Selection of an optimal cysteine-containing peptide-based chelator for labeling of affibody molecules with (188)Re.

PubMed

Altai, Mohamed; Honarvar, Hadis; Wållberg, Helena; Strand, Joanna; Varasteh, Zohreh; Rosestedt, Maria; Orlova, Anna; Dunås, Finn; Sandström, Mattias; Löfblom, John; Tolmachev, Vladimir; Ståhl, Stefan

2014-11-24

Affibody molecules constitute a class of small (7 kDa) scaffold proteins that can be engineered to have excellent tumor targeting properties. High reabsorption in kidneys complicates development of affibody molecules for radionuclide therapy. In this study, we evaluated the influence of the composition of cysteine-containing C-terminal peptide-based chelators on the biodistribution and renal retention of (188)Re-labeled anti-HER2 affibody molecules. Biodistribution of affibody molecules containing GGXC or GXGC peptide chelators (where X is G, S, E or K) was compared with biodistribution of a parental affibody molecule ZHER2:2395 having a KVDC peptide chelator. All constructs retained low picomolar affinity to HER2-expressing cells after labeling. The biodistribution of all (188)Re-labeled affibody molecules was in general comparable, with the main observed difference found in the uptake and retention of radioactivity in excretory organs. The (188)Re-ZHER2:V2 affibody molecule with a GGGC chelator provided the lowest uptake in all organs and tissues. The renal retention of (188)Re-ZHER2:V2 (3.1 ± 0.5 %ID/g at 4 h after injection) was 55-fold lower than retention of the parental (188)Re-ZHER2:2395 (172 ± 32 %ID/g). We show that engineering of cysteine-containing peptide-based chelators can be used for significant improvement of biodistribution of (188)Re-labeled scaffold proteins, particularly reduction of their uptake in excretory organs. Copyright © 2014 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Collison-Induced Absorption of Oxygen Molecule as Studied by High Sensitivity Spectroscopy

NASA Astrophysics Data System (ADS)

Kashihara, Wataru; Shoji, Atsushi; Kawai, Akio

2017-06-01

Oxygen dimol is transiently generated when two oxygen molecules collide. At this short period, the electron clouds of molecules are distorted and some forbidden transition electronic transitions become partially allowed. This transition is called CIA (Collision-induced absorption). There are several CIA bands appearing in the spectral region from UV to near IR. Absorption of solar radiation by oxygen dimol is a small but significant part of the total budget of incoming shortwave radiation. However, a theory predicting the lineshape of CIA is still under developing. In this study, we measured CIA band around 630 nm that is assigned to optical transition, a^{1}Δ_{g}(v=0):a^{1}Δ_{g}(v=0)-X^{3}Σ_{g}^{-}(v=0):X^{3}Σ_{g}^{-}(v=0) of oxygen dimol. CRDS(Cavity Ring-down Spectroscopy) was employed to measure weak absorption CIA band of oxygen. Laser beam around 630 nm was generated by a dye laser that was pumped by a YAG Laser. Multiple reflection of the probe light was performed within a vacuum chamber that was equipped with two high reflective mirrors. We discuss the measured line shape of CIA on the basis of collision pair model.

Reactive oxygen species, essential molecules, during plant-pathogen interactions.

PubMed

Camejo, Daymi; Guzmán-Cedeño, Ángel; Moreno, Alexander

2016-06-01

Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications

PubMed Central

Scheler, Ott; Glynn, Barry; Parkel, Sven; Palta, Priit; Toome, Kadri; Kaplinski, Lauris; Remm, Maido; Maher, Majella; Kurg, Ants

2009-01-01

Background Here we present a novel promising microbial diagnostic method that combines the sensitivity of Nucleic Acid Sequence Based Amplification (NASBA) with the high information content of microarray technology for the detection of bacterial tmRNA molecules. The NASBA protocol was modified to include aminoallyl-UTP (aaUTP) molecules that were incorporated into nascent RNA during the NASBA reaction. Post-amplification labeling with fluorescent dye was carried out subsequently and tmRNA hybridization signal intensities were measured using microarray technology. Significant optimization of the labeled NASBA protocol was required to maintain the required sensitivity of the reactions. Results Two different aaUTP salts were evaluated and optimum final concentrations were identified for both. The final 2 mM concentration of aaUTP Li-salt in NASBA reaction resulted in highest microarray signals overall, being twice as high as the strongest signals with 1 mM aaUTP Na-salt. Conclusion We have successfully demonstrated efficient combination of NASBA amplification technology with microarray based hybridization detection. The method is applicative for many different areas of microbial diagnostics including environmental monitoring, bio threat detection, industrial process monitoring and clinical microbiology. PMID:19445684

High Throughput, Label-free Screening Small Molecule Compound Libraries for Protein-Ligands using Combination of Small Molecule Microarrays and a Special Ellipsometry-based Optical Scanner.

PubMed

Landry, James P; Fei, Yiyan; Zhu, X D

2011-12-01

Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.

Copper-catalyzed oxidative desulfurization-oxygenation of thiocarbonyl compounds using molecular oxygen: an efficient method for the preparation of oxygen isotopically labeled carbonyl compounds.

PubMed

Shibahara, Fumitoshi; Suenami, Aiko; Yoshida, Atsunori; Murai, Toshiaki

2007-06-21

A novel copper-catalyzed oxidative desulfurization reaction of thiocarbonyl compounds, using molecular oxygen as an oxidant and leading to formation of carbonyl compounds, has been developed, and the utility of the process is demonstrated by its application to the preparation of a carbonyl-18O labeled sialic acid derivative.

Evaluation of a maleimido derivative of CHX-A” DTPA for site-specific labeling of Affibody molecules

PubMed Central

Tolmachev, Vladimir; Xu, Heng; Wållberg, Helena; Ahlgren, Sara; Hjertman, Magnus; Sjöberg, Anna; Sandström, Mattias; Abrahmsén, Lars; Brechbiel, Martin W.; Orlova, Anna

2008-01-01

Affibody molecules are a new class of small targeting proteins based on a common threehelix bundle structure. Affibody molecules binding a desired target may be selected using phage-display technology. An Affibody molecule ZHER2:342 binding with subnanomolar affinity to the tumor antigen HER2 has recently been developed for radionuclide imaging in vivo. Introduction of a single cysteine into the cysteine-free Affibody scaffold provides a unique thiol group for site-specific labeling of recombinant Affibody molecules. The recently developed maleimido-CHX-A” DTPA was site-specifically conjugated at the C-terminal cysteine of ZHER2:2395-C, a variant of ZHER2:342, providing a homogenous conjugate with a dissociation constant of 56 pM. The yield of labeling with 111In was > 99% after 10 min at room temperature. In vitro cell tests demonstrated specific binding of 111In-CHX-A” DTPAZ2395-C to HER2-expressing cell-line SKOV-3 and good cellular retention of radioactivity. In normal mice, the conjugate demonstrated rapid clearance from all non-specific organs except kidney. In mice bearing SKOV-3 xenografts, the tumor uptake of 111In-CHX-A” DTPAZ2395-C was 17.3 ± 4.8 % IA/g and the tumor-to-blood ratio 86 ± 46 (4 h post-injection). HER2-exprssing xenografts were clearly visualized 1 h post-injection. In conclusion, coupling of maleimido-CHX-A” DTPA to cysteine-containing Affibody molecules provides welldefined uniform conjugate, which can be rapidly labeled at room temperature and provides high-contrast imaging of molecular targets in vivo. PMID:18620447

The study of excited oxygen molecule gas species production and quenching on thermal protection system materials

NASA Technical Reports Server (NTRS)

Nordine, Paul C.; Fujimoto, Gordon T.; Greene, Frank T.

1987-01-01

The detection of excited oxygen and ozone molecules formed by surface catalyzed oxygen atom recombination and reaction was investigated by laser induced fluorescence (LIF), molecular beam mass spectrometric (MBMS), and field ionization (FI) techniques. The experiment used partially dissociated oxygen flows from a microwave discharge at pressures in the range from 60 to 400 Pa or from an inductively coupled RF discharge at atmospheric pressure. The catalyst materials investigated were nickel and the reaction cured glass coating used for Space Shuttle reusable surface insulation tiles. Nonradiative loss processes for the laser excited states makes LIF detection of O2 difficult such that formation of excited oxygen molecules could not be detected in the flow from the microwave discharge or in the gaseous products of atom loss on nickel. MBMS experiments showed that ozone was a product of heterogeneous O atom loss on nickel and tile surfaces at low temperatures and that ozone is lost on these materials at elevated temperatures. FI was separately investigated as a method by which excited oxygen molecules may be conveniently detected. Partial O2 dissociation decreases the current produced by FI of the gas.

DETECTION OF WHOLE BODY OXIDATIVE STRESS IN URINE USING OXYGEN-18 LABELING

EPA Science Inventory

DETECTION OF WHOLE BODY OXIDATIVE STRESS IN URINE USING OXYGEN-18 LABELING. R Slade, J L McKee and G E Hatch. PTB, ETD, NHEERL, ORD, USEPA, Research Triangle Park, NC, USA.
Reliable non-invasive markers for detecting oxidative stress in vivo are currently not available. We pr...

Oxygen-doped carbon nanotubes for near-infrared fluorescent labels and imaging probes.

PubMed

Iizumi, Yoko; Yudasaka, Masako; Kim, Jaeho; Sakakita, Hajime; Takeuchi, Tsukasa; Okazaki, Toshiya

2018-04-19

Chemical modification of carbon nanotube surface can controllably modulate their optical properties. Here we report a simple and effective synthesis method of oxygen-doped single-walled carbon nanotubes (o-SWCNTs), in which a thin film of SWCNTs is just irradiated under the UV light for a few minutes in air. By using this method, the epoxide-type oxygen-adducts (ep-SWCNTs) were produced in addition to the ether-type oxygen-adducts (eth-SWCNTs). The Treated (6, 5) ep-SWCNTs show a red-shifted luminescence at ~1280 nm, which corresponds to the most transparent regions for bio-materials. Immunoassay, fluorescence vascular angiography and observation of the intestinal contractile activity of mice were demonstrated by using the produced o-SWCNTs as infrared fluorescent labels and imaging agents.

Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.

Quantum chemical calculations were employed to model the interactions of the [(NH 4 +) 4(HSO 4 -) 4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH 4 +) 4(SOmore » 4 -) 4] cluster, is able to adsorb an oxygenated organic molecule. Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.« less

Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

DOE PAGES

DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.; ...

2015-10-21

Quantum chemical calculations were employed to model the interactions of the [(NH 4 +) 4(HSO 4 -) 4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH 4 +) 4(SOmore » 4 -) 4] cluster, is able to adsorb an oxygenated organic molecule. Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.« less

Four-color single-molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes.

PubMed

DeRocco, Vanessa; Anderson, Trevor; Piehler, Jacob; Erie, Dorothy A; Weninger, Keith

2010-11-01

To enable studies of conformational changes within multimolecular complexes, we present a simultaneous, four-color single molecule fluorescence methodology implemented with total internal reflection illumination and camera-based, wide-field detection. We further demonstrate labeling histidine-tagged proteins noncovalently with Tris-nitrilotriacetic acid (Tris-NTA)-conjugated dyes to achieve single molecule detection. We combine these methods to colocalize the mismatch repair protein MutSα on DNA while monitoring MutSα-induced DNA bending using Förster resonance energy transfer (FRET) and to monitor assembly of membrane-tethered SNARE protein complexes.

Four-color single molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes

PubMed Central

DeRocco, Vanessa C.; Anderson, Trevor; Piehler, Jacob; Erie, Dorothy A.; Weninger, Keith

2010-01-01

To allow studies of conformational changes within multi-molecular complexes, we present a simultaneous, 4-color single molecule fluorescence methodology implemented with total internal reflection illumination and camera based, wide-field detection. We further demonstrate labeling histidine-tagged proteins non-covalently with tris-Nitrilotriacetic acid (tris-NTA) conjugated dyes to achieve single molecule detection. We combine these methods to co-localize the mismatch repair protein MutSα on DNA while monitoring MutSα-induced DNA bending using Förster resonance energy transfer (FRET) and to monitor assembly of membrane-tethered SNARE protein complexes. PMID:21091445

Label-free optical imaging of nonfluorescent molecules by stimulated radiation.

PubMed

Min, Wei

2011-12-01

Imaging contrasts other than fluorescence are highly desirable for label-free detection and interrogation of nonfluorescent molecular species inside live cells, tissues, and organisms. The recently developed stimulated Raman scattering (SRS) and stimulated emission microscopy techniques provide sensitive and specific contrast mechanisms for nonfluorescent species, by employing the light amplification aspect of stimulated radiation. Compared to their spontaneous counterparts, stimulated radiation can enhance the imaging performance significantly, making the previously 'dark' molecules observable. Here we review and summarize the underlying principles of this emerging class of molecular imaging techniques. Copyright © 2011 Elsevier Ltd. All rights reserved.

Label-free detection of protein molecules secreted from an organ-on-a-chip model for drug toxicity assays

NASA Astrophysics Data System (ADS)

Morales, Andres W.; Zhang, Yu S.; Aleman, Julio; Alerasool, Parissa; Dokmeci, Mehmet R.; Khademhosseini, Ali; Ye, Jing Yong

2016-03-01

Clinical attrition is about 30% from failure of drug candidates due to toxic side effects, increasing the drug development costs significantly and slowing down the drug discovery process. This partly originates from the fact that the animal models do not accurately represent human physiology. Hence there is a clear unmet need for developing drug toxicity assays using human-based models that are complementary to traditional animal models before starting expensive clinical trials. Organ-on-a-chip techniques developed in recent years have generated a variety of human organ models mimicking different human physiological conditions. However, it is extremely challenging to monitor the transient and long-term response of the organ models to drug treatments during drug toxicity tests. First, when an organ-on-a-chip model interacts with drugs, a certain amount of protein molecules may be released into the medium due to certain drug effects, but the amount of the protein molecules is limited, since the organ tissue grown inside microfluidic bioreactors have minimum volume. Second, traditional fluorescence techniques cannot be utilized for real-time monitoring of the concentration of the protein molecules, because the protein molecules are continuously secreted from the tissue and it is practically impossible to achieve fluorescence labeling in the dynamically changing environment. Therefore, direct measurements of the secreted protein molecules with a label-free approach is strongly desired for organs-on-a-chip applications. In this paper, we report the development of a photonic crystal-based biosensor for label-free assays of secreted protein molecules from a liver-on-a-chip model. Ultrahigh detection sensitivity and specificity have been demonstrated.

Surface Chemical Conversion of Organosilane Self-Assembled Monolayers with Active Oxygen Species Generated by Vacuum Ultraviolet Irradiation of Atmospheric Oxygen Molecules

NASA Astrophysics Data System (ADS)

Kim, Young-Jong; Lee, Kyung-Hwang; Sano, Hikaru; Han, Jiwon; Ichii, Takashi; Murase, Kuniaki; Sugimura, Hiroyuki

2008-01-01

The chemical conversion of the top surface of n-octadecyltrimethoxy silane self-assembled monolayers (ODS-SAMs) on oxide-covered Si substrates using active oxygen species generated from atmospheric oxygen molecules irradiated with vacuum ultraviolet (VUV) light at 172 nm in wavelength has been studied on the basis of water contact angle measurements, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy. An ODS-SAM whose water contact angle was 104° on average was prepared using chemical vapor deposition with substrate and vapor temperatures of 150 °C. The VUV treatment of an ODS-SAM sample was carried out by placing the sample in air and then irradiating the sample surface with a Xe-excimer lamp. The distance between the lamp and the sample was regulated so that the VUV light emitted from the lamp was almost entirely absorbed by atmospheric oxygen molecules to generate active oxygen species, such as ozone and atomic oxygen before reaching the sample surface. Hence, the surface chemical conversion of the ODS-SAM was primarily promoted through chemical reactions with the active oxygen species. Photochemical changes in the ODS-SAM were found to be the generation of polar functional groups, such as -COOH, -CHO, and -OH, on the surface and the subsequent etching of the monolayer. Irradiation parameters, such as irradiation time, were optimized to achieve a better functionalization of the SAM top surface while minimizing the etching depth of the ODS-SAM. The ability to graft another SAM onto the modified ODS-SAM bearing polar functional groups was demonstrated by the formation of alkylsilane bilayers.

Light-Driven Nano-oscillators for Label-Free Single-Molecule Monitoring of MicroRNA.

PubMed

Chen, Zixuan; Peng, Yujiao; Cao, Yue; Wang, Hui; Zhang, Jian-Rong; Chen, Hong-Yuan; Zhu, Jun-Jie

2018-06-13

Here, we present a mapping tool based on individual light-driven nano-oscillators for label-free single-molecule monitoring of microRNA. This design uses microRNA as a single-molecule damper for nano-oscillators by forming a rigid dual-strand structure in the gap between nano-oscillators and the immobilized surface. The ultrasensitive detection is attributed to comparable dimensions of the gap and microRNA. A developed surface plasmon-coupled scattering imaging technology enables us to directly measure the real-time gap distance vibration of multiple nano-oscillators with high accuracy and fast dynamics. High-level and low-level states of the oscillation amplitude indicate melting and hybridization statuses of microRNA. Lifetimes of two states reveal that the hybridization rate of microRNA is determined by the three-dimensional diffusion. This imaging technique contributes application potentials in a single-molecule detection and nanomechanics study.

Lysozyme oxidation by singlet molecular oxygen: Peptide characterization using [18 O]-labeling oxygen and nLC-MS/MS.

PubMed

Marques, Emerson Finco; Medeiros, Marisa H G; Di Mascio, Paolo

2017-11-01

Singlet molecular oxygen ( 1 O 2 ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for 1 O 2 , and His, Tyr, Met, Cys, and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by 1 O 2 was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine, and tryptophan oxidation. The experiments were achieved using [ 18 O]-labeled 1 O 2 released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry. The structural characterization by nLC-MS/MS of the amino acids in the tryptic peptides of the proteins showed addition of [ 18 O]-labeling atoms in different amino acids. Copyright © 2017 John Wiley & Sons, Ltd.

Comparative Evaluation of Anti-HER2 Affibody Molecules Labeled with 64Cu Using NOTA and NODAGA

PubMed Central

Yim, Cheng-Bin; Rajander, Johan; Perols, Anna; Karlström, Amelie Eriksson; Haaparanta-Solin, Merja; Grönroos, Tove J.; Solin, Olof; Orlova, Anna

2017-01-01

Imaging using affibody molecules enables discrimination between breast cancer metastases with high and low expression of HER2, making appropriate therapy selection possible. This study aimed to evaluate if the longer half-life of 64Cu (T1/2 = 12.7 h) would make 64Cu a superior nuclide compared to 68Ga for PET imaging of HER2 expression using affibody molecules. The synthetic ZHER2:S1 affibody molecule was conjugated with the chelators NOTA or NODAGA and labeled with 64Cu. The tumor-targeting properties of 64Cu-NOTA-ZHER2:S1 and 64Cu-NODAGA-ZHER2:S1 were evaluated and compared with the targeting properties of 68Ga-NODAGA-ZHER2:S1 in mice. Both 64Cu-NOTA-ZHER2:S1 and 64Cu-NODAGA-ZHER2:S1 demonstrated specific targeting of HER2-expressing xenografts. At 2 h after injection of 64Cu-NOTA-ZHER2:S1, 64Cu-NODAGA-ZHER2:S1, and 68Ga-NODAGA-ZHER2:S1, tumor uptakes did not differ significantly. Renal uptake of 64Cu-labeled conjugates was dramatically reduced at 6 and 24 h after injection. Notably, radioactivity uptake concomitantly increased in blood, lung, liver, spleen, and intestines, which resulted in decreased tumor-to-organ ratios compared to 2 h postinjection. Organ uptake was lower for 64Cu-NODAGA-ZHER2:S1. The most probable explanation for this biodistribution pattern was the release and redistribution of renal radiometabolites. In conclusion, monoamide derivatives of NOTA and NODAGA may be suboptimal chelators for radiocopper labeling of anti-HER2 affibody molecules and, possibly, other scaffold proteins with high renal uptake. PMID:29097939

Label-free in-flow detection of single DNA molecules using glass nanopipettes.

PubMed

Gong, Xiuqing; Patil, Amol V; Ivanov, Aleksandar P; Kong, Qingyuan; Gibb, Thomas; Dogan, Fatma; deMello, Andrew J; Edel, Joshua B

2014-01-07

With the view of enhancing the functionality of label-free single molecule nanopore-based detection, we have designed and developed a highly robust, mechanically stable, integrated nanopipette-microfluidic device which combines the recognized advantages of microfluidic systems and the unique properties/advantages of nanopipettes. Unlike more typical planar solid-state nanopores, which have inherent geometrical constraints, nanopipettes can be easily positioned at any point within a microfluidic channel. This is highly advantageous, especially when taking into account fluid flow properties. We show that we are able to detect and discriminate between DNA molecules of varying lengths when motivated through a microfluidic channel, upon the application of appropriate voltage bias across the nanopipette. The effects of applied voltage and volumetric flow rates have been studied to ascertain translocation event frequency and capture rate. Additionally, by exploiting the advantages associated with microfluidic systems (such as flow control and concomitant control over analyte concentration/presence), we show that the technology offers a new opportunity for single molecule detection and recognition in microfluidic devices.

Label-free electrochemical biosensing of small-molecule inhibition on O-GlcNAc glycosylation.

PubMed

Yang, Yu; Gu, Yuxin; Wan, Bin; Ren, Xiaomin; Guo, Liang-Hong

2017-09-15

O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) plays a critical role in modulating protein function in many cellular processes and human diseases such as Alzheimer's disease and type II diabetes, and has emerged as a promising new target. Specific inhibitors of OGT could be valuable tools to probe the biological functions of O-GlcNAcylation, but a lack of robust nonradiometric assay strategies to detect glycosylation, has impeded efforts to identify such compounds. Here we have developed a novel label-free electrochemical biosensor for the detection of peptide O-GlcNAcylation using protease-protection strategy and electrocatalytic oxidation of tyrosine mediated by osmium bipyridine as a signal reporter. There is a large difference in the abilities of proteolysis of the glycosylated and the unglycosylated peptides by protease, thus providing a sensing mechanism for OGT activity. When the O-GlcNAcylation is achieved, the glycosylated peptides cannot be cleaved by proteinase K and result in a high current response on indium tin oxide (ITO) electrode. However, when the O-GlcNAcylation is successfully inhibited using a small molecule, the unglycosylated peptides can be cleaved easily and lead to low current signal. Peptide O-GlcNAcylation reaction was performed in the presence of a well-defined small-molecule OGT inhibitor. The results indicated that the biosensor could be used to screen the OGT inhibitors effectively. Our label-free electrochemical method is a promising candidate for protein glycosylation pathway research in screening small-molecule inhibitors of OGT. Copyright © 2017 Elsevier B.V. All rights reserved.

Minimizing ATP depletion by oxygen scavengers for single-molecule fluorescence imaging in live cells.

PubMed

Jung, Seung-Ryoung; Deng, Yi; Kushmerick, Christopher; Asbury, Charles L; Hille, Bertil; Koh, Duk-Su

2018-06-19

The stability of organic dyes against photobleaching is critical in single-molecule tracking and localization microscopy. Since oxygen accelerates photobleaching of most organic dyes, glucose oxidase is commonly used to slow dye photobleaching by depleting oxygen. As demonstrated here, pyranose-2-oxidase slows bleaching of Alexa647 dye by ∼20-fold. However, oxygen deprivation may pose severe problems for live cells by reducing mitochondrial oxidative phosphorylation and ATP production. We formulate a method to sustain intracellular ATP levels in the presence of oxygen scavengers. Supplementation with metabolic intermediates including glyceraldehyde, glutamine, and α-ketoisocaproate maintained the intracellular ATP level for at least 10 min by balancing between FADH 2 and NADH despite reduced oxygen levels. Furthermore, those metabolites supported ATP-dependent synthesis of phosphatidylinositol 4,5-bisphosphate and internalization of PAR2 receptors. Our method is potentially relevant to other circumstances that involve acute drops of oxygen levels, such as ischemic damage in the brain or heart or tissues for transplantation.

On the influence of singlet oxygen molecules on characteristics of HCCI combustion: A numerical study

NASA Astrophysics Data System (ADS)

Starik, A. M.; Kozlov, V. E.; Titova, N. S.

2013-08-01

Mechanisms of homogeneous charge compression ignition (HCCI) combustion enhancement are investigated numerically when excited O2(a 1Δg) molecules are produced at different points in the compression stroke. The analysis is conducted with the use of an extended kinetic model involving the submechanism of nitric oxide formation in the presence of singlet oxygen O2(a 1Δg) or O2(b 1Σg +) molecules in the methane-air mixture. It is demonstrated that the abundance of excited O2(a 1Δg) molecules in the mixture even in a small amounts intensifies the ignition and combustion and allows one to control the ignition event in the HCCI engine. Such a method of energy supply in the HCCI engine is much more effective in advancement of combustion timing than mere heating of the mixture, because it leads to acceleration of the chain-branching mechanism. The excitation of O2 molecules to the a 1Δg electronic state makes it possible to organise the successful combustion in the cylinder at diminished initial temperature of the mixture and increase the effective energy released during HCCI combustion. The advance in the value of this energy is much higher than the energy needed for the excitation of oxygen molecules. Moreover, in this case, the output concentration of NO and CO can be reduced significantly.

End labeling procedures: an overview.

PubMed

Hilario, Elena

2004-09-01

There are two ways to label a DNA molecular; by the ends or all along the molecule. End labeling can be performed at the 3'- or 5'-end. Labeling at the 3' end is performed by filling 3'-end recessed ends with a mixture or labeled and unlabeled dNTPs using Klenow or T4 DNA polymerases. Both reactions are template dependent. Terminal deoxynucleotide transferase incorporates dNTPs at the 3' end of any kind of DNA molecule or RNA. Labels incorporated at the 3'-end of the DNA molecule prevent any further extension or ligation to any other molecule, but this can be overcome by labeling the 5'-end of the desired DNA molecule. 5'-end labeling is performed by enzymatic methods (T4 polynucleotide kinase exchange and forward reactions), by chemical modification of sensitized oligonucleotides with phosphoroamidite, or by combined methods. Probe cleanup is recommended when high background problems occur, but caution should be taken not to damage the attached probe with harsh chemicals or by light exposure.

Attosecond Coherent Control of the Photo-Dissociation of Oxygen Molecules

NASA Astrophysics Data System (ADS)

Sturm, Felix; Ray, Dipanwita; Wright, Travis; Shivaram, Niranjan; Bocharova, Irina; Slaughter, Daniel; Ranitovic, Predrag; Belkacem, Ali; Weber, Thorsten

2016-05-01

Attosecond Coherent Control has emerged in recent years as a technique to manipulate the absorption and ionization in atoms as well as the dissociation of molecules on an attosecond time scale. Single attosecond pulses and attosecond pulse trains (APTs) can coherently excite multiple electronic states. The electronic and nuclear wave packets can then be coupled with a second pulse forming multiple interfering quantum pathways. We have built a high flux extreme ultraviolet (XUV) light source delivering APTs based on HHG that allows to selectively excite neutral and ion states in molecules. Our beamline provides spectral selectivity and attosecond interferometric control of the pulses. In the study presented here, we use APTs, generated by High Harmonic Generation in a high flux extreme ultraviolet light source, to ionize highly excited states of oxygen molecules. We identify the ionization/dissociation pathways revealing vibrational structure with ultra-high resolution ion 3D-momentum imaging spectroscopy. Furthermore, we introduce a delay between IR pulses and XUV/IR pulses to constructively or destructively interfere the ionization and dissociation pathways, thus, enabling the manipulation of both the O2+and the O+ ion yields with attosecond precision. Supported by DOE under Contract No. DE-AC02-05CH11231.

