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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions

On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers.

Liquid chromatography↗
DOE OSTI2019

Design, synthesis, molecular docking, antimicrobial, and antioxidant activities of new phenylsulfamoyl carboxylic acids of pharmacological interest

Abstracts: The research explores the facile synthesis of some new phenylsulfamoyl carboxylic acids, their molecular docking, antimicrobial, and antioxidant activities. The procedure involved the mild reaction of amino acids with benzenesulfonyl chloride in a medium of aqueous base. The compounds were characterized using FTIR, {sup 1}H-NMR, {sup 13}C-NMR, and an elemental analysis. They were tested for their antimicrobial activities against Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Salmonella typhi, Candida albicans, and Aspergillus niger microorganisms. The antioxidant activity of the compounds were measured in vitro by the inhibition of generated stable 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical. The molecular docking was carried out properly and five different disease conditions were studied, namely: trypanosomiasis, malaria, bacterial, fungal infections, and oxidative stress. From the results, compounds 4c, 4d, 4e, and 4g possess more excellent in vitro antibacterial and antifungal activities than the standard drug Ofloxacin used. Compound 4e displayed the most excellent antioxidant activity. Compound 4g showed significant 2D interaction with amino acid residue of urate oxidase from Aspergillus flavus complexed with uracil. Interestingly, compounds 4a, 4c, 4d, 4e, and 4g exhibited excellent antibacterial, antifungal, antioxidant, antitrypanosome, and antimalaria activities comparable to the corresponding standard drugs such as Penicillin, Ketoconazole; α-Tocopherol, Melarsoprol, and Chloroquine respectively. All the compounds were confirmed drug-like according to “Lipinski’s rule of five”. The compounds were found to be promising antibacterial, antifungal, antioxidant, and antitrypanosome agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Prognostic Factors for Survival and Resection in Patients With Initial Nonresectable Locally Advanced Pancreatic Cancer Treated With Chemoradiotherapy

Background and Purpose: Controversies regarding the optimal therapy for patients with locally advanced pancreatic cancer (LAPC) exist. Although the prognosis as a whole remains dismal, subgroups are known to benefit from intensive therapy, including chemoradiotherapy (CRT). We describe the results in 178 patients treated from 2001 to 2010 and have developed a prognostic model for both survival and the possibility of a subsequent resection in these patients. Methods and Materials: From 2001 until 2010, 178 consecutive patients with LAPC were treated and included in the present study, with CRT consisting of 50 Gy in 27 fractions combined with tegafur-uracil(UFT)/folinic acid(FA). Results: The median survival from diagnosis was 11.5 months. Adverse events of Grade 3 or above were seen in 36% of the patients. Ninety-three percent of the patients completed all fractions. A Cox regression model for survival demonstrated resection (hazard ratio [HR] 0.12; 95% confidence interval [CI], 0.1-0.3) and pre-CRT gemcitabine-based therapy (HR 0.57; 95% CI, 0.4-0.9) as being associated with a favorable outcome, increasing gross tumor volume (HR 1.14; 95% CI, 1.0-1.3) was associated with shorter survival. A logistic regression model showed Stage III disease (odds ratio [OR] 0.16; 95% CI, 0.0-1.1) and abnormal hemoglobin (OR 0.26; 95% CI, 0.0-1.2) as being associated with lower odds of resection. Conclusion: This study confirms the favorable prognosis for patients receiving gemcitabine therapy before CRT and the poor prognosis associated with increasing tumor volume. In addition, CRT in patients with abnormal hemoglobin and Stage III disease rarely induced tumor shrinkage allowing subsequent resection.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Metronomic Adjuvant Chemotherapy Improves Treatment Outcome in Nasopharyngeal Carcinoma Patients With Postradiation Persistently Detectable Plasma Epstein-Barr Virus Deoxyribonucleic Acid

