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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Overall and cause‐specific mortality in the Sentinel system: A power analysis

Abstract Purpose Mortality data within the Sentinel Death Tables remain generally uncharacterized. Assessment of mortality data within Sentinel will help inform its utility for medical product safety studies. Methods To determine if Sentinel contains sufficient all‐cause and cause‐specific mortality events to power postmarketing safety studies. We calculated crude rates of all‐cause mortality and suicide and proportional mortality from suicide from 2004 to 2012 in seven Sentinel data partners. Results were stratified by data partner, sex, age group, and calendar year and compared with national estimates from Centers for Disease Control and Prevention Wide‐ranging ONline Data for Epidemiologic Research. We performed sample size estimations for all‐cause mortality and 10 leading causes of death. Results We observed 479 694 deaths, including 5811 suicides, during 68 million person‐years of follow‐up. Pooled mean death and suicide rates in the data partners were 710 and 8.6 per 100 000 person‐years, respectively (vs 810 and 11.8 nationally). The mean proportional mortality from suicide among the data partners was 1.2%, compared with 1.5% nationally. National trends of decreasing overall mortality and increasing proportional mortality for suicide were reflected within Sentinel. We estimated that detecting hazard ratios of 1.25 and 3 would require 16 442 and 460 exposed patients, respectively, for overall mortality, and 1.3 million and 37 411, respectively, for suicide. Conclusions This was the first study to investigate mortality data in the Sentinel death tables. We found that all‐cause mortality appeared well powered for use as a safety outcome and cause‐specific mortality outcomes may be adequately powered in certain circumstances. Further investigation into the quality of the Sentinel death data is needed.

Swain, Richard S.↗
DOE OSTI2025

Search for long-lived charged particles using large specific ionisation loss and time of flight in 140 fb −1 of pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

This paper presents a search for massive, charged, long-lived particles with the ATLAS detector at the Large Hadron Collider using an integrated luminosity of 140 fb −1 of proton-proton collisions at $\sqrt{s}$ = 13 TeV. These particles are expected to move significantly slower than the speed of light. In this paper, two signal regions provide complementary sensitivity. In one region, events are selected with at least one charged-particle track with high transverse momentum, large specific ionisation measured in the pixel detector, and time of flight to the hadronic calorimeter inconsistent with the speed of light. In the other region, events are selected with at least two tracks of opposite charge which both have a high transverse momentum and an anomalously large specific ionisation. The search is sensitive to particles with lifetimes greater than about 3 ns with masses ranging from 200 GeV to 3 TeV. The results are interpreted to set constraints on the supersymmetric pair production of long-lived R-hadrons, charginos and staus, with mass limits extending beyond those from previous searches in broad ranges of lifetime.

beyond Standard Model↗
DOE OSTI2014

Investigating Commercial Cellulase Performances Toward Specific Biomass Recalcitrance Factors Using Reference Substrates

Three commercial cellulase preparations, Novozymes Cellic® Ctec2, Dupont Accellerase® 1500, and DSM Cytolase CL, were evaluated for their hydrolytic activity using a set of reference biomass substrates with controlled substrate characteristics. It was found that lignin remains a significant recalcitrance factor to all the preparations, although different enzyme preparations respond to the inhibitory effect of lignin differently. Also, different types of biomass lignin can inhibit cellulose enzymes in different manners. Enhancing enzyme activity toward biomass fiber swelling is an area significantly contributing to potential improvement in cellulose performance. While the degree of polymerization of cellulose in the reference substrates did not present a major recalcitrance factor to Novozymes Cellic® Ctec2, cellulose crystallite has been shown to have a significant lower reactivity toward all enzyme mixtures. The presence of polysaccharide monooxygenases (PMOs) in Novozymes Ctec2 appears to enhance enzyme activity toward decrystallization of cellulose. This study demonstrated that reference substrates with controlled chemical and physical characteristics of structural features can be applied as an effective and practical strategy to identify cellulosic enzyme activities toward specific biomass recalcitrance factor(s) and provide specific targets for enzyme improvement.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2026