Detection of ultra-low oxygen concentration based on the fluorescence blinking dynamics of single molecules

NASA Astrophysics Data System (ADS)

Wu, Ruixiang; Chen, Ruiyun; Zhou, Haitao; Qin, Yaqiang; Zhang, Guofeng; Qin, Chengbing; Gao, Yan; Gao, Yajun; Xiao, Liantuan; Jia, Suotang

2018-01-01

We present a sensitive method for detection of ultra-low oxygen concentrations based on the fluorescence blinking dynamics of single molecules. The relationship between the oxygen concentration and the fraction of time spent in the off-state, stemming from the population and depopulation of triplet states and radical cationic states, can be fitted with a two-site quenching model in the Stern-Volmer plot. The oxygen sensitivity is up to 43.42 kPa-1 in the oxygen partial pressure region as low as 0.01-0.25 kPa, which is seven times higher than that of the fluorescence intensity indicator. This method avoids the limitation of the sharp and non-ignorable fluctuations that occur during the measurement of fluorescence intensity, providing potential applications in the field of low oxygen-concentration monitoring in life science and industry.

The small molecule probe PT-Yellow labels the renal proximal tubules in zebrafish.

PubMed

Sander, Veronika; Patke, Shantanu; Sahu, Srikanta; Teoh, Chai Lean; Peng, Zhenzhen; Chang, Young-Tae; Davidson, Alan J

2015-01-01

We report the development of a small fluorescent molecule, BDNCA3-D2, herein referred to as PT-Yellow. Soaking zebrafish embryos in PT-Yellow or intraperitoneal injection into adults results in non-toxic in vivo fluorescent labeling of the renal proximal tubules, the major site of blood filtrate reabsorption and a common target of injury in acute kidney injury. We demonstrate the applicability of this new compound as a rapid and simple readout for zebrafish kidney filtration and proximal tubule reabsorption function.

Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

DOEpatents

Salafsky, Joshua S.; Eisenthal, Kenneth B.

2005-10-11

This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

Specific Effects of Oxygen Molecule and Plasma on Thin-Film Growth of Y-Ba-Cu-O and Bi-Sr-(Ca)-Cu-O Systems

NASA Astrophysics Data System (ADS)

Endo, Tamio; Horie, Munehiro; Hirate, Naoki; Itoh, Katsutoshi; Yamada, Satoshi; Tada, Masaki; Itoh, Ken-ichi; Sugiyama, Morihiro; Sano, Shinji; Watabe, Kinji

1998-07-01

Thin films of a-oriented YBa2Cu3Ox (YBCO), Ca-doped c-oriented Bi2(Sr,Ca)2CuOx and nondoped c-oriented Bi2Sr2CuOx (Bi2201) were prepared at low temperatures by ion beam sputtering with supply of oxygen molecules or plasma. The plasma enhances crystal growth of the a-YBCO and Ca-doped Bi2201 phases. This can be interpreted in terms of their higher surface energies. The growth and quality of nondoped Bi2201 are improved with the supply of oxygen molecules. This particular result could be interpreted by the collision process between the oxygen molecules and the sputtered particles.

The Cloud Paradigm: Geostable molecules as proxies for surface oxygenation

NASA Astrophysics Data System (ADS)

Summons, R. E.; Hallmann, C.

2011-12-01

Geoscientists continue to puzzle over when and by which means Earth's surface environment became oxygenated. One of the prevailing scenarios, articulated by Cloud, Holland and Walker, proposes an initially anoxic or very low O2 atmosphere. Although photosystem II is thought to have appeared early, there was an extended period of imbalance between sources & sinks of O2 due to pervasive feedback between biosphere, atmosphere, hydrosphere & lithosphere. Ultimately O2 accumulated in the atmosphere to such levels that it left geochemical and physical evidence for mobilization of redox-sensitive elements in what is currently referred to as the 'Great Oxidation Event' or GOE at c. 2.45 Ga. While some researchers hold that the GOE marks the advent of oxygenic photosynthesis (e.g. Kopp et al., 2005), a wealth of geochemical and paleontological data is consistent with the presence of both cyanobacteria (e.g. Bosak et al., 2009) and traces of environmental oxygen (e.g. Anbar et al., 2007) several hundred million years prior. Further, molecular fossils present in 2.7-2.5 Ga rocks from the Transvaal Supergroup of the Kaapvaal Craton include steroids and other molecules indicative of oxygen-dependent biosynthesis and oxygen-respiring methanotrophic bacteria (Waldbauer et al., 2008). New molecular data for samples from the Mount McRae Formation in the Mt Bruce Supergroup, Pilbara Craton, identifies a diverse array of hydrocarbons including steroids and carotenoid residues diagnostic of phototrophic green sulfur bacteria. Co-variance of biomarker ratios with inorganic proxies-each leading to similar environmental reconstructions- confirm the authenticity of this signal. The carotenoid biomarkers indicate that the surface waters of the Hamersley Basin provided a sustained supply of hydrogen sulfide for anoxygenic photosynthesis and, indirectly, suggest the presence of precursor sulfate derived from the oxidative weathering of metal sulfides. Anbar A.D. et al. A whiff of oxygen

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

Overview of Single-Molecule Speckle (SiMS) Microscopy and Its Electroporation-Based Version with Efficient Labeling and Improved Spatiotemporal Resolution.

PubMed

Yamashiro, Sawako; Watanabe, Naoki

2017-07-06

Live-cell single-molecule imaging was introduced more than a decade ago, and has provided critical information on remodeling of the actin cytoskeleton, the motion of plasma membrane proteins, and dynamics of molecular motor proteins. Actin remodeling has been the best target for this approach because actin and its associated proteins stop diffusing when assembled, allowing visualization of single-molecules of fluorescently-labeled proteins in a state specific manner. The approach based on this simple principle is called Single-Molecule Speckle (SiMS) microscopy. For instance, spatiotemporal regulation of actin polymerization and lifetime distribution of actin filaments can be monitored directly by tracking actin SiMS. In combination with fluorescently labeled probes of various actin regulators, SiMS microscopy has contributed to clarifying the processes underlying recycling, motion and remodeling of the live-cell actin network. Recently, we introduced an electroporation-based method called eSiMS microscopy, with high efficiency, easiness and improved spatiotemporal precision. In this review, we describe the application of live-cell single-molecule imaging to cellular actin dynamics and discuss the advantages of eSiMS microscopy over previous SiMS microscopy.

Electron Paramagnetic Resonance Studies of Spin-Labeled Hemoglobins and Their Implications to the Nature of Cooperative Oxygen Binding to Hemoglobin*

PubMed Central

Ho, Chien; Baldassare, Joseph J.; Charache, Samuel

1970-01-01

The spin label technique has been used to study human hemoglobins A, F, Zürich, and Chesapeake as a function of carbon monoxide saturation. The experimental results suggest that the changes in the electron paramagnetic resonance spectra of hemoglobin labeled with N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)iodoacetamide depend on the state of ligation of more than one heme group. For those hemoglobins with full or large cooperative ligand binding (such as A, F, and Zürich), there is a lack of isosbestic points in the spectra as a function of CO saturation. However, for those hemoglobins with little or no cooperative ligand binding (such as Chesapeake and methemoglobins), there is a sharp set of isosbestic points. These findings confirm and extend the early work of McConnell and co-workers. The absence of a set of isosbestic points in those hemoglobins with full cooperative ligand binding is consistent with the sequential model of Koshland, Némethy, and Filmer for cooperative oxygen binding to hemoglobin. The present results, with hemoglobin variants having known amino acid substitutions, also focus on the importance of the interactions among the amino acid residues located at α1-β2 or α2-β1 subunit contacts for the functioning of hemoglobin as an oxygen carrier. In addition, the resonance spectra of the spin label are very sensitive to small structural variations around the heme groups in the β- or γ-chains where the labels are attached. The results of the spin label experiment are discussed in relation to recent findings on the mechanism of oxygenation of hemoglobin from the nuclear magnetic resonance studies of this laboratory and the x-ray crystallographic analysis of Perutz and co-workers. PMID:4316679

The use of radiocobalt as a label improves imaging of EGFR using DOTA-conjugated Affibody molecule.

PubMed

Garousi, Javad; Andersson, Ken G; Dam, Johan H; Olsen, Birgitte B; Mitran, Bogdan; Orlova, Anna; Buijs, Jos; Ståhl, Stefan; Löfblom, John; Thisgaard, Helge; Tolmachev, Vladimir

2017-07-20

Several anti-cancer therapies target the epidermal growth factor receptor (EGFR). Radionuclide imaging of EGFR expression in tumours may aid in selection of optimal cancer therapy. The 111 In-labelled DOTA-conjugated Z EGFR:2377 Affibody molecule was successfully used for imaging of EGFR-expressing xenografts in mice. An optimal combination of radionuclide, chelator and targeting protein may further improve the contrast of radionuclide imaging. The aim of this study was to evaluate the targeting properties of radiocobalt-labelled DOTA-Z EGFR:2377 . DOTA-Z EGFR:2377 was labelled with 57 Co (T 1/2  = 271.8 d), 55 Co (T 1/2  = 17.5 h), and, for comparison, with the positron-emitting radionuclide 68 Ga (T 1/2  = 67.6 min) with preserved specificity of binding to EGFR-expressing A431 cells. The long-lived cobalt radioisotope 57 Co was used in animal studies. Both 57 Co-DOTA-Z EGFR:2377 and 68 Ga-DOTA-Z EGFR:2377 demonstrated EGFR-specific accumulation in A431 xenografts and EGFR-expressing tissues in mice. Tumour-to-organ ratios for the radiocobalt-labelled DOTA-Z EGFR:2377 were significantly higher than for the gallium-labelled counterpart already at 3 h after injection. Importantly, 57 Co-DOTA-Z EGFR:2377 demonstrated a tumour-to-liver ratio of 3, which is 7-fold higher than the tumour-to-liver ratio for 68 Ga-DOTA-Z EGFR:2377 . The results of this study suggest that the positron-emitting cobalt isotope 55 Co would be an optimal label for DOTA-Z EGFR:2377 and further development should concentrate on this radionuclide as a label.

49 CFR 172.405 - Authorized label modifications.

Code of Federal Regulations, 2011 CFR

2011-10-01

... subsidiary label. (b) For a package containing Oxygen, compressed, or Oxygen, refrigerated liquid, the OXIDIZER label specified in § 172.426 of this subpart, modified to display the word “OXYGEN” instead of... OXIDIZER labels. Notwithstanding the provisions of paragraph (a) of this section, the word “OXYGEN” must...

Oxygen in Orion

NASA Image and Video Library

2011-08-01

This graphic illustrates where astronomers at last found oxygen molecules in space -- near the star-forming core of the Orion nebula. The squiggly lines, or spectra, reveal the signatures of oxygen molecules, detected by ESA Hershel Space Observatory.

Fluorescent Affibody Molecule Administered In Vivo at a Microdose Level Labels EGFR Expressing Glioma Tumor Regions.

PubMed

de Souza, Ana Luiza Ribeiro; Marra, Kayla; Gunn, Jason; Samkoe, Kimberley S; Hoopes, P Jack; Feldwisch, Joachim; Paulsen, Keith D; Pogue, Brian W

2017-02-01

Fluorescence guidance in surgical oncology provides the potential to realize enhanced molecular tumor contrast with dedicated targeted tracers, potentially with a microdose injection level. For most glioma tumors, the blood brain barrier is compromised allowing some exogenous drug/molecule delivery and accumulation for imaging. The aberrant overexpression and/or activation of epidermal growth factor receptor (EGFR) is associated with many types of cancers, including glioblastoma, and so the use of a near-infrared (NIR) fluorescent molecule targeted to the EGFR receptor provides the potential for improving tumor contrast during surgery. Fluorescently labeled affibody molecule (ABY-029) has high EGFR affinity and high potential specificity with reasonably fast plasma clearance. In this study, ABY-29 was evaluated in glioma versus normal brain uptake from intravenous injection at a range of doses, down to a microdose injection level. Nude rats were inoculated with the U251 human glioma cell line in the brain. Tumors were allowed to grow for 3-4 weeks. ABY-029 fluorescence ex vivo imaging of brain slices was acquired at different time points (1-48 h) and varying injection doses from 25 to 122 μg/kg (from human protein microdose equivalent to five times microdose levels). The tumor was most clearly visualized at 1-h post-injection with 8- to 16-fold average contrast relative to normal brain. However, the tumor still could be identified after 48 h. In all cases, the ABY-029 fluorescence appeared to localize preferentially in EGFR-positive regions. Increasing the injected dose from a microdose level to five times, a microdose level increased the signal by 10-fold, and the contrast was from 8 to 16, showing that there was value in doses slightly higher than the microdose restriction. Normal tissue uptake was found to be affected by the tumor size, indicating that edema was a likely factor affecting the expected tumor to normal tissue contrast. These results suggest

The molecular inventory around protostars: water, organic molecules, and the missing oxygen problem

NASA Astrophysics Data System (ADS)

Neufeld, David A.

2018-06-01

Massive star formation is accompanied by significant chemical evolution in the surrounding interstellar gas. Here, grains are heated up and icy mantles evaporate, releasing a rich inventory of water and organic molecules into the gas-phase within “hot core” regions surrounding massive protostars. Because molecules on the grain surface present broad infrared features without rotational structure, only the most abundant molecules can be identified unambiguously in the solid phase; once released into the gas-phase, however, where they are free to rotate, the constituents of grain mantles can be identified easily by means of rotational spectroscopy at millimeter and submillimeter wavelengths or through rovibrational spectroscopy in the mid-infrared. While observations of pure-rotational emission lines provide a broad view of hot core chemistry, absorption line spectroscopy of rovibrational transitions can probe the very hottest material closest to the protostar. With access to the mid-infrared spectral region from above 99% of Earth’s water vapor, SOFIA provides a unique platform for high-resolution rovibrational spectroscopy of water and organic molecules, many of which have vibrational transitions in the 5 – 8 micron spectral region that is unobservable from the ground. High spectral resolution is essential for disentangling the rotational structure and providing reliable measurements of the molecular column densities and temperatures. Future SOFIA observations will help elucidate the inventory of water and organic molecules around young protostars, and can address a puzzle related to the “oxygen budget” in the interstellar medium: surprisingly, the main interstellar reservoirs of the third-most abundant element in the Universe have yet to be identified.

Theoretical analysis of bimetallic nanorod dimer biosensors for label-free molecule detection

NASA Astrophysics Data System (ADS)

Das, Avijit; Talukder, Muhammad Anisuzzaman

2018-02-01

In this work, we theoretically analyze a gold (Au) core within silver (Ag) shell (Au@Ag) nanorod dimer biosensor for label-free molecule detection. The incident light on an Au@Ag nanorod strongly couples to localized surface plasmon modes, especially around the tip region. The field enhancement around the tip of a nanorod or between the tips of two longitudinally aligned nanorods as in a dimer can be exploited for sensitive detection of biomolecules. We derive analytical expressions for the interactions of an Au@Ag nanorod dimer with the incident light. We also study the detail dynamics of an Au@Ag nanorod dimer with the incident light computationally using finite difference time domain (FDTD) technique when core-shell ratio, relative position of the nanorods, and angle of incidence of light change. We find that the results obtained using the developed analytical model match well with that obtained using FDTD simulations. Additionally, we investigate the sensitivity of the Au@Ag nanorod dimer, i.e., shift in the resonance wavelength, when a target biomolecule such as lysozyme (Lys), human serum albumin (HSA), anti-biotin (Abn), human catalase (CAT), and human fibrinogen (Fb) protein molecules are attached to the tips of the nanorods.

Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

NASA Astrophysics Data System (ADS)

Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro

2011-10-01

Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

Heme Amplifies the Innate Immune Response to Microbial Molecules through Spleen Tyrosine Kinase (Syk)-dependent Reactive Oxygen Species Generation*

PubMed Central

Fernandez, Patricia L.; Dutra, Fabianno F.; Alves, Letícia; Figueiredo, Rodrigo T.; Mourão-Sa, Diego; Fortes, Guilherme B.; Bergstrand, Sophie; Lönn, David; Cevallos, Ricardo R.; Pereira, Renata M. S.; Lopes, Ulisses G.; Travassos, Leonardo H.; Paiva, Claudia N.; Bozza, Marcelo T.

2010-01-01

Infectious diseases that cause hemolysis are among the most threatening human diseases, because of severity and/or global distribution. In these conditions, hemeproteins and heme are released, but whether heme affects the inflammatory response to microorganism molecules remains to be characterized. Here, we show that heme increased the lethality and cytokine secretion induced by LPS in vivo and enhanced the secretion of cytokines by macrophages stimulated with various agonists of innate immune receptors. Activation of nuclear factor κB (NF-κB) and MAPKs and the generation of reactive oxygen species were essential to the increase in cytokine production induced by heme plus LPS. This synergistic effect of heme and LPS was blocked by a selective inhibitor of spleen tyrosine kinase (Syk) and was abrogated in dendritic cells deficient in Syk. Moreover, inhibition of Syk and the downstream molecules PKC and PI3K reduced the reactive oxygen species generation by heme. Our results highlight a mechanism by which heme amplifies the secretion of cytokines triggered by microbial molecule activation and indicates possible pathways for therapeutic intervention during hemolytic infectious diseases. PMID:20729208

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Spin-labeled small unilamellar vesicles with the T1-sensitive saturation-recovery EPR display as an oxygen sensitive analyte for measurement of cellular respiration

PubMed Central

Mainali, Laxman; Vasquez-Vivar, Jeannette; Hyde, James S.; Subczynski, Witold K.

2015-01-01

This study validated the use of small unilamellar vesicles (SUVs) made of 1-palmitoyl-2-oleoylphosphatidylcholine with 1 mol% spin label of 1-palmitoyl-2-(16-doxylstearoyl)phosphatidylcholine (16-PC) as an oxygen sensitive analyte to study cellular respiration. In the analyte the hydrocarbon environment surrounds the nitroxide moiety of 16-PC. This ensures high oxygen concentration and oxygen diffusion at the location of the nitroxide as well as isolation of the nitroxide moiety from cellular reductants and paramagnetic ions that might interfere with spin-label oximetry measurements. The saturation-recovery EPR approach was applied in the analysis since this approach is the most direct method to carry out oximetric studies. It was shown that this display (spin-lattice relaxation rate) is linear in oxygen partial pressure up to 100% air (159 mmHg). Experiments using a neuronal cell line in suspension were carried out at X-band for closed chamber geometry. Oxygen consumption rates showed a linear dependence on the number of cells. Other significant benefits of the analyte are: the fast effective rotational diffusion and slow translational diffusion of the spin-probe is favorable for the measurements, and there is no cross reactivity between oxygen and paramagnetic ions in the lipid bilayer. PMID:26441482

Spin-labeled small unilamellar vesicles with the T1-sensitive saturation-recovery EPR display as an oxygen sensitive analyte for measurement of cellular respiration.

PubMed

Mainali, Laxman; Vasquez-Vivar, Jeannette; Hyde, James S; Subczynski, Witold K

2015-08-01

This study validated the use of small unilamellar vesicles (SUVs) made of 1-palmitoyl-2-oleoylphosphatidylcholine with 1 mol% spin label of 1-palmitoyl-2-(16-doxylstearoyl)phosphatidylcholine (16-PC) as an oxygen sensitive analyte to study cellular respiration. In the analyte the hydrocarbon environment surrounds the nitroxide moiety of 16-PC. This ensures high oxygen concentration and oxygen diffusion at the location of the nitroxide as well as isolation of the nitroxide moiety from cellular reductants and paramagnetic ions that might interfere with spin-label oximetry measurements. The saturation-recovery EPR approach was applied in the analysis since this approach is the most direct method to carry out oximetric studies. It was shown that this display (spin-lattice relaxation rate) is linear in oxygen partial pressure up to 100% air (159 mmHg). Experiments using a neuronal cell line in suspension were carried out at X-band for closed chamber geometry. Oxygen consumption rates showed a linear dependence on the number of cells. Other significant benefits of the analyte are: the fast effective rotational diffusion and slow translational diffusion of the spin-probe is favorable for the measurements, and there is no cross reactivity between oxygen and paramagnetic ions in the lipid bilayer.

Preparation of goat and rabbit anti-camel immunoglobulin G whole molecule labeled with horseradish peroxidase

PubMed Central

Abdel-Rahman, Eman Hussein; El-Jakee, Jakeen Kamal; Hatem, Mahmoud Essam; Ata, Nagwa Sayed; Fouad, Ehab Ali

2017-01-01

Aim: As the labeled anti-camel immunoglobulins (Igs) with enzymes for enzyme-linked immunosorbent assay (ELISA) are unavailable in the Egyptian market, the present investigation was directed for developing local labeled anti-camel IgG with horseradish peroxidase (HRP) to save hard curacy. Materials and Methods: For purification of camel IgG whole molecule, camel sera was preliminary precipitated with 50% saturated ammonium sulfate and dialyzed against 15 mM phosphate-buffered saline pH 7.2 then concentrated. This preparation was further purified by protein A sepharose affinity column chromatography. The purity of the eluted camel IgG was tested by sodium dodecyl sulfate polyacrylamide gel electrophoresi. Anti-camel IgG was prepared by immunization of goats and rabbits separately, with purified camel IgG. The anti-camel IgG was purified by protein A sepharose affinity column chromatography. Whole molecule anti-camel IgG was conjugated with HRP using glutraldehyde based assay. Sensitivity and specificity of prepared conjugated secondary antibodies were detected using positive and negative camel serum samples reacted with different antigens in ELISA, respectively. The potency of prepared conjugated antibodies was evaluated compared with protein A HRP. The stability of the conjugate at −20°C during 1 year was assessed by ELISA. Results: The electrophoretic profile of camel IgG showed four bands of molecular weight 63, 52, 40 and 33 kDa. The recorded sensitivity and specificity of the product are 100%. Its potency is also 100% compared to 58-75% of commercial protein A HRP. The conjugates are stable for 1 year at −20°C as proved by ELISA. Conclusion: Collectively, this study introduces goat and rabbit anti-camel IgG whole molecules with simple, inexpensive method, with 100% sensitivity, 100% specificity and stability up to 1 year at −20°C. The important facet of the current study is saving hard curacy. Future investigations are necessary for preparation of Ig

Oxygen depletion speeds and simplifies diffusion in HeLa cells.

PubMed

Edwald, Elin; Stone, Matthew B; Gray, Erin M; Wu, Jing; Veatch, Sarah L

2014-10-21

Many cell types undergo a hypoxic response in the presence of low oxygen, which can lead to transcriptional, metabolic, and structural changes within the cell. Many biophysical studies to probe the localization and dynamics of single fluorescently labeled molecules in live cells either require or benefit from low-oxygen conditions. In this study, we examine how low-oxygen conditions alter the mobility of a series of plasma membrane proteins with a range of anchoring motifs in HeLa cells at 37°C. Under high-oxygen conditions, diffusion of all proteins is heterogeneous and confined. When oxygen is reduced with an enzymatic oxygen-scavenging system for ≥ 15 min, diffusion rates increase by > 2-fold, motion becomes unconfined on the timescales and distance scales investigated, and distributions of diffusion coefficients are remarkably consistent with those expected from Brownian motion. More subtle changes in protein mobility are observed in several other laboratory cell lines examined under both high- and low-oxygen conditions. Morphological changes and actin remodeling are observed in HeLa cells placed in a low-oxygen environment for 30 min, but changes are less apparent in the other cell types investigated. This suggests that changes in actin structure are responsible for increased diffusion in hypoxic HeLa cells, although superresolution localization measurements in chemically fixed cells indicate that membrane proteins do not colocalize with F-actin under either experimental condition. These studies emphasize the importance of controls in single-molecule imaging measurements, and indicate that acute response to low oxygen in HeLa cells leads to dramatic changes in plasma membrane structure. It is possible that these changes are either a cause or consequence of phenotypic changes in solid tumor cells associated with increased drug resistance and malignancy.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

PubMed Central

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

Formation of highly oxygenated organic molecules from aromatic compounds

NASA Astrophysics Data System (ADS)

Molteni, Ugo; Bianchi, Federico; Klein, Felix; El Haddad, Imad; Frege, Carla; Rossi, Michel J.; Dommen, Josef; Baltensperger, Urs

2018-02-01

Anthropogenic volatile organic compounds (AVOCs) often dominate the urban atmosphere and consist to a large degree of aromatic hydrocarbons (ArHCs), such as benzene, toluene, xylenes, and trimethylbenzenes, e.g., from the handling and combustion of fuels. These compounds are important precursors for the formation of secondary organic aerosol. Here we show that the oxidation of aromatics with OH leads to a subsequent autoxidation chain reaction forming highly oxygenated molecules (HOMs) with an O : C ratio of up to 1.09. This is exemplified for five single-ring ArHCs (benzene, toluene, o-/m-/p-xylene, mesitylene (1,3,5-trimethylbenzene) and ethylbenzene), as well as two conjugated polycyclic ArHCs (naphthalene and biphenyl). We report the elemental composition of the HOMs and show the differences in the oxidation patterns of these ArHCs. A potential pathway for the formation of these HOMs from aromatics is presented and discussed. We hypothesize that AVOCs may contribute substantially to new particle formation events that have been detected in urban areas.

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

NASA Astrophysics Data System (ADS)

Yu, Dindi; Ruangchaithaweesuk, Songtham; Yao, Li; Xu, Shoujun

2012-09-01

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/√Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 μm with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 μm, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Noncompetitive Homogeneous Detection of Small Molecules Using Synthetic Nanopeptamer-Based Luminescent Oxygen Channeling.

PubMed

Lassabe, Gabriel; Kramer, Karl; Hammock, Bruce D; González-Sapienza, Gualberto; González-Techera, Andrés

2018-05-15

Our group has previously developed immunoassays for noncompetitive detection of small molecules based on the use of phage borne anti-immunocomplex peptides. Recently, we substituted the phage particles by biotinylated synthetic anti-immunocomplex peptides complexed with streptavidin and named these constructs nanopeptamers. In this work, we report the results of combining AlphaLisa, a commercial luminescent oxygen channeling bead system, with nanopeptamers for the development of a noncompetitive homogeneous assay for the detection of small molecules. The signal generation of AlphaLisa assays relies on acceptor-donor bead proximity induced by the presence of the analyte (a macromolecule) simultaneously bound by antibodies immobilized on the surface of these beads. In the developed assay, termed as nanoAlphaLisa, bead proximity is sustained by the presence of a small model molecule (atrazine, MW = 215) using an antiatrazine antibody captured on the acceptor bead and an atrazine nanopeptamer on the donor bead. Atrazine is one of the most used pesticides worldwide, and its monitoring in water has relevant human health implications. NanoAlphaLisa allowed the homogeneous detection of atrazine down to 0.3 ng/mL in undiluted water samples in 1 h, which is 10-fold below the accepted limit in drinking water. NanoAlphaLisa has the intrinsic advantages for automation and high-throughput, simple, and fast homogeneous detection of target analytes that AlphaLisa assay provides.

How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient.

PubMed

Blomberg, Margareta R A; Siegbahn, Per E M

2015-03-01

Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover. Copyright © 2014 Elsevier B.V. All rights reserved.

Singlet oxygen generation in gas discharge for oxygen-iodine laser pumping

NASA Astrophysics Data System (ADS)

Lopaev, D. V.; Braginsky, O. V.; Klopovsky, K. S.; Kovalev, A. S.; Mankelevich, Yu. A.; Popov, N. A.; Rakhimov, A. T.; Rakhimova, T. V.; Vasilieva, A. N.

2004-09-01

The possibility of development of effective discharged singlet oxygen (SO) generator (DSOG) for oxygen-iodine laser (OIL) is studied in detail. Researches of kinetics of oxygen atoms and oxygen molecules in the lowest metastable singlet states have been carried out in the different discharges and its afterglow (DC discharges, E-beam controlled discharge and RF discharges) in both CW and pulsed mode in a wide range of conditions (pressures, gas mixtures, energy deposits etc.). The models developed for all the discharges have allowed us to analyze SO generation and loss mechanisms and to find out the key-parameters controlling the highest SO yield. It is shown that in addition to spatial plasma uniformity at low E/N and high specific energy deposit per oxygen molecule, DSOG must be oxygen atom free to avoid fast three-body quenching of SO by atomic oxygen with increasing pressure and thereby to provide pressure scaling (in tens Torrs) for applying to real OIL systems.

