Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “CIS”

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.

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

At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

THE CM-, MM-, AND SUB-MM-WAVE SPECTRUM OF ALLYL ISOCYANIDE AND RADIOASTRONOMICAL OBSERVATIONS IN ORION KL AND THE SgrB2 LINE SURVEYS

Organic isocyanides have an interesting astrochemistry and some of these molecules have been detected in the interstellar medium (ISM). However, rotational spectral data for this class of compounds are still scarce. We provide laboratory spectra of the four-carbon allyl isocyanide covering the full microwave region, thus allowing a potential astrophysical identification in the ISM. We assigned the rotational spectrum of the two cis (synperiplanar) and gauche (anticlinal) conformations of allyl isocyanide in the centimeter-wave region (4-18 GHz), resolved its {sup 14}N nuclear quadrupole coupling (NQC) hyperfine structure, and extended the measurements into the millimeter and submillimeter-wave (150-900 GHz) ranges for the title compound. Rotational constants for all the monosubstituted {sup 13}C and {sup 15}N isotopologues are additionally provided. Laboratory observations are supplemented with initial radioastronomical observations. Following analysis of an extensive dataset (>11000 rotational transitions), accurate ground-state molecular parameters are reported for the cis and gauche conformations of the molecule, including rotational constants, NQC parameters, and centrifugal distortion terms up to octic contributions. Molecular parameters have also been obtained for the two first excited states of the cis conformation, with a dataset of more than 3300 lines. The isotopic data allowed determining substitution and effective structures for the title compound. We did not detect allyl isocyanide either in the IRAM 30 m line survey of Orion KL or in the PRIMOS survey toward SgrB2. Nevertheless, we provided an upper limit to its column density in Orion KL.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Doppler coherence imaging of divertor and SOL flows in ASDEX upgrade and Wendelstein 7-X

Measurement of ion dynamics is of great importance to the study of plasma exhaust and impurity particle flows in the scrape-off-layer (SOL) and divertor in magnetic confinement experiments. Doppler coherence imaging spectroscopy (CIS) is a passive optical diagnostic that produces 2D images of line-integrated ion flow velocity. Doppler CIS flow measurements of neutral deuterium and impurities were conducted for the first time in the divertor of the medium-sized tokamak experiment ASDEX Upgrade. A detailed sightline, emission and magnetic field analysis was undertaken to identify location and direction of flows. Under the assumption of toroidal axisymmetry, they revealed mainly parallel impurity flows in the proximity of the X-point and target plates on the order of 20 km s -1 . Two Doppler CIS systems are currently set up for the optimized stellarator Wendelstein 7-X (W7-X). With this being said, the main task of this diagnostic will be the measurement of impurity ion flows in one of the island divertors of W7-X. EMC3-EIRENE simulations have been carried out to estimate the flow behaviour in the W7-X SOL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

2D coherence imaging measurements of C 2+ ion temperatures in the divertor of Wendelstein 7-X

For the first time, 2D ion temperature values are derived from coherence imaging spectroscopy (CIS) fringe contrast measurements by taking Zeeman line broadening effects into account during the analysis procedure of a spatial-heterodyne CIS instrument. This allowed 2D images of C 2+ ion temperatures (T i ) across the 3D-shaped island divertor of the Wendelstein 7-X stellarator. Ion temperatures ranging from 10 to 20 eV are observed for the C 2+ impurity species in the region above the divertor targets. During the transition from the attached to the detached plasma state, the C 2+ radiation zone moves from close to the divertor target towards the last closed flux surface. Within this radiation zone, C 2+ temperature does not decrease significantly. Experimentally, the coherence imaging measurements were cross-calibrated at one poloidal cross-section using a high resolution Echelle spectrometer, that shared its sightlines with the coherence imaging diagnostic. The spectra demonstrated that, apart from Doppler broadening, the Zeeman effect significantly contributes to the spectral line broadening and cannot be neglected when analyzing the CIS contrast data for T i extraction in the edge and scrape-off-layer of Wendelstein 7-X (W7-X), due to the relatively low temperatures (T i < 100 eV) and high magnetic fields (B ≈ 2.5 T).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

