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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Chromosome-level assembly and analysis of Camelina neglecta : a novel diploid model for Camelina biotechnology research

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis between C. neglecta and C. sativa, we successfully used the method of calculating Ks to distinguish the three subgenomes of C. sativa and determined that C. neglecta was closest to the first subgenome (SG1) of C. sativa. Further, transcriptomic analysis revealed the key genes associated with seed oil biosynthesis and its transcriptional regulation, including SAD, FAD2, FAD3, FAE1, ABI3, WRI1 and FUS3 displaying high expression levels in C. neglecta seeds. The high representability of C. neglecta as a model species for Camelina-based biotechnology research has been demonstrated for the first time. In particular, floral Agrobacterium tumefaciens infiltration-based transformation of C. neglecta, leading to overexpression of CvLPAT2, CpDGAT1 and CvFatB1 transgenes, was demonstrated for medium-chain fatty acid accumulation in C. neglecta seed oil. This study provides an important genomic resource and establishes C. neglecta as a new model for oilseed biotechnology research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

High-resolution linkage map and chromosome-scale genome assembly for cassava ( Manihot esculenta Crantz) from 10 populations

Cassava Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculent Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. Here, we used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum , Clostridium sporogenes , and Clostridium argentinense

At least 40 toxin subtypes of botulinum neurotoxins (BoNTs), a heterogenous group of bacterial proteins, are produced by seven different clostridial species. A key factor that drives the diversity of neurotoxigenic clostridia is the association of bont gene clusters with various genomic locations including plasmids, phages and the chromosome. Analysis of Clostridium sporogenes BoNT/B1 strain CDC 1632, C. argentinense BoNT/G strain CDC 2741, and Clostridium parabotulinum BoNT/B1 strain DFPST0006 genomes revealed bont gene clusters within plasmid-like sequences within the chromosome or nested in large contigs, with no evidence of extrachromosomal elements. A nucleotide sequence (255,474 bp) identified in CDC 1632 shared 99.5% identity (88% coverage) with bont/B1-containing plasmid pNPD7 of C. sporogenes CDC 67071; CDC 2741 contig AYSO01000020 (1.1 MB) contained a ~140 kb region which shared 99.99% identity (100% coverage) with plasmid pRSJ17_1 of C. argentinense BoNT/G strain 89G; and DFPST0006 contig JACBDK0100002 (573 kb) contained a region that shared 100% identity (99%) coverage with the bont/B1-containing plasmid pCLD of C. parabotulinum Okra. This is the first report of full-length plasmid DNA-carrying complete neurotoxin gene clusters integrated in three distinct neurotoxigenic species: C. parabotulinum, C. sporogenes and C. argentinense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons

The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases ( KCS ), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.

09 BIOMASS FUELS↗
DOE OSTI2018

The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea ‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1969

Microscopes and computers combined for analysis of chromosomes

Scanning machine CHLOE, developed for photographic use, is combined with a digital computer to obtain quantitative and statistically significant data on chromosome shapes, distribution, density, and pairing. CHLOE permits data acquisition about a chromosome complement to be obtained two times faster than by manual pairing.

Butler, J. W.↗
NASA NTRS1976

An Automated System for Chromosome Analysis

The design, construction, and testing of a complete system to produce karyotypes and chromosome measurement data from human blood samples, and to provide a basis for statistical analysis of quantitative chromosome measurement data are described.

Castleman, K. R.↗
NASA NTRS1978

Effect of ultrasonic irradiation on mammalian cells and chromosomes in vitro

Human peripheral blood and HeLa cells were irradiated in vitro at the ultrasonic frequency of 65 kHz. The whole blood and HeLa cell suspensions were exposed to continuous and pulsed ultrasonic power levels of 0.12, 0.16, 0.72, 1.12 and 2.24 W for a period of one minute. The method of ultrasonic irradiation was carried out with the whole blood or HeLa cell suspensions coupled directly to a cylindrical transducer while heating of the cell suspensions in excess of 41 C was avoided. Irradiated and unirradiated peripheral blood lymphocyte chromosome cultures were prepared and scored for selected numerical and morphological aberrations. There was no significant difference in the frequency of chromosomal aberrations between irradiated and unirradiated cells.