Investigation of Oxygen-Induced Quenching of Phosphorescence in Photoexcited Aromatic Molecules by Positron Annihilation Spectroscopy

NASA Technical Reports Server (NTRS)

Singh, Jag J.; Eftekhari, Abe

1996-01-01

Platinum OctaEthyl Porphyrin (Pt.OEP) is an efficient phosphor under ultraviolet excitation. The phosphorescent triplet state P(T(Sup 1)) is readily quenched by the oxygen O2 molecules. This phenomenon is being utilized as the basis for global air pressure measurements in aerodynamic facilities at various laboratories. The exact mechanism by which O2 molecules quench the P(T(Sup 1) approaches P(S(Sub O)) transitions is still unknown. The diamagnetic singlet states P(S(Sub n)), which feed P(T(Sub 1)) states via intersystem crossings, would presumably not be affected by O2. It must be only the magnetic P(T(Sub 1)) states, which can interact with the paramagnetic O2 molecules, that are affected. However, our positron lifetime and Doppler broadening studies suggest the formation of O2P(S(Sub n)), complexes which can also eventually reduce the population of the P(T(Sub 1)) states (i.e., quench phosphorescence). This reduction is possible because higher triplet states in (Pt.OEP) are admixed with the P(S(Sub 1)), states via spin orbit interactions. The experimental procedures and the results of various measurements are presented in this paper.

Understanding Trends in Autoignition of Biofuels: Homologous Series of Oxygenated C5 Molecules

DOE PAGES

Ciesielski, Peter N.; Robichaud, David J.; Kim, Seonah; ...

2017-07-05

Oxygenated biofuels provide a renewable, domestic source of energy that can enable adoption of advanced, high-efficiency internal combustion engines, such as those based on homogeneously charged compression ignition (HCCI). Of key importance to such engines is the cetane number (CN) of the fuel, which is determined by the autoignition of the fuel under compression at relatively low temperatures (550-800 K). For the plethora of oxygenated biofuels possible, it is desirable to know the ignition delay times and the CN of these fuels to help guide conversion strategies so as to focus efforts on the most desirable fuels. For alkanes, themore » chemical pathways leading to radical chain-branching reactions giving rise to low-temperature autoignition are well-known and are highly coincident with the buildup of reactive radicals such as OH. Key in the mechanisms leading to chain branching are the addition of molecular oxygen to alkyl radicals and the rearrangement and dissociation of the resulting peroxy radials. Prediction of the temperature and pressure dependence of reactions that lead to the buildup of reactive radicals requires a detailed understanding of the potential energy surfaces (PESs) of these reactions. In this study, we used quantum mechanical modeling to systematically compare the effects of oxygen functionalities on these PESs and associated kinetics so as to understand how they affect experimental trends in autoignition and CN. The molecules studied here include pentane, pentanol, pentanal, 2-heptanone, methylpentyl ether, methyl hexanoate, and pentyl acetate. All have a saturated five-carbon alkyl chain with an oxygen functional group attached to the terminal carbon atom. The results of our systematic comparison may be summarized as follows: (1) Oxygen functionalities activate C-H bonds by lowering the bond dissociation energy (BDE) relative to alkanes. (2) The R-OO bonds in peroxy radicals adjacent to carbonyl groups are weaker than corresponding alkyl

Understanding Trends in Autoignition of Biofuels: Homologous Series of Oxygenated C5 Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ciesielski, Peter N.; Robichaud, David J.; Kim, Seonah

Oxygenated biofuels provide a renewable, domestic source of energy that can enable adoption of advanced, high-efficiency internal combustion engines, such as those based on homogeneously charged compression ignition (HCCI). Of key importance to such engines is the cetane number (CN) of the fuel, which is determined by the autoignition of the fuel under compression at relatively low temperatures (550-800 K). For the plethora of oxygenated biofuels possible, it is desirable to know the ignition delay times and the CN of these fuels to help guide conversion strategies so as to focus efforts on the most desirable fuels. For alkanes, themore » chemical pathways leading to radical chain-branching reactions giving rise to low-temperature autoignition are well-known and are highly coincident with the buildup of reactive radicals such as OH. Key in the mechanisms leading to chain branching are the addition of molecular oxygen to alkyl radicals and the rearrangement and dissociation of the resulting peroxy radials. Prediction of the temperature and pressure dependence of reactions that lead to the buildup of reactive radicals requires a detailed understanding of the potential energy surfaces (PESs) of these reactions. In this study, we used quantum mechanical modeling to systematically compare the effects of oxygen functionalities on these PESs and associated kinetics so as to understand how they affect experimental trends in autoignition and CN. The molecules studied here include pentane, pentanol, pentanal, 2-heptanone, methylpentyl ether, methyl hexanoate, and pentyl acetate. All have a saturated five-carbon alkyl chain with an oxygen functional group attached to the terminal carbon atom. The results of our systematic comparison may be summarized as follows: (1) Oxygen functionalities activate C-H bonds by lowering the bond dissociation energy (BDE) relative to alkanes. (2) The R-OO bonds in peroxy radicals adjacent to carbonyl groups are weaker than corresponding alkyl

Calcium manganese oxides as oxygen evolution catalysts: O2 formation pathways indicated by 18O-labelling studies.

PubMed

Shevela, Dmitriy; Koroidov, Sergey; Najafpour, M Mahdi; Messinger, Johannes; Kurz, Philipp

2011-05-02

Oxygen evolution catalysed by calcium manganese and manganese-only oxides was studied in (18)O-enriched water. Using membrane-inlet mass spectrometry, we monitored the formation of the different O(2) isotopologues (16)O(2), (16)O(18)O and (18)O(2) in such reactions simultaneously with good time resolution. From the analysis of the data, we conclude that entirely different pathways of dioxygen formation catalysis exist for reactions involving hydrogen peroxide (H(2)O(2)), hydrogen persulfate (HSO(5)(-)) or single-electron oxidants such as Ce(IV) and [Ru(III) (bipy)(3)](3+) . Like the studied oxide catalysts, the active sites of manganese catalase and the oxygen-evolving complex (OEC) of photosystem II (PSII) consist of μ-oxido manganese or μ-oxido calcium manganese sites. The studied processes show very similar (18)O-labelling behaviour to the natural enzymes and are therefore interesting model systems for in vivo oxygen formation by manganese metalloenzymes such as PSII. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Balancing the (carbon) budget: Using linear inverse models to estimate carbon flows and mass-balance 13C:15N labelling experiments in low oxygen sediments.

NASA Astrophysics Data System (ADS)

Hunter, William Ross; Van Oevelen, Dick; Witte, Ursula

2013-04-01

Over 1 million km2 of seafloor experience permanent low-oxygen conditions within oxygen minimum zones (OMZs). OMZs are predicted to grow as a consequence of climate change, potentially affecting oceanic biogeochemical cycles. The Arabian Sea OMZ impinges upon the western Indian continental margin at bathyal depths (150 - 1500m) producing a strong depth dependent oxygen gradient at the sea floor. The influence of the OMZ upon the short term processing of organic matter by sediment ecosystems was investigated using in situ stable isotope pulse chase experiments. These deployed doses of 13C:15N labeled organic matter onto the sediment surface at four stations from across the OMZ (water depth 540 - 1100 m; [O2] = 0.35 - 15 μM). In order to prevent experimentally anoxia, the mesocosms were not sealed. 13C and 15N labels were traced into sediment, bacteria, fauna and 13C into sediment porewater DIC and DOC. However, the DIC and DOC flux to the water column could not be measured, limiting our capacity to obtain mass-balance for C in each experimental mesocosm. Linear Inverse Modeling (LIM) provides a method to obtain a mass-balanced model of carbon flow that integrates stable-isotope tracer data with community biomass and biogeochemical flux data from a range of sources. Here we present an adaptation of the LIM methodology used to investigate how ecosystem structure influenced carbon flow across the Indian margin OMZ. We demonstrate how oxygen conditions affect food-web complexity, affecting the linkages between the bacteria, foraminifera and metazoan fauna, and their contributions to benthic respiration. The food-web models demonstrate how changes in ecosystem complexity are associated with oxygen availability across the OMZ and allow us to obtain a complete carbon budget for the stationa where stable-isotope labelling experiments were conducted.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels.

PubMed

Sevenler, Derin; Daaboul, George G; Ekiz Kanik, Fulya; Ünlü, Neşe Lortlar; Ünlü, M Selim

2018-05-21

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Spin-Label Oximetry at Q- and W-Band

PubMed Central

Subczynski, W.K.; Mainali, L.; Camenisch, T.G.; Froncisz, W.; Hyde, J.S.

2011-01-01

Spin-lattice relaxation times (T1s) of both small water-soluble spin labels in the aqueous phase as well as lipid-type spin labels in membranes increase when the microwave frequency increases from 2 to 35 GHz (Hyde et al., J. Phys. Chem. B 108 [2004] 9524–9529). The T1 measured at W-band (94 GHz) for the water-soluble spin labels CTPO and TEMPONE (Froncisz et al., J. Magn. Reson. 193 [2008] 297–304) is, however, shorter than when measured at Q-band (35 GHz). In this paper, the decreasing trends at W-band have been confirmed for commonly used lipid-type spin labels in model membranes. It is concluded that the longest values of T1 will generally be found at Q-band, noting that long values are advantageous for measurement of bimolecular collisions with oxygen. The contribution of dissolved molecular oxygen to the relaxation rate was found to be independent of microwave frequency up to 94 GHz for lipid-type spin labels in membranes. This contribution is expressed in terms of the oxygen transport parameter W = T1−1(Air) − T1−1(N2), which is a function of both concentration and translational diffusion of oxygen in the local environment of a spin label. The new capabilities in measurement of the oxygen transport parameter using saturation-recovery (SR) EPR at Q- and W-band have been demonstrated in saturated (DMPC) and unsaturated (POPC) lipid bilayer membranes with the use of stearic acid (n-SASL) and phosphatidylcholine (n-PC) spin labels, and compared with results obtained earlier at X-band. SR EPR spin-label oximetry at Q- and W-band has the potential to be a powerful tool for studying samples of small volume, ~30 nL. These benefits, together with other factors such as a higher resonator efficiency parameter and a new technique for canceling free induction decay signals, are discussed. PMID:21277814

Label-Free, LC-MS-Based Assays to Quantitate Small-Molecule Antagonist Binding to the Mammalian BLT1 Receptor.

PubMed

Chen, Xun; Stout, Steven; Mueller, Uwe; Boykow, George; Visconti, Richard; Siliphaivanh, Phieng; Spencer, Kerrie; Presland, Jeremy; Kavana, Michael; Basso, Andrea D; McLaren, David G; Myers, Robert W

2017-08-01

We have developed and validated label-free, liquid chromatography-mass spectrometry (LC-MS)-based equilibrium direct and competition binding assays to quantitate small-molecule antagonist binding to recombinant human and mouse BLT1 receptors expressed in HEK 293 cell membranes. Procedurally, these binding assays involve (1) equilibration of the BLT1 receptor and probe ligand, with or without a competitor; (2) vacuum filtration through cationic glass fiber filters to separate receptor-bound from free probe ligand; and (3) LC-MS analysis in selected reaction monitoring mode for bound probe ligand quantitation. Two novel, optimized probe ligands, compounds 1 and 2, were identified by screening 20 unlabeled BLT1 antagonists for direct binding. Saturation direct binding studies confirmed the high affinity, and dissociation studies established the rapid binding kinetics of probe ligands 1 and 2. Competition binding assays were established using both probe ligands, and the affinities of structurally diverse BLT1 antagonists were measured. Both binding assay formats can be executed with high specificity and sensitivity and moderate throughput (96-well plate format) using these approaches. This highly versatile, label-free method for studying ligand binding to membrane-associated receptors should find broad application as an alternative to traditional methods using labeled ligands.

Appreciating Oxygen

ERIC Educational Resources Information Center

Weiss, Hilton M.

2008-01-01

Photosynthetic flora and microfauna utilize light from the sun to convert carbon dioxide and water into carbohydrates and oxygen. While these carbohydrates and their derivative hydrocarbons are generally considered to be fuels, it is the thermodynamically energetic oxygen molecule that traps, stores, and provides almost all of the energy that…

How plasma induced oxidation, oxygenation, and de-oxygenation influences viability of skin cells

NASA Astrophysics Data System (ADS)

Oh, Jun-Seok; Strudwick, Xanthe; Short, Robert D.; Ogawa, Kotaro; Hatta, Akimitsu; Furuta, Hiroshi; Gaur, Nishtha; Hong, Sung-Ha; Cowin, Allison J.; Fukuhara, Hideo; Inoue, Keiji; Ito, Masafumi; Charles, Christine; Boswell, Roderick W.; Bradley, James W.; Graves, David B.; Szili, Endre J.

2016-11-01

The effect of oxidation, oxygenation, and de-oxygenation arising from He gas jet and He plasma jet treatments on the viability of skin cells cultured in vitro has been investigated. He gas jet treatment de-oxygenated cell culture medium in a process referred to as "sparging." He plasma jet treatments oxidized, as well as oxygenated or de-oxygenated cell culture medium depending on the dissolved oxygen concentration at the time of treatment. He gas and plasma jets were shown to have beneficial or deleterious effects on skin cells depending on the concentration of dissolved oxygen and other oxidative molecules at the time of treatment. Different combinations of treatments with He gas and plasma jets can be used to modulate the concentrations of dissolved oxygen and other oxidative molecules to influence cell viability. This study highlights the importance of a priori knowledge of the concentration of dissolved oxygen at the time of plasma jet treatment, given the potential for significant impact on the biological or medical outcome. Monitoring and controlling the dynamic changes in dissolved oxygen is essential in order to develop effective strategies for the use of cold atmospheric plasma jets in biology and medicine.

Acetone in Orion BN/KL. High-resolution maps of a special oxygen-bearing molecule

NASA Astrophysics Data System (ADS)

Peng, T.-C.; Despois, D.; Brouillet, N.; Baudry, A.; Favre, C.; Remijan, A.; Wootten, A.; Wilson, T. L.; Combes, F.; Wlodarczak, G.

2013-06-01

Aims: As one of the prime targets of interstellar chemistry study, Orion BN/KL clearly shows different molecular distributions between large nitrogen- (e.g., C2H5CN) and oxygen-bearing (e.g., HCOOCH3) molecules. However, acetone (CH3)2CO, a special complex O-bearing molecule, has been shown to have a very different distribution from other typical O-bearing molecules in the BN/KL region. Therefore, it is worth investigating acetone in detail at high angular resolutions, which will help us understand the formation of this molecule and its chemical role in the complex BN/KL region. Methods: We searched for acetone within our IRAM Plateau de Bure Interferometer 3 mm and 1.3 mm data sets. Twenty-two acetone lines were searched within these data sets. The angular resolution ranged from 1farcs8×0farcs8 to 6farcs0×2farcs3, and the spectral resolution ranged from 0.4 to 1.9 km s-1. Results: Nine of the acetone lines appear free of contamination. Three main acetone peaks (Ace-1, 2, and 3) are identified in Orion BN/KL. The new acetone source Ace-3 and the extended emission in the north of the hot core region have been found for the first time. An excitation temperature of about 150 K is determined toward Ace-1 and Ace-2, and the acetone column density is estimated to be 2-4 × 1016 cm-2 with a relative abundance of 1-6 × 10-8 toward these two peaks. Acetone is a few times less abundant toward the hot core and Ace-3 compared with Ace-1 and Ace-2. Conclusions: We find that the overall distribution of acetone in BN/KL is similar to that of N-bearing molecules, e.g., NH3 and C2H5CN, and very different from those of large O-bearing molecules, e.g., HCOOCH3 and (CH3)2O. Our findings show the acetone distribution is more extended than in previous studies and does not originate only in those areas where both N-bearing and O-bearing species are present. Moreover, because the N-bearing molecules may be associated with shocked gas in Orion BN/KL, this suggests that the formation and

Validity of using a 3-dimensional PET scanner during inhalation of 15O-labeled oxygen for quantitative assessment of regional metabolic rate of oxygen in man

NASA Astrophysics Data System (ADS)

Hori, Yuki; Hirano, Yoshiyuki; Koshino, Kazuhiro; Moriguchi, Tetsuaki; Iguchi, Satoshi; Yamamoto, Akihide; Enmi, Junichiro; Kawashima, Hidekazu; Zeniya, Tsutomu; Morita, Naomi; Nakagawara, Jyoji; Casey, Michael E.; Iida, Hidehiro

2014-09-01

Use of 15O labeled oxygen (15O2) and positron emission tomography (PET) allows quantitative assessment of the regional metabolic rate of oxygen (CMRO2) in vivo, which is essential to understanding the pathological status of patients with cerebral vascular and neurological disorders. The method has, however, been challenging, when a 3D PET scanner is employed, largely attributed to the presence of gaseous radioactivity in the trachea and the inhalation system, which results in a large amount of scatter and random events in the PET assessment. The present study was intended to evaluate the adequacy of using a recently available commercial 3D PET scanner in the assessment of regional cerebral radioactivity distribution during an inhalation of 15O2. Systematic experiments were carried out on a brain phantom. Experiments were also performed on a healthy volunteer following a recently developed protocol for simultaneous assessment of CMRO2 and cerebral blood flow, which involves sequential administration of 15O2 and C15O2. A particular intention was to evaluate the adequacy of the scatter-correction procedures. The phantom experiment demonstrated that errors were within 3% at the practically maximum radioactivity in the face mask, with the greatest radioactivity in the lung. The volunteer experiment demonstrated that the counting rate was at peak during the 15O gas inhalation period, within a verified range. Tomographic images represented good quality over the entire FOV, including the lower part of the cerebral structures and the carotid artery regions. The scatter-correction procedures appeared to be important, particularly in the process to compensate for the scatter originating outside the FOV. Reconstructed images dramatically changed if the correction was carried out using inappropriate procedures. This study demonstrated that accurate reconstruction could be obtained when the scatter compensation was appropriately carried out. This study also suggested the

Fate of Pathologically Bound Oxygen Resulting from Inhalation of Labeled Ozone in Rats

PubMed Central

Hatch, Gary E.; Slade, Ralph; McKee, John

2013-01-01

Inhaled ozone (O3) reacts chemically with respiratory tract biomolecules where it forms covalently bound oxygen adducts. We investigated the fate of these adducts following inhalation exposure of rats to labeled ozone (18O3, 2 ppm, 6 hr or 5 ppm, 2 hr). Increased 18O was detected in blood plasma at 7 hr post exposure and was continuously present in urine for 4 days. Total 18O excreted was ~53% of the estimated amount of 18O3 retained by the rats during 18O3 exposure suggesting that only moderate recycling of the adduct material occurs. The time course of excretion, as well as properties of the excreted 18O were determined to provide guidance to future searches for urinary oxidative stress markers. These results lend plausibility to published findings that O3 inhalation could exert influences outside the lung, such as enhancement of atherosclerotic plaques. PMID:24052692

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

PubMed Central

2017-01-01

Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle–single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics. PMID:28762723

Combustion method for assay of biological materials labeled with carbon-14 or tritium, or double-labeled

NASA Technical Reports Server (NTRS)

Huebner, L. G.; Kisieleski, W. E.

1969-01-01

Dry catalytic combustion at high temperatures is used for assaying biological materials labeled carbon-14 and tritium, or double-labeled. A modified oxygen-flask technique is combined with standard vacuum-line techniques and includes convenience of direct in-vial collection of final combustion products, giving quantitative recovery of tritium and carbon-14.

99mTc: Labeling Chemistry and Labeled Compounds

NASA Astrophysics Data System (ADS)

Alberto, R.; Abram, U.

This chapter reviews the radiopharmaceutical chemistry of technetium related to the synthesis of perfusion agents and to the labeling of receptor-binding biomolecules. To understand the limitations of technetium chemistry imposed by future application of the complexes in nuclear medicine, an introductory section analyzes the compulsory requirements to be considered when facing the incentive of introducing a novel radiopharmaceutical into the market. Requirements from chemistry, routine application, and market are discussed. In a subsequent section, commercially available 99mTc-based radiopharmaceuticals are treated. It covers the complexes in use for imaging the most important target organs such as heart, brain, or kidney. The commercially available radiopharmaceuticals fulfill the requirements outlined earlier and are discussed with this background. In a following section, the properties and perspectives of the different generations of radiopharmaceuticals are described in a general way, covering characteristics for perfusion agents and for receptor-specific molecules. Technetium chemistry for the synthesis of perfusion agents and the different labeling approaches for target-specific biomolecules are summarized. The review comprises a general introduction to the common approaches currently in use, employing the N x S4-x , [3+1] and 2-hydrazino-nicotinicacid (HYNIC) method as well as more recent strategies such as the carbonyl and the TcN approach. Direct labeling without the need of a bifunctional chelator is briefly reviewed as well. More particularly, recent developments in the labeling of concrete targeting molecules, the second generation of radiopharmaceuticals, is then discussed and prominent examples with antibodies/peptides, neuroreceptor targeting small molecules, myocardial imaging agents, vitamins, thymidine, and complexes relevant to multidrug resistance are given. In addition, a new approach toward peptide drug development is described. The section

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

PubMed Central

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; Li, Jinyang; Schwab, Mark J.; Brudvig, Gary W.; Taylor, André D.

2016-01-01

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. However, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. Here, we show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O2 batteries. The heme's oxygen binding capability facilitates battery recharge by accepting and releasing dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. This study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage. PMID:27759005

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

Heme biomolecule as redox mediator and oxygen shuttle for efficient charging of lithium-oxygen batteries

DOE PAGES

Ryu, Won-Hee; Gittleson, Forrest S.; Thomsen, Julianne M.; ...

2016-10-19

One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. But, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. We show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O 2 batteries. The heme’s oxygen binding capability facilitates battery recharge by accepting and releasingmore » dissociated oxygen species while benefiting charge transfer with the cathode. We reveal the chemical change of heme redox molecules where synergy exists with the electrolyte species. Our study brings focus to the rational design of solution-based catalysts and suggests a sustainable cross-link between biomolecules and advanced energy storage.« less

Vascular Cell Adhesion Molecule-1 Expression and Signaling During Disease: Regulation by Reactive Oxygen Species and Antioxidants

PubMed Central

Marchese, Michelle E.; Abdala-Valencia, Hiam

2011-01-01

Abstract The endothelium is immunoregulatory in that inhibiting the function of vascular adhesion molecules blocks leukocyte recruitment and thus tissue inflammation. The function of endothelial cells during leukocyte recruitment is regulated by reactive oxygen species (ROS) and antioxidants. In inflammatory sites and lymph nodes, the endothelium is stimulated to express adhesion molecules that mediate leukocyte binding. Upon leukocyte binding, these adhesion molecules activate endothelial cell signal transduction that then alters endothelial cell shape for the opening of passageways through which leukocytes can migrate. If the stimulation of this opening is blocked, inflammation is blocked. In this review, we focus on the endothelial cell adhesion molecule, vascular cell adhesion molecule-1 (VCAM-1). Expression of VCAM-1 is induced on endothelial cells during inflammatory diseases by several mediators, including ROS. Then, VCAM-1 on the endothelium functions as both a scaffold for leukocyte migration and a trigger of endothelial signaling through NADPH oxidase-generated ROS. These ROS induce signals for the opening of intercellular passageways through which leukocytes migrate. In several inflammatory diseases, inflammation is blocked by inhibition of leukocyte binding to VCAM-1 or by inhibition of VCAM-1 signal transduction. VCAM-1 signal transduction and VCAM-1-dependent inflammation are blocked by antioxidants. Thus, VCAM-1 signaling is a target for intervention by pharmacological agents and by antioxidants during inflammatory diseases. This review discusses ROS and antioxidant functions during activation of VCAM-1 expression and VCAM-1 signaling in inflammatory diseases. Antioxid. Redox Signal. 15, 1607–1638. PMID:21050132

Potential energy surfaces for atomic oxygen reactions: Formation of singlet and triplet biradicals as primary reaction products with unsaturated organic molecules

NASA Technical Reports Server (NTRS)

Jaffe, Richard L.

1987-01-01

The experimental study of the interaction of atomic oxygen with organic polymer films under LEO conditions has been hampered by the inability to conduct detailed experiments in situ. As a result, studies of the mechanism of oxygen atom reactions have relied on laboratory O-atom sources that do not fully reproduce the orbital environment. For example, it is well established that only ground electronic state O atoms are present at LEO, yet most ground-based sources are known to produce singlet O atoms and molecules and ions in addition to O(3P). Engineers should not rely on such facilities unless it can be demonstrated either that these different O species are inert or that they react in the same fashion as ground state atoms. Ab initio quantum chemical calculations have been aimed at elucidating the biradical intermediates formed during the electrophilic addition of ground and excited-state O atoms to carbon-carbon double bonds in small olefins and aromatic molecules. These biradicals are critical intermediates in any possible insertion, addition and elimination reaction mechanisms. Through these calculations, we will be able to comment on the relative importance of these pathways for O(3P) and O(1D) reactions. The reactions of O atoms with ethylene and benzene are used to illustrate the important features of the mechanisms of atomic oxygen reaction with unsaturated organic compounds and polymeric materials.

Influence of DOTA chelator position on biodistribution and targeting properties of (111)In-labeled synthetic anti-HER2 affibody molecules.

PubMed

Perols, Anna; Honarvar, Hadis; Strand, Joanna; Selvaraju, Ramkumar; Orlova, Anna; Karlström, Amelie Eriksson; Tolmachev, Vladimir

2012-08-15

Affibody molecules are a class of affinity proteins. Their small size (7 kDa) in combination with the high (subnanomolar) affinity for a number of cancer-associated molecular targets makes them suitable for molecular imaging. Earlier studies demonstrated that the selection of radionuclide and chelator may substantially influence the tumor-targeting properties of affibody molecules. Moreover, the placement of chelators for labeling of affibody molecules with (99m)Tc at different positions in affibody molecules influenced both blood clearance rate and uptake in healthy tissues. This introduces an opportunity to improve the contrast of affibody-mediated imaging. In this comparative study, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was conjugated to the synthetic affibody molecule Z(HER2:S1) at three different positions: DOTA-A1-Z(HER2:S1) (N-terminus), DOTA-K58-Z(HER2:S1) (C-terminus), and DOTA-K50-Z(HER2:S1) (middle of helix 3). The affinity for HER2 differed slightly among the variants and the K(D) values were determined to be 133 pM, 107 pM and 94 pM for DOTA-A1-Z(HER2:S1), DOTA-K50-Z(HER2:S1), and DOTA-K58-Z(HER2:S1), respectively. Z(HER2:S1)-K50-DOTA showed a slightly lower melting point (57 °C) compared to DOTA-A1-Z(HER2:S1) (64 °C) and DOTA-K58-Z(HER2:S1) (62 °C), but all variants showed good refolding properties after heat treatment. All conjugates were successfully labeled with (111)In resulting in a radiochemical yield of 99% with preserved binding capacity. In vitro specificity studies using SKOV-3 and LS174T cell lines showed that the binding of the radiolabeled compounds was HER2 receptor-mediated, which also was verified in vivo using BALB/C nu/nu mice with LS174T and Ramos lymphoma xenografts. The three conjugates all showed specific uptake in LS174T xenografts in nude mice, where DOTA-A1-Z(HER2:S1)and DOTA-K58-Z(HER2:S1) showed the highest uptake. Overall, DOTA-K58-Z(HER2:S1) provided the highest tumor-to-blood ratio, which is

Fluorescent labels and their use in separations

DOEpatents

Mathies, Richard A.; Glazer, Alexander; Ju, Jingyue

1997-01-01

Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids.

Probes labelled with energy transfer coupled dyes

DOEpatents

Mathies, Richard A.; Glazer, Alexander; Ju, Jingyue

1997-01-01

Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids.

Probes labelled with energy transfer coupled dyes

DOEpatents

Mathies, R.A.; Glazer, A.; Ju, J.

1997-11-18

Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids. 7 figs.

Interactions of Oxygen and Water Molecules with Pyrite Surface: A New Insight.

PubMed

Li, Yuqiong; Chen, Jianhua; Chen, Ye; Zhao, Cuihua; Zhang, Yibing; Ke, Baolin

2018-02-06

Pyrite is the most common sulfide in nature, and it is well-known for its roles in acid mine drainage, flotation separation of useful metal (Cu, Pb, Zn, and Mo) sulfide minerals, optoelectronic and photovoltaic application, pneumoconiosis, and even in the origin of life. However, the detailed oxidation behaviors of pyrite are still unclear and not well-understood. New oxidation pathways by O 2 on the pyrite (100) surface have been found in this work for the first time using density functional theory simulation; that is, besides Fe sites, S sites are also possible oxidation sites in the initial oxidation state of pyrite, where easier and stronger oxidation may occur. This is the first time to confirm the other researchers' conjecture on the direct oxidation of S sites, which explains the isotopic composition experiments that a minor amount of O 2 is permanently incorporated into SO 4 2- during pyrite oxidation (O in SO 4 2- is mainly derived from water). We constructed various H 2 O-O 2 coadsorption models on the pyrite surface by considering the adsorption sequence of H 2 O and O 2 . It is found that the H 2 O molecule undergoes step-wise dissociation in the presence of the O 2 molecule. Hydroxyl radical •OH is the reactive oxygen species during H 2 O dissociation. Cyclic voltammetric measurements confirm the presence of •OH. In addition, H 2 O 2 may also be formed on the surface in terms of H 2 O-then-O 2 sequence adsorption.