2D measurements of parallel counter-streaming flows in the W7-X scrape-off layer for attached and detached plasmas

Abstract Investigations of particle parallel flow velocities have been carried out for the scrape-off layer (SOL) of the Wendelstein 7-X (W7-X) stellarator, in order to gain insights on the SOL transport properties during attached and detached plasma scenarios. The experimental evidence is based on the coherence imaging spectroscopy (CIS) diagnostic, able to measure 2D impurity emission intensity and flow velocity. The impurity monitored by CIS is C 2+ , characterized by a line-emission intensity observed to be linearly proportional to the total plasma radiated power in both attached and detached plasmas. The related C 2+ velocity shows a strong dependence on the line-averaged electron density while remaining insensitive to the input power. During attached plasmas, the velocity increases with increasing line-averaged density. The tendency reverses in the transition to and during detachment, in which the velocity decreases by at least a factor of 2. The sharp drop in velocity, together with a rise in line-emission intensity, is reliably correlated to the detachment transition and can therefore be used as one of its signatures. The impurity flow velocity appears to be well coupled with the main ions’ one, thus implying the dominant role of impurity-main ion friction in the parallelimpurity transport dynamics. In view of this SOL impurity transport regime, the CIS measurement results are here interpreted with the help of EMC3-Eirene simulations, and their major trends are already explainable with a simple 1D fluid model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F 1 and F 2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F 1 progeny individuals. We show that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Lastly, altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improved genome editing by an engineered CRISPR-Cas12a

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis - and trans -DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2–18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A novel conformity index for intensity modulated radiation therapy plan evaluation

Purpose: Intensity modulated radiation therapy (IMRT) has gained popularity in the treatment of cancers. Manual evaluation of IMRT plans for head-and-neck cancers has been especially challenging necessitating efficient and objective assessment tools. In this work, the authors address this issue by developing a personalized conformity index (CI) for comparison of IMRT plans for head-and-neck cancers and evaluating its plan quality discerning power in comparison with other widely used CIs. Methods: A two-dimensional CI with dose and distance incorporated (CI{sub DD}) was developed using the MATLAB program language, to quantify the planning target volume (PTV) coverage. Valuable information contained in the digital imaging and communication in medicine (DICOM) RT objects were harvested for computation of each of the CI{sub DD} components. Apart from the dose penalty factor, a distance-based exponential function was employed by varying the penalty weight associated with the location of cold spots within the PTV. With the goal of deriving a customized penalty factor, the distances between individual pixel and its nearest PTV boundary was found. Using the exponential function, the impact of distance penalty was substantially larger for cold spots closer to the PTV centroid but petered out quickly wherever they were situated in the vicinity of PTV border. In order to evaluate the CI{sub DD} scoring system, three CT image data sets of nasopharyngeal carcinoma (NPC) patients were collected. Ten IMRT plans with degrading qualities were generated from each dataset and were ranked based on CI{sub DD} and other existing indices. The coefficient of variance was calculated for each dataset to compare the degree of variation. Results: The CI{sub DD} scoring system that considered spatial importance of each voxel within the PTV was successfully developed. The results demonstrated that the CI{sub DD} including four discrete factors could provide accurate rankings of plan quality by examining the relative importance of each cold spot within the PTVs. Apart from the dose penalty factor, a distance-based exponential function was employed taking the specific tumor geometry into account. Compared with other commonly used CIs, the CI{sub DD} resulted in the largest coefficient of variance among the ten IMRT plans for each dataset, indicating that its discerning power was the best among the CIs being compared. Conclusions: The CI{sub DD} scoring system was successfully developed to incorporate patient-specific spatial dose information and provide a geometry-based physical index for comparison of IMRT plans for head-and-neck cancers. By taking individual tumor geometry into account, the superiority of CI{sub DD} in plan discerning power was demonstrated. The use of CI{sub DD} could provide an effective means of benchmarking performance, reducing treatment plan variability, and advancing the quality of current IMRT planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Deletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble Substrates