Purpose: To investigate the effects of adjuvant chemotherapy in nasopharyngeal carcinoma (NPC) patients with persistently detectable plasma Epstein-Barr virus DNA (pEBV DNA) after curative radiation therapy plus induction/concurrent chemotherapy. Methods and Materials: The study population consisted of 625 NPC patients with available pEBV DNA levels before and after treatment. Eighty-five patients with persistently detectable pEBV DNA after 1 week of completing radiation therapy were eligible for this retrospective study. Of the 85 patients, 33 were administered adjuvant chemotherapy consisting of oral tegafur-uracil (2 capsules twice daily) for 12 months with (n=4) or without (n=29) preceding intravenous chemotherapy of mitomycin-C, epirubicin, and cisplatin. The remaining 52 patients who did not receive adjuvant chemotherapy served as the control group. Results: Baseline patient characteristics at diagnosis (age, sex, pathologic type, performance status, T classification, N classification, and overall stage), as well as previous treatment modality, were comparable in both arms. After a median follow-up of 70 months for surviving patients, 45.5% (15 of 33 patients) with adjuvant chemotherapy and 71.2% (37 of 52 patients) without adjuvant chemotherapy experienced tumor relapses (P=.0323). There were a significant reduction in distant failure (P=.0034) but not in local or regional recurrence. The 5-year overall survival rate was 71.6% for patients with adjuvant chemotherapy and 28.7% for patients without adjuvant chemotherapy (hazard ratio 0.27; 95% confidence interval 0.17-0.55; P<.0001). Conclusions: Our retrospective data showed that adjuvant chemotherapy can reduce distant failure and improve overall survival in NPC patients with persistently detectable pEBV DNA after curative radiation therapy plus induction/concurrent chemotherapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Long-Term Results of a Randomized Trial in Locally Advanced Rectal Cancer: No Benefit From Adding a Brachytherapy Boost

Purpose/Objective(s): Mature data on tumor control and survival are presented from a randomized trial of the addition of a brachytherapy boost to long-course neoadjuvant chemoradiation therapy (CRT) for locally advanced rectal cancer. Methods and Materials: Between March 2005 and November 2008, 248 patients with T3-4N0-2M0 rectal cancer were prospectively randomized to either long-course preoperative CRT (50.4 Gy in 28 fractions, per oral tegafur-uracil and L-leucovorin) alone or the same CRT schedule plus a brachytherapy boost (10 Gy in 2 fractions). The primary trial endpoint was pathologic complete response (pCR) at the time of surgery; secondary endpoints included overall survival (OS), progression-free survival (PFS), and freedom from locoregional failure. Results: Results for the primary endpoint have previously been reported. This analysis presents survival data for the 224 patients in the Danish part of the trial. In all, 221 patients (111 control arm, 110 brachytherapy boost arm) had data available for analysis, with a median follow-up time of 5.4 years. Despite a significant increase in tumor response at the time of surgery, no differences in 5-year OS (70.6% vs 63.6%, hazard ratio [HR] = 1.24, P=.34) and PFS (63.9% vs 52.0%, HR=1.22, P=.32) were observed. Freedom from locoregional failure at 5 years were 93.9% and 85.7% (HR=2.60, P=.06) in the standard and in the brachytherapy arms, respectively. There was no difference in the prevalence of stoma. Explorative analysis based on stratification for tumor regression grade and resection margin status indicated the presence of response migration. Conclusions: Despite increased pathologic tumor regression at the time of surgery, we observed no benefit on late outcome. Improved tumor regression does not necessarily lead to a relevant clinical benefit when the neoadjuvant treatment is followed by high-quality surgery.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Activation-induced cytidine deaminase (AID) is localized to subnuclear domains enriched in splicing factors

Activation-induced cytidine deaminase (AID) is the mutator enzyme in adaptive immunity. AID initiates the antibody diversification processes in activated B cells by deaminating cytosine to uracil in immunoglobulin genes. To some extent other genes are also targeted, which may lead to genome instability and B cell malignancy. Thus, it is crucial to understand its targeting and regulation mechanisms. AID is regulated at several levels including subcellular compartmentalization. However, the complex nuclear distribution and trafficking of AID has not been studied in detail previously. In this work, we examined the subnuclear localization of AID and its interaction partner CTNNBL1 and found that they associate with spliceosome-associated structures including Cajal bodies and nuclear speckles. Moreover, protein kinase A (PKA), which activates AID by phosphorylation at Ser38, is present together with AID in nuclear speckles. Importantly, we demonstrate that AID physically associates with the major spliceosome subunits (small nuclear ribonucleoproteins, snRNPs), as well as other essential splicing components, in addition to the transcription machinery. Based on our findings and the literature, we suggest a transcription-coupled splicing-associated model for AID targeting and activation. - Highlights: • AID and its interaction partner CTNNBL1 localize to Cajal bodies and nuclear speckles. • AID associates with its activating kinase PKA in nuclear speckles. • AID is linked to the splicing machinery in switching B-cells. • Our findings suggest a transcription-coupled splicing associated mechanism for AID targeting and activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Exact-Factorization-Based Surface Hopping for Multistate Dynamics

A surface-hopping algorithm recently derived from the exact factorization approach, SHXF, introduces an additional term in the electronic equation of surface hopping that couples electronic states through the quantum momentum. Furthermore, this term not only provides a first-principles description of decoherence, but here we show it is crucial to accurately capture nonadiabatic dynamics when more than two states are occupied at any given time. Using a vibronic coupling model of the uracil cation, we show that the lack of this term in traditional surface-hopping methods, including those with decoherence corrections, leads to failure to predict the dynamics through a three-state intersection, while SHXF performs similarly to the multiconfiguration time-dependent Hartree quantum dynamics benchmark.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Photoelectron spectroscopic studies of 5-halouracil anions

