaptation to fast lung tumor motion for couch tracking and to prostate motion perpendicular to the MLC leaves for MLC tracking. Conclusions: Couch and MLC tracking markedly improved the geometric and dosimetric accuracies of VMAT delivery. However, the two tracking types have different strengths and weaknesses. While couch tracking can correct perfectly for slowly moving targets such as the prostate, MLC tracking may have considerably larger dose errors for persistent target shift perpendicular to the MLC leaves. Advantages of MLC tracking include faster dynamics with better adaptation to fast moving targets, the avoidance of moving the patient, and the potential to track target rotations and deformations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗

NASA NTRSDate not supplied

Cleanroom Microbes Survive Drying, Vacuum, and Proton Irradiation

Introduction : The goal of planetary protection at NASA is to mitigate the risk of contaminating sensitive target bodies with biological life. While many cleaning procedures have been put in place to reduce bioburden on spacecraft, microbes are experts at evolving to survive harsh conditions. Specifically, the dry, low-nutrient environment of a cleanroom (commonly used for assembly of spacecraft) can represent an environment where extremophiles can survive. Methods : Scientists at NASA MSFC wished to gather a snapshot of the microbial population within a variety of cleanrooms on site. A study was undertaken to collect air, surface, and floor samples from clean-rooms and isolate unique morphologies. From this study, 95 isolates were collected and saved in a microbial library. About 86% of these were identified at least to a genus level. Following identification, 24 microbes were selected, based on a literature review, as potential extremophiles. These were grown in liquid cultures, diluted to a set optical density, washed with water, and then applied to a sterilized Kapton coupon. Droplets were allowed to dry overnight in a biosafety cabinet. Coupons were then installed in a pelletron and pumped down to high vacuum (~1E-6 Torr). Samples were then subjected 100 keV protons at a fluence of 2x10 15 p+/cm 2 up to 4x10 15 p+/cm 2 . Following exposure, samples were returned to the microbiology lab where they were pro-cessed by submerging in water, vortexing, and then plating either droplets or spread plates. Recovery data collected was qualitative with a ranking or +, minor, or – for growth. Some selected radiotolerant strains were sequenced using the Illumina sequencing platform. The resulting genomes were annotated with the Rapid Annotations using Subsystems Technology (RAST) server and analyzed for conserved and unique stress response relevant genomic signatures to identify clues related to specific tolerances. Results and Discussion : After five rounds of proton radiation, we narrowed our isolates to five, non-spore forming bacteria that demonstrated survival: Arthrobacter koreensis, Paenarthrobacter nitroguajacolicus, Mycetocola manganoxydans , and an Erwinia sp. Furthermore, we exposed these four microbes to 254 nm wavelength light at an intensity of 80 W/m 2 at a distance of ~18 cm for 10 minutes. Only A. koreensis demonstrated survival following UV exposure. Finally, we performed whole genome sequencing on the four strains to look for genetic markers of stress resistance. When we compared the genomes of the four strains, we found that genes coding for GGDEF and EAL domains with PAS/PAC sensors were only found in A. koreensis . These domains, modulated by PAS/PAC sensors, are hypothesized to facilitate survival under drying, desiccation, and proton irradiation. Drying and Desiccation : PAS domains sense hydration changes and modulate GGDEF and EAL domain activity to adjust c-di-GMP levels, enhancing resistance to desiccation. For instance, in Pseudomonas aeruginosa , the PAS domain of RbdA modulates activity under varying hydration conditions, affecting stress responses [1]. Proton Irradiation : Proton irradiation causes oxidative stress, leading to ROS generation. PAS domains detect this stress and modulate GGDEF and EAL domains to manage oxidative stress responses. In Shewanella , EAL domain proteins modulated by PAS sensors help bacteria adapt to extreme conditions [2]. These genes upregulate other stress response genes, protecting membrane function, protein stability, DNA repair, and antioxidant defenses. The modulation of c-di-GMP by PAS domains is crucial for bacterial adaptation to stress conditions, enabling dynamic physio-logical adjustments [3]. Understanding these mechanisms provides insights into bacterial stress responses and strategies for controlling bacterial growth [4]. Conclusions : These findings indicate that clean-rooms harbor extremophile microbes that may be able to survive conditions in deep space. Furthermore, while we identified certain stress-response genes that may be at least partly responsible for the phenotypes observed in this study, there are likely unidentified genes or characteristics about A. koreensis , and other bacteria, that may allow them to survive in harsh environments. Future studies will focus on identifying these unknown genes and characteristics, further elucidating the mechanisms of extremophile survival and potentially informing the development of new biotechnologies for space exploration and other extreme environments.