Roseboro, J. A.↗
NASA NTRS1987

Evaluation of an automated karyotyping system for chromosome aberration analysis

Chromosome aberration analysis is a promising complement to conventional radiation dosimetry, particularly in the complex radiation fields encountered in the space environment. The capabilities of a recently developed automated karyotyping system were evaluated both to determine current capabilities and limitations and to suggest areas where future development should be emphasized. Cells exposed to radiometric chemicals and to photon and particulate radiation were evaluated by manual inspection and by automated karyotyping. It was demonstrated that the evaluated programs were appropriate for image digitization, storage, and transmission. However, automated and semi-automated scoring techniques must be advanced significantly if in-flight chromosome aberration analysis is to be practical. A degree of artificial intelligence may be necessary to realize this goal.

Prichard, Howard M.↗
NASA NTRS1994

Capillary electrophoresis: Biotechnology for separation of DNA and chromosomes

Electrophoresis has been used for the separation of particles, ions, and molecules for a number of years. The technology for separation and detection of the results has many applications in the life sciences. One of the major goals of the scientific community is to separate DNA molecules and intact chromosomes based upon their different lengths or number of base pairs. This may be achieved by using some of the commercially available and widely used methods, but these processes require a considerable amount of time. The challenge is to achieve separation of intact chromosomes in a short time, preferably in a matter of minutes.

Williams, George O., Jr.↗
NASA NTRS1985

Automated Chromosome Breakage Assessment

An automated karyotyping machine was built at JPL in 1972. It does computerized karyotyping, but it has some hardware limitations. The image processing hardware that was available at a reasonable price in 1972 was marginal, at best, for this job. In the meantime, NASA has developed an interest in longer term spaceflights and an interest in using chromosome breakage studies as a dosimeter for radiation or perhaps other damage that might occur to the tissues. This uses circulating lymphocytes as a physiological dosimeter looking for chromosome breakage on long-term spaceflights. For that reason, we have reactivated the automated karyotyping work at JPL. An update on that work, and a description of where it appears to be headed is presented.

Castleman, Kenneth↗
NASA NTRS2007

Painting Analysis of Chromosome Aberrations Induced by Energetic Heavy Ions in Human Cells

This viewgraph presentation reviews some of the techniques used to analyze the damage done to chromosome from ion radiation. Fluorescence in situ hybridization (FISH), mFISH, mBAND, telomere and centromereprobes have been used to study chromosome aberrations induced in human cells exposed to low-and high-LET radiation in vitro. There is some comparison of the different results from the various techniques. The results of the study are summarized.

Wu, Honglu↗
NASA NTRS2010

Distribution of Chromosome Breakpoints in Human Epithelial Cells Exposed to Low- and High-LET Radiation

Low-and high-LET radiations produced distinct breakpoint distributions. The difference of the breakpoint distributions between low-and high-LET only appeared in break ends involved in interchromosome exchanges. The breakpoint distributions for break ends participating in intrachromosome exchanges were similar. Gene-rich regions do not necessarily have more chromosome breaks. High-LET appeared to produce long live (data not shown) or longer live breaks that can migrate a longer distance before rejoining with other breaks. Domains occupied by different segments of the chromosomes may be responsible for the breakpoint distribution. The dose responses for interchromosomal exchanges were linear in all four exposures. However, the dose response for intrachromosomal exchanges were none linear. Increasing dose of high dose rate exposure (Fe-ions or -rays) increase the fraction of cells with intrachromosome aberrations, whereas increasing dose of low dose rate exposure (neutrons or -rays) does not affect the fraction of cells with intrachromosome aberrations.

Hada, Megumi↗
NASA NTRS2011

Space Radiation Effects on Human Cells: Modeling DNA Breakage, DNA Damage Foci Distribution, Chromosomal Aberrations and Tissue Effects

Future long-tem space travel will face challenges from radiation concerns as the space environment poses health risk to humans in space from radiations with high biological efficiency and adverse post-flight long-term effects. Solar particles events may dramatically affect the crew performance, while Galactic Cosmic Rays will induce a chronic exposure to high-linear-energy-transfer (LET) particles. These types of radiation, not present on the ground level, can increase the probability of a fatal cancer later in astronaut life. No feasible shielding is possible from radiation in space, especially for the heavy ion component, as suggested solutions will require a dramatic increase in the mass of the mission. Our research group focuses on fundamental research and strategic analysis leading to better shielding design and to better understanding of the biological mechanisms of radiation damage. We present our recent effort to model DNA damage and tissue damage using computational models based on the physics of heavy ion radiation, DNA structure and DNA damage and repair in human cells. Our particular area of expertise include the clustered DNA damage from high-LET radiation, the visualization of DSBs (DNA double strand breaks) via DNA damage foci, image analysis and the statistics of the foci for different experimental situations, chromosomal aberration formation through DSB misrepair, the kinetics of DSB repair leading to a model-derived spectrum of chromosomal aberrations, and, finally, the simulation of human tissue and the pattern of apoptotic cell damage. This compendium of theoretical and experimental data sheds light on the complex nature of radiation interacting with human DNA, cells and tissues, which can lead to mutagenesis and carcinogenesis later in human life after the space mission.