Fab fragment labeled with ICG-derivative for detecting digestive tract cancer.

PubMed

Yano, Hiromi; Muguruma, Naoki; Ito, Susumu; Aoyagi, Eriko; Kimura, Tetsuo; Imoto, Yoshitaka; Cao, Jianxin; Inoue, Shohei; Sano, Shigeki; Nagao, Yoshimitsu; Kido, Hiroshi

2006-09-01

In previous studies, we generated infrared ray fluorescence-labeled monoclonal antibodies and developed an infrared ray fluorescence endoscope capable of detecting the monoclonal antibodies to establish a novel diagnostic technique for gastrointestinal cancer. Although the whole IgG molecule has commonly been used for preparation of labeled antibodies, labeled IgG displays insufficient sensitivity and specificity, probably resulting from non-specific binding of the Fc fragment to target cells or interference between fluorochromes on the identical labeled antibody, which might be caused by molecular structure. In this in vitro study, we characterized an Fc-free fluorescence-labeled Fab fragment, which was expected to yield more specific binding to target cells than the whole IgG molecule. An anti-mucin antibody and ICG-ATT, an ICG derivative, were used as the labeled antibody and labeling compound, respectively. Paraffin sections of excised gastric cancer tissues were subjected to staining. The labeled whole IgG molecule (ICG-ATT-labeled IgG) and the labeled Fab fragment (ICG-ATT-labeled Fab) were prepared according to a previous report, and the fluorescence properties, antibody activities, and features of fluorescence microscope images obtained from paraffin sections were compared. Both ICG-ATT-labeled Fab and ICG-ATT-labeled IgG were excited by a near infrared ray of 766nm, and maximum emission occurred at 804nm. Antibody activities of ICG-ATT-labeled Fab were shown to be similar to those of unlabeled anti-MUC1 antibody. The fluorescence intensity obtained from paraffin sections of excised gastric cancer tissues revealed a tendency to be greater with ICG-ATT-labeled Fab than with ICG-ATT-labeled IgG. The infrared ray fluorescence-labeled Fab fragment was likely to be more specific than the conventionally labeled antibodies. Fragmentation of antibodies is considered to contribute to improved sensitivity and specificity of labeled antibodies for detection of micro

Does photodissociation of molecular oxygen from myoglobin and hemoglobin yield singlet oxygen?

PubMed

Lepeshkevich, Sergei V; Stasheuski, Alexander S; Parkhats, Marina V; Galievsky, Victor A; Dzhagarov, Boris M

2013-03-05

Time-resolved luminescence measurements in the near-infrared region indicate that photodissociation of molecular oxygen from myoglobin and hemoglobin does not produce detectable quantities of singlet oxygen. A simple and highly sensitive method of luminescence quantification is developed and used to determine the upper limit for the quantum yield of singlet oxygen production. The proposed method was preliminarily evaluated using model data sets and confirmed with experimental data for aqueous solutions of 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin. A general procedure for error estimation is suggested. The method is shown to provide a determination of the integral luminescence intensity in a wide range of values even for kinetics with extremely low signal-to-noise ratio. The present experimental data do not deny the possibility of singlet oxygen generation during the photodissociation of molecular oxygen from myoglobin and hemoglobin. However, the photodissociation is not efficient to yield singlet oxygen escaped from the proteins into the surrounding medium. The upper limits for the quantum yields of singlet oxygen production in the surrounding medium after the photodissociation for oxyhemoglobin and oxymyoglobin do not exceed 3.4×10(-3) and 2.3×10(-3), respectively. On the average, no more than one molecule of singlet oxygen from every hundred photodissociated oxygen molecules can succeed in escaping from the protein matrix. Copyright © 2013 Elsevier B.V. All rights reserved.

Single molecule resolution of the antimicrobial action of quantum dot-labeled sushi peptide on live bacteria.

PubMed

Leptihn, Sebastian; Har, Jia Yi; Chen, Jianzhu; Ho, Bow; Wohland, Thorsten; Ding, Jeak Ling

2009-05-11

Antimicrobial peptides are found in all kingdoms of life. During the evolution of multicellular organisms, antimicrobial peptides were established as key elements of innate immunity. Most antimicrobial peptides are thought to work by disrupting the integrity of cell membranes, causing pathogen death. As antimicrobial peptides target the membrane structure, pathogens can only acquire resistance by a fundamental change in membrane composition. Hence, the evolution of pathogen resistance has been a slow process. Therefore antimicrobial peptides are valuable alternatives to classical antibiotics against which multiple drug-resistant bacteria have emerged. For potential therapeutic applications as antibiotics a thorough knowledge of their mechanism of action is essential. Despite the increasingly comprehensive understanding of the biochemical properties of these peptides, the actual mechanism by which antimicrobial peptides lyse microbes is controversial. Here we investigate how Sushi 1, an antimicrobial peptide derived from the horseshoe crab (Carcinoscorpius rotundicauda), induces lysis of Gram-negative bacteria. To follow the entire process of antimicrobial action, we performed a variety of experiments including transmission electron microscopy and fluorescence correlation spectroscopy as well as single molecule tracking of quantum dot-labeled antimicrobial peptides on live bacteria. Since in vitro measurements do not necessarily correlate with the in vivo action of a peptide we developed a novel fluorescent live bacteria lysis assay. Using fully functional nanoparticle-labeled Sushi 1, we observed the process of antimicrobial action at the single-molecule level. Recently the hypothesis that many antimicrobial peptides act on internal targets to kill the bacterium has been discussed. Here, we demonstrate that the target sites of Sushi 1 are outer and inner membranes and are not cytosolic. Further, our findings suggest four successive steps of the bactericidal process

Vibrational Relaxation of Ground-State Oxygen Molecules With Atomic Oxygen and Carbon Dioxide

NASA Astrophysics Data System (ADS)

Saran, D. V.; Pejakovic, D. A.; Copeland, R. A.

2008-12-01

Vertical water vapor profiles are key to understanding the composition and energy budget in the mesosphere and lower thermosphere (MLT). The SABER instrument onboard NASA's TIMED satellite measures such profiles by detecting H2O(ν2) emission in the 6.8 μm region. Collisional deactivation of vibrationally excited O2, O2(X3Σ-g, υ = 1) + H2O ↔ O2(X3Σ-g, υ = 0) + H2O(ν2), is an important source of H2O(ν2). A recent study has identified two other processes involving excited O2 that control H2O(ν2) population in the MLT: (1) the vibrational-translational (V-T) relaxation of O2(X3Σ-g, υ = 1) level by atomic oxygen and (2) the V-V exchange between CO2 and excited O2 molecules [1]. Over the past few years SRI researchers have measured the atomic oxygen removal process mentioned above at room temperature [2] and 240 K [3]. These measurements have been incorporated into the models for H2O(ν2) emission [1]. Here we report laboratory studies of the collisional removal of O2(X3Σ-g, υ = 1) by O(3P) at room temperature and below, reaching temperatures relevant to mesopause and polar summer MLT (~150 K). Instead of directly detecting the O2(X3Σ-g, υ = 1) population, a technically simpler approach is used in which the υ = 1 level of the O2(a1Δg) state is monitored. A two-laser method is employed, in which the pulsed output of the first laser near 285 nm photodissociates ozone to produce atomic oxygen and O2(a1Δg, υ = 1), and the pulsed output of the second laser detects O2(a1Δg, υ = 1) via resonance-enhanced multiphoton ionization. With ground-state O2 present, owing to the rapid equilibration of the O2(X3Σ-g, υ = 1) and O2(a1Δg, υ = 1) populations via the processes O2(a1Δg, υ = 1) + O2(X3Σ-g, υ = 0) ↔ O2(a1Δg, υ = 0) + O2(X3Σ-g, υ = 1), the information on the O2(X3Σ-g, υ = 1) kinetics is extracted from the O2(a1Δg, υ = 1) temporal evolution. In addition, measurements of the removal of O2(X3Σ-g, υ = 1) by CO2 at room temperature will also

Catalytic Oxidation of Methane into Methanol over Copper-Exchanged Zeolites with Oxygen at Low Temperature

PubMed Central

2016-01-01

The direct catalytic conversion of methane to liquid oxygenated compounds, such as methanol or dimethyl ether, at low temperature using molecular oxygen is a grand challenge in C–H activation that has never been met with synthetic, heterogeneous catalysts. We report the first demonstration of direct, catalytic oxidation of methane into methanol with molecular oxygen over copper-exchanged zeolites at low reaction temperatures (483–498 K). Reaction kinetics studies show sustained catalytic activity and high selectivity for a variety of commercially available zeolite topologies under mild conditions (e.g., 483 K and atmospheric pressure). Transient and steady state measurements with isotopically labeled molecules confirm catalytic turnover. The catalytic rates and apparent activation energies are affected by the zeolite topology, with caged-based zeolites (e.g., Cu-SSZ-13) showing the highest rates. Although the reaction rates are low, the discovery of catalytic sites in copper-exchanged zeolites will accelerate the development of strategies to directly oxidize methane into methanol under mild conditions. PMID:27413787

Improved Dye Stability in Single-Molecule Fluorescence Experiments

NASA Astrophysics Data System (ADS)

EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

Reaction Kinetics of Water Molecules with Oxygen Vacancies on Rutile TiO 2(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Nikolay G.; Kimmel, Gregory A.

2015-09-16

The formation of bridging hydroxyls (OHb) via reactions of water molecules with oxygen vacancies (VO) on reduced TiO 2(110) surfaces is studied using infrared reflection-absorption spectroscopy (IRAS), electron-stimulated desorption (ESD), and photon-stimulated desorption (PSD). Narrow IRAS peaks at 2737 cm-1 and 3711 cm -1 are observed for stretching vibrations of OD b and OH b on TiO 2(110), respectively. IRAS measurements with s- and p-polarized light demonstrate that the bridging hydroxyls are oriented normal to the (110) surface. The IR peaks disappear after the sample is exposed to O 2 or annealed in the temperature range of 400 – 600more » K (correlating with the temperature at which pairs of OHb’s reform water and then desorb), which is consistent with their identification as bridging hydroxyls. We have studied the kinetics of water reacting with the vacancies by monitoring the formation of bridging hydroxyls (using IRAS) as a function of the annealing temperature for a small amount of water initially dosed on the TiO 2(110) at low temperature. Separate experiments have also monitored the loss of water molecules (using water ESD) and vacancies (using the CO photooxidation reaction) due to the reactions of water molecules with the vacancies. All three techniques show that the reaction rate becomes appreciable for T > 150 K and that the reactions largely complete for T > 250 K. The temperature-dependent water-VO reaction kinetics are consistent with a Gaussian distribution of activation energies with E a = 0.545 eV, ΔE a(FWHM) = 0.125 eV, and a “normal” prefactor, v = 10 12 s -1. In contrast, a single activation energy with a physically reasonable prefactor does not fit the data well. Our experimental activation energy is close to theoretical estimates for the diffusion of water molecules along the Ti 5c rows on the reduced TiO 2(110) surface, which suggests that the diffusion of water controls the water – V O reaction rate.« less

Dextran hydrogel coated surface plasmon resonance imaging (SPRi) sensor for sensitive and label-free detection of small molecule drugs

NASA Astrophysics Data System (ADS)

Li, Shaopeng; Yang, Mo; Zhou, Wenfei; Johnston, Trevor G.; Wang, Rui; Zhu, Jinsong

2015-11-01

The label-free and sensitive detection of small molecule drugs on SPRi is still a challenging task, mainly due to the limited surface immobilization capacity of the sensor. In this research, a dextran hydrogel-coated gold sensor chip for SPRi was successfully fabricated via photo-cross-linking for enhanced surface immobilization capacity. The density of the dextran hydrogel was optimized for protein immobilization and sensitive small molecule detection. The protein immobilization capacity of the hydrogel was 10 times greater than a bare gold surface, and 20 times greater than an 11-mercaptoundecanoic acid (MUA) surface. Such a drastic improvement in immobilization capacity allowed the SPRi sensor to detect adequate response signals when probing small molecule binding events. The binding signal of 4 nM liquid-phase biotin to streptavidin immobilized on the dextran surface reached 435 RU, while no response was observed on bare gold or MUA surfaces. The dextran hydrogel-coated SPRi sensor was also applied in a kinetic study of the binding between an immunosuppressive drug (FK506) and its target protein (FKBP12) in a high-throughput microarray format. The measured binding affinity was shown to be consistent with reported literature values, and a detection limit of 0.5 nM was achieved.

Precursor state of oxygen molecules on the Si(001) surface during the initial room-temperature adsorption

NASA Astrophysics Data System (ADS)

Hwang, Eunkyung; Chang, Yun Hee; Kim, Yong-Sung; Koo, Ja-Yong; Kim, Hanchul

2012-10-01

The initial adsorption of oxygen molecules on Si(001) is investigated at room temperature. The scanning tunneling microscopy images reveal a unique bright O2-induced feature. The very initial sticking coefficient of O2 below 0.04 Langmuir is measured to be ˜0.16. Upon thermal annealing at 250-600 °C, the bright O2-induced feature is destroyed, and the Si(001) surface is covered with dark depressions that seem to be oxidized structures with -Si-O-Si- bonds. This suggests that the observed bright O2-induced feature is an intermediate precursor state that may be either a silanone species or a molecular adsorption structure.

Nanopipette Delivery of Individual Molecules to Cellular Compartments for Single-Molecule Fluorescence Tracking

PubMed Central

Bruckbauer, Andreas; James, Peter; Zhou, Dejian; Yoon, Ji Won; Excell, David; Korchev, Yuri; Jones, Roy; Klenerman, David

2007-01-01

We have developed a new method, using a nanopipette, for controlled voltage-driven delivery of individual fluorescently labeled probe molecules to the plasma membrane which we used for single-molecule fluorescence tracking (SMT). The advantages of the method are 1), application of the probe to predefined regions on the membrane; 2), release of only one or a few molecules onto the cell surface; 3), when combined with total internal reflection fluorescence microscopy, very low background due to unbound molecules; and 4), the ability to first optimize the experiment and then repeat it on the same cell. We validated the method by performing an SMT study of the diffusion of individual membrane glycoproteins labeled with Atto 647-wheat germ agglutin in different surface domains of boar spermatozoa. We found little deviation from Brownian diffusion with a mean diffusion coefficient of 0.79 ± 0.04 μm2/s in the acrosomal region and 0.10 ± 0.02 μm2/s in the postacrosomal region; this difference probably reflects different membrane structures. We also showed that we can analyze diffusional properties of different subregions of the cell membrane and probe for the presence of diffusion barriers. It should be straightforward to extend this new method to other probes and cells, and it can be used as a new tool to investigate the cell membrane. PMID:17631532

Oxygen in wound healing: nutrient, antibiotic, signaling molecule, and therapeutic agent.

PubMed

Eisenbud, David E

2012-07-01

Disturbances to healing observed under hypoxic conditions have given insights into the roles of oxygen. Wound hypoxia is more prevalent than generally appreciated, and occurs even in patients who are free of arterial occlusive disease. There is a strong scientific basis for oxygen treatment as prophylaxis against infection, to facilitate wound closure, and to prevent amputation in wounded patients. This article reviews extensive data from preclinical and human trials of supplemental inhaled oxygen, hyperbaric oxygen, and topical oxygen treatment. Oxygen supports biochemical metabolism and cellular function, and has roles in combating infection and facilitating the wound healing cascade. Copyright © 2012 Elsevier Inc. All rights reserved.

Single-Molecule Denaturation Mapping of Genomic DNA in Nanofluidic Channels

NASA Astrophysics Data System (ADS)

Reisner, Walter; Larsen, Niels; Kristensen, Anders; Tegenfeldt, Jonas O.; Flyvbjerg, Henrik

2009-03-01

We have developed a new DNA barcoding technique based on the partial denaturation of extended fluorescently labeled DNA molecules. We partially melt DNA extended in nanofluidic channels via a combination of local heating and added chemical denaturants. The melted molecules, imaged via a standard fluorescence videomicroscopy setup, exhibit a nonuniform fluorescence profile corresponding to a series of local dips and peaks in the intensity trace along the stretched molecule. We show that this barcode is consistent with the presence of locally melted regions and can be explained by calculations of sequence-dependent melting probability. We believe this melting mapping technology is the first optically based single molecule technique sensitive to genome wide sequence variation that does not require an additional enzymatic labeling or restriction scheme.

Kinetics of highly vibrationally excited O2(X) molecules in inductively-coupled oxygen plasmas

NASA Astrophysics Data System (ADS)

Annušová, Adriana; Marinov, Daniil; Booth, Jean-Paul; Sirse, Nishant; Lino da Silva, Mário; Lopez, Bruno; Guerra, Vasco

2018-04-01

The high degree of vibrational excitation of O2 ground state molecules recently observed in inductively coupled plasma discharges is investigated experimentally in more detail and interpreted using a detailed self-consistent 0D global kinetic model for oxygen plasmas. Additional experimental results are presented and used to validate the model. The vibrational kinetics considers vibrational levels up to v = 41 and accounts for electron impact excitation and de-excitation (e-V), vibration-to-translation relaxation (V-T) in collisions with O2 molecules and O atoms, vibration-to-vibration energy exchanges (V-V), excitation of electronically excited states, dissociative electron attachment, and electron impact dissociation. Measurements were performed at pressures of 10–80 mTorr (1.33 and 10.67 Pa) and radio frequency (13.56 MHz) powers up to 500 W. The simulation results are compared with the absolute densities in each O2 vibrational level obtained by high sensitivity absorption spectroscopy measurements of the Schumann–Runge bands for O2(X, v = 4–18), O(3 P) atom density measurements by two-photon absorption laser induced fluorescence (TALIF) calibrated against Xe, and laser photodetachment measurements of the O‑ negative ions. The highly excited O2(X, v) distribution exhibits a shape similar to a Treanor-Gordiets distribution, but its origin lies in electron impact e-V collisions and not in V-V up-pumping, in contrast to what happens in all other molecular gases known to date. The relaxation of vibrational quanta is mainly due to V-T energy-transfer collisions with O atoms and to electron impact dissociation of vibrationally excited molecules, e+O2(X, v)→O(3P)+O(3P).

Fluorine-18 Radiochemistry, Labeling Strategies and Synthetic Routes

PubMed Central

2015-01-01

Fluorine-18 is the most frequently used radioisotope in positron emission tomography (PET) radiopharmaceuticals in both clinical and preclinical research. Its physical and nuclear characteristics (97% β+ decay, 109.7 min half-life, 635 keV positron energy), along with high specific activity and ease of large scale production, make it an attractive nuclide for radiochemical labeling and molecular imaging. Versatile chemistry including nucleophilic and electrophilic substitutions allows direct or indirect introduction of 18F into molecules of interest. The significant increase in 18F radiotracers for PET imaging accentuates the need for simple and efficient 18F-labeling procedures. In this review, we will describe the current radiosynthesis routes and strategies for 18F labeling of small molecules and biomolecules. PMID:25473848

49 CFR 175.501 - Special requirements for oxidizers and compressed oxygen.

Code of Federal Regulations, 2012 CFR

2012-10-01

... oxygen. 175.501 Section 175.501 Transportation Other Regulations Relating to Transportation PIPELINE AND... Special requirements for oxidizers and compressed oxygen. (a) Compressed oxygen, when properly labeled Oxidizer or Oxygen, may be loaded and transported as provided in this section. Except for Oxygen...

49 CFR 175.501 - Special requirements for oxidizers and compressed oxygen.

Code of Federal Regulations, 2014 CFR

2014-10-01

... oxygen. 175.501 Section 175.501 Transportation Other Regulations Relating to Transportation PIPELINE AND... Special requirements for oxidizers and compressed oxygen. (a) Compressed oxygen, when properly labeled Oxidizer or Oxygen, may be loaded and transported as provided in this section. Except for Oxygen...

49 CFR 175.501 - Special requirements for oxidizers and compressed oxygen.

Code of Federal Regulations, 2010 CFR

2010-10-01

... oxygen. 175.501 Section 175.501 Transportation Other Regulations Relating to Transportation PIPELINE AND... Special requirements for oxidizers and compressed oxygen. (a) Compressed oxygen, when properly labeled Oxidizer or Oxygen, may be loaded and transported as provided in this section. Except for Oxygen...

49 CFR 175.501 - Special requirements for oxidizers and compressed oxygen.

Code of Federal Regulations, 2013 CFR

2013-10-01

... oxygen. 175.501 Section 175.501 Transportation Other Regulations Relating to Transportation PIPELINE AND... Special requirements for oxidizers and compressed oxygen. (a) Compressed oxygen, when properly labeled Oxidizer or Oxygen, may be loaded and transported as provided in this section. Except for Oxygen...

49 CFR 175.501 - Special requirements for oxidizers and compressed oxygen.

Code of Federal Regulations, 2011 CFR

2011-10-01

... oxygen. 175.501 Section 175.501 Transportation Other Regulations Relating to Transportation PIPELINE AND... Special requirements for oxidizers and compressed oxygen. (a) Compressed oxygen, when properly labeled Oxidizer or Oxygen, may be loaded and transported as provided in this section. Except for Oxygen...

Isotopic measurements (C,N,O) of detonation soot produced from labeled and unlabeled Composition B-3 indicate source of solid carbon residues

NASA Astrophysics Data System (ADS)

Podlesak, David; Manner, Virginia; Amato, Ronald; Dattelbaum, Dana; Gusavsen, Richard; Huber, Rachel

2017-06-01

Detonation of HE is an exothermic process whereby metastable complex molecules are converted to simple stable molecules such as H2 O, N2, CO, CO2, and solid carbon. The solid carbon contains various allotropes such as detonation nanodiamonds, graphite, and amorphous carbon. It is well known that certain HE formulations such as Composition B (60% RDX, 40% TNT) produce greater amounts of solid carbon than other more oxygen-balanced formulations. To develop a greater understanding of how formulation and environment influence solid carbon formation, we synthesized TNT and RDX with 13 C and 15 N at levels slightly above natural abundance levels. Synthesized RDX and TNT were mixed at a ratio of 60:40 to form Composition B and solid carbon residues were collected from detonations of isotopically-labeled as well as un-labelled Composition B. The raw HE and detonation residues were analyzed isotopically for C, N, O isotopic compositions. We will discuss differences between treatments groups as a function of formulation and environment. LA-UR - 17-21266.

Consistent assignment of the vibrations of symmetric and asymmetric para-disubstituted benzene molecules

NASA Astrophysics Data System (ADS)

Andrejeva, Anna; Gardner, Adrian M.; Tuttle, William D.; Wright, Timothy G.

2016-03-01

We give a description of the phenyl-ring-localized vibrational modes of the ground states of the para-disubstituted benzene molecules including both symmetric and asymmetric cases. In line with others, we quickly conclude that the use of Wilson mode labels is misleading and ambiguous; we conclude the same regarding the related ones of Varsányi. Instead we label the modes consistently based upon the Mulliken (Herzberg) method for the modes of para-difluorobenzene (pDFB). Since we wish the labelling scheme to cover both symmetrically- and asymmetrically-substituted molecules, we apply the Mulliken labelling under C2v symmetry. By studying the variation of the vibrational wavenumbers with mass of the substituent, we are able to identify the corresponding modes across a wide range of molecules and hence provide consistent assignments. Particularly interesting are pairs of vibrations that evolve from in- and out-of-phase motions in pDFB to more localized modes in asymmetric molecules. We consider the para isomers of the following: the symmetric dihalobenzenes, xylene, hydroquinone, the asymmetric dihalobenzenes, halotoluenes, halophenols and cresol.

The role of highly oxygenated molecules (HOMs) in determining the composition of ambient ions in the boreal forest

NASA Astrophysics Data System (ADS)

Bianchi, Federico; Garmash, Olga; He, Xucheng; Yan, Chao; Iyer, Siddharth; Rosendahl, Ida; Xu, Zhengning; Rissanen, Matti P.; Riva, Matthieu; Taipale, Risto; Sarnela, Nina; Petäjä, Tuukka; Worsnop, Douglas R.; Kulmala, Markku; Ehn, Mikael; Junninen, Heikki

2017-11-01

In order to investigate the negative ions in the boreal forest we have performed measurements to chemically characterise the composition of negatively charged clusters containing highly oxygenated molecules (HOMs). Additionally, we compared this information with the chemical composition of the neutral gas-phase molecules detected in the ambient atmosphere during the same period. The chemical composition of the ions was retrieved using an atmospheric pressure interface time-of-flight mass spectrometer (APi-TOF-MS) while the gas-phase neutral molecules (mainly sulfuric acid and HOMs) were characterised using the same mass spectrometer coupled to a nitrate-based chemical ionisation unit (CI-APi-TOF). Overall, we divided the identified HOMs in two classes: HOMs containing only carbon, hydrogen and oxygen and nitrogen-containing HOMs or organonitrates (ONs). During the day, among the ions, in addition to the well-known pure sulfuric acid clusters, we found a large number of HOMs clustered with nitrate (NO3-) or bisulfate (HSO4-), with the first one being more abundant. During the night, the distribution of ions, mainly composed of HOM clustered with NO3-, was very similar to the neutral compounds that are detected in the CI-APi-TOF as adducts with the artificially introduced primary ion (NO3-). For the first time, we identified several clusters containing up to 40 carbon atoms. These ions are formed by up to four oxidised α-pinene units clustered with NO3-. While we know that dimers (16-20 carbon atoms) are probably formed by a covalent bond between two α-pinene oxidised units, it is still unclear what bonding formed larger clusters. Finally, diurnal profiles of the negative ions were consistent with the neutral compounds revealing that ONs peak during the day while HOMs are more abundant at night-time. However, during the day, a large fraction of the negative charge is taken up by the pure sulfuric acid clusters causing differences between ambient ions and neutral

Positron emission reconstruction tomography for the assessment of regional myocardial metabolism by the administration of substrates labeled with cyclotron produced radionuclides

NASA Technical Reports Server (NTRS)

Ter-Pogossian, M. M.; Hoffman, E. J.; Weiss, E. S.; Coleman, R. E.; Phelps, M. E.; Welch, M. J.; Sobel, B. E.

1975-01-01

A positron emission transverse tomograph device was developed which provides transaxial sectional images of the distribution of positron-emitting radionuclides in the heart. The images provide a quantitative three-dimensional map of the distribution of activity unencumbered by the superimposition of activity originating from regions overlying and underlying the plane of interest. PETT is used primarily with the cyclotron-produced radionuclides oxygen-15, nitrogen-13 and carbon-11. Because of the participation of these atoms in metabolism, they can be used to label metabolic substrates and intermediary molecules incorporated in myocardial metabolism.

Enzymatic production of single-molecule FISH and RNA capture probes.

PubMed

Gaspar, Imre; Wippich, Frank; Ephrussi, Anne

2017-10-01

Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed. © 2017 Gaspar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Fluorescein isothiocyanate-labeled human plasma fibronectin in extracellular matrix remodeling.

PubMed

Hoffmann, Celine; Leroy-Dudal, Johanne; Patel, Salima; Gallet, Olivier; Pauthe, Emmanuel

2008-01-01

Fluorescein isothiocyanate (FITC) is a well-known probe for labeling biologically relevant proteins. However, the impact of the labeling procedure on protein structure and biological activities remains unclear. In this work, FITC-labeled human plasma fibronectin (Fn) was developed to gain insight into the dynamic relationship between cells and Fn. The similarities and differences concerning the structure and function between Fn-FITC and standard Fn were evaluated using biochemical as well as cellular approaches. By varying the FITC/Fn ratio, we demonstrated that overlabeling (>10 FITC molecules/Fn molecule) induces probe fluorescence quenching, protein aggregation, and cell growth modifications. A correct balance between reliable fluorescence for detection and no significant modifications to structure and biological function compared with standard Fn was obtained with a final ratio of 3 FITC molecules per Fn molecule (Fn-FITC3). Fn-FITC3, similar to standard Fn, is correctly recruited into the cell matrix network. Also, Fn-FITC3 is proposed to be a powerful molecular tool to investigate Fn organization and cellular behavior concomitantly.