Chelsi Cassilly↗

DOE OSTI2015

Molecular characterization of free tropospheric aerosol collected at the Pico Mountain Observatory: a case study with a long-range transported biomass burning plume

Free tropospheric aerosol was sampled at the Pico Mountain Observatory located at 2225 m above mean sea level on Pico Island of the Azores archipelago in the North Atlantic. The observatory is located ~ 3900 km east and downwind of North America, which enables studies of free tropospheric air transported over long distances. Aerosol samples collected on filters from June to October 2012 were analyzed to characterize organic carbon, elemental carbon, and inorganic ions. The average ambient concentration of aerosol was 0.9 ± 0.7 μg m -3 . On average, organic aerosol components represent the largest mass fraction of the total measured aerosol (60 ± 51%), followed by sulfate (23 ± 28%), nitrate (13 ± 10%), chloride (2 ± 3%), and elemental carbon (2 ± 2%). Water-soluble organic matter (WSOM) extracted from two aerosol samples (9/24 and 9/25) collected consecutively during a pollution event were analyzed using ultrahigh-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Approximately 4000 molecular formulas were assigned to each of the mass spectra in the range of m/z 100–1000. The majority of the assigned molecular formulas had unsaturated structures with CHO and CHNO elemental compositions. FLEXPART retroplume analyses showed the sampled air masses were very aged (average plume age > 12 days). These aged aerosol WSOM compounds had an average O/C ratio of ~ 0.45, which is relatively low compared to O/C ratios of other aged aerosol. The increase in aerosol loading during the measurement period of 9/24 was linked to biomass burning emissions from North America by FLEXPART retroplume analysis and Moderate Resolution Imaging Spectroradiometer (MODIS) fire counts. This was confirmed with biomass burning markers detected in the WSOM and with the morphology and mixing state of particles as determined by scanning electron microscopy. The presence of markers characteristic of aqueous-phase reactions of phenolic species suggests that the aerosol collected at the Pico Mountain Observatory had undergone cloud processing before reaching the site. Finally, the air masses of 9/25 were more aged and influenced by marine emissions, as indicated by the presence of organosulfates and other species characteristic of marine aerosol. The change in the air masses for the two samples was corroborated by the changes in ethane, propane, and ozone, morphology of particles, as well as by the FLEXPART retroplume simulations. This paper presents the first detailed molecular characterization of free tropospheric aged aerosol intercepted at a lower free troposphere remote location and provides evidence of low oxygenation after long-range transport. We hypothesize this is a result of the selective removal of highly aged and polar species during long-range transport, because the aerosol underwent a combination of atmospheric processes during transport facilitating aqueous-phase removal (e.g., clouds processing) and fragmentation (e.g., photolysis) of components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Combined effects of microplastics and chemical contaminants on the organ toxicity of zebrafish (Danio rerio)

Highlights: • Microplastics did not produce effects on gene expression in zebrafish after 3 weeks. • Microplastics and sorbed chemicals had a greater effect than chemicals alone. • Effects were detected mainly in the liver. • Perfluorinated compounds were detected mainly in the liver. • Adverse effect of microplastics and sorbed chemicals should be considered in risk assessment. Microplastics contamination of the aquatic environment is considered a growing problem. The ingestion of microplastics has been documented for a variety of aquatic animals. Studies have shown the potential of microplastics to affect the bioavailability and uptake route of sorbed co-contaminants of different nature in living organisms. Persistent organic pollutants and metals have been the co-contaminants majorly investigated in this field. The combined effect of microplastics and sorbed co-contaminants in aquatic organisms still needs to be properly understood. To address this, we have subjected zebrafish to four different feeds: A) untreated feed; B) feed supplemented with microplastics (LD-PE 125–250 µm of diameter); C) feed supplemented with 2% microplastics to which a mixture of PCBs, BFRs, PFCs and methylmercury were sorbed; and D) feed supplemented with the mixture of contaminants only. After 3 weeks of exposure fish were dissected and liver, intestine, muscular tissue and brain were extracted. After visual observation, evaluation of differential gene expression of some selected biomarker genes in liver, intestine and brain were carried out. Additionally, quantification of perfluorinated compounds in liver, brain, muscular tissue and intestine of some selected samples were performed. The feed supplemented with microplastics with sorbed contaminants produced the most evident effects especially on the liver. The results indicate that microplastics alone does not produce relevant effects on zebrafish in the experimental conditions tested; on the contrary, the combined effect of microplastics and sorbed contaminants altered significantly their organs homeostasis in a greater manner than the contaminants alone.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