Ponomarev, A. L.↗
NASA NTRS2020

A Bi-Exponential Repair Algorithm for Radiation-Induced Double-Strand Breaks: Application to Chromosome Aberrations

Chromosome aberrations (CAs) are one of the effects of radiation exposure and are used as a biomarker. A new simulation program, named RITCARD (Radiation induced tracks, chromosome aberrations, repair, and damage) was developed to simulate radiation-induced CA. RITCARD is used with the program RITRACKS (Relativistic Ion Tracks), which simulates the radiation tracks. The restitution kinetics algorithm presented here is a significant improvement over the one used in the first version. Simulations of radiation-induced CA were performed for several ion types and mixed irradiation fields. These simulations will be useful to help interpreting experiments of galactic cosmic rays (GCR) simulator.

Plante, Ianik↗
DOE OSTI2022

Chromosome aberrations among atomic-bomb survivors exposed in utero: updated analysis accounting for revised radiation doses and smoking

A previous study of peripheral blood lymphocyte translocations around age 40 among atomic-bomb survivors exposed in utero revealed no overall association with radiation dose—despite a clear association between translocations and dose among their mothers—but the data suggested an increase at doses below 100 mGy with a definite peak. That analysis of the in utero-exposed survivors did not adjust for their subsequent smoking behavior, an established cause of chromosomal aberrations, or their subsequent exposures to medical irradiation, a potential mediator. In addition, atomic-bomb survivor radiation dose estimates have subsequently been updated and refined. We therefore re-estimated the dose response using the latest DS02R1 dose estimates and adjusting for smoking as well as for city and proximal–distal location at the time of exposure to the atomic bomb. Sex of the survivor, mother’s age around the time of conception, and approximate trimester of gestation at the time of exposure were also considered as explanatory variables and modifiers. Precision of the estimated dose response was slightly lower due to greater variability near zero in the updated dose estimates, but there was little change in evidence of a low-dose increase and still no suggestion of an overall increase across the entire dose range. Adjustment for smoking behavior led to a decline in background number of translocations (the dose–response intercept), but smoking did not interact with dose overall (across the entire dose range). Adjustment for medical irradiation did not alter the association between dose and translocation frequency. Sex, mother’s age, and trimester were not associated with number of translocations, nor did they interact with dose overall. Interactions with dose in the low-dose range could not be evaluated because of numerical instability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness

Quercus variabilis is a deciduous woody species with high ecological and economic value and is a major source of cork in East Asia. Cork from thick softwood sheets have higher commercial value than those from thin sheets. It is extremely difficult to genetically improve Q. variabilis to produce high quality softwood due to the lack of genomic information. Here, we present a high-quality chromosomal genome assembly for Q. variabilis with length of 791,89 Mb and 54,606 predicted genes. Comparative analysis of protein sequences of Q. variabilis with 11 other species revealed that specific and expanded gene families were significantly enriched in the "fatty acid biosynthesis" pathway in Q. variabilis, which may contribute to the formation of its unique cork. Additionally, based on weighted correlation network analysis of time-course (i.e., five important developmental ages) gene expression data in thick-cork versus thin-cork genotypes of Q. variabilis, we identified one co-expression gene module associated with the thick-cork trait. Within this co-expression gene module, 10 hub genes were associated with suberin biosynthesis. Furthermore, we identified a total of 198 suberin biosynthesis-related new candidate genes that were up-regulated in trees with a thick cork layer relative to those with a thin cork layer. Also, we found that some genes related to cell expansion and cell division were highly expressed in trees with a thick cork layer. Collectively, our results revealed that two metabolic pathways (i.e., suberin biosynthesis, fatty acid biosynthesis), along with other genes involved in cell expansion, cell division, and transcriptional regulation, were associated with the thick-cork trait in Q. variabilis, providing insights into the molecular basis of cork development and knowledge for informing genetic improvement of cork thickness in Q. variabilis and closely related species.

59 BASIC BIOLOGICAL SCIENCES↗