Group specific internal standard technology (GSIST) for simultaneous identification and quantification of small molecules

DOEpatents

Adamec, Jiri; Yang, Wen-Chu; Regnier, Fred E

2014-01-14

Reagents and methods are provided that permit simultaneous analysis of multiple diverse small molecule analytes present in a complex mixture. Samples are labeled with chemically identical but isotopically distince forms of the labeling reagent, and analyzed using mass spectrometry. A single reagent simultaneously derivatizes multiple small molecule analytes having different reactive functional groups.

Two-Way Gold Nanoparticle Label-Free Sensing of Specific Sequence and Small Molecule Targets Using Switchable Concatemers.

PubMed

Zhu, Longjiao; Shao, Xiangli; Luo, Yunbo; Huang, Kunlung; Xu, Wentao

2017-05-19

A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1 and H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained a single-stranded DNA (ssDNA) loop and sticky end to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change. This process then starts the alternate-opening of H1 and H2 through HCR, and dsDNA concatemers grow from the target sequence. As a result, unmodified GNPs undergo salt-induced aggregation because the formed dsDNA concatemers are stiffer and provide less stabilization. A light purple-to-blue color variation was observed in the bulk solution, termed the light-off sensing way. Furthermore, H1 ingeniously inserted an aptamer sequence to generate dsDNA concatemers with multiple small molecule binding sites. In the presence of small molecule targets, concatemers can be disassembled into mixtures with ssDNA sticky ends. A blue-to-purple reverse color variation was observed due to the regeneration of the ssDNA, termed the light-on way. The two-way biosensor can detect both nucleic acids and small molecule targets with one sensing device. This switchable sensing element is label-free, enzyme-free, and sophisticated-instrumentation-free. The detection limits of both targets were below nanomolar.

Singlet oxygen detection in biological systems: Uses and limitations.

PubMed

Koh, Eugene; Fluhr, Robert

2016-07-02

The study of singlet oxygen in biological systems is challenging in many ways. Singlet oxygen is a relatively unstable ephemeral molecule, and its properties make it highly reactive with many biomolecules, making it difficult to quantify accurately. Several methods have been developed to study this elusive molecule, but most studies thus far have focused on those conditions that produce relatively large amounts of singlet oxygen. However, the need for more sensitive methods is required as one begins to explore the levels of singlet oxygen required in signaling and regulatory processes. Here we discuss the various methods used in the study of singlet oxygen, and outline their uses and limitations.

A new interstellar molecule - Tricarbon monoxide

NASA Technical Reports Server (NTRS)

Matthews, H. E.; Irvine, W. M.; Friberg, P.; Brown, R. D.; Godfrey, P. D.

1984-01-01

The C3O molecule, whose pure rotational spectrum has only recently been studied in the laboratory, has been detected in the cold, dark interstellar Taurus Molecular Cloud 1. Since C3O is the first interstelar carbon chain molecule to contain oxygen, its existence places an important new constraint on chemical schemes for cold interstellar clouds. The abundance of C3O can be understood in terms of purely gas-phase ion-molecule chemistry.

Selective photooxidation of hydrocarbons in zeolites by oxygen

DOEpatents

Frei, Heinz; Blatter, Fritz; Sun, Hai

1998-01-01

A selective photooxidation process for the conversion of hydrocarbon molecules to partially oxygenated derivatives, which comprises the steps of adsorbing a hydrocarbon and oxygen onto a dehydrated zeolite support matrix to form a hydrocarbon-oxygen contact pair, and subsequently exposing the hydrocarbon-oxygen contact pair to visible light, thereby forming a partially oxygenated derivative.

A Single-Molecule Barcoding System using Nanoslits for DNA Analysis

NASA Astrophysics Data System (ADS)

Jo, Kyubong; Schramm, Timothy M.; Schwartz, David C.

Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels

Small-molecule-based protein-labeling technology in live cell studies: probe-design concepts and applications.

PubMed

Mizukami, Shin; Hori, Yuichiro; Kikuchi, Kazuya

2014-01-21

The use of genetic engineering techniques allows researchers to combine functional proteins with fluorescent proteins (FPs) to produce fusion proteins that can be visualized in living cells, tissues, and animals. However, several limitations of FPs, such as slow maturation kinetics or issues with photostability under laser illumination, have led researchers to examine new technologies beyond FP-based imaging. Recently, new protein-labeling technologies using protein/peptide tags and tag-specific probes have attracted increasing attention. Although several protein-labeling systems are com mercially available, researchers continue to work on addressing some of the limitations of this technology. To reduce the level of background fluorescence from unlabeled probes, researchers have pursued fluorogenic labeling, in which the labeling probes do not fluoresce until the target proteins are labeled. In this Account, we review two different fluorogenic protein-labeling systems that we have recently developed. First we give a brief history of protein labeling technologies and describe the challenges involved in protein labeling. In the second section, we discuss a fluorogenic labeling system based on a noncatalytic mutant of β-lactamase, which forms specific covalent bonds with β-lactam antibiotics such as ampicillin or cephalosporin. Based on fluorescence (or Förster) resonance energy transfer and other physicochemical principles, we have developed several types of fluorogenic labeling probes. To extend the utility of this labeling system, we took advantage of a hydrophobic β-lactam prodrug structure to achieve intracellular protein labeling. We also describe a small protein tag, photoactive yellow protein (PYP)-tag, and its probes. By utilizing a quenching mechanism based on close intramolecular contact, we incorporated a turn-on switch into the probes for fluorogenic protein labeling. One of these probes allowed us to rapidly image a protein while avoiding washout. In

Exotic Metal Molecules in Oxygen-rich Envelopes: Detection of AlOH (X1Σ+) in VY Canis Majoris

NASA Astrophysics Data System (ADS)

Tenenbaum, E. D.; Ziurys, L. M.

2010-03-01

A new interstellar molecule, AlOH, has been detected toward the envelope of VY Canis Majoris (VY CMa), an oxygen-rich red supergiant. Three rotational transitions of AlOH were observed using the facilities of the Arizona Radio Observatory (ARO). The J = 9 → 8 and J = 7 → 6 lines at 1 mm were measured with the ARO Submillimeter Telescope, while the J = 5 → 4 transition at 2 mm was observed with the ARO 12 m antenna on Kitt Peak. The AlOH spectra exhibit quite narrow line widths of 16-23 km s-1, as found for NaCl in this source, indicating that the emission arises from within the dust acceleration zone of the central circumstellar outflow. From a radiative transfer analysis, the abundance of AlOH relative to H2 was found to be ~1 × 10-7 for a source size of 0.26'' or 22 R* . In contrast, AlCl was not detected with f <= 5 × 10-8. AlOH is likely formed just beyond the photosphere via thermodynamic equilibrium chemistry and then disappears due to dust condensation. The AlOH/AlO abundance ratio found in VY CMa is ~17. Therefore, AlOH appears to be the dominant gas-phase molecular carrier of aluminum in this oxygen-rich shell. Local thermodynamic equilibrium calculations predict that the monohydroxides should be the major carriers of Al, Ca, and Mg in O-rich envelopes, as opposed to the oxides or halides. The apparent predominance of aluminum-bearing molecules in VY CMa may reflect proton addition processes in H-shell burning.

Optically (solar) pumped oxygen-iodine lasers

NASA Astrophysics Data System (ADS)

Danilov, O. B.; Zhevlakov, A. P.; Yur'ev, M. S.

2014-07-01

We present the results of theoretical and experimental studies demonstrating the possibility of developing an oxygen-iodine laser (OIL) with direct optical pumping of molecular oxygen involving inter-molecular interaction with charge transfer from donor molecule (buffer gas) to acceptor molecule (oxygen). This interaction lifts degeneracy of the lower energy states of molecular oxygen and increases its absorption cross section in the visible spectral region and the UV Herzberg band, where high quantum yield of singlet oxygen is achieved (QY ˜ 1 and QY ˜ 2, respectively) at the same time. A pulse-periodic optical pump sources with pulse energy of ˜50 kJ, pulse duration of ˜25 μs, and repetition rate of ˜10 Hz, which are synchronized with the mechanism of singlet oxygen generation, are developed. This allows implementation of a pulse-periodic oxygen-iodine laser with an efficiency of ˜25%, optical efficiency of ˜40%, and parameter L/ T ˜ 1/1.5, where T is the thermal energy released in the laser active medium upon generation of energy L. It is demonstrated that, under direct solar pumping of molecular oxygen, the efficiency parameter of the OIL can reach L/ T ˜ 1/0.8 in a wide range of scaling factors.

Singlet oxygen detection in biological systems: Uses and limitations

PubMed Central

Koh, Eugene; Fluhr, Robert

2016-01-01

ABSTRACT The study of singlet oxygen in biological systems is challenging in many ways. Singlet oxygen is a relatively unstable ephemeral molecule, and its properties make it highly reactive with many biomolecules, making it difficult to quantify accurately. Several methods have been developed to study this elusive molecule, but most studies thus far have focused on those conditions that produce relatively large amounts of singlet oxygen. However, the need for more sensitive methods is required as one begins to explore the levels of singlet oxygen required in signaling and regulatory processes. Here we discuss the various methods used in the study of singlet oxygen, and outline their uses and limitations. PMID:27231787

Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

PubMed

Braun, Joerg E; Serebrov, Victor

2017-01-01

Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

Click strategies for single-molecule protein fluorescence.

PubMed

Milles, Sigrid; Tyagi, Swati; Banterle, Niccolò; Koehler, Christine; VanDelinder, Virginia; Plass, Tilman; Neal, Adrian P; Lemke, Edward A

2012-03-21

Single-molecule methods have matured into central tools for studies in biology. Foerster resonance energy transfer (FRET) techniques, in particular, have been widely applied to study biomolecular structure and dynamics. The major bottleneck for a facile and general application of these studies arises from the need to label biological samples site-specifically with suitable fluorescent dyes. In this work, we present an optimized strategy combining click chemistry and the genetic encoding of unnatural amino acids (UAAs) to overcome this limitation for proteins. We performed a systematic study with a variety of clickable UAAs and explored their potential for high-resolution single-molecule FRET (smFRET). We determined all parameters that are essential for successful single-molecule studies, such as accessibility of the probes, expression yield of proteins, and quantitative labeling. Our multiparameter fluorescence analysis allowed us to gain new insights into the effects and photophysical properties of fluorescent dyes linked to various UAAs for smFRET measurements. This led us to determine that, from the extended tool set that we now present, genetically encoding propargyllysine has major advantages for state-of-the-art measurements compared to other UAAs. Using this optimized system, we present a biocompatible one-step dual-labeling strategy of the regulatory protein RanBP3 with full labeling position freedom. Our technique allowed us then to determine that the region encompassing two FxFG repeat sequences adopts a disordered but collapsed state. RanBP3 serves here as a prototypical protein that, due to its multiple cysteines, size, and partially disordered structure, is not readily accessible to any of the typical structure determination techniques such as smFRET, NMR, and X-ray crystallography.

Enhancing Dissociative Adsorption of Water on Cu(111) via Chemisorbed Oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qianqian; Li, Jonathan; Tong, Xiao

We have used X-ray photoelectron spectroscopy to study the dehydrogenation of H 2O molecules on the clean and oxygenated Cu(111) surfaces. The clean surface does not show reactivity toward H 2O dehydrogenation. By contrast, H 2O molecules on the oxygenated Cu(111) dissociate into OH species by reacting with chemisorbed oxygen until the complete consumption of the chemisorbed oxygen at which the surface loses its reactivity toward H 2O dehydrogenation. Increasing the temperature to 200 °C and above decreases molecularly adsorbed H 2O for dehydrogenation, thereby resulting in less loss of chemisorbed O. In conjunction with density-functional theory calculations, a three-stepmore » reaction pathway is proposed to account for the chemisorbed O assisted dehydrogenation of H 2O molecules and the net loss of surface oxygen. Finally, these results provide insight into understanding the elemental steps of the dehydrogenation of H 2O molecules and the controllable conditions for tuning H 2O dissociation on metal surfaces.« less

Enhancing Dissociative Adsorption of Water on Cu(111) via Chemisorbed Oxygen

DOE PAGES

Liu, Qianqian; Li, Jonathan; Tong, Xiao; ...

2017-05-16

We have used X-ray photoelectron spectroscopy to study the dehydrogenation of H 2O molecules on the clean and oxygenated Cu(111) surfaces. The clean surface does not show reactivity toward H 2O dehydrogenation. By contrast, H 2O molecules on the oxygenated Cu(111) dissociate into OH species by reacting with chemisorbed oxygen until the complete consumption of the chemisorbed oxygen at which the surface loses its reactivity toward H 2O dehydrogenation. Increasing the temperature to 200 °C and above decreases molecularly adsorbed H 2O for dehydrogenation, thereby resulting in less loss of chemisorbed O. In conjunction with density-functional theory calculations, a three-stepmore » reaction pathway is proposed to account for the chemisorbed O assisted dehydrogenation of H 2O molecules and the net loss of surface oxygen. Finally, these results provide insight into understanding the elemental steps of the dehydrogenation of H 2O molecules and the controllable conditions for tuning H 2O dissociation on metal surfaces.« less

Single DNA molecule detection using nanopipettes and nanoparticles.

PubMed

Karhanek, Miloslav; Kemp, Jennifer T; Pourmand, Nader; Davis, Ronald W; Webb, Chris D

2005-02-01

Single DNA molecules labeled with nanoparticles can be detected by blockades of ionic current as they are translocated through a nanopipette tip formed by a pulled glass capillary. The nanopipette detection technique can provide not only tools for detection and identification of single DNA and protein molecules but also deeper insight and understanding of stochastic interactions of various biomolecules with their environment.

The Three Forms of Molecular Oxygen.

ERIC Educational Resources Information Center

Laing, Michael

1989-01-01

Finds that a logical application of the simple rules of the molecular orbital bonding theory for diatomic molecules predicted the existence of three spin isomers of the oxygen molecule: one triplet form with two unpaired electrons and two singlet forms with all electrons paired. (MVL)

Detection of an oxygen atmosphere on Jupiter's moon Europa.

PubMed

Hall, D T; Strobel, D F; Feldman, P D; McGrath, M A; Weaver, H A

1995-02-23

Europa, the second large satellite out from Jupiter, is roughly the size of Earth's Moon, but unlike the Moon, it has water ice on its surface. There have been suggestions that an oxygen atmosphere should accumulate around such a body, through reactions which break up the water molecules and form molecular hydrogen and oxygen. The lighter H2 molecules would escape from Europa relatively easily, leaving behind an atmosphere rich in oxygen. Here we report the detection of atomic oxygen emission from Europa, which we interpret as being produced by the simultaneous dissociation and excitation of atmospheric O2 by electrons from Jupiter's magnetosphere. Europa's molecular oxygen atmosphere is very tenuous, with a surface pressure about 10(-11) that of the Earth's atmosphere at sea level.

Two-photon absorption in conjugated energetic molecule

DOE PAGES

Bjorgaard, Josiah August; Sifain, Andrew; Nelson, Tammie Renee; ...

2016-06-03

Time-dependent density functional theory (TD-DFT) is used to investigate the relationship between molecular structure and one- and two-photon absorption (OPA and TPA, respectively) properties in novel and recently synthesized conjugated energetic molecules (CEMs). The molecular structure of CEMs can be strategically altered to influence the heat of formation and oxygen balance, two factors that can contribute to the sensitivity and strength of an explosive material. OPA and TPA are sensitive to changes in molecular structure as well, influencing optical range of excitation. We find calculated vertical excitation energies in good agreement with experiment for most molecules. Peak TPA intensities aremore » significant and on the order of 102 GM. Natural transition orbitals for essential electronic states defining TPA peaks of relatively large intensity to examine the character of relevant transitions. Minor modification of molecular substituents, such as additional oxygen and other functional groups, produces significant changes in electronic structure, OPA, TPA, and improves the oxygen balance. Results show that select molecules are apt to nonlinear absorption, opening the possibility for controlled, direct optical initiation of CEMs through photochemical pathways.« less

Laser Ablation Molecular Isotopic Spectrometry for Molecules Formation Chemistry in Femtosecond-Laser Ablated Plasmas.

PubMed

Hou, Huaming; Mao, Xianglei; Zorba, Vassilia; Russo, Richard E

2017-07-18

Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser-induced plasma in addition to isotope analysis. LAMIS is a powerful tool for tracking the origination of atoms that is involved in formation of investigated molecules by labeling atoms with their isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C 2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma. This research focuses on elucidating the formation pathways of AlO radicals in femtosecond laser ablated plasma from 18 O-labeled Al 2 O 3 pellet. Plasmas expanding with strong forward bias in the direction normal to the sample surface were generated in the wake of a weakly ionized channel created by a femtosecond laser. The formation mechanism of AlO and influence of air were investigated with multiple plasma diagnostic methods such as monochromatic fast gating imaging, spatiotemporal resolved optical emission spectroscopy, and LAMIS. An advanced LAMIS fitting procedure was used to deduce the spatiotemporal distributions of Al 18 O and Al 16 O number densities and also their ratios. We found that the Al 16 O/Al 18 O number density ratio is higher for plasma portion closer to the sample surface, which suggests that chemical reactions between the plasma plume and ambient air are more intense at the tail of the plasma. The results also reveals that direct association of free Al and O atoms is the main mechanism for the formation of AlO at the early stage of the plasma. To the contrast, chemical reactions between plasma materials and ambient oxygen molecules and the isotope exchange effect are the dominant mechanisms of the formation of AlO and evolution of Al 16 O/Al 18 O number density ratio at the late stage of the plasma.

X-ray induced singlet oxygen generation by nanoparticle-photosensitizer conjugates for photodynamic therapy: determination of singlet oxygen quantum yield.

PubMed

Clement, Sandhya; Deng, Wei; Camilleri, Elizabeth; Wilson, Brian C; Goldys, Ewa M

2016-01-28

Singlet oxygen is a primary cytotoxic agent in photodynamic therapy. We show that CeF3 nanoparticles, pure as well as conjugated through electrostatic interaction with the photosensitizer verteporfin, are able to generate singlet oxygen as a result of UV light and 8 keV X-ray irradiation. The X-ray stimulated singlet oxygen quantum yield was determined to be 0.79 ± 0.05 for the conjugate with 31 verteporfin molecules per CeF3 nanoparticle, the highest conjugation level used. From this result we estimate the singlet oxygen dose generated from CeF3-verteporfin conjugates for a therapeutic dose of 60 Gy of ionizing radiation at energies of 6 MeV and 30 keV to be (1.2 ± 0.7) × 10(8) and (2.0 ± 0.1) × 10(9) singlet oxygen molecules per cell, respectively. These are comparable with cytotoxic doses of 5 × 10(7)-2 × 10(9) singlet oxygen molecules per cell reported in the literature for photodynamic therapy using light activation. We confirmed that the CeF3-VP conjugates enhanced cell killing with 6 MeV radiation. This work confirms the feasibility of using X- or γ- ray activated nanoparticle-photosensitizer conjugates, either to supplement the radiation treatment of cancer, or as an independent treatment modality.

Exploring the Diffusion of Molecular Oxygen in the Red Fluorescent Protein mCherry Using Explicit Oxygen Molecular Dynamics Simulations

PubMed Central

Regmi, Chola K.; Bhandari, Yuba R.; Gerstman, Bernard S.; Chapagain, Prem P.

2013-01-01

The development of fluorescent proteins (FPs) has revolutionized cell biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for tagging and tracking cellular processes in vivo. Determining oxygen diffusion pathways in FPs can be important for improving photostability and for understanding maturation of the chromophore. We use molecular dynamics (MD) calculations to investigate the diffusion of molecular oxygen in one of the most useful monomeric RFPs, mCherry. We describe a pathway that allows oxygen molecules to enter from the solvent and travel through the protein barrel to the chromophore. We calculate the free-energy of an oxygen molecule at points along the path. The pathway contains several oxygen hosting pockets, which are identified by the amino acid residues that form the pocket. We also investigate an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins. PMID:23363049

Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins.

PubMed

Venkataramani, Varun; Kardorff, Markus; Herrmannsdörfer, Frank; Wieneke, Ralph; Klein, Alina; Tampé, Robert; Heilemann, Mike; Kuner, Thomas

2018-04-03

With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the 'labeling barrier' and to bypass photobleaching in multi-plane, whole-cell 3D experiments.

Analyzing the dependence of oxygen incorporation current density on overpotential and oxygen partial pressure in mixed conducting oxide electrodes.

PubMed

Guan, Zixuan; Chen, Di; Chueh, William C

2017-08-30

The oxygen incorporation reaction, which involves the transformation of an oxygen gas molecule to two lattice oxygen ions in a mixed ionic and electronic conducting solid, is a ubiquitous and fundamental reaction in solid-state electrochemistry. To understand the reaction pathway and to identify the rate-determining step, near-equilibrium measurements have been employed to quantify the exchange coefficients as a function of oxygen partial pressure and temperature. However, because the exchange coefficient contains contributions from both forward and reverse reaction rate constants and depends on both oxygen partial pressure and oxygen fugacity in the solid, unique and definitive mechanistic assessment has been challenging. In this work, we derive a current density equation as a function of both oxygen partial pressure and overpotential, and consider both near and far from equilibrium limits. Rather than considering specific reaction pathways, we generalize the multi-step oxygen incorporation reaction into the rate-determining step, preceding and following quasi-equilibrium steps, and consider the number of oxygen ions and electrons involved in each. By evaluating the dependence of current density on oxygen partial pressure and overpotential separately, one obtains the reaction orders for oxygen gas molecules and for solid-state species in the electrode. We simulated the oxygen incorporation current density-overpotential curves for praseodymium-doped ceria for various candidate rate-determining steps. This work highlights a promising method for studying the exchange kinetics far away from equilibrium.

Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens?

PubMed

Plesnar, Elzbieta; Szczelina, Robert; Subczynski, Witold K; Pasenkiewicz-Gierula, Marta

2018-02-01

In the eye lens, the oxygen partial pressure is very low and the cholesterol (Chol) content in cell membranes is very high. Disturbance of these quantities results in cataract development. In human lens membranes, both bulk phospholipid-Chol domains and the pure Chol bilayer domains (CBDs) were experimentally detected. It is hypothesized that the CBD constitutes a significant barrier to oxygen transport into the lens. Transmembrane profiles of the oxygen diffusion-concentration product, obtained with electron paramagnetic resonance spin-labeling methods, allow evaluation of the oxygen permeability (P M ) of phospholipid membranes but not the CBD. Molecular dynamics simulation can independently provide components of the product across any bilayer domain, thus allowing evaluation of the P M across the CBD. Therefore, to test the hypothesis, MD simulation was used. Three bilayers containing palmitoyl-oleoyl-phosphorylcholine (POPC) and Chol were built. The pure Chol bilayer modeled the CBD, the 1:1 POPC-Chol bilayer modeled the bulk membrane in which the CBD is embedded, and the POPC bilayer was a reference. To each model, 200 oxygen molecules were added. After equilibration, the oxygen concentration and diffusion profiles were calculated for each model and multiplied by each other. From the respective product profiles, the P M of each bilayer was calculated. Favorable comparison with experimental data available only for the POPC and POPC-Chol bilayers validated these bilayer models and allowed the conclusion that oxygen permeation across the CBD is ~10 smaller than across the bulk membrane, supporting the hypothesis that the CBD is a barrier to oxygen transport into the eye lens. Copyright © 2017 Elsevier B.V. All rights reserved.

Methods for the selective detection of alkyne-presenting molecules and related compositions and systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdez, Carlos A.; Vu, Alexander K.

Provided herein are methods for selectively detecting an alkyne-presenting molecule in a sample and related detection reagents, compositions, methods and systems. The methods include contacting a detection reagent with the sample for a time and under a condition to allow binding of the detection reagent to the one or more alkyne-presenting molecules possibly present in the matrix to the detection reagent. The detection reagent includes an organic label moiety presenting an azide group. The binding of the azide group to the alkyne-presenting molecules results in emission of a signal from the organic label moiety.

Labeled nucleotide phosphate (NP) probes

DOEpatents

Korlach, Jonas [Ithaca, NY; Webb, Watt W [Ithaca, NY; Levene, Michael [Ithaca, NY; Turner, Stephen [Ithaca, NY; Craighead, Harold G [Ithaca, NY; Foquet, Mathieu [Ithaca, NY

2009-02-03

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Factors Determining the Oxygen Permeability of Biological Membranes: Oxygen Transport Across Eye Lens Fiber-Cell Plasma Membranes.

PubMed

Subczynski, Witold Karol; Widomska, Justyna; Mainali, Laxman

2017-01-01

Electron paramagnetic resonance (EPR) spin-label oximetry allows the oxygen permeability coefficient to be evaluated across homogeneous lipid bilayer membranes and, in some cases, across coexisting membrane domains without their physical separation. The most pronounced effect on oxygen permeability is observed for cholesterol, which additionally induces the formation of membrane domains. In intact biological membranes, integral proteins induce the formation of boundary and trapped lipid domains with a low oxygen permeability. The effective oxygen permeability coefficient across the intact biological membrane is affected not only by the oxygen permeability coefficients evaluated for each lipid domain but also by the surface area occupied by these domains in the membrane. All these factors observed in fiber cell plasma membranes of clear human eye lenses are reviewed here.

Physics and chemistry of the influence of excited molecules on combustion enhancement

PubMed Central

Starik, A. M.; Loukhovitski, B. I.; Sharipov, A. S.; Titova, N. S

2015-01-01

The paper addresses detailed analysis of kinetic processes in the H2−O2, CO−O2 and CH4−O2-reactive systems upon the presence of singlet oxygen molecules O2(a1Δg) and and the influence of the activation of oxygen molecules in electric discharge on the acceleration of ignition in the H2−O2 and CH4−O2 mixtures. The possibility of the intensification of CO oxidation due to excitation of O2 and N2 molecule vibrations and generation of singlet oxygen molecules is also considered. It is shown that the effect of accelerating the ignition strongly depends on the reduced electric field and, as a consequence, on the composition of discharge plasma as well as on the features of chain mechanism development in oxy-fuel systems. It is revealed that the most effective approach for the intensification of CO oxidation both in the moist air and in the products of hydrocarbon combustion in air is the generation of O2(a1Δg) molecules by electric discharge. Computations showed that the presence of 1% O2(a1Δg) in the total oxygen allowed one to convert CO to CO2 even at the temperature T=850–900 K in the time of 10−2 s. The excitation of O2 and N2 molecule vibrations is less effective for such a conversion. PMID:26170425

Influence of oxygen concentration on ethylene removal using dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Takahashi, Katsuyuki; Motodate, Takuma; Takaki, Koichi; Koide, Shoji

2018-01-01

Ethylene gas is decomposed using a dielectric barrier discharge plasma reactor for long-period preservation of fruits and vegetables. The oxygen concentration in ambient gas is varied from 2 to 20% to simulate the fruit and vegetable transport container. The experimental results show that the efficiency of ethylene gas decomposition increases with decreasing oxygen concentration. The reactions of ethylene molecules with ozone are analyzed by Fourier transform infrared spectrometry. The analysis results show that the oxidization process by ozone is later than that by oxygen atoms. The amount of oxygen atoms that contribute to ethylene removal increases with decreasing oxygen concentration because the reaction between oxygen radicals and oxygen molecules is suppressed at low oxygen concentrations. Ozone is completely removed and the energy efficiency of C2H4 removal is increased using manganese dioxide as a catalyst.

A spectroscopic experimental and computer-assisted empirical model for the production and energetics of excited oxygen molecules formed by atom recombination on shuttle tile surfaces

NASA Technical Reports Server (NTRS)

Owan, D. A.

1981-01-01

A visible emission spectroscopic method was developed. The amounts of excited singlet and triplet oxygen molecules produced by recombination on the Space Shuttle Orbiter thermal protective tiles at elevated temperatures are determined. Rate constants and energetics of the extremely exothermic reaction are evaluated in terms of a chemical and mathematical model. Implications for potential contribution to Shuttle surface reentry heating fluxes are outlined.

Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging

PubMed Central

Cronin, Bríd; de Wet, Ben; Wallace, Mark I.

2009-01-01

We apply the astronomical data-analysis technique, Lucky imaging, to improve resolution in single molecule fluorescence microscopy. We show that by selectively discarding data points from individual single-molecule trajectories, imaging resolution can be improved by a factor of 1.6 for individual fluorophores and up to 5.6 for more complex images. The method is illustrated using images of fluorescent dye molecules and quantum dots, and the in vivo imaging of fluorescently labeled linker for activation of T cells. PMID:19348772

The effect of oxygen molecule adsorption on lead iodide perovskite surface by first-principles calculation

NASA Astrophysics Data System (ADS)

Ma, Xia-Xia; Li, Ze-Sheng

2018-01-01

Oxygen molecule has a negative effect on perovskite solar cells, which has been investigated experimentally. However, detailed theoretical research is still rare. This study presents a microscopic view to reveal the interaction mechanism between O2 and perovskite based on the first-principles calculation. The results show that O2 is adsorbed on the (100) surface of MAPbI3 perovskite mainly by Van der Waals force. O2 adsorption makes the MAPbI3 surface generate a small number of positive charges, which leads to the increase of the work function of the MAPbI3 surface. This is in agreement with the experimental measurement. And increased work function of MAPbI3 surface is not beneficial to electron transfer from perovskite to electronic extraction layer (such as TiO2). Comparison of the density of states (DOS) of the clean (100) surface and the adsorbed system shows that an in-gap state belonging to O2 appears, which can explain the phenomenon observed from experiments that electron transfers from the surface of perovskite to O2 to form superoxide. The theoretical power conversion efficiency of the system with and without O2 adsorption is evaluated, and it turns out that the power conversion efficiency of the system with O2 adsorption is slightly lower than that of the system without O2 adsorption. This result indicates that avoiding the introduction of O2 molecules between perovskite and electronic extraction layer is beneficial to the perovskite solar cell.

In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines.

PubMed

Custer, Thomas C; Walter, Nils G

2017-07-01

RNA plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexes-"molecular machines"-used to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of RNAs involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular RNA functions, including those of protein coding messenger RNAs (mRNAs). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label RNA molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 RNA polymerase to body label an RNA with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2'-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mRNA, whereas protein coding is severely diminished in the case of body labeling. © 2016 The Protein Society.

Method for sequencing nucleic acid molecules

DOEpatents

Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

2006-06-06

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Method for sequencing nucleic acid molecules

DOEpatents

Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

2006-05-30

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

The Comparative Study of the Effects of Extremely Low Frequency Electromagnetic Fields and Infrasound on Water Molecule Dissociation and Generation of Reactive Oxygen Species

DTIC Science & Technology

2008-11-01

ISTC Project No. #1592P The Comparative Study of The Effects of Extremely Low Frequency Electromagnetic Fields and Infrasound on Water Molecule...performed under the agreement with the International Science and Technology Center ( ISTC ), Moscow. REPORT DOCUMENTATION PAGE Form Approved OMB No. 0704...dissociation and generation of reactive oxygen spaces. 5a. CONTRACT NUMBER ISTC Registration No: A-1592p 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH.

PubMed

Bolková, Jitka; Lanctôt, Christian

2016-04-01

Advances in fluorescent probe design and synthesis have allowed the uniform in situ labeling of individual RNA molecules. In a technique referred to as single molecule RNA FISH (smRNA FISH), the labeled RNA molecules can be imaged as diffraction-limited spots and counted using image analysis algorithms. Single RNA counting has provided valuable insights into the process of gene regulation. This microscopy-based method has often revealed a high cell-to-cell variability in expression levels, which has in turn led to a growing interest in investigating the biological significance of gene expression noise. Here we describe the application of the smRNA FISH technique to samples of Caenorhabditis elegans, a well-characterized model organism. Copyright © 2015 Elsevier Inc. All rights reserved.

Adsorption of squaraine molecules to Au(111) and Ag(001) surfaces

NASA Astrophysics Data System (ADS)

Luft, Maike; Groß, Boris; Schulz, Matthias; Lützen, Arne; Schiek, Manuela; Nilius, Niklas

2018-02-01

The adsorption of anilino squaraines, an important chromophore for the use in organic solar cells, to Ag(001) and Au(111) has been studied with scanning tunneling microscopy. Self-assembly into square building blocks with eight molecules per unit cell is revealed on the Ag surface, while no ordering effects occur on gold. The squaraine-silver interaction is mediated by the carbonyl and hydroxyl oxygens located in the center of the molecule. The intermolecular coupling, on the other hand, is governed by hydrogen bonds formed between the terminal isobutyl groups and oxygen species of adjacent molecules. The latter gets maximized by rotating the molecules by a few degrees against a perfect square alignment. A similar molecular pattern does not form on Au(111) due to symmetry mismatch. Moreover, the high electronegativity of gold reduces the directing effect of oxygen-metal bonds that trigger the ordering process on silver. As a consequence, only frustrated three-fold symmetric units that do not expand into an ordered molecular network are present on the gold surface.

Cytochrome c-promoted cardiolipin oxidation generates singlet molecular oxygen.

PubMed

Miyamoto, Sayuri; Nantes, Iseli L; Faria, Priscila A; Cunha, Daniela; Ronsein, Graziella E; Medeiros, Marisa H G; Di Mascio, Paolo

2012-10-01

The interaction of cytochrome c (cyt c) with cardiolipin (CL) induces protein conformational changes that favor peroxidase activity. This process has been correlated with CL oxidation and the induction of cell death. Here we report evidence demonstrating the generation of singlet molecular oxygen [O(2)((1)Δ(g))] by a cyt c-CL complex in a model membrane containing CL. The formation of singlet oxygen was directly evidenced by luminescence measurements at 1270 nm and by chemical trapping experiments. Singlet oxygen generation required cyt c-CL binding and occurred at pH values higher than 6, consistent with lipid-protein interactions involving fully deprotonated CL species and positively charged residues in the protein. Moreover, singlet oxygen formation was specifically observed for tetralinoleoyl CL species and was not observed with monounsaturated and saturated CL species. Our results show that there are at least two mechanisms leading to singlet oxygen formation: one with fast kinetics involving the generation of singlet oxygen directly from CL hydroperoxide decomposition and the other involving CL oxidation. The contribution of the first mechanism was clearly evidenced by the detection of labeled singlet oxygen [(18)O(2)((1)Δ(g))] from liposomes supplemented with 18-oxygen-labeled CL hydroperoxides. However quantitative analysis showed that singlet oxygen yield from CL hydroperoxides was minor (<5%) and that most of the singlet oxygen is formed from the second mechanism. Based on these data and previous findings we propose a mechanism of singlet oxygen generation through reactions involving peroxyl radicals (Russell mechanism) and excited triplet carbonyl intermediates (energy transfer mechanism).

Oligonucleotide labeling methods. 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1,3-propanediol backbone.

PubMed Central

Nelson, P S; Kent, M; Muthini, S

1992-01-01

Novel CE-phosphoramidite (7a-e) and CPG (8a, c, d, e) reagents have been prepared from a unique 2-aminobutyl-1,3-propanediol backbone. The reagents have been used to directly label oligonucleotides with fluorescein, acridine, and biotin via automated DNA synthesis. The versatile 2-aminobutyl-1,3-propanediol backbone allows for labeling at any position (5', internal, and 3') during solid phase oligonucleotide synthesis. Multiple labels can be achieved by repetitive coupling cycles. Furthermore, the 3-carbon atom internucleotide phosphate distance is retained when inserted internally. Using this method, individual oligonucleotides possessing two and three different reporter molecules have been prepared. PMID:1475185

Polymer physics experiments with single DNA molecules

NASA Astrophysics Data System (ADS)

Smith, Douglas E.

1999-11-01

Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

Non-invasive MRI measurements of venous oxygenation, oxygen extraction fraction and oxygen consumption in neonates.

PubMed

De Vis, J B; Petersen, E T; Alderliesten, T; Groenendaal, F; de Vries, L S; van Bel, F; Benders, M J N L; Hendrikse, J

2014-07-15

Brain oxygen consumption reflects neuronal activity and can therefore be used to investigate brain development or neuronal injury in neonates. In this paper we present the first results of a non-invasive MRI method to evaluate whole brain oxygen consumption in neonates. For this study 51 neonates were included. The T1 and T2 of blood in the sagittal sinus were fitted using the 'T2 prepared tissue relaxation inversion recovery' pulse sequence (T2-TRIR). From the T1 and the T2 of blood, the venous oxygenation and the oxygen extraction fraction (OEF) were calculated. The cerebral metabolic rate of oxygen (CMRO2) was the resultant of the venous oxygenation and arterial spin labeling whole brain cerebral blood flow (CBF) measurements. Venous oxygenation was 59±14% (mean±sd), OEF was 40±14%, CBF was 14±5ml/100g/min and CMRO2 was 30±12μmol/100g/min. The OEF in preterms at term-equivalent age was higher than in the preterms and in the infants with hypoxic-ischemic encephalopathy (p<0.01). The OEF, CBF and CMRO2 increased (p<0.01, <0.05 and <0.01, respectively) with postnatal age. We presented an MRI technique to evaluate whole-brain oxygen consumption in neonates non-invasively. The measured values are in line with reference values found by invasive measurement techniques. Preterms and infants with HIE demonstrated significant lower oxygen extraction fraction than the preterms at term-equivalent age. This could be due to decreased neuronal activity as a reflection of brain development or as a result of tissue damage, increased cerebral blood flow due to immature or impaired autoregulation, or could be caused by differences in postnatal age. Copyright © 2014 Elsevier Inc. All rights reserved.

Reactions of small organic molecules on silver(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ayre, C.R.

1992-01-01

The interaction of two pairs of molecules (1) acetone (CH[sub 3])[sub 2]C=O and isobutylene (CH[sub 3])[sub 2] C=CH[sub 2] and (2) 1,2-propanediol CH[sub 3] CH (OH)CH[sub 2]OH and 1,3-propanediol HOCH[sub 2]CH[sub 2]CH[sub 2]OH with clean and oxygen-activated Ag(110) has been explored to investigate the effects of molecular structure on reactivity. Experimental techniques employed include temperature programmed reaction spectroscopy, isotopic labelling, surface displacement reactions, and electron energy loss spectroscopy. Acetone and isobutylene were studied to explore the relative importance of C=O and C=C bonds in governing the reactivity of structurally similar compounds. Nucleophilic attack by oxygen at the electron-deficient carbonyl carbonmore » in acetone results in reversible formation of the metallacycle (CH[sub 3])[sub 2]COO[sub (a)] at 110 K. Upon heating C-H bond activation by O[sub (a)] occurs near 215 K to yield acetone enolate CH[sub 2]=C(CH[sub 3])O[sub (a)] and evolve H[sub 2]O[sub (g)]. Atomic oxygen activates methyl C-H bonds in isobutylene via an acid-base mechanism. Although the major products are CO[sub 2(g)] and H[sub 2]O[sub (g)], a small amount of (CH[sub 3])[sub 2]C=CH[sub 2(g)] evolves near 310 K. Evidence for the formation of [pi]-2-methylallyl CH[sub 3]C(CH[sub 2])[sub 2(a)] and trimethylenementhane C(CH[sub 2])[sub 3(a)] is presented. The reaction of 1,2-propanediol CH[sub 3] CH(OH)CH[sub 2] OH with oxygen-activated Ag(110) has been compared with that of 1,3-propanediol HOCH[sub 2]CH[sub 2]CH[sub 2]OH to evaluate the effects of varying the position of O-H bonds in both diols to produce the corresponding dialkoxides.« less

A tandem mass spectrometric method for singlet oxygen measurement.

PubMed

Karonen, Maarit; Mattila, Heta; Huang, Ping; Mamedov, Fikret; Styring, Stenbjörn; Tyystjärvi, Esa

2014-01-01

Singlet oxygen, a harmful reactive oxygen species, can be quantified with the substance 2,2,6,6-tetramethylpiperidine (TEMP) that reacts with singlet oxygen, forming a stable nitroxyl radical (TEMPO). TEMPO has earlier been quantified with electron paramagnetic resonance (EPR) spectroscopy. In this study, we designed an ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-ESI-MS/MS) quantification method for TEMPO and showed that the method based on multiple reaction monitoring (MRM) can be used for the measurements of singlet oxygen from both nonbiological and biological samples. Results obtained with both UHPLC-ESI-MS/MS and EPR methods suggest that plant thylakoid membranes produce 3.7 × 10(-7) molecules of singlet oxygen per chlorophyll molecule in a second when illuminated with the photosynthetic photon flux density of 2000 μmol m(-2 ) s(-1). © 2014 The American Society of Photobiology.

Label-Enhanced Surface Plasmon Resonance: A New Concept for Improved Performance in Optical Biosensor Analysis

PubMed Central

Granqvist, Niko; Hanning, Anders; Eng, Lars; Tuppurainen, Jussi; Viitala, Tapani

2013-01-01

Surface plasmon resonance (SPR) is a well-established optical biosensor technology with many proven applications in the study of molecular interactions as well as in surface and material science. SPR is usually applied in the label-free mode which may be advantageous in cases where the presence of a label may potentially interfere with the studied interactions per se. However, the fundamental challenges of label-free SPR in terms of limited sensitivity and specificity are well known. Here we present a new concept called label-enhanced SPR, which is based on utilizing strongly absorbing dye molecules in combination with the evaluation of the full shape of the SPR curve, whereby the sensitivity as well as the specificity of SPR is significantly improved. The performance of the new label-enhanced SPR method was demonstrated by two simple model assays: a small molecule assay and a DNA hybridization assay. The small molecule assay was used to demonstrate the sensitivity enhancement of the method, and how competitive assays can be used for relative affinity determination. The DNA assay was used to demonstrate the selectivity of the assay, and the capabilities in eliminating noise from bulk liquid composition variations. PMID:24217357

First results on label-free detection of DNA and protein molecules using a novel integrated sensor technology based on gravimetric detection principles.

PubMed

Gabl, R; Feucht, H-D; Zeininger, H; Eckstein, G; Schreiter, M; Primig, R; Pitzer, D; Wersing, W

2004-01-15

A novel integrated bio-sensor technology based on thin-film bulk acoustic wave resonators on silicon is presented and the feasibility of detecting DNA and protein molecules proofed. The detection principle of these sensors is label-free and relies on a resonance frequency shift caused by mass loading of an acoustic resonator, a principle very well known from quartz crystal micro balances. Integrated ZnO bulk acoustic wave resonators with resonance frequencies around 2 GHz have been fabricated, employing an acoustic mirror for isolation from the silicon substrate. DNA oligos have been thiol-coupled to the gold electrode by on-wafer dispensing. In a further step, samples have either been hybridised or alternatively a protein has been coupled to the receptor. The measurement results show the new bio-sensor being capable of both, detecting proteins as well as the DNA hybridisation without using a label. Due to the substantially higher oscillation frequency, these sensors already show much higher sensitivity and resolution comparable to quartz crystal micro balances. The potential for these sensors and sensors arrays as well as technological challenges will be discussed in detail.

Infrared Auroral Emissions Driven by Resonant Electron Impact Excitation of NO Molecules

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.; Petrovic, Z. Lj.; Jelisavcic, M.; Panajotovic, R.; Buckman, S. J.

2004-05-01

Although only a minor constituent of the earth's upper atmosphere, nitric oxide (NO) plays a major role in infrared auroral emissions due to radiation from vibrationally excited (NO*) states. The main process leading to the production of these excited molecules was thought to be chemiluminescence, whereby excited nitrogen atoms interact with oxygen molecules to form vibrationally excited nitric oxide (NO*) and atomic oxygen. Here we show evidence that a different production mechanism for NO*, due to low energy electron impact excitation of NO molecules, is responsible for more than 30% of the NO auroral emission near 5 μm.

Small molecule CP-31398 induces reactive oxygen species-dependent apoptosis in human multiple myeloma.

PubMed

Arihara, Yohei; Takada, Kohichi; Kamihara, Yusuke; Hayasaka, Naotaka; Nakamura, Hajime; Murase, Kazuyuki; Ikeda, Hiroshi; Iyama, Satoshi; Sato, Tsutomu; Miyanishi, Koji; Kobune, Masayoshi; Kato, Junji

2017-09-12

Reactive oxygen species (ROS) are normal byproducts of a wide variety of cellular processes. ROS have dual functional roles in cancer cell pathophysiology. At low to moderate levels, ROS act as signaling transducers to activate cell proliferation, migration, invasion, and angiogenesis. In contrast, high levels of ROS induce cell death. In multiple myeloma (MM), ROS overproduction is the trigger for apoptosis induced by several anticancer compounds, including proteasome inhibitors. However, no drugs for which oxidative stress is the main mechanism of action are currently used for treatment of MM in clinical situations. In this study, we demonstrate that the p53-activating small molecule CP-31398 (CP) effectively inhibits the growth of MM cell lines and primary MM isolates from patients. CP also suppresses the growth of MM xenografts in mice. Mechanistically, CP was found to induce intrinsic apoptosis in MM cells via increasing ROS production. Interestingly, CP-induced apoptosis occurs regardless of the p53 status, suggesting that CP has additional mechanisms of action. Our findings thus indicate that CP could be an attractive candidate for treatment of MM patients harboring p53 abnormalities; this satisfies an unmet clinical need, as such individuals currently have a poor prognosis.

Single molecule optical measurements of orientation and rotations of biological macromolecules

PubMed Central

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-01-01

The subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measuring their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292

Single molecule optical measurements of orientation and rotations of biological macromolecules.

PubMed

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-11-22

Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

A Simple Picaxe Microcontroller Pulse Source for Juxtacellular Neuronal Labelling.

PubMed

Verberne, Anthony J M

2016-10-19

Juxtacellular neuronal labelling is a method which allows neurophysiologists to fill physiologically-identified neurons with small positively-charged marker molecules. Labelled neurons are identified by histochemical processing of brain sections along with immunohistochemical identification of neuropeptides, neurotransmitters, neurotransmitter transporters or biosynthetic enzymes. A microcontroller-based pulser circuit and associated BASIC software script is described for incorporation into the design of a commercially-available intracellular electrometer for use in juxtacellular neuronal labelling. Printed circuit board construction has been used for reliability and reproducibility. The current design obviates the need for a separate digital pulse source and simplifies the juxtacellular neuronal labelling procedure.

Electrochemical cell for obtaining oxygen from carbon dioxide atmospheres

NASA Technical Reports Server (NTRS)

Hooker, M. W.; Rast, H. E.; Rogers, D. K.

1989-01-01

For manned missions to Mars to become a reality, an efficient and reliable means of obtaining oxygen from the carbon dioxide-rich atmosphere will be required. Otherwise, the high cost of transporting the oxygen needed to sustain the astronauts will severely restrict the expedition to the martian surface. Recently, the use of electrochemical devices has been explored as a means of obtaining oxygen from the carbon dioxide-rich atmosphere. In these devices, oxygen ions diffuse through solid oxide membranes, thus, separating oxygen from the other gases presented. This phenomenon has only recently been explored as a means of obtaining large quantities of oxygen from toxic atmospheres, although first observed by Walter nernst in 1899. Nernst observed that stabilized zirconia will conduct oxygen ions when an electrical potential is applied across metallic electrodes applied to the ceramic membrane. Diatomic oxygen molecules are dissociated at the positive electrode/electrolyte interface. The oxygen ions enter the ceramic body due to the ion density gradient which is produced by the electrical potential across the electrolytic membrane. Once the ions have diffused through the membrane, they reform diatomic oxygen molecules at the anode. The separation of oxygen from carbon dioxide is achieved by the combination of thermal and electrochemical processes. The thermal decomposition of carbon dioxide (at 1000 C) results in the production of carbon monoxide and oxygen by the reaction.

Single-molecule imaging at high fluorophore concentrations by local activation of dye

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geertsema, Hylkje J.; Mangel, Walter F.; Schulte, Aartje C.

Single-molecule fluorescence microscopy is a powerful approach to observe biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual, labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Then, making use ofmore » short-distance energy-transfer mechanisms, the fluorescence from only those proteins bound to their substrate are selectively activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 (IFI16) with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease (pVIc-AVP) on DNA in the presence of a background of hundreds of nM Cy5 fluorophore.« less

Single-molecule imaging at high fluorophore concentrations by local activation of dye

DOE PAGES

Geertsema, Hylkje J.; Mangel, Walter F.; Schulte, Aartje C.; ...

2015-02-17

Single-molecule fluorescence microscopy is a powerful approach to observe biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual, labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Then, making use ofmore » short-distance energy-transfer mechanisms, the fluorescence from only those proteins bound to their substrate are selectively activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 (IFI16) with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease (pVIc-AVP) on DNA in the presence of a background of hundreds of nM Cy5 fluorophore.« less

3'-End labeling of nucleic acids by a polymerase ribozyme.

PubMed

Samanta, Biswajit; Horning, David P; Joyce, Gerald F

2018-06-13

A polymerase ribozyme can be used to label the 3' end of RNA or DNA molecules by incorporating a variety of functionalized nucleotide analogs. Guided by a complementary template, the ribozyme adds a single nucleotide that may contain a fluorophore, biotin, azide or alkyne moiety, thus enabling the detection and/or capture of selectively labeled materials. Employing a variety of commercially available nucleotide analogs, efficient labeling was demonstrated for model RNAs and DNAs, human microRNAs and natural tRNA.

Mechanism of singlet oxygen deactivation in an electric discharge oxygen – iodine laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azyazov, V N; Mikheyev, P A; Torbin, A P

2014-12-31

We have determined the influence of the reaction of molecular singlet oxygen with a vibrationally excited ozone molecule O{sub 2}(a {sup 1}Δ) + O{sub 3}(ν) → 2O{sub 2} + O on the removal rate of O{sub 2}(a {sup 1}Δ) in an electric-discharge-driven oxygen – iodine laser. This reaction has been shown to be a major channel of O{sub 2}(a {sup 1}Δ) loss at the output of an electric-discharge singlet oxygen generator. In addition, it can also contribute significantly to the loss of O{sub 2}(a {sup 1}Δ) in the discharge region of the generator. (lasers)

Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

NASA Astrophysics Data System (ADS)

Chirvi, Sajal

Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

PubMed

Qin, Yan; Du, Qi-Shi; Xie, Neng-Zhong; Li, Jian-Xiu; Huang, Ri-Bo

2017-05-01

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 -2H 2 interaction structure is smaller than the dimension of CO 2 -2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 +2H 2 ) cluster in clathrate hydrate. Copyright © 2017 Elsevier Inc. All rights reserved.

Fingerprinting Bacterial and Fungal Manganese Oxidation via Stable Oxygen Isotopes of Manganese Oxides

NASA Astrophysics Data System (ADS)

Sutherland, K. M.; Wankel, S. D.; Hansel, C. M.

2016-12-01

Manganese (Mn) oxides are a ubiquitous mineralogical component of surface Earth and Mars. Mn(III/IV) oxides are potent environmental sorbents and oxidants that play a crucial role in the fate of organic matter. The processes by which Mn(II) oxidation occurs in natural systems are poorly understood, but a number of studies have implicated microogranisms as the primary agents of Mn(II) oxidation in terrestrial and marine environments. The ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides transcends the boundaries of biological domain, with an abundance of well-characterized prokaryotes as well as eukaryotic fungi with the ability to oxidize Mn(II) to Mn(III/IV) oxides. Biological Mn(II) oxidation proceeds directly through enzymatic activity or indirectly through the production of reactive oxygen species. Building upon earlier research suggesting that stable oxygen isotope fractionation could be used to fingerprint unique Mn(II)-oxidizing organisms or distinct oxidation pathways, here we use culture-based studies of Mn(II)-oxidizing bacteria and fungi to determine the kinetic oxygen isotope effects associated with Mn(II) oxidation. Since the oxygen molecules in Mn(III/IV) oxides are comprised of oxygen from both precursor water and molecular oxygen, we used a two-fold approach to constrain isotope fractionation with respect to each oxygen source. We used open system oxidation experiments using oxygen-18 labeled water in parallel with closed system Rayleigh distillation oxidation experiments to fully constrain isotope fractionation associated with oxygen atom incorporation during Mn(II) oxidation. Our results suggest commonalities among fractionation factors from groups of Mn(II)-oxidizing organisms that have similar oxidation mechanisms. These results suggest that stable oxygen isotopes of Mn(III/IV) oxides have the potential to distinguish between Mn(II) oxidation pathways in nature, providing a way to determine which groups of Mn(II) oxidizers may be

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

NASA Astrophysics Data System (ADS)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

PubMed Central

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-01-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level. PMID:28382928

A systematization of spectral data on the methanol molecule

NASA Astrophysics Data System (ADS)

Akhlyostin, A. Yu.; Voronina, S. S.; Lavrentiev, N. A.; Privezentsev, A. I.; Rodimova, O. B.; Fazliev, A. Z.

2015-11-01

Problems underlying a systematization of spectral data on the methanol molecule are formulated. Data on the energy levels and vacuum wavenumbers acquired from the published literature are presented in the form of information sources imported into the W@DIS information system. Sets of quantum numbers and labels used to describe the CH3OH molecular states are analyzed. The set of labels is different from universally accepted sets. A system of importing the data sources into W@DIS is outlined. The structure of databases characterizing transitions in an isolated CH3OH molecule is introduced and a digital library of the relevant published literature is discussed. A brief description is given of an imported data quality analysis and representation of the results obtained in the form of ontologies for subsequent computer processing.

Real-time monitoring of specific oxygen uptake rates of embryonic stem cells in a microfluidic cell culture device.

PubMed

Super, Alexandre; Jaccard, Nicolas; Cardoso Marques, Marco Paulo; Macown, Rhys Jarred; Griffin, Lewis Donald; Veraitch, Farlan Singh; Szita, Nicolas

2016-09-01

Oxygen plays a key role in stem cell biology as a signaling molecule and as an indicator of cell energy metabolism. Quantification of cellular oxygen kinetics, i.e. the determination of specific oxygen uptake rates (sOURs), is routinely used to understand metabolic shifts. However current methods to determine sOUR in adherent cell cultures rely on cell sampling, which impacts on cellular phenotype. We present real-time monitoring of cell growth from phase contrast microscopy images, and of respiration using optical sensors for dissolved oxygen. Time-course data for bulk and peri-cellular oxygen concentrations obtained for Chinese hamster ovary (CHO) and mouse embryonic stem cell (mESCs) cultures successfully demonstrated this non-invasive and label-free approach. Additionally, we confirmed non-invasive detection of cellular responses to rapidly changing culture conditions by exposing the cells to mitochondrial inhibiting and uncoupling agents. For the CHO and mESCs, sOUR values between 8 and 60 amol cell(-1) s(-1) , and 5 and 35 amol cell(-1) s(-1) were obtained, respectively. These values compare favorably with literature data. The capability to monitor oxygen tensions, cell growth, and sOUR, of adherent stem cell cultures, non-invasively and in real time, will be of significant benefit for future studies in stem cell biology and stem cell-based therapies. © 2016 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

PubMed

Liu, Jie; Jiang, Xiangang; Cao, Yu; Zhang, Chen; Zhao, Guangyao; Zhao, Maoshuang; Feng, Li

2018-05-07

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Mechanochemical Association Reaction of Interfacial Molecules Driven by Shear.

PubMed

Khajeh, Arash; He, Xin; Yeon, Jejoon; Kim, Seong H; Martini, Ashlie

2018-05-29

Shear-driven chemical reaction mechanisms are poorly understood because the relevant reactions are often hidden between two solid surfaces moving in relative motion. Here, this phenomenon is explored by characterizing shear-induced polymerization reactions that occur during vapor phase lubrication of α-pinene between sliding hydroxylated and dehydroxylated silica surfaces, complemented by reactive molecular dynamics simulations. The results suggest that oxidative chemisorption of the α-pinene molecules at reactive surface sites, which transfers oxygen atoms from the surface to the adsorbate molecule, is the critical activation step. Such activation takes place more readily on the dehydroxylated surface. During this activation, the most strained part of the α-pinene molecules undergoes a partial distortion from its equilibrium geometry, which appears to be related to the critical activation volume for mechanical activation. Once α-pinene molecules are activated, association reactions occur between the newly attached oxygen and one of the carbon atoms in another molecule, forming ether bonds. These findings have general implications for mechanochemistry because they reveal that shear-driven reactions may occur through reaction pathways very different from their thermally induced counterparts and specifically the critical role of molecular distortion in such reactions.