Input specific neural networks

Neural networks have emerged as powerful tools for mapping between inputs and outputs. However, their black-box nature limits the ability to encode or impose specific structural relationships between inputs and outputs. Many scientific and engineering problems, such as constitutive modeling in solid mechanics, require networks that can enforce convexity, monotonicity, or other structural constraints to ensure physical consistency. Here, we introduce the Input Specific Neural Network (ISNN), a new architecture that enables multiple, distinct constraints to be imposed on different input subsets for scalar-valued outputs. This framework unifies convex, monotone–convex, monotone, and arbitrary mappings within a single network for the first time. Two ISNN architectures with analytical first- and second-order derivatives are developed. We demonstrate the performance on synthetic toy problems, inverse problems in isotropic hyperelasticity, and finite element simulations. ISNNs achieve improved extrapolation behavior, require fewer invariant inputs than standard input convex networks for polyconvex potentials, and enable significant computational savings via manual differentiation. We also show how ISNNs can be used to learn structural relationships between inputs and outputs via a binary gating mechanism. Particularly, ISNNs are employed to model a homogenized anisotropic free energy potential in a decoupled multiscale setting. The network learns whether or not the potential should be modeled as polyconvex and retains only the relevant layers while using the minimum number of inputs. ISNNs provide a flexible foundation for embedding structural priors into neural networks, enhancing both interpretability and stability. They are broadly applicable across computational mechanics and other scientific domains requiring constrained functional relationships.

Jadoon, Asghar A. [Univ. of Texas, Austin, TX (Uni↗
DOE OSTI2017

New fructan — the O-specific polysaccharide from Escherichia coli O92

The structure of the O-specific polysaccharide (O-antigen) from Escherichia coli O92 was established. The acid-labile polysaccharide was produced by O-deacylation of the lipopolysaccharide under mild alkaline conditions. The methylation analysis combined with 1D and 2D {sup 1}H and {sup 13}C NMR spectroscopy demonstrated that the O-specific polysaccharide chain of the lipopolysaccharide is a linear fructan composed of mono-О-acetylated disaccharide repeating units having the structure →1)-β-D-Fruf3Ac-(2→3)-β-D-Fruf-(2→. To the best of our knowledge, this fructan has been hitherto unknown in bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Tissue-specific differences in metabolites and transcripts contribute to the heterogeneity of ricinoleic acid accumulation in Ricinus communis L. (castor) seeds

Castor ( Ricinus communis L.) seeds are valued for their production of oils which can comprise up to 90% hydroxy-fatty acids (ricinoleic acid). Castor oil contains mono-, di- and tri- ricinoleic acid containing triacylglycerols (TAGs). Although the enzymatic synthesis of ricinoleic acid is well described, the differential compartmentalization of these TAG molecular species has remained undefined. To examine the distribution of hydroxy fatty acid accumulation within the endosperm and embryo tissues of castor seeds. Matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was used to map the distribution of triacylglycerols in tissue sections of castor seeds. In addition, the endosperm and embryo (cotyledons and embryonic axis) tissues were dissected and extracted for quantitative lipidomics analysis and Illumina-based RNA deep sequencing. Results: This study revealed an unexpected heterogeneous tissue distribution of mono-, di- and tri- hydroxy-triacylglycerols in the embryo and endosperm tissues of castor seeds. Pathway analysis based on transcript abundance suggested that distinct embryo- and endosperm-specific mechanisms may exist for the shuttling of ricinoleic acid away from phosphatidylcholine (PC) and into hydroxy TAG production. The embryo-biased mechanism appears to favor removal of ricinoleic acid from PC through phophatidylcholine: diacylglycerol acylytransferase (PDAT) while the endosperm pathway appears to remove ricinoleic acid from the PC pool by preferences of phospholipase A (PLA 2 α) and/or phosphatidylcholine: diacylglycerol cholinepshphotransferase PDCT. In conclusion, collectively, a combination of lipidomics and transcriptomics analyses revealed previously undefined spatial aspects of hydroxy fatty acid metabolism in castor seeds. These studies underscore a need for tissue-specific studies as a means to better understand the regulation of triacylglycerol accumulation in oilseeds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Transseptal Puncture: Devices, Techniques, and Considerations for Specific Interventions