Caldicellulosiruptor bescii secretes a large number of complementary multifunctional enzymes with unique activities for biomass deconstruction. The most abundant enzymes in the C. bescii secretome are found in a unique gene cluster containing a glycosyl transferase (GT39) and a putative peptidyl prolyl cis-trans isomerase. Deletion of the glycosyl transferase in this cluster resulted in loss of detectable protein glycosylation in C. bescii, and its activity has been shown to be responsible for the glycosylation of the proline-threonine rich linkers found in many of the multifunctional cellulases. The presence of a putative peptidyl prolyl cis-trans isomerase within this gene cluster suggested that it might also play a role in cellulase modification. Here, we identify this gene as a putative prsA prolyl cis-trans isomerase. Deletion of prsA2 leads to the inability of C. bescii to grow on insoluble substrates such as Avicel, the model cellulose substrate, while exhibiting no differences in phenotype with the wild-type strain on soluble substrates. Finally, we provide evidence that the prsA2 gene is likely needed to increase solubility of multifunctional cellulases and that this unique gene cluster was likely acquired by members of the Caldicellulosiruptor genus with a group of genes to optimize the production and activity of multifunctional cellulases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Background: Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results: Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions: Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

From Vibrational Spectroscopy to Force Fields and Structures of Saccharides: New Computational Algorithms and Applications

This work was undertaken with the main objective to investigate basic reactions that take place in relatively simple saccharides (mono-saccharides and cellobiose - the building block of cellulose) , in isolation and in cluster with few water molecules or with (gas-phase) clusters of few waters and ionic compounds (salt, isolated ions like H + or OH - ). Within the context of this work, different potentials were investigated; among them, were the PM3 semi empirical potential, DFT/BLYP and a new hybrid potential constructed from MP2 for the harmonic part and from adjusted Hartree-Fock anharmonic interactions (VSCF-PT2). These potentials were evaluated by comparison with experimental data from published sources and from several collaborating groups. The findings show excellent agreement between experiments and predictions with the hybrid VSCF-PT2 potential and very good agreement with predictions obtained from dynamics with dispersion corrected DFT/BLYP potential. Investigation of hydration of cellobiose, was another topic of interest. Guided by a hydration motif demonstrated by our experimental collaborators (team of Prof J.P. Simons), we demonstrated large energetic and structural differences between the two species of cellobiose: cis and trans. The later, which is dominant in solid and liquid phases, is higher in energy in the gas-phase and compared to pure water, it does not disturb as much the network of H bonds. In contrast, the cis species exhibits asymmetric hydration in cluster with up to 25 waters, indicating that it has surfactant properties. Another highlight of this research effort was the successful first time spectrometric and spectroscopic study of a gas-phase protonated sugar derivative (alpha-D-Galactopyranoside) and its interpretation by Ab Initio molecular dynamics (AIMD) simulations. The findings demonstrate the formation of a motif in which a proton bridges between two Oxygen atoms (belonging to OH groups) at the sugar; The vibrational bands involving the shared proton were strongly shifted to lower frequencies ( by about ~ 500 cm -1 for the symmetric mode, in this case). A similar motif was also observed recently by us in protonated cellobiose, indicating that this might be a common mechanism for interaction of a proton with sugars, perhaps similar to the proton wires observed in proteins. The simulations with protonated sugars also shed light on different mechanisms of interaction of a sugar with a proton, including formation of a carboxonium ion, mutarotation events, ring puckering and in the disaccharide cellobiose, the breaking of the glycosidic bond (in both forms of cis and trans). One final highlight to note in this summary, is the finding that in the monosaccharide beta-D-Galactose a hydroxyl ion abstracts a proton (forming water) in a barrierless process at room temperature, but the water remains bound to the sugar backbone, though it migrates around it; actual degradation occurs at ~500 K when water leaves the sugar. However, the study also shows that the water abstraction reaction can be reversed in the presence of 2 additional water molecules complexed with the sugar.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Carbon Intensities of Refining Products in Petroleum Refineries with Co-Processed Biofeedstocks