Single molecule fluorescence microscopy for ultra-sensitive RNA expression profiling

NASA Astrophysics Data System (ADS)

Hesse, Jan; Jacak, Jaroslaw; Regl, Gerhard; Eichberger, Thomas; Aberger, Fritz; Schlapak, Robert; Howorka, Stefan; Muresan, Leila; Frischauf, Anna-Maria; Schütz, Gerhard J.

2007-02-01

We developed a microarray analysis platform for ultra-sensitive RNA expression profiling of minute samples. It utilizes a novel scanning system for single molecule fluorescence detection on cm2 size samples in combination with specialized biochips, optimized for low autofluorescence and weak unspecific adsorption. 20 μg total RNA was extracted from 10 6 cells of a human keratinocyte cell line (HaCaT) and reversely transcribed in the presence of Alexa647-aha-dUTP. 1% of the resulting labeled cDNA was used for complex hybridization to a custom-made oligonucleotide microarray representing a set of 125 different genes. For low abundant genes, individual cDNA molecules hybridized to the microarray spots could be resolved. Single cDNA molecules hybridized to the chip surface appeared as diffraction limited features in the fluorescence images. The à trous wavelet method was utilized for localization and counting of the separated cDNA signals. Subsequently, the degree of labeling of the localized cDNA molecules was determined by brightness analysis for the different genes. Variations by factors up to 6 were found, which in conventional microarray analysis would result in a misrepresentation of the relative abundance of mRNAs.

Combined phosphorescence-holographic approach for singlet oxygen detection in biological media

NASA Astrophysics Data System (ADS)

Semenova, I. V.; Belashov, A. V.; Beltukova, D. M.; Petrov, N. V.; Vasyutinskii, O. S.

2015-06-01

The paper presents a novel combined approach aimed to detect and monitor singlet oxygen molecules in biological specimens by means of the simultaneous recording and monitoring of their deactivation dynamics in the two complementary channels: radiative and nonradiative. The approach involves both the direct registration of phosphorescence at the wavelength of about 1270 nm caused by radiative relaxation of excited singlet oxygen molecules and holographic recording of thermal disturbances in the medium produced by their nonradiative relaxation. The data provides a complete set of information on singlet oxygen location and dynamics in the medium. The approach was validated in the case study of photosensitized generation of singlet oxygen in onion cell structures.

Single-molecule fluorescence study of the inhibition of the oncogenic functionality of STAT3

NASA Astrophysics Data System (ADS)

Liu, Baoxu; Badali, Daniel; Fletcher, Steven; Avadisian, Miriam; Gunning, Patrick; Gradinaru, Claudiu

2009-06-01

Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein plays an important role in the onset of cancers such as leukemia and lymphoma. In this study, we aim to test the effectiveness of a novel peptide drug designed to tether STAT3 to the phospholipid bilayer of the cell membrane and thus inhibit unwanted transcription. As a first step, STAT3 proteins were successfully labelled with tetramethylrhodamine (TMR), a fluorescent dye with suitable photostability for single molecule studies. The effectiveness of labelling was determined using fluorescence correlation spectroscopy in a custom built confocal microscope, from which diffusion times and hydrodynamic radii of individual proteins were determined. A newly developed fluorescein derivative label (F-NAc) has been designed to be incorporated into the structure of the peptide drug so that peptide-STAT3 interactions can be examined. This dye is spectrally characterized and is found to be well suited for its application to this project, as well as other single-molecule studies. The membrane localization via high-affinity cholesterol-bound small-molecule binding agents can be demonstrated by encapsulating TMR-labeled STAT3 and inhibitors within a vesicle model cell system. To this end, unilaminar lipid vesicles were examined for size and encapsulation ability. Preliminary results of the efficiency and stability of the STAT3 anchoring in lipid membranes obtained via quantitative confocal imaging and single-molecule spectroscopy using a custom-built multiparameter fluorescence microscope are reported here.

Production of isotopically labeled standards from a uniformly labeled precursor for quantitative volatile metabolomic studies.

PubMed

Gómez-Cortés, Pilar; Brenna, J Thomas; Sacks, Gavin L

2012-06-19

Optimal accuracy and precision in small-molecule profiling by mass spectrometry generally requires isotopically labeled standards chemically representative of all compounds of interest. However, preparation of mixed standards from commercially available pure compounds is often prohibitively expensive and time-consuming, and many labeled compounds are not available in pure form. We used a single-prototype uniformly labeled [U-(13)C]compound to generate [U-(13)C]-labeled volatile standards for use in subsequent experimental profiling studies. [U-(13)C]-α-Linolenic acid (18:3n-3, ALA) was thermally oxidized to produce labeled lipid degradation volatiles which were subsequently characterized qualitatively and quantitatively. Twenty-five [U-(13)C]-labeled volatiles were identified by headspace solid-phase microextraction-gas chromatography/time-of-flight mass spectrometry (HS-SPME-GC/TOF-MS) by comparison of spectra with unlabeled volatiles. Labeled volatiles were quantified by a reverse isotope dilution procedure. Using the [U-(13)C]-labeled standards, limits of detection comparable to or better than those of previous HS-SPME reports were achieved, 0.010-1.04 ng/g. The performance of the [U-(13)C]-labeled volatile standards was evaluated using a commodity soybean oil (CSO) oxidized at 60 °C from 0 to 15 d. Relative responses of n-decane, an unlabeled internal standard otherwise absent from the mixture, and [U-(13)C]-labeled oxidation products changed by up to 8-fold as the CSO matrix was oxidized, demonstrating that reliance on a single standard in volatile profiling studies yields inaccurate results due to changing matrix effects. The [U-(13)C]-labeled standard mixture was used to quantify 25 volatiles in oxidized CSO and low-ALA soybean oil with an average relative standard deviation of 8.5%. Extension of this approach to other labeled substrates, e.g., [U-(13)C]-labeled sugars and amino acids, for profiling studies should be feasible and can dramatically improve

Quantum dots as strain- and metabolism-specific microbiological labels

NASA Technical Reports Server (NTRS)

Kloepfer, J. A.; Mielke, R. E.; Wong, M. S.; Nealson, K. H.; Stucky, G.; Nadeau, J. L.

2003-01-01

Biologically conjugated quantum dots (QDs) have shown great promise as multiwavelength fluorescent labels for on-chip bioassays and eukaryotic cells. However, use of these photoluminescent nanocrystals in bacteria has not previously been reported, and their large size (3 to 10 nm) makes it unclear whether they inhibit bacterial recognition of attached molecules and whether they are able to pass through bacterial cell walls. Here we describe the use of conjugated CdSe QDs for strain- and metabolism-specific microbial labeling in a wide variety of bacteria and fungi, and our analysis was geared toward using receptors for a conjugated biomolecule that are present and active on the organism's surface. While cell surface molecules, such as glycoproteins, make excellent targets for conjugated QDs, internal labeling is inconsistent and leads to large spectral shifts compared with the original fluorescence, suggesting that there is breakup or dissolution of the QDs. Transmission electron microscopy of whole mounts and thin sections confirmed that bacteria are able to extract Cd and Se from QDs in a fashion dependent upon the QD surface conjugate.

Chemical complexity in the winds of the oxygen-rich supergiant star VY Canis Majoris

NASA Astrophysics Data System (ADS)

Ziurys, L. M.; Milam, S. N.; Apponi, A. J.; Woolf, N. J.

2007-06-01

The interstellar medium is enriched primarily by matter ejected from old, evolved stars. The outflows from these stars create spherical envelopes, which foster gas-phase chemistry. The chemical complexity in circumstellar shells was originally thought to be dominated by the elemental carbon to oxygen ratio. Observations have suggested that envelopes with more carbon than oxygen have a significantly greater abundance of molecules than their oxygen-rich analogues. Here we report observations of molecules in the oxygen-rich shell of the red supergiant star VY Canis Majoris (VY CMa). A variety of unexpected chemical compounds have been identified, including NaCl, PN, HNC and HCO+. From the spectral line profiles, the molecules can be distinguished as arising from three distinct kinematic regions: a spherical outflow, a tightly collimated, blue-shifted expansion, and a directed, red-shifted flow. Certain species (SiO, PN and NaCl) exclusively trace the spherical flow, whereas HNC and sulphur-bearing molecules (amongst others) are selectively created in the two expansions, perhaps arising from shock waves. CO, HCN, CS and HCO+ exist in all three components. Despite the oxygen-rich environment, HCN seems to be as abundant as CO. These results suggest that oxygen-rich shells may be as chemically diverse as their carbon counterparts.

Chemical complexity in the winds of the oxygen-rich supergiant star VY Canis Majoris.

PubMed

Ziurys, L M; Milam, S N; Apponi, A J; Woolf, N J

2007-06-28

The interstellar medium is enriched primarily by matter ejected from old, evolved stars. The outflows from these stars create spherical envelopes, which foster gas-phase chemistry. The chemical complexity in circumstellar shells was originally thought to be dominated by the elemental carbon to oxygen ratio. Observations have suggested that envelopes with more carbon than oxygen have a significantly greater abundance of molecules than their oxygen-rich analogues. Here we report observations of molecules in the oxygen-rich shell of the red supergiant star VY Canis Majoris (VY CMa). A variety of unexpected chemical compounds have been identified, including NaCl, PN, HNC and HCO+. From the spectral line profiles, the molecules can be distinguished as arising from three distinct kinematic regions: a spherical outflow, a tightly collimated, blue-shifted expansion, and a directed, red-shifted flow. Certain species (SiO, PN and NaCl) exclusively trace the spherical flow, whereas HNC and sulphur-bearing molecules (amongst others) are selectively created in the two expansions, perhaps arising from shock waves. CO, HCN, CS and HCO+ exist in all three components. Despite the oxygen-rich environment, HCN seems to be as abundant as CO. These results suggest that oxygen-rich shells may be as chemically diverse as their carbon counterparts.

A Simple Picaxe Microcontroller Pulse Source for Juxtacellular Neuronal Labelling †

PubMed Central

Verberne, Anthony J. M.

2016-01-01

Juxtacellular neuronal labelling is a method which allows neurophysiologists to fill physiologically-identified neurons with small positively-charged marker molecules. Labelled neurons are identified by histochemical processing of brain sections along with immunohistochemical identification of neuropeptides, neurotransmitters, neurotransmitter transporters or biosynthetic enzymes. A microcontroller-based pulser circuit and associated BASIC software script is described for incorporation into the design of a commercially-available intracellular electrometer for use in juxtacellular neuronal labelling. Printed circuit board construction has been used for reliability and reproducibility. The current design obviates the need for a separate digital pulse source and simplifies the juxtacellular neuronal labelling procedure. PMID:28952589

Mitochondrial reactive oxygen species (ROS) as signaling molecules of intracellular pathways triggered by the cardiac renin-angiotensin II-aldosterone system (RAAS)

PubMed Central

De Giusti, V. C.; Caldiz, C. I.; Ennis, I. L.; Pérez, N. G.; Cingolani, H. E.; Aiello, E. A.

2013-01-01

Mitochondria represent major sources of basal reactive oxygen species (ROS) production of the cardiomyocyte. The role of ROS as signaling molecules that mediate different intracellular pathways has gained increasing interest among physiologists in the last years. In our lab, we have been studying the participation of mitochondrial ROS in the intracellular pathways triggered by the renin-angiotensin II-aldosterone system (RAAS) in the myocardium during the past few years. We have demonstrated that acute activation of cardiac RAAS induces mitochondrial ATP-dependent potassium channel (mitoKATP) opening with the consequent enhanced production of mitochondrial ROS. These oxidant molecules, in turn, activate membrane transporters, as sodium/hydrogen exchanger (NHE-1) and sodium/bicarbonate cotransporter (NBC) via the stimulation of the ROS-sensitive MAPK cascade. The stimulation of such effectors leads to an increase in cardiac contractility. In addition, it is feasible to suggest that a sustained enhanced production of mitochondrial ROS induced by chronic cardiac RAAS, and hence, chronic NHE-1 and NBC stimulation, would also result in the development of cardiac hypertrophy. PMID:23755021

Mitochondrial reactive oxygen species (ROS) as signaling molecules of intracellular pathways triggered by the cardiac renin-angiotensin II-aldosterone system (RAAS).

PubMed

De Giusti, V C; Caldiz, C I; Ennis, I L; Pérez, N G; Cingolani, H E; Aiello, E A

2013-01-01

Mitochondria represent major sources of basal reactive oxygen species (ROS) production of the cardiomyocyte. The role of ROS as signaling molecules that mediate different intracellular pathways has gained increasing interest among physiologists in the last years. In our lab, we have been studying the participation of mitochondrial ROS in the intracellular pathways triggered by the renin-angiotensin II-aldosterone system (RAAS) in the myocardium during the past few years. We have demonstrated that acute activation of cardiac RAAS induces mitochondrial ATP-dependent potassium channel (mitoKATP) opening with the consequent enhanced production of mitochondrial ROS. These oxidant molecules, in turn, activate membrane transporters, as sodium/hydrogen exchanger (NHE-1) and sodium/bicarbonate cotransporter (NBC) via the stimulation of the ROS-sensitive MAPK cascade. The stimulation of such effectors leads to an increase in cardiac contractility. In addition, it is feasible to suggest that a sustained enhanced production of mitochondrial ROS induced by chronic cardiac RAAS, and hence, chronic NHE-1 and NBC stimulation, would also result in the development of cardiac hypertrophy.

Reversible oxygen addition on a triplet sensitizer molecule: protection from excited state depopulation.

PubMed

Filatov, Mikhail A; Heinrich, Ernesta; Busko, Dmitry; Ilieva, Iliyana Z; Landfester, Katharina; Baluschev, Stanislav

2015-03-07

We demonstrate that photoactivated oxygen addition to diphenylanthracene moities can be used as a tool for protection of porphyrin's phosphorescence against oxygen quenching. Phosphorescent palladium(II) tetrabenzoporphyrin, covalently linked to four diphenylanthracene moieties, was synthesized and studied. Upon irradiation with ambient light or red laser in solution in air, addition of oxygen and formation of the corresponding endoperoxides were observed. Heating of the irradiated samples afforded the parent porphyrin material.

A new fluorogenic small molecule labeling tool for surface diffusion analysis and advanced fluorescence imaging of β-site amyloid precursor protein (APP)-cleaving enzyme 1 based on silicone rhodamine: SiR-BACE1.

PubMed

Karch, Sandra; Broichhagen, Johannes; Schneider, Julia; Böning, Daniel; Hartmann, Stephanie; Schmid, Benjamin; Tripal, Philipp; Palmisano, Ralf; Alzheimer, Christian; Johnsson, Kai; Huth, Tobias

2018-06-25

β-site APP-cleaving enzyme 1 (BACE1) is a major player in the pathogenesis of Alzheimer's disease. Structural and functional fluorescence microscopy offers a powerful approach to learn about the physiology and pathophysiology of this protease. Up to now, however, common labeling techniques either require genetic manipulation, use large antibodies, or are not compatible with live cell imaging. Fluorescent small molecules that specifically bind to the protein of interest can overcome these limitations. Herein, we introduce SiR-BACE1, a conjugate of the BACE1 inhibitor S-39 and SiR647, as a novel fluorogenic, tag-free, and antibody-free label for BACE1. We present its chemical development, characterize its photo-physical and pharmacologic properties, and evaluate its behavior in solution, in over-expression systems, and in native brain tissue. We demonstrate its applicability in confocal, stimulated emission depletion (STED), and dynamic single molecule microscopy. First functional studies with SiR-BACE1 on the surface mobility of BACE1 revealed a markedly confined diffusion pattern.

Study and development of label-free optical biosensors for biomedical applications

NASA Astrophysics Data System (ADS)

Choi, Charles J.

For the majority of assays currently performed, fluorescent or colorimetric chemical labels are commonly attached to the molecules under study so that they may be readily visualized. The methods of using labels to track biomolecular binding events are very sensitive and effective, and are employed as standardized assay protocol across research labs worldwide. However, using labels induces experimental uncertainties due to the effect of the label on molecular conformation, active binding sites, or inability to find an appropriate label that functions equivalently for all molecules in an experiment. Therefore, the ability to perform highly sensitive biochemical detection without the use of fluorescent labels would further simplify assay protocols and would provide quantitative kinetic data, while removing experimental artifacts from fluorescent quenching, shelf-life, and background fluorescence phenomena. In view of the advantages mentioned above, the study and development of optical label-free sensor technologies have been undertaken here. In general, label-free photonic crystal (PC) biosensors and metal nanodome array surface-enhanced Raman scattering (SERS) substrates, both of which are fabricated by nanoreplica molding process, have been used as the method to attack the problem. Chapter 1 shows the work on PC label-free biosensor incorporated microfluidic network for bioassay performance enhancement and kinetic reaction rate constant determination. Chapter 2 describes the work on theoretical and experimental comparison of label-free biosensing in microplate, microfluidic, and spot-based affinity capture assays. Chapter 3 shows the work on integration of PC biosensor with actuate-to-open valve microfluidic chip for pL-volume combinatorial mixing and screening application. In Chapter 4, the development and characterization of SERS nanodome array is shown. Lastly, Chapter 5 describes SERS nanodome sensor incorporated tubing for point-of-care monitoring of

Graphite grain-size spectrum and molecules from core-collapse supernovae

NASA Astrophysics Data System (ADS)

Clayton, Donald D.; Meyer, Bradley S.

2018-01-01

Our goal is to compute the abundances of carbon atomic complexes that emerge from the C + O cores of core-collapse supernovae. We utilize our chemical reaction network in which every atomic step of growth employs a quantum-mechanically guided reaction rate. This tool follows step-by-step the growth of linear carbon chain molecules from C atoms in the oxygen-rich C + O cores. We postulate that once linear chain molecules reach a sufficiently large size, they isomerize to ringed molecules, which serve as seeds for graphite grain growth. We demonstrate our technique for merging the molecular reaction network with a parallel program that can follow 1017 steps of C addition onto the rare seed species. Due to radioactivity within the C + O core, abundant ambient oxygen is unable to convert C to CO, except to a limited degree that actually facilitates carbon molecular ejecta. But oxygen severely minimizes the linear-carbon-chain abundances. Despite the tiny abundances of these linear-carbon-chain molecules, they can give rise to a small abundance of ringed-carbon molecules that serve as the nucleations on which graphite grain growth builds. We expand the C + O-core gas adiabatically from 6000 K for 109 s when reactions have essentially stopped. These adiabatic tracks emulate the actual expansions of the supernova cores. Using a standard model of 1056 atoms of C + O core ejecta having O/C = 3, we calculate standard ejection yields of graphite grains of all sizes produced, of the CO molecular abundance, of the abundances of linear-carbon molecules, and of Buckminsterfullerene. None of these except CO was expected from the C + O cores just a few years past.

A general electrochemical method for label-free screening of protein–small molecule interactions†

PubMed Central

Cash, Kevin J.; Ricci, Francesco

2010-01-01

Here we report a versatile method by which the interaction between a protein and a small molecule, and the disruption of that interaction by competition with other small molecules, can be monitored electrochemically directly in complex sample matrices. PMID:19826675

Super-Chelators for Advanced Protein Labeling in Living Cells.

PubMed

Gatterdam, Karl; Joest, Eike F; Dietz, Marina S; Heilemann, Mike; Tampé, Robert

2018-05-14

Live-cell labeling, super-resolution microscopy, single-molecule applications, protein localization, or chemically induced assembly are emerging approaches, which require specific and very small interaction pairs. The minimal disturbance of protein function is essential to derive unbiased insights into cellular processes. Herein, we define a new class of hexavalent N-nitrilotriacetic acid (hexaNTA) chelators, displaying the highest affinity and stability of all NTA-based small interaction pairs described so far. Coupled to bright organic fluorophores with fine-tuned photophysical properties, the super-chelator probes were delivered into human cells by chemically gated nanopores. These super-chelators permit kinetic profiling, multiplexed labeling of His 6 - and His 12 -tagged proteins as well as single-molecule-based super-resolution imaging. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small molecule CP-31398 induces reactive oxygen species-dependent apoptosis in human multiple myeloma

PubMed Central

Arihara, Yohei; Takada, Kohichi; Kamihara, Yusuke; Hayasaka, Naotaka; Nakamura, Hajime; Murase, Kazuyuki; Ikeda, Hiroshi; Iyama, Satoshi; Sato, Tsutomu; Miyanishi, Koji; Kobune, Masayoshi; Kato, Junji

2017-01-01

Reactive oxygen species (ROS) are normal byproducts of a wide variety of cellular processes. ROS have dual functional roles in cancer cell pathophysiology. At low to moderate levels, ROS act as signaling transducers to activate cell proliferation, migration, invasion, and angiogenesis. In contrast, high levels of ROS induce cell death. In multiple myeloma (MM), ROS overproduction is the trigger for apoptosis induced by several anticancer compounds, including proteasome inhibitors. However, no drugs for which oxidative stress is the main mechanism of action are currently used for treatment of MM in clinical situations. In this study, we demonstrate that the p53-activating small molecule CP-31398 (CP) effectively inhibits the growth of MM cell lines and primary MM isolates from patients. CP also suppresses the growth of MM xenografts in mice. Mechanistically, CP was found to induce intrinsic apoptosis in MM cells via increasing ROS production. Interestingly, CP-induced apoptosis occurs regardless of the p53 status, suggesting that CP has additional mechanisms of action. Our findings thus indicate that CP could be an attractive candidate for treatment of MM patients harboring p53 abnormalities; this satisfies an unmet clinical need, as such individuals currently have a poor prognosis. PMID:29029480

Advantages and application of label-free detection assays in drug screening.

PubMed

Cunningham, Brian T; Laing, Lance G

2008-08-01

Adoption is accelerating for a new family of label-free optical biosensors incorporated into standard format microplates owing to their ability to enable highly sensitive detection of small molecules, proteins and cells for high-throughput drug discovery applications. Label-free approaches are displacing other detection technologies owing to their ability to provide simple assay procedures for hit finding/validation, accessing difficult target classes, screening the interaction of cells with drugs and analyzing the affinity of small molecule inhibitors to target proteins. This review describes several new drug discovery applications that are under development for microplate-based photonic crystal optical biosensors and the key issues that will drive adoption of the technology. Microplate-based optical biosensors are enabling a variety of cell-based assays, inhibition assays, protein-protein binding assays and protein-small molecule binding assays to be performed with high-throughput and high sensitivity.

DNA-length-dependent quenching of fluorescently labeled iron oxide nanoparticles with gold, graphene oxide and MoS2 nanostructures.

PubMed

Balcioglu, Mustafa; Rana, Muhit; Robertson, Neil; Yigit, Mehmet V

2014-08-13

We controlled the fluorescence emission of a fluorescently labeled iron oxide nanoparticle using three different nanomaterials with ultraefficient quenching capabilities. The control over the fluorescence emission was investigated via spacing introduced by the surface-functionalized single-stranded DNA molecules. DNA molecules were conjugated on different templates, either on the surface of the fluorescently labeled iron oxide nanoparticles or gold and nanographene oxide. The efficiency of the quenching was determined and compared with various fluorescently labeled iron oxide nanoparticle and nanoquencher combinations using DNA molecules with three different lengths. We have found that the template for DNA conjugation plays significant role on quenching the fluorescence emission of the fluorescently labeled iron oxide nanoparticles. We have observed that the size of the DNA controls the quenching efficiency when conjugated only on the fluorescently labeled iron oxide nanoparticles by setting a spacer between the surfaces and resulting change in the hydrodynamic size. The quenching efficiency with 12mer, 23mer and 36mer oligonucleotides decreased to 56%, 54% and 53% with gold nanoparticles, 58%, 38% and 32% with nanographene oxide, 46%, 38% and 35% with MoS2, respectively. On the other hand, the presence, not the size, of the DNA molecules on the other surfaces quenched the fluorescence significantly with different degrees. To understand the effect of the mobility of the DNA molecules on the nanoparticle surface, DNA molecules were attached to the surface with two different approaches. Covalently immobilized oligonucleotides decreased the quenching efficiency of nanographene oxide and gold nanoparticles to ∼22% and ∼21%, respectively, whereas noncovalently adsorbed oligonucleotides decreased it to ∼25% and ∼55%, respectively. As a result, we have found that each nanoquencher has a powerful quenching capability against a fluorescent nanoparticle, which can be

Device and method for separating oxygen isotopes

DOEpatents

Rockwood, Stephen D.; Sander, Robert K.

1984-01-01

A device and method for separating oxygen isotopes with an ArF laser which produces coherent radiation at approximately 193 nm. The output of the ArF laser is filtered in natural air and applied to an irradiation cell where it preferentially photodissociates molecules of oxygen gas containing .sup.17 O or .sup.18 O oxygen nuclides. A scavenger such as O.sub.2, CO or ethylene is used to collect the preferentially dissociated oxygen atoms and recycled to produce isotopically enriched molecular oxygen gas. Other embodiments utilize an ArF laser which is narrowly tuned with a prism or diffraction grating to preferentially photodissociate desired isotopes. Similarly, desired mixtures of isotopic gas can be used as a filter to photodissociate enriched preselected isotopes of oxygen.

A simple procedure for parallel sequence analysis of both strands of 5'-labeled DNA.

PubMed

Razvi, F; Gargiulo, G; Worcel, A

1983-08-01

Ligation of a 5'-labeled DNA restriction fragment results in a circular DNA molecule carrying the two 32Ps at the reformed restriction site. Double digestions of the circular DNA with the original enzyme and a second restriction enzyme cleavage near the labeled site allows direct chemical sequencing of one 5'-labeled DNA strand. Similar double digestions, using an isoschizomer that cleaves differently at the 32P-labeled site, allows direct sequencing of the now 3'-labeled complementary DNA strand. It is possible to directly sequence both strands of cloned DNA inserts by using the above protocol and a multiple cloning site vector that provides the necessary restriction sites. The simultaneous and parallel visualization of both DNA strands eliminates sequence ambiguities. In addition, the labeled circular molecules are particularly useful for single-hit DNA cleavage studies and DNA footprint analysis. As an example, we show here an analysis of the micrococcal nuclease-induced breaks on the two strands of the somatic 5S RNA gene of Xenopus borealis, which suggests that the enzyme may recognize and cleave small AT-containing palindromes along the DNA helix.

Progress of new label-free techniques for biosensors: a review.

PubMed

Sang, Shengbo; Wang, Yajun; Feng, Qiliang; Wei, Ye; Ji, Jianlong; Zhang, Wendong

2016-01-01

The detection techniques used in biosensors can be broadly classified into label-based and label-free. Label-based detection relies on the specific properties of labels for detecting a particular target. In contrast, label-free detection is suitable for the target molecules that are not labeled or the screening of analytes which are not easy to tag. Also, more types of label-free biosensors have emerged with developments in biotechnology. The latest developed techniques in label-free biosensors, such as field-effect transistors-based biosensors including carbon nanotube field-effect transistor biosensors, graphene field-effect transistor biosensors and silicon nanowire field-effect transistor biosensors, magnetoelastic biosensors, optical-based biosensors, surface stress-based biosensors and other type of biosensors based on the nanotechnology are discussed. The sensing principles, configurations, sensing performance, applications, advantages and restriction of different label-free based biosensors are considered and discussed in this review. Most concepts included in this survey could certainly be applied to the development of this kind of biosensor in the future.

Effect of oxygen atoms dissociated by non-equilibrium plasma on flame of methane oxygen and argon pre-mixture gas

NASA Astrophysics Data System (ADS)

Akashi, Haruaki; Yoshinaga, Tomokazu; Sasaki, Koichi

2014-10-01

For more efficient way of combustion, plasma-assisted combustion has been investigated by many researchers. But it is very difficult to clarify the effect of plasma even on the flame of methane. Because there are many complex chemical reactions in combustion system. Sasaki et al. has reported that the flame length of methane and air premixed burner shortened by irradiating microwave power. They also measured emission from Second Positive Band System of nitrogen during the irradiation. The emission indicates existence of high energy electrons which are accelerated by the microwave. The high energy electrons also dissociate oxygen molecules easily and oxygen atom would have some effects on the flame. But the dissociation ratio of oxygen molecules by the non-equilibrium plasma is significantly low, compared to that in the combustion reaction. To clarify the effect of dissociated oxygen atoms on the flame, dependence of dissociation ratio of oxygen on the flame has been examined using CHEMKIN. It is found that in the case of low dissociation ratio of 10-6, the ignition of the flame becomes slightly earlier. It is also found that in the case of high dissociation ratio of 10-3, the ignition time becomes significantly earlier by almost half. This work was supported by KAKENHI (22340170).