Tamoxifen affects glucose and lipid metabolism parameters, causes browning of subcutaneous adipose tissue and transient body composition changes in C57BL/6NTac mice

Tamoxifen is a selective estrogen receptor (ER) modulator which is widely used to generate inducible conditional transgenic mouse models. Activation of ER signaling plays an important role in the regulation of adipose tissue (AT) metabolism. We therefore tested the hypothesis that tamoxifen administration causes changes in AT biology in vivo. 12 weeks old male C57BL/6NTac mice were treated with either tamoxifen (n = 18) or vehicle (n = 18) for 5 consecutive days. Tamoxifen treatment effects on body composition, energy homeostasis, parameters of AT biology, glucose and lipid metabolism were investigated up to an age of 18 weeks. We found that tamoxifen treatment causes: I) significantly increased HbA{sub 1c}, triglyceride and free fatty acid serum concentrations (p < 0.01), II) browning of subcutaneous AT and increased UCP-1 expression, III) increased AT proliferation marker Ki67 mRNA expression, IV) changes in adipocyte size distribution, and V) transient body composition changes. Tamoxifen may induce changes in body composition, whole body glucose and lipid metabolism and has significant effects on AT biology, which need to be considered when using Tamoxifen as a tool to induce conditional transgenic mouse models. Our data further suggest that tamoxifen-treated wildtype mice should be characterized in parallel to experimental transgenic models to control for tamoxifen administration effects. - Highlights: • Tamoxifen treatment causes significantly increased HbA{sub 1c}, triglyceride and free fatty acid serum concentrations. • Tamoxifen induces browning of subcutaneous AT and increased UCP-1 expression. • Tamoxifen changes adipocyte size distribution, and transient body composition.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Clinical Usefulness of {sup 18}F-Fluorodeoxyglucose-Positron Emission Tomography in Patients With Locally Advanced Pancreatic Cancer Planned to Undergo Concurrent Chemoradiation Therapy

Purpose: To assess the role of coregistered {sup 18}F-fluorodeoxyglucose positron emission tomography (FDG-PET) in detecting radiographically occult distant metastasis (DM) at staging in patients with locally advanced pancreatic cancer (LAPC) and to study whether FDG-PET parameters can predict relatively long-term survival in patients who are more likely to benefit from chemoradiation therapy (CRT). Methods and Materials: From our institutional database, we identified 388 LAPC patients with M0 on conventional computed tomography (CT) who were planned to undergo CRT. Coregistered FDG-PET staging was offered to all patients, and follow-up FDG-PET was used at the clinical discretion of the physician. Results: FDG-PET detected unsuspected CT-occult DM in 33% of all 388 patients and allowed them to receive systemic therapy immediately. The remaining 260 patients (PET-M0) underwent CRT selectively as an initial treatment. Early DM arose in 13.1% of 260 patients, and the 1-year estimated locoregional recurrence rate was 5.4%. Median overall survival (OS) and progression-free survival (PFS) were 14.6 and 9.3 months, respectively, at a median follow-up time of 32.3 months (range, 10-99.1 months). Patients with a baseline standardized uptake value (SUV) <3.5 and/or SUV decline ≥60% had significantly better OS and PFS than those having none, even after adjustment for all potential confounding variables (all P<.001). Conclusions: FDG-PET can detect radiographically occult DM at staging in one-third of patients and spare them from the potentially toxic therapy. Additionally, FDG-PET parameters including baseline SUV and SUV changes may serve as useful clinical markers for predicting the prognosis in LAPC patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