Petroleum refineries increasingly seek to generate fuels with lower carbon intensities (CIs; a measure of life cycle greenhouse gas [GHG] emissions per unit of energy of fuel; well-to-wheel [WTW]) to meet growing demand. Co-processing refers to a process that adds biomass-derived feedstocks to the fossil-based feedstocks of existing petroleum refinery process units. With the use of biofeedstocks, it is expected that co-processed fuels would have lower CIs than their petroleum counterparts without requiring changes in the existing infrastructure for producing, transporting, and using fuels. To quantify the GHG emissions reduction benefits of co-processing, this study uses a linear programming model to simulate petroleum refinery conditions with and without co-processing. The co-processing cases include three biofeedstocks (soy oil, tallow, and used cooking oil or UCO) used as 10 vol.% of the feedstock to a hydrotreater or hydrocracker since these lipid-based feedstocks have favorable properties to be treated in a hydrotreater or hydrocracker. In addition, we considered pyrolysis oil used as 10 vol.% of the feedstock to a fluid catalytic cracking (FCC) unit in the modeled refinery due to its higher oxygen content compared to other lipid-based feedstocks. Life cycle analysis (LCA) using two distinct approaches—process-level energy allocation and a refinery-level marginal approach—has been conducted for each case. The LCA results using process-level allocation show that there are no noticeable changes in emissions or energy use impacts at the facility level. The life cycle GHG emission reductions of co-processing cases are mainly related to the fraction of biogenic carbon embedded in each fuel product. For example, co-processed jet fuels (a mixture of fossil and biogenic fuels) made via hydrotreating or hydrocracking have higher biogenic carbon, which results in jet fuel CI reductions of 3.9%–8.6% compared to the CI of baseline petroleum jet fuels on a WTW basis. However, analysis of co-processed pyrolysis oil in an FCC shows that a higher fraction of biofeedstocks (29%) becomes process emissions (i.e., CO and CO 2 ), mainly due to the oxygenates in pyrolysis oil, and so it generates less renewable fuel than biofeedstocks co-processed via hydrotreating or hydrocracking. Using the refinery-level marginal approach, the changes in energy use and emissions of co-processing cases compared to the petroleum-only baseline case are allocated to the changes in fuel production (assuming renewable fuels). This approach generates the life cycle GHG emission values of co-processed renewable fuels, which are comparable to the CIs of standalone biofuel production pathways. However, as this approach relies on a rough assumption that product yields and emissions from co-processing units on fossil feedstocks remain the same with and without biofeedstock inputs, co-processing cases like FCC pyrolysis oil may generate quite skewed results.

02 PETROLEUM↗
DOE OSTI2022

Feedstock Carbon Intensity Calculator (FD-CIC): Users’ Manual and Technical Documentation

The carbon intensities (CIs) of biofuels are determined with the life cycle analysis (LCA) technique, which accounts for the energy/material uses and emissions during the complete supply chain of biofuel including feedstock production and fuel conversion stages. Regulatory agencies such as California Air Resources Board (CARB) adopts LCA to calculate biofuel CIs. The Low Carbon Fuel Standard (LCFS) program developed by CARB allows individual biofuel conversion facilities to submit their own biofuel CIs with their facility input data and incentivizes the reduction in the CI specific to that particular facility compared to a reference fuel’s CI (Liu et al 2020). Such an incentive program has driven innovations in biorefineries to reduce their greenhouse gas (GHG) emissions by linking their revenue directly to its CI score through LCFS credit trading. Besides the biofuel conversion stage, different farming practices for feedstock growth can result in significant CI variations for feedstocks, thus for biofuels. To provide evidence-based research findings, the U.S. Department of Energy’s Advanced Research Projects Agency–Energy (ARPA-E) has supported the Systems Assessment Center of the Energy Systems and Infrastructure Analysis Division at Argonne National Laboratory to examine CI variations of different farming practices to grow agricultural crops for biofuel production. Meanwhile, the ARPA-E has launched the Systems for Monitoring and Analytics for Renewable Transportation Fuels from Agricultural Resources and Management (SMARTFARM) program to develop technologies and data platforms that enable an accurate measurement of key farming parameters that can help robust accounting of the GHG benefits of sustainable, low-carbon agronomic practices at farm level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Test Plan for DOE-GENIORS Dyanamic Irradiation Tests