The parent negative ions of 5-chlorouracil, UCl{sup -} and 5-fluorouracil, UF{sup -} have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl{sup -} and UF{sup -} and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr{sup -}, we did not observe it, the mass spectrum exhibiting only Br{sup -} fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Infrared Spectroscopy of Charge Transfer Complexes of Purines and Pyrimidines

The FTIR spectra of charge transfer complexes of purines and pyrimidines with organic acceptors such as TCNQ, TCNE, DDQ, chloranil and iodine are obtained and studied in the present work. Adenine, guanine, thymine, cytosine and uracil are the purines and pyrimidines which are found as constituent of DNA and RNA. Charge transfer induced hydrogen bonding is concluded on the basis of indirect transitions observed in the infrared range in these CTCs. Some CTCs show gaussian bands revealing delocalization of charge carriers. The CTCs show interband transition in three-dimensions rather than two-dimensions unlike CTCs of amino acids. There is no extended hydrogen bonded network spanning the whole crystal. This leads to indirect transition due to locally deformed lattice furnishing a phonon-assisted transition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linear response have been implemented in a development version of DALTON. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality to CASSCF/CASPT2 benchmarks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A source for microhydrated biomolecules

We describe the construction of an apparatus for the production of a molecular jet of microhydrated biomolecules. Our design uses a water reservoir producing water vapour, which then passes through a separate reservoir containing a vapour of a sublimated biomolecule. The mixture coexpands into a molecular beam apparatus through a conical nozzle. Mass spectra showing water-adenin and water-uracil complexes are shown as typical examples. Suitable expansion conditions are reached without the use of an inert carrier gas.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV)

Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N–H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N–H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π{sub 1}{sup −} and π{sub 2}{sup −} states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

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

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

Biochemistry & Molecular Biology↗
DOE OSTI2012

Closing the Carbon Balance for Fermentation by Clostridium thermocellum (ATCC 27405)

Our lab and most others have not been able to close a carbon balance for fermentation by the thermophilic, cellulolytic anaerobe, Clostridium thermocellum. We undertook a detailed accounting of product formation in C. thermocellum ATCC 27405. Elemental analysis revealed that for both cellulose (Avicel) and cellobiose, {>=}92% of the substrate carbon utilized could be accounted for in the pellet, supernatant and off-gas when including sampling. However, 11.1% of the original substrate carbon was found in the liquid phase and not in the form of commonly-measured fermentation products - ethanol, acetate, lactate, and formate. Further detailed analysis revealed all the products to be <720 da and have not usually been associated with C. thermocellum fermentation, including malate, pyruvate, uracil, soluble glucans, and extracellular free amino acids. By accounting for these products, 92.9% and 93.2% of the final product carbon was identified during growth on cellobiose and Avicel, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Competitive sorption of microbial metabolites on an iron oxide mineral

A large fraction of soil organic matter (SOM) is composed of small molecules of microbial origin. However, the biotic and abiotic cycling of these nutrients is poorly understood and is a critical component of the global carbon cycle. Although there are many factors controlling the accessibility of SOM to microbes, sorption to mineral surfaces is among the most significant. We investigated the competitive sorption of a complex pool of microbial metabolites on ferrihydrite, an iron oxide mineral, using a lysate prepared from a soil bacterium, Pseudomonas stutzeri RCH2. After a 24-h incubation with a range of mineral concentrations, more than half of the metabolites showed significant decreases in solution concentration. Phosphate-containing metabolites showed the greatest degree of sorption followed by dicarboxylates and metabolites containing both nitrogen and an aromatic moiety. Similar trends were observed when comparing sorption of metabolites with an equimolar metabolite mixture rather than a bacterial lysate. Interestingly, ectoine, lysine, two disaccharides and uracil were found not to sorb and may be more bioavailable in iron oxide-rich soils. Additionally, the highest-sorbing metabolites were examined for their ability to mobilize mineral-sorbed phosphate. All phosphate-containing metabolites tested and glutathione released phosphate from the mineral surface within 30 min of metabolite addition. These findings of preferential sorption behavior within a complex pool of microbial metabolites may provide insight into the cycling of SOM and specific nutrient availability. Finally, the release of highly-sorptive metabolites may be an underexplored mechanism utilized by microbial communities to gain access to limited environmental nutrients.

54 ENVIRONMENTAL SCIENCES↗