Purpose of Review: Transseptal puncture is a routinely performed interventional cardiology procedure for an array of cardiac diseases. We aimed to review the current status of available devices and techniques of transseptal puncture with consideration to specific interventions. Recent Findings: Except for a few modifications, devices for transseptal puncture technique has not changed much compared to when it was first described almost 60 years ago. For difficult transseptal puncture, a few newer techniques such as radio frequency needle puncture system have been used but there is lack of robust clinical study. Advanced imaging, such as intracardiac echocardiography and transesophageal echocardiography, has been found to make transseptal puncture safer. A new transseptal approach that incorporates 3D non-fluoroscopic catheter tracking systems has shown promising results in two human studies. Summary: While various modifications in the transseptal technique tailored to the specific interventions have improved procedural safety, further improvement in existing devices focusing on distinct procedure might be needed in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Impact of non-specific normal databases on perfusion quantification of low-dose myocardial SPECT studies

Aim: To evaluate the impact of non-specific normal databases on the percent summed rest score (SR%) and stress score (SS%) from simulated low-dose SPECT studies by shortening the acquisition time/projection. Methods: Forty normal-weight and 40 overweight/obese patients underwent myocardial studies with a conventional gamma-camera (BrightView, Philips) using three different acquisition times/projection: 30, 15, and 8 s (100%-counts, 50%-counts, and 25%-counts scan, respectively) and reconstructed using the iterative algorithm with resolution recovery (IRR) Astonish{sup TM} (Philips). Three sets of normal databases were used: (1) full-counts IRR; (2) half-counts IRR; and (3) full-counts traditional reconstruction algorithm database (TRAD). The impact of these databases and the acquired count statistics on the SR% and SS% was assessed by ANOVA analysis and Tukey test (P < 0.05). Results: Significantly higher SR% and SS% values (> 40%) were found for the full-counts TRAD databases respect to the IRR databases. For overweight/obese patients, significantly higher SS% values for 25%-counts scans (+19%) are confirmed compared to those of 50%-counts scan, independently of using the half-counts or the full-counts IRR databases. Conclusions: Astonish{sup TM} requires the adoption of the own specific normal databases in order to prevent very high overestimation of both stress and rest perfusion scores. Conversely, the count statistics of the normal databases seems not to influence the quantification scores.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Development of performance specifications for hybrid modeling of floating wind turbines in wave basin tests

Hybrid modeling—combining physical testing and numerical simulation in real time$-$opens new opportunities in floating wind turbine research. Wave basin testing is an important validation step for floating support structure design, but the conventional approaches that use physical wind above the basin are limited by scaling problems in the aerodynamics. Applying wind turbine loads with an actuation system that is controlled by a simulation responding to the basin test in real time offers a way to avoid scaling problems and reduce cost barriers for floating wind turbine design validation in realistic coupled wind and wave conditions. This paper demonstrates the development of performance specifications for a system that couples a wave basin experiment with a wind turbine simulation. Two different points for the hybrid coupling are considered: the tower-base interface and the aero-rotor interface (the boundary between aerodynamics and the rotor structure). Analyzing simulations of three floating wind turbine designs across seven load cases reveals the motion and force requirements of the coupling system. By simulating errors in the hybrid coupling system, the sensitivity of the floating wind turbine response to coupling quality can be quantified. The sensitivity results can then be used to determine tolerances for motion tracking errors, force actuation errors, bandwidth limitations, and latency in the hybrid coupling system. These tolerances can guide the design of hybrid coupling systems to achieve desired levels of accuracy. An example demonstrates how the developed methods can be used to generate performance specifications for a system at 1:50 scale. Results show that sensitivities vary significantly between support structure designs and that coupling at the aero-rotor interface has less stringent requirements than those for coupling at the tower base. As a result, the methods and results presented here can inform design of future hybrid coupling systems and enhance understanding of how test results are affected by hybrid coupling quality.