Dynamic irradiation tests will be performed within the DOE-GENIORS collaboration, to be finished by the end of March 2021. These tests will be performed using three different setups, one at INL, one at CEA, and one at CIEMAT. The cis-mTDDGA/PTD chemical system will be used, applying both "extraction" (cis-mTDDGA - n-dodecane/HNO3) and "stripping" (cis-mTDDGA - n-dodecane/PTD - HNO3) conditions. This test plan provides the details and parameters to be used to perform irradiation at the INL using the INL Radiolysis Test Loop.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2025

Combining genome-wide association studies and expression quantitative trait nucleotide mapping with molecular and genetic validations to identify transcriptional networks regulating drought tolerance in Populus

Objectives: (i). To deploy a large-scale experimental drought trial for up to 1000 unique genotypes of Populus equipping the sites with controlled irrigation and drought treatments that are fully automated and monitored. FULLY COMPLETED (ii) To test the hypothesis that a suite of traits identified for drought tolerance in P. nigra can be measured in drought and control treatments in the wide germplasm collection of P. trichocarpa. FULLY COMPLETED (iii) To use established and novel GWAS model approaches to identify gene loci linked to drought tolerance traits on interest in P. trichocarpa. FULLY COMPLETED (iv) To undertake comparative analysis of GWAS results for drought tolerance traits in P. nigra and P. trichocarpa. PARTIALLY COMPLETED – remains active (v) Using RNAseq in P. trichocarpa, in droughted and control treatments to identify cis- and trans-regulated eQTN. FULLY COMPLETED (vi) Validate up to 50 cis-QTNs, from network hubs using transient protoplast assays. FULLY COMPLETED (vii) To establish Agrobacterium-based gene editing protocols in Populus. FULLY COMPLETED (viii) To utilize early leads from previous research to investigate at least 6 candidate genes for drought tolerance in Populus. FULLY COMPLETED (ix) To validate up to 20 candidate genes for drought tolerance in P. trichocarpa refined from the long-list tested in the transient assays for cis-acting hub gene targets. PARTIALLY COMPLETED- remains active.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3

In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Chlorine Isotope Effects from Isotope Ratio Mass Spectrometry Suggest Intramolecular C-Cl Bond Competition in Trichloroethene (TCE) Reductive Dehalogenation

Chlorinated ethenes are prevalent groundwater contaminants. To better constrain (bio)chemical reaction mechanisms of reductive dechlorination, the position-specificity of reductive trichloroethene (TCE) dehalogenation was investigated. Selective biotransformation reactions (i) of tetrachloroethene (PCE) to TCE in cultures of Desulfitobacterium sp. strain Viet1; and (ii) of TCE to cis-1,2-dichloroethene (cis-DCE) in cultures of Geobacter lovleyi strain SZ were investigated. Compound-average carbon isotope effects were -19.0‰ ± 0.9‰ (PCE) and -12.2‰ ± 1.0‰ (TCE) (95% confidence intervals). Using instrumental advances in chlorine isotope analysis by continuous flow isotope ratio mass spectrometry, compound-average chorine isotope effects were measured for PCE (-5.0‰ ± 0.1‰) and TCE (-3.6‰ ± 0.2‰). In addition, position-specific kinetic chlorine isotope effects were determined from fits of reactant and product isotope ratios. In PCE biodegradation, primary chlorine isotope effects were substantially larger (by -16.3‰ ± 1.4‰ (standard error)) than secondary. In TCE biodegradation, in contrast, the product cis-DCE reflected an average isotope effect of -2.4‰ ± 0.3‰ and the product chloride an isotope effect of -6.5‰ ± 2.5‰, in the original positions of TCE from which the products were formed (95% confidence intervals). A greater difference would be expected for a position-specific reaction (chloride would exclusively reflect a primary isotope effect). These results therefore suggest that both vicinal chlorine substituents of TCE were reactive (intramolecular competition). This finding puts new constraints on mechanistic scenarios and favours either nucleophilic addition by Co(I) or single electron transfer as reductive dehalogenation mechanisms.

organohalide respiration↗
DOE OSTI2017

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ = - 100° left-handed or right-handed?). This report provides a new metric for backbone handedness ( h ) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ , both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ , ψ and ω . In particular, h equals sin( θ ) d / d |, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis ( ω = 0°) and trans ( ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran ( φ , ψ ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

59 BASIC BIOLOGICAL SCIENCES↗