NASA NTRS1999

The Role of Calcium in the Response of Osteoblasts to Mechanical Stimulation

A major biomedical concern in the exploration and development of space is the rapid loss of bone associated with extended periods of spaceflight. Mineral content, bone formation, matrix protein production and total body calcium are all reduced during long-term periods of weightlessness. These effects of weightlessness appears to be due to decreases in the anabolic function of osteoblasts and osteocytes rather than changes in the resorptive activity of osteoclasts. Conversely, subjecting the skeleton to exogenous mechanical loading increases matrix protein synthesis and bone formation rate, a process which also appears mediated through osteogenic cells. Osteoblasts have been shown to respond to a number of types of mechanical stimulation. However recently we have demonstrated that osteoblasts respond to fluid shear, but not physiologic levels of mechanical strain, with increases in expression of the matrix protein, osteopontin. We have also shown similar responses in other markers for the anabolic response in bone. The expression of the early response gene, c-fos, and the inducible-isoform of the prostaglandin synthetic enzyme, cyclooygenase-2 (COX-2), both increase rapidly in response to fluid shear, but not strain. How osteoblasts and osteocytes perceive mechanical stimuli and convert this stimulus into a biochemical event within the cell is still unknown. However, examination of the cellular events following mechanical stimulation indicate that two of the earliest responses are a rapid increase in intracellular calcium ([Ca(2+)](sub i)) and a reorganization of the actin cytoskeleton. The increase in [Ca(2+)](sub i) is dependent on the presence of extracellular Ca(2+), suggesting the activation of membrane Ca(2+) channel. We have previously characterized a mechanosensitive, cation-selective channel (MSCC) in osteoblast-like clonal cells, which we postulate is important in this early response to mechanical loading. Using an antisense oligodeoxynucleotide strategy, we have tentatively identified this channel as an isoform of the alc subunit of the dihydropyridine-sensitive, voltage sensitive Ca(2+) channel (VSCC). However, a major component in this mechanically induced rise in [Ca(2+)](sub i) is the release of Ca(2+) from intracellular stores. The actin cytoskeleton also rapidly responds to fluid shear with an increase in stress fiber formation and a realignment of the cell parallel to the direction of flow. To ascertain whether these two observations are related and how they effect shear-induced gene expression, we examined the role of Ca(2+) channels and intracellular Ca(2+) release on cytoskeletal reorganization and the resultant increases in the expression and production of c-fos and COX-2 in response to fluid shear.

Duncan, R. L.↗

DOE OSTI2016

Correlation between ECM guidance and actin polymerization on osteogenic differentiation of human adipose-derived stem cells

The correlation between extracellular matrix (ECM) components, cell shape, and stem cell guidance can shed light in understanding and mimicking the functionality of stem cell niches for various applications. This interplay on osteogenic guidance of human adipose-derived stem cells (hASCs) was focus of this study. Proliferation and osteogenic markers like alkaline phosphatase activity and calcium mineralization were slightly increased by the ECM components laminin (LA), collagen I (COL), and fibronectin (FIB); with control medium no differentiation occurred. ECM guided differentiation was rather dependent on osterix than on Runx2 pathway. FIB significantly enhanced cell elongation even in presence of actin polymerization blockers cytochalasin D (CytoD) and ROCK inhibitor Y-27632, which generally caused more rounded cells. Except for the COL surface, both inhibitors increased the extent of osterix, while the Runx2 pathway was more sensitive to the culture condition. Both inhibitors did not affect hASC proliferation. CytoD enabled osteogenic differentiation independently from the ECM, while it was rather blocked via Y-27632 treatment; on FIB the general highest extent of differentiation occurred. Taken together, the ECM effect on hASCs occurs indirectly and selectively via a dominant role of FIB: it sustains osteogenic differentiation in case of a tension-dependent control of actin polymerization. - Highlights: • Interplay of ECM and cell shape guides osteogenic differentiation of hASCs. • ECM components only present a promotive but not stimulative effect. • No direct correlation between ECM-enhanced cell elongation and differentiation. • Suppression of differentiation depends on a specific actin polymerization blocking. • Fibronectin sustains cell elongation and differentiation in case of blocking actin.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-BRA-07: Megavoltage Spectral Imaging with a Layered Detector

Purpose: The aim of the current work is to investigate the feasibility of megavoltage spectral imaging using a multiple layered detector for enhancement of low contrast detectability through material segmentation and discrimination (such as bone, markers and metal implants). Potentially the technique can be applied to improve detection and reduce dose in Megavoltage Cone Beam Computed Tomography (MV-CBCT). Methods: Experiments were performed with a prototype multi-layer imager (MLI) which has higher detective efficiency and lower noise characteristics than conventional Electronic Portal Imaging Devices (EPIDs). Images of a solid water phantom were acquired at 2.5 MV, 6MV and 6MV without flattening filter (FFF). The following materials were placed within a stack of solid water: aluminum, copper and gold. Material separation was assessed based on Contrast-to-Noise Ratio (CNR) of the weighted image, formed by a weighted subtraction of the images from two layers of the MLI. A range of weighting factors were investigated for material separation. Results: CNR can be minimized for each material by appropriate selection of the subtraction weighting factor. This is equivalent to a selective subtraction of specific materials from the image. Using multiple layers simultaneously also decreases the dose requirement and removes any registration errors. The minimum CNR for aluminum, copper and gold at the weighted image formed with 2.5MV was obtained at weighting factors equal to 0.92, 0.76 and 0.64 respectively. The corresponding values at 6MVFFF were 0.99, 0.92 and 0.78 respectively. Conclusion: In the current work, an MV spectral imaging feasibility study was attempted using a novel multi-layer prototype EPID imager. Initial results suggest that material separation based on spectral differences between different layers is possible. This spectral imaging technique has potential advantages in MV-CBCT for real-time target tracking, patient set-up imaging and adaptive radiotherapy. The project was supported, partially, by a grant from Varian Medical Systems, Inc., and Award No. R01CA188446-01 from the National Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis

Abstract Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M . × giganteus (M×g) ‘1993–1780', in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus , this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis . Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F 1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47 . The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 ( CEX13 ), WRKY2 transcription factor, and cold shock domain ( CSDP1 ). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Data from Winter Hardiness of Miscanthus (III): Genome‐Wide Association and Genomic Prediction for Overwintering Ability in Miscanthus sinensis

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780′, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus , this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis . Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47 . The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

Biomass Analytics↗

DOE OSTI2022

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗

NASA NTRS2006

Stable Carbon Isotopic Signatures of Abiotic Organics from Hydrothermal Synthesis Experiments

Stable carbon isotopes can be powerful biogeochemical markers in the study of life's origins. Biogenic carbon fixation produces organics that are depleted in C-13 by about -20 to -30%0. Less attention has been paid to the isotopic signatures of abiotic processes. The possibility of abiotic processes producing organics with morphologies and isotopic signatures in the biogenic range has been at the center of recent debate over the Earth's earliest microfossils. The abiotic synthesis of organic compounds in hydrothermal environments is one possible source of endogenous organic matter to the prebiotic earth. Simulated hydrothermal settings have been shown to synthesize, among other things, single chain amphiphiles and simple lipids from a mix of CO, CO2, and H2. A key characteristic of these amphiphilic molecules is the ability to self-assemble in aqueous phases into more organized structures called vesicles, which form a selectively permeable boundary and serve the function of containing and concentrating other organic molecules. The ability to form cell like structures also makes these compounds more likely to be mistaken for biogenic. Hydrothermal simulation experiments were conducted from oxalic or formic acid in water at 175 C for 72 hr. The molecular and isotopic composition of the products of these reactions were determined and compared to biogenic fractionations . Preliminary results indicate isotopic fractionation during abiotic hydrocarbon synthesis in hydrothermal environments is on par with biological carbon fixation.

Stern, Jennifer C.↗

DOE OSTI2019

Design, synthesis and biological evaluation of a new series of thiazolyl-pyrazolines as dual EGFR and HER2 inhibitors

Epidermal growth factor receptor (EGFR, also known as HER1) and HER2, prominent members of receptor tyrosine kinase (RTK) superfamily, have been reported as diagnostic or prognostic markers in tumor progression. Based on the importance of molecular hybridization of pyrazoline and thiazole scaffolds in the discovery of potent anticancer agents, new thiazolyl-pyrazoline derivatives (3a-v) were synthesized and screened for their cytotoxic effects on A549 human lung adenocarcinoma, MCF-7 human breast adenocarcinoma and A375 human melanoma cell lines. 1-(4-(4-Fluorophenyl)thiazol-2-yl)-3-(4-morpholinophenyl)-5-(4-chlorophenyl)-2-pyrazoline (3c),1-(4-(4-cyanophenyl)thiazol-2-yl)-3-(4-morpholinophenyl)-5-(4-chlorophenyl)-2-pyrazoline (3f) and 1-(4-(4-cyanophenyl)thiazol-2-yl)-3-(4-piperidinophenyl)-5-(4-chlorophenyl)-2-pyrazoline (3q) were found as the most potent anticancer agents against A549 and MCF-7 cell lines compared to erlotinib. Compound 3q also showed moderate cytotoxic activity against A375 cell line. Moreover, these compounds exert a cancer cell–selective action against Jurkat cell line posing no toxicity on peripheral blood mononuclear cells (PBMCs). In order to enlighten the mechanism of action underlying anticancer activity, compounds 3c, 3f and 3q were investigated for their apoptotic effects on A549 and MCF-7 cell lines and inhibitory potencies against eight different RTKs including EGFR and HER2 compared to erlotinib. The results indicated that compounds 3f and 3q induced apoptosis in both cell lines and showed significant EGFR inhibitory activity with IC50 values of 4.34 ± 0.66 μM and 4.71 ± 0.84 μM, respectively when compared with erlotinib (IC 50 = 0.05 ± 0.01 μM). Besides, compound 3f also inhibited HER2 notably with an IC 50 value of 2.28 ± 0.53 μM making it a dual EGFR and HER2 inhibitor. Molecular docking studies, which were conducted to support the in vitro assays, pointed out that compound 3f showed high affinity into the ATP binding sites of EGFR and HER2.

60 APPLIED LIFE SCIENCES↗