16 TIDAL AND WAVE POWER↗
DOE OSTI2016

Specific features of defect and mass transport in concentrated fcc alloys

We report that diffusion and mass transport are basic properties that control materials performance, such as phase stability, solute decomposition and radiation tolerance. While understanding diffusion in dilute alloys is a mature field, concentrated alloys are much less studied. Here, atomic-scale diffusion and mass transport via vacancies and interstitial atoms are compared in fcc Ni, Fe and equiatomic Ni-Fe alloy. High temperature properties were determined using conventional molecular dynamics on the microsecond timescale, whereas the kinetic activation-relaxation (k-ART) approach was applied at low temperatures. The k-ART was also used to calculate transition states in the alloy and defect transport coefficients. The calculations reveal several specific features. For example, vacancy and interstitial defects migrate via different alloy components, diffusion is more sluggish in the alloy and, notably, mass transport in the concentrated alloy cannot be predicted on the basis of diffusion in its pure metal counterparts. Lastly, the percolation threshold for the defect diffusion in the alloy is discussed and it is suggested that this phenomenon depends on the properties and diffusion mechanisms of specific defects.

36 MATERIALS SCIENCE↗
DOE OSTI2023

DISCOVR strain pipeline screening – Part I: Maximum specific growth rate as a function of temperature and salinity for 38 candidate microalgae for biofuels production

Here, to identify high productivity strains for microalgal biofuels generation, the maximum specific growth rate of 38 strains was measured as a function of salinity (i.e., 5, 15, and 35 PSU) and temperature (i.e., at 8 temperatures along a linear gradient from ca. 5 to 45°C) to determine the most suitable growth medium salinity and best growing season, respectively, for outdoor raceway pond cultivation. The following strains were evaluated: Agmenellum quadruplicatum UTEX 2268, Anabaena sp. ATCC 33081, Arthrospira fusiformis UTEX 2721, Arthrospira platensis UTEX 3086, Chlorella vulgaris NREL 4-C12, Chlorella autotrophica CCMP 243, Chlorella sorokiniana DOE1044, Chlorella sorokiniana DOE 1116, Chlorella sorokiniana DOE 1412 (UTEXB3016), Chlorella vulgaris LRB AZ-1201, Chlorococcum littorale UTEX 117, Chlorococcum sp. UTEX-B P7, Chloromonas reticulata CCALA 870, Coelastrella sp. DOE 0202, Cyanobacterium sp. AB1, Micractinium reisseri NREL 14-F2, Microchloropsis gaditana CCMP1894, Microchloropsis salina CCMP 1776, Monoraphidium sp. MONOR1, Monoraphidium minutum 26B-AM, Nannochloropsis oceanica CCAP 849/10, Oscillatoria cf. priestleyi CCMEE 5020.1-1, Picochlorum celeri TG2-WT-CSM/EMRE, Picochlorum oklahomensis CCMP 2329, Picochlorum renovo NREL 39-A8, Picochlorum soloecismus DOE 101, Porphyridium cruentum CCMP 675, Scenedesmus acutus LRB-AP-0401, Scenedesmus obliquus DOE 0152.z, Scenedesmus obliquus UTEX393,Scenedesmus rubescens NREL 46B-D3, Scenedesmus sp. IITRIND2, Stichococcus minor CCMP 819, Stichococcus minutus CCALA 727, Synechococcus elongatus UTEX2973.1, Tetraselmis striata LANL 1001, Tisochrysis lutea CCMP 1324, and Tribonema minus UTEXB3156. For each strain, the identity and the presence of bacterial cohorts was determined using 18S and 16S rDNA sequencing, respectively. The maximum specific growth rate versus temperature data were also used to determine the activation energies (Arrhenius equation) for most strains. For all strains, the measured salinity and temperature tolerance data were compared to those reported in the literature. The fastest growing strains were down-selected for subsequent biomass productivity measurements in climate-simulation photobioreactors, as reported in the next paper in the issue.

18S and 16S rDNA sequencing↗
DOE OSTI2017

Automated cassette-based production of high specific activity [ 203/212 Pb]peptide-based theranostic radiopharmaceuticals for image-guided radionuclide therapy for cancer

A method for preparation of Pb-212 and Pb-203 labeled chelator-modified peptide-based radiopharmaceuticals for cancer imaging and radionuclide therapy has been developed and adapted for automated clinical production. Pre-concentration and isolation of radioactive Pb2+ from interfering metals in dilute hydrochloric acid was optimized using a commercially-available Pb-specific chromatography resin packed in disposable plastic columns. The pre-concentrated radioactive Pb2+ is eluted in NaOAc buffer directly to the reaction vessel containing chelator-modified peptides. Radiolabeling was found to proceed efficiently at 85 °C (45 min; pH 5.5). The specific activity of radiolabeled conjugates was optimized by separation of radiolabeled conjugates from unlabeled peptide via HPLC. Preservation of bioactivity was confirmed by in vivo biodistribution of Pb-203 and Pb-212 labeled peptides in melanoma-tumor-bearing mice. The approach has been found to be robustly adaptable to automation and a cassette-based fluid-handling system (Modular Lab Pharm Tracer) has been customized for clinical radiopharmaceutical production. Our findings demonstrate that the Pb-203/Pb-212 combination is a promising elementally-matched radionuclide pair for image-guided radionuclide therapy for melanoma, neuroendocrine tumors, and potentially other cancers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Ubiquitination and degradation of the hominoid-specific oncoprotein TBC1D3 is regulated by protein palmitoylation

Highlights: •Hominoid-specific oncogene TBC1D3 is targeted to plasma membrane by palmitoylation. •TBC1D3 is palmitoylated on two cysteine residues: 318 and 325. •TBC1D3 palmitoylation governs growth factors-induced TBC1D3 degradation. •Post-translational modifications may regulate oncogenic properties of TBC1D3. -- Abstract: Expression of the hominoid-specific oncoprotein TBC1D3 promotes enhanced cell growth and proliferation by increased activation of signal transduction through several growth factors. Recently we documented the role of CUL7 E3 ligase in growth factors-induced ubiquitination and degradation of TBC1D3. Here we expanded our study to discover additional molecular mechanisms that control TBC1D3 protein turnover. We report that TBC1D3 is palmitoylated on two cysteine residues: 318 and 325. The expression of double palmitoylation mutant TBC1D3:C318/325S resulted in protein mislocalization and enhanced growth factors-induced TBC1D3 degradation. Moreover, ubiquitination of TBC1D3 via CUL7 E3 ligase complex was increased by mutating the palmitoylation sites, suggesting that depalmitoylation of TBC1D3 makes the protein more available for ubiquitination and degradation. The results reported here provide novel insights into the molecular mechanisms that govern TBC1D3 protein degradation. Dysregulation of these mechanisms in vivo could potentially result in aberrant TBC1D3 expression and promote oncogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Canonical Wnts, specifically Wnt-10b, show ability to maintain dermal papilla cells

Highlights: •First report on effects of various Wnts on DP cells. •Wnt-10b promoted trichogenesis, while Wnt-3a showed to a limited extent. •Canonical Wnts, specifically Wnt-10b, is important for DP cells maintenance. -- Abstract: Although Wnts are expressed in hair follicles (HFs) and considered to be crucial for maintaining dermal papilla (DP) cells, the functional differences among them remain largely unknown. In the present study, we investigated the effects of Wnts (Wnt-3a, 5a, 10b, 11) on the proliferation of mouse-derived primary DP cells in vitro as well as their trichogenesis-promoting ability using an in vivo skin reconstitution protocol. Wnt-10b promoted cell proliferation and trichogenesis, while Wnt-3a showed those abilities to a limited extent, and Wnt-5a and 11 had no effects. Furthermore, we investigated the effects of these Wnts on cultured DP cells obtained from versican-GFP transgenic mice and found that Wnt-10b had a potent ability to sustain their GFP-positivity. These results suggest that canonical Wnts, specifically Wnt-10b, play important roles in the maintenance of DP cells and trichogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

21-Methylpyrenyl-cholesterol stably and specifically associates with lipoprotein peripheral hemi-membrane: A new labelling tool

Highlights: •21-Methylpyrenyl-cholesterol specifically and stably associates to lipoproteins. •It is not esterified by LCAT, and thus reliably labels their peripheral hemi-membrane. •HDL vs. LDL are well distinguishable by various fluorescent labelling characteristics. •LDL peripheral hemi-membrane harbors cholesterol-rich ordered lipid (micro)domains. •Cultured cells can be stained by such labelled lipoproteins-mediated delivery. -- Abstract: Lipoproteins are important biological components. However, they have few convenient fluorescent labelling probes currently reported, and their physiological reliability can be questioned. We compared the association of two fluorescent cholesterol derivatives, 22-nitrobenzoxadiazole-cholesterol (NBD-Chol) and 21-methylpyrenyl-cholesterol (Pyr-met-Chol), to serum lipoproteins and to purified HDL and LDL. Both lipoproteins could be stably labelled by Pyr-met-Chol, but virtually not by NBD-Chol. At variance with NBD-Chol, LCAT did not esterify Pyr-met-Chol. The labelling characteristics of lipoproteins by Pyr-met-Chol were well distinguishable between HDL and LDL, regarding dializability, associated probe amount and labelling kinetics. We took benefit of the pyrene labelling to approach the structural organization of LDL peripheral hemi-membrane, since Pyr-met-Chol-labelled LDL, but not HDL, presented a fluorescence emission of pyrene excimers, indicating that the probe was present in an ordered lipid micro-environment. Since the peripheral membrane of LDL contains more sphingomyelin (SM) than HDL, this excimer formation was consistent with the existence of cholesterol- and SM-enriched lipid microdomains in LDL, as already suggested in model membranes of similar composition and reminiscent to the well-described “lipid rafts” in bilayer membranes. Finally, we showed that Pyr-met-Chol could stain cultured PC-3 cells via lipoprotein-mediated delivery, with a staining pattern well different to that observed with NBD-Chol non-specifically delivered to the cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

The Ca{sup 2+} channel TRPML3 specifically interacts with the mammalian ATG8 homologue GATE16 to regulate autophagy

Highlights: •Split-ubiquitin MY2H screen identified GATE16 as an interacting protein of TRPML3. •TRPML3 specifically binds to a mammalian ATG8 homologue GATE16, not to LC3B. •The interaction of TRPML3 with GATE16 facilitates autophagosome formation. •GATE16 is expressed in both autophagosome and extra-autophagosomal compartments. -- Abstract: TRPML3 is a Ca{sup 2+} permeable cation channel expressed in multiple intracellular compartments. Although TRPML3 is implicated in autophagy, how TRPML3 can regulate autophagy is not understood. To search interacting proteins with TRPML3 in autophagy, we performed split-ubiquitin membrane yeast two-hybrid (MY2H) screening with TRPML3-loop as a bait and identified GATE16, a mammalian ATG8 homologue. GST pull-down assay revealed that TRPML3 and TRPML3-loop specifically bind to GATE16, not to LC3B. Co-immunoprecipitation (co-IP) experiments showed that TRPML3 and TRPML3-loop pull down only the lipidated form of GATE16, indicating that the interaction occurs exclusively at the organellar membrane. The interaction of TRPML3 with GATE16 and GATE16-positive vesicle formation were increased in starvation induced autophagy, suggesting that the interaction facilitates the function of GATE16 in autophagosome formation. However, GATE16 was not required for TRPML3 trafficking to autophagosomes. Experiments using dominant-negative (DN) TRPML3(D458K) showed that GATE16 is localized not only in autophagosomes but also in extra-autophagosomal compartments, by contrast with LC3B. Since GATE16 acts at a later stage of the autophagosome biogenesis, our results suggest that TRPML3 plays a role in autophagosome maturation through the interaction with GATE16, by providing Ca{sup 2+} in the fusion process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K{sub d} 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K{sub d} 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy.

60 APPLIED LIFE SCIENCES↗