Label-free, real-time interaction and adsorption analysis 1: surface plasmon resonance.

PubMed

Fee, Conan J

2013-01-01

A key requirement for the development of proteins for use in nanotechnology is an understanding of how individual proteins bind to other molecules as they assemble into larger structures. The introduction of labels to enable the detection of biomolecules brings the inherent risk that the labels themselves will influence the nature of biomolecular interactions. Thus, there is a need for label-free interaction and adsorption analysis. In this and the following chapter, two biosensor techniques are reviewed: surface plasmon resonance (SPR) and the quartz crystal microbalance (QCM). Both allow real-time analysis of biomolecular interactions and both are label-free. The first of these, SPR, is an optical technique that is highly sensitive to the changes in refractive index that occur with protein (or other molecule) accumulation near an illuminated gold surface. Unlike QCM ( Chapter 18 ) SPR is not affected by the water that may be associated with the adsorbed layer nor by conformational changes in the adsorbed species. SPR thus provides unique information about the interaction of a protein with its binding partners.

Interactions between nitrogen and oxygen molecules studied by gas-phase NMR spectroscopy

NASA Astrophysics Data System (ADS)

Garbacz, Piotr; Misiak, Maria; Jackowski, Karol

2018-05-01

Gas-phase 14N and 15N NMR studies of nitrogen and synthetic air pressurized up to 300 bar were performed. It was found that the magnetic shielding of an isolated N2 molecule, σ0(N) = -63.4(2) ppm, is in good agreement with the results of ab initio calculations. The binary N2-O2 interactions contribute to shielding an order of the magnitude larger than the N2-N2 pairs. For nitrogen the three body collisions become observable by NMR for pressure higher than 200 bar and the appropriate coefficient can be practically assigned to the interaction between one molecule of N2 and a pair of O2 molecules.

Emerging applications of label-free optical biosensors

NASA Astrophysics Data System (ADS)

Zanchetta, Giuliano; Lanfranco, Roberta; Giavazzi, Fabio; Bellini, Tommaso; Buscaglia, Marco

2017-01-01

Innovative technical solutions to realize optical biosensors with improved performance are continuously proposed. Progress in material fabrication enables developing novel substrates with enhanced optical responses. At the same time, the increased spectrum of available biomolecular tools, ranging from highly specific receptors to engineered bioconjugated polymers, facilitates the preparation of sensing surfaces with controlled functionality. What remains often unclear is to which extent this continuous innovation provides effective breakthroughs for specific applications. In this review, we address this challenging question for the class of label-free optical biosensors, which can provide a direct signal upon molecular binding without using secondary probes. Label-free biosensors have become a consolidated approach for the characterization and screening of molecular interactions in research laboratories. However, in the last decade, several examples of other applications with high potential impact have been proposed. We review the recent advances in label-free optical biosensing technology by focusing on the potential competitive advantage provided in selected emerging applications, grouped on the basis of the target type. In particular, direct and real-time detection allows the development of simpler, compact, and rapid analytical methods for different kinds of targets, from proteins to DNA and viruses. The lack of secondary interactions facilitates the binding of small-molecule targets and minimizes the perturbation in single-molecule detection. Moreover, the intrinsic versatility of label-free sensing makes it an ideal platform to be integrated with biomolecular machinery with innovative functionality, as in case of the molecular tools provided by DNA nanotechnology.

EPR spin trapping of oxygen radicals in plants: a methodological overview.

PubMed

Bacić, Goran; Mojović, Milos

2005-06-01

We present a brief account of the difficulties involved in detection of oxygen free radicals in plants and give a rationale for using the EPR spin trapping technique in such studies. Comparative analysis of characteristics of different spin traps is given, having in mind their suitability in trapping oxygen-centered free radicals. Certain technical aspects of EPR experiments related to successful trapping of free radicals are discussed. Previous studies of trapping of oxygen radicals in plants are reviewed in terms of how efficient the experimental approach employed has been in their detection and how this influences conclusions about the mechanisms of their production. In addition, we analyze the potential of spin labels in the analysis of free radical production in plants and demonstrate that the combination of EPR spin traps and spin labels is extremely efficient for this purpose.

A spin labelling study of immunomodulating peptidoglycan monomer and adamantyltripeptides entrapped into liposomes.

PubMed

Frkanec, Ruza; Noethig-Laslo, Vesna; Vranesić, Branka; Mirosavljević, Krunoslav; Tomasić, Jelka

2003-04-01

The interaction of immunostimulating compounds, the peptidoglycan monomer (PGM) and structurally related adamantyltripeptides (AdTP1 and AdTP2), respectively, with phospholipids in liposomal bilayers were investigated by electron paramagnetic resonance spectroscopy. (1). The fatty acids bearing the nitroxide spin label at different positions along the acyl chain were used to investigate the interaction of tested compounds with negatively charged multilamellar liposomes. Electron spin resonance (ESR) spectra were studied at 290 and 310 K. The entrapment of the adamantyltripeptides affected the motional properties of all spin labelled lipids, while the entrapment of PGM had no effect. (2). Spin labelled PGM was prepared and the novel compound bearing the spin label attached via the amino group of diaminopimelic acid was chromatographically purified and chemically characterized. The rotational correlation time of the spin labelled molecule dissolved in buffer at pH 7.4 was studied as a function of temperature. The conformational change was observed above 300 K. The same effect was observed with the spin labelled PGM incorporated into liposomes. Such effect was not observed when the spin labelled PGM was studied at alkaline pH, probably due to the hydrolysis of PGM molecule. The study of possible interaction with liposomal membrane is relevant to the use of tested compounds incorporated into liposomes, as adjuvants in vivo.

Photophysical properties of fluorescently-labeled peptoids.

PubMed

Rudat, Birgit; Birtalan, Esther; Vollrath, Sidonie B L; Fritz, Daniel; Kölmel, Dominik K; Nieger, Martin; Schepers, Ute; Müllen, Klaus; Eisler, Hans-Jürgen; Lemmer, Uli; Bräse, Stefan

2011-09-01

Fluorescently-labeled biomolecules are often utilized in biochemical or cellular experiments without further detailed spectroscopical characterization. This report is intended to narrow this gap and therefore presents the photophysical investigation of a library of 17 fluorescently-labeled molecules, namely peptoid transporters. First, one peptoid structure is labeled with seven different fluorophores and the spectroscopical properties are examined. Absorption and fluorescence maxima are almost identical for free dyes and conjugated dyes, suggesting free choice of a spectrally suitable fluorophore for different applications. Otherwise, extinction coefficients and quantum yields, and therefore the brightness of all seven dyes are strongly influenced. For the fluorophores, e.g. rhodamine B, the extent of this influence depends on the peptoid itself. This is shown by comparing different structures in the second part of this report. Especially the side chain functionalities influence the brightness. And finally, peptoids having two identical fluorescent labels are presented, which show decreased quantum yields. Possible reasons for the observed photophysical properties are discussed. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Fluorescent Labeling of Proteins.

PubMed

Modesti, Mauro

2018-01-01

Many single-molecule experimental techniques exploit fluorescence as a tool to investigate conformational dynamics, molecular interactions, or track the movement of proteins in order to gain insight into their biological functions. A prerequisite to these experimental approaches is to graft one or more fluorophores on the protein of interest with the desired photophysical properties. Here, we describe procedures for efficient methods used to covalently attach fluorophores to proteins. Alternative direct and indirect labeling strategies are also described.

Energy expenditure in space flight (doubly labelled water method) (8-IML-1)

NASA Technical Reports Server (NTRS)

Parsons, Howard G.

1992-01-01

The objective of the Energy Expenditure in Space Flight (ESS) experiment is to demonstrate and evaluate the doubly labeled water method of measuring the energy expended by crew members during approximately 7 days in microgravity. The doubly labeled water technique determines carbon dioxide production which is then used to calculate energy expenditure. The method relies on the equilibrium between oxygen in respiratory carbon dioxide and oxygen in body water. Because of this equilibrium, the kinetic of water turnover and respiration are interdependent. Under normal conditions, man contains small but significant amounts of deuterium and oxygen 18. Deuterium is eliminated from the body as water while oxygen 18 is eliminated as water and carbon dioxide. The difference in the turnover rates in the two isotopes is proportional to the carbon dioxide production. Deliberately enriching the total body water with both of these isotopes allows the isotope turnovers to be accurately measured in urine, plasma, or saliva samples. The samples are taken to the laboratory for analysis using an ion-ratio spectrometer.

Discovery of competing anaerobic and aerobic pathways in umpolung amide synthesis allows for site-selective amide 18O-labeling

PubMed Central

Shackleford, Jessica P.; Shen, Bo; Johnston, Jeffrey N.

2012-01-01

The mechanism of umpolung amide synthesis was probed by interrogating potential sources for the oxygen of the product amide carbonyl that emanates from the α-bromo nitroalkane substrate. Using a series of 18O-labeled substrates and reagents, evidence is gathered to advance two pathways from the putative tetrahedral intermediate. Under anaerobic conditions, a nitro-nitrite isomerization delivers the amide oxygen from nitro oxygen. The same homolytic nitro-carbon fragmentation can be diverted by capture of the carbon radical intermediate with oxygen gas (O2) to deliver the amide oxygen from O2. This understanding was used to develop a straightforward protocol for the preparation of 18O-labeled amides in peptides by simply performing the umpolung amide synthesis reaction under an atmosphere of . PMID:22184227

Analysis of carbon-oxygen reactions by use of a square-input response technique and {sup 18}O isotope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miura, Kouichi; Nakagawa, Hiroyuki

1996-12-31

Carbon gasification reaction has been investigated for decades including the pioneering works of Walker and his co-workers, but its mechanism has not been completely elucidated. The concept of the active surface area (ASA) was proposed by them, and its importance has been recognized. However, since ASA was measured by O{sub 2} chemisorption at below 300{degrees}C where carbon loss through gasification is negligible, it does not reflect the actual gasification situation. To overcome this weak point, measurements of ASA in a batch reactor and the so-called transient kinetic (TK) method were proposed. Ahmed and Back successfully measured the chemisorbed oxygen duringmore » the gasification using a batch reactor, and proposed a new mechanistic sequence for carbon-oxygen reaction which stresses the importance of the reaction between the gaseous oxygen and the chemisorbed oxygen. Radovic et al. proposed the concept of the reactive surface area (RSA), and reported excellent proportionality between the CO{sub 2} gasification rate and the RSA estimated by the TK and the TPD methods. Kapteijn et al. showed that the TK method with labeled molecules is more powerful to examine the mechanism. They found the presence of two types of surface oxygen complexes which desorb at different rates. A Square-input response (SIR) method is applied to the carbon-oxygen reaction. This method allows the observation of transient changes on two step changes. This method has been successfully applied to the analysis of a coal char gasification.« less

Complex molecules in the W51 North region

NASA Astrophysics Data System (ADS)

Rong, Jialei; Qin, Sheng-Li; Zapata, Luis A.; Wu, Yuefang; Liu, Tie; Zhang, Chengpeng; Peng, Yaping; Zhang, Li; Liu, Ying

2016-01-01

We present Submillimeter Array (SMA) molecular-line observations in two 2-GHz wide bands centred at 217.5 and 227.5 GHz, towards the massive star-forming region W51 North. We identified 84 molecular-line transitions from 17 species and their isotopologues. The molecular gas distribution of these lines mainly peaks in the continuum position of W51 North, and has a small tail extending to the west, probably associated with W51 d2. In addition to the commonly detected nitrogen- and oxygen-bearing species, we detected a large number of transitions of acetone (CH3COCH3) and methyl formate (CH3OCHO), which might suggest that these molecules are present in an early evolutionary stage of massive stars. We have also found that W51 North is an ethanol-rich source. There is no obvious difference in the molecular gas distributions between the oxygen-bearing and nitrogen-bearing molecules. Under the assumption of local thermodynamic equilibrium, with the XCLASS tool, the molecular column densities and rotation temperatures are estimated. We have found that the oxygen-bearing molecules have considerably higher column densities and fractional abundances than the nitrogen-bearing molecules. The rotation temperatures range from 100 to 200 K, suggesting that the molecular emission could originate from a warm environment. Finally, based on the gas distributions, fractional abundances and the rotation temperatures, we conclude that CH3OH, C2H5OH, CH3COCH3 and CH3CH2CN might be synthesized on the grain surface, while gas phase chemistry is responsible for the production of CH3OCH3, CH3OCHO and CH2CHCN.

Near-infrared oxygen airglow from the Venus nightside

NASA Technical Reports Server (NTRS)

Crisp, D.; Meadows, V. S.; Allen, D. A.; Bezard, B.; Debergh, C.; Maillard, J.-P.

1992-01-01

Groundbased imaging and spectroscopic observations of Venus reveal intense near-infrared oxygen airglow emission from the upper atmosphere and provide new constraints on the oxygen photochemistry and dynamics near the mesopause (approximately 100 km). Atomic oxygen is produced by the Photolysis of CO2 on the dayside of Venus. These atoms are transported by the general circulation, and eventually recombine to form molecular oxygen. Because this recombination reaction is exothermic, many of these molecules are created in an excited state known as O2(delta-1). The airglow is produced as these molecules emit a photon and return to their ground state. New imaging and spectroscopic observations acquired during the summer and fall of 1991 show unexpected spatial and temporal variations in the O2(delta-1) airglow. The implications of these observations for the composition and general circulation of the upper venusian atmosphere are not yet understood but they provide important new constraints on comprehensive dynamical and chemical models of the upper mesosphere and lower thermosphere of Venus.

Femtogram-scale photothermal spectroscopy of explosive molecules on nanostrings.

PubMed

Biswas, T S; Miriyala, N; Doolin, C; Liu, X; Thundat, T; Davis, J P

2014-11-18

We demonstrate detection of femtogram-scale quantities of the explosive molecule 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) via combined nanomechanical photothermal spectroscopy and mass desorption. Photothermal spectroscopy provides a spectroscopic fingerprint of the molecule, which is unavailable using mass adsorption/desorption alone. Our measurement, based on thermomechanical measurement of silicon nitride nanostrings, represents the highest mass resolution ever demonstrated via nanomechanical photothermal spectroscopy. This detection scheme is quick, label-free, and is compatible with parallelized molecular analysis of multicomponent targets.

Bioorthogonal Metabolic DNA Labelling using Vinyl Thioether-Modified Thymidine and o-Quinolinone Quinone Methide.

PubMed

Gubu, Amu; Li, Long; Ning, Yan; Zhang, Xiaoyun; Lee, Seonghyun; Feng, Mengke; Li, Qiang; Lei, Xiaoguang; Jo, Kyubong; Tang, Xinjing

2018-04-17

Bioorthogonal metabolic DNA labeling with fluorochromes is a powerful strategy to visualize DNA molecules and their functions. Here, we report the development of a new DNA metabolic labeling strategy enabled by the catalyst-free bioorthogonal ligation using vinyl thioether modified thymidine and o-quinolinone quinone methide. With the newly designed vinyl thioether-modified thymidine (VTdT), we added labeling tags on cellular DNA, which could further be linked to fluorochromes in cells. Therefore, we successfully visualized the DNA localization within cells as well as single DNA molecules without other staining reagents. In addition, we further characterized this bioorthogonal DNA metabolic labeling using DNase I digestion, MS characterization of VTdT as well as VTdT-oQQF conjugate in cell nuclei or mitochondria. This technique provides a powerful strategy to study DNA in cells, which paves the way to achieve future spatiotemporal deciphering of DNA synthesis and functions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Labeling proteins inside living cells using external fluorophores for microscopy.

PubMed

Teng, Kai Wen; Ishitsuka, Yuji; Ren, Pin; Youn, Yeoan; Deng, Xiang; Ge, Pinghua; Lee, Sang Hak; Belmont, Andrew S; Selvin, Paul R

2016-12-09

Site-specific fluorescent labeling of proteins inside live mammalian cells has been achieved by employing Streptolysin O, a bacterial enzyme which forms temporary pores in the membrane and allows delivery of virtually any fluorescent probes, ranging from labeled IgG's to small ligands, with high efficiency (>85% of cells). The whole process, including recovery, takes 30 min, and the cell is ready to be imaged immediately. A variety of cell viability tests were performed after treatment with SLO to ensure that the cells have intact membranes, are able to divide, respond normally to signaling molecules, and maintains healthy organelle morphology. When combined with Oxyrase, a cell-friendly photostabilizer, a ~20x improvement in fluorescence photostability is achieved. By adding in glutathione, fluorophores are made to blink, enabling super-resolution fluorescence with 20-30 nm resolution over a long time (~30 min) under continuous illumination. Example applications in conventional and super-resolution imaging of native and transfected cells include p65 signal transduction activation, single molecule tracking of kinesin, and specific labeling of a series of nuclear and cytoplasmic protein complexes.

Cellular Metabolic Activity and the Oxygen and Hydrogen Stable Isotope Composition of Intracellular Water and Metabolites

NASA Astrophysics Data System (ADS)

Kreuzer-Martin, H. W.; Hegg, E. L.

2008-12-01

Intracellular water is an important pool of oxygen and hydrogen atoms for biosynthesis. Intracellular water is usually assumed to be isotopically identical to extracellular water, but an unexpected experimental result caused us to question this assumption. Heme O isolated from Escherichia coli cells grown in 95% H218O contained only a fraction of the theoretical value of labeled oxygen at a position where the O atom was known to be derived from water. In fact, fewer than half of the oxygen atoms were labeled. In an effort to explain this surprising result, we developed a method to determine the isotope ratios of intracellular water in cultured cells. The results of our experiments showed that during active growth, up to 70% of the oxygen atoms and 50% of the hydrogen atoms in the intracellular water of E. coli are generated during metabolism and can be isotopically distinct from extracellular water. The fraction of isotopically distinct atoms was substantially less in stationary phase and chilled cells, consistent with our hypothesis that less metabolically-generated water would be present in cells with lower metabolic activity. Our results were consistent with and explained the result of the heme O labeling experiment. Only about 40% of the O atoms on the heme O molecule were labeled because, presumably, only about 40% of the water inside the cells was 18O water that had diffused in from the culture medium. The rest of the intracellular water contained 16O atoms derived from either nutrients or atmospheric oxygen. To test whether we could also detect metabolically-derived hydrogen atoms in cellular constituents, we isolated fatty acids from log-phase and stationary phase E. coli and determined the H isotope ratios of individual fatty acids. The results of these experiments showed that environmental water contributed more H atoms to fatty acids isolated in stationary phase than to the same fatty acids isolated from log-phase cells. Stable isotope analyses of

Single-molecule studies of multi-protein machines

NASA Astrophysics Data System (ADS)

van Oijen, Antoine

2010-03-01

Advances in optical imaging and molecular manipulation techniques have made it possible to observe individual enzymes and record molecular movies that provide new insight into their dynamics and reaction mechanisms. In a biological context, most of these enzymes function in concert with other enzymes in multi-protein complexes, so an important future direction will be the utilization of single-molecule techniques to unravel the orchestration of large macromolecular assemblies. Our group is developing the single-molecule tools that will make it possible to study biochemical pathways of arbitrary complexity at the single-molecule level. I will discuss results of single-molecule experiments on the replisome, the molecular machinery that is responsible for replication of DNA. We stretch individual DNA molecules and use their elastic properties to obtain dynamic information on the proteins that unwind the double helix and copy its genetic information. Furthermore, we visualize fluorescently labeled components of the replisome and thus obtain information on stochiometry and exchange kinetics. This simultaneous observation of catalytic activity and composition allows us to gain deeper insight into the structure-function relationship of the replisome.

Labeling Biomolecules with Radiorhenium - a Review of the Bifunctional Chelators

PubMed Central

Liu, Guozheng; Hnatowich, Donald J.

2007-01-01

For radiotherapy, biomolecules such as intact antibodies, antibody fragments, peptides, DNAs and other oligomers have all been labeled with radiorhenium (186Re and 188Re). Three different approaches have been employed that may be referred to as direct, indirect and integral labeling. Direct labeling applies to proteins and involves the initial reduction of endogenous disulfide bridges to provide chelation sites. Indirect labeling can apply to most biomolecules and involves the initial attachment of an exogenous chelator. Finally, integral labeling is a special case applying only to small molecules in which the metallic radionuclide serves to link two parts of a biomolecule together in forming the labeled complex. While the number of varieties for the direct and integral radiolabeling approaches is rather limited, a fairly large and diverse number of chelators have been reported in the case of indirect labeling. Our objective herein is to provide an overview of the various chelators that have been used in the indirect labeling of biomolecules with radiorhenium, including details on the labeling procedures, the stability of the radiolabel and, where possible, the influence of the label on biological properties. PMID:17504162

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Generation of singlet oxygen in fullerene-containing media: 1. Photodesorption of singlet oxygen from fullerene-containing surfaces

NASA Astrophysics Data System (ADS)

Belousova, I. M.; Belousov, V. P.; Danilov, O. B.; Ermakov, A. V.; Kiselev, V. M.; Kislyakov, I. M.; Sosnov, E. N.

2008-03-01

It is shown that upon irradiation of fullerene-containing surfaces by laser or flashlamp pulses, oxygen adsorbed by these surfaces efficiently escapes to the gas phase. The observation of luminescence pulses in the spectral region of 762 and 1268 nm confirms the presence of oxygen molecules in the excited singlet state in the desorbed oxygen. The conditions for optimisation of the efficiency of singlet-oxygen production are studied. It is shown that singlet oxygen at the concentration sufficient for obtaining operation of a fullerene-oxygen-iodine laser can be produced in this way.

Preparation and characterization of dextran nanobubbles for oxygen delivery.

PubMed

Cavalli, R; Bisazza, A; Giustetto, P; Civra, A; Lembo, D; Trotta, G; Guiot, C; Trotta, M

2009-11-03

Dextran nanobubbles were prepared with a dextran shell and a perfluoropentan core in which oxygen was stored. To increase the stability polyvinylpirrolidone was also added to the formulation as stabilizing agent. Rhodamine B was used as fluorescent marker to obtain fluorescent nanobubbles. The nanobubble formulations showed sizes of about 500nm, a negative surface charge and a good capacity of loading oxygen, no hemolytic activity or toxic effect on cell lines. The fluorescent labelled nanobubbles could be internalized in Vero cells. Oxygen-filled nanobubbles were able to release oxygen in different hypoxic solutions at different time after their preparation in in vitro experiments. The oxygen release kinetics could be enhanced after nanobubble insonation with ultrasound at 2.5MHz. The oxygen-filled nanobubble formulations might be proposed for therapeutic applications in various diseases.

Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.

PubMed

Koh, Hye Ran; Wang, Xinlei; Myong, Sua

2016-08-01

TRBP, one of double strand RNA binding proteins (dsRBPs), is an essential cofactor of Dicer in the RNA interference pathway. Previously we reported that TRBP exhibits repetitive diffusion activity on double strand (ds)RNA in an ATP independent manner. In the TRBP-Dicer complex, the diffusion mobility of TRBP facilitates Dicer-mediated RNA cleavage. Such repetitive diffusion of dsRBPs on a nucleic acid at the nanometer scale can be appropriately captured by several single molecule detection techniques. Here, we provide a step-by-step guide to four different single molecule fluorescence assays by which the diffusion activity of dsRBPs on dsRNA can be detected. One color assay, termed protein induced fluorescence enhancement enables detection of unlabeled protein binding and diffusion on a singly labeled RNA. Two-color Fluorescence Resonance Energy Transfer (FRET) in which labeled dsRBPs is applied to labeled RNA, allows for probing the motion of protein along the RNA axis. Three color FRET reports on the diffusion movement of dsRBPs from one to the other end of RNA. The single molecule pull down assay provides an opportunity to collect dsRBPs from mammalian cells and examine the protein-RNA interaction at single molecule platform. Copyright © 2016 Elsevier Inc. All rights reserved.

Visualization of DNA molecules in time during electrophoresis

NASA Technical Reports Server (NTRS)

Lubega, Seth

1991-01-01

For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.

Spectroscopic and kinetic studies of photochemical reaction of magnesium tetraphenylporphyrin with oxygen.

PubMed

Zhang, Jianbin; Zhang, Pengyan; Zhang, Zhengfu; Wei, Xionghui

2009-05-07

Magnesium tetraphenylporphyrin (MgTPP) was synthesized from meso-tetraphenylporphyrin (H(2)TPP) in N,N-dimethylformamide (DMF). The photochemical properties of MgTPP in the presence of oxygen were investigated in dichloromethane (CH(2)Cl(2)) by conventional fluorescence, UV-vis, (1)H NMR, MALDI-TOF-MS, FTIR, and XPS spectroscopic techniques. Spectral analyses showed that under irradiation, MgTPP molecules reacted with O(2) molecules, and a stable 1:1 adduct was produced. During the photochemical reaction process, one oxygen molecule was bound to the pyrrolenine nitrogens in the MgTPP molecule, and the characteristic N-O bonds were identified using the FTIR and XPS techniques. The kinetics of the photochemical reaction of MgTPP with O(2) has been studied in an oxygen-saturated solution. Under irradiation conditions, the experimental rate follows a pseudo-first-order reaction for MgTPP, having a half-life from 40 to 130 min under various irradiation intensities. The kinetic rate constant of photochemical reaction of MgTPP with O(2) showed a linear dependence.

Topological events in single molecules of E. coli DNA confined in nanochannels

PubMed Central

Reifenberger, Jeffrey G.; Dorfman, Kevin D.; Cao, Han

2015-01-01

We present experimental data concerning potential topological events such as folds, internal backfolds, and/or knots within long molecules of double-stranded DNA when they are stretched by confinement in a nanochannel. Genomic DNA from E. coli was labeled near the ‘GCTCTTC’ sequence with a fluorescently labeled dUTP analog and stained with the DNA intercalator YOYO. Individual long molecules of DNA were then linearized and imaged using methods based on the NanoChannel Array technology (Irys® System) available from BioNano Genomics. Data were collected on 189,153 molecules of length greater than 50 kilobases. A custom code was developed to search for abnormal intensity spikes in the YOYO backbone profile along the length of individual molecules. By correlating the YOYO intensity spikes with the aligned barcode pattern to the reference, we were able to correlate the bright intensity regions of YOYO with abnormal stretching in the molecule, which suggests these events were either a knot or a region of internal backfolding within the DNA. We interpret the results of our experiments involving molecules exceeding 50 kilobases in the context of existing simulation data for relatively short DNA, typically several kilobases. The frequency of these events is lower than the predictions from simulations, while the size of the events is larger than simulation predictions and often exceeds the molecular weight of the simulated molecules. We also identified DNA molecules that exhibit large, single folds as they enter the nanochannels. Overall, topological events occur at a low frequency (~7% of all molecules) and pose an easily surmountable obstacle for the practice of genome mapping in nanochannels. PMID:25991508

A protocol for a systematic review to identify allergenic tree nuts and the molecules responsible for their allergenic properties.

PubMed

Javed, Bushra; Padfield, Philip; Sperrin, Matthew; Simpson, Angela; Mills, E N Clare

2017-08-01

Food regulations require that tree nuts and derived ingredients are included on food labels in order to help individuals with IgE-mediated allergies to avoid them. However, there is no consensus regarding which tree nut species should be included in this definition and specified on food labels. Allergen detection methods used for monitoring foods target allergen molecules, but it not clear which are the most relevant molecules to choose. A modified population-exposure-comparators-outcome (PECO) approach has been developed to systematically review the evidence regarding (1) which allergenic tree nuts should be included in food allergen labelling lists and (2) which are the clinically relevant allergens which should be used as analytical targets. A search strategy and criteria against which the evidence will be evaluated have been developed. The resulting evidence will be used to rank tree nuts with regards their ability to cause IgE-mediated allergies, and allergen molecules regarding their capacity to elicit an allergic reaction. The results of the systematic review will enable risk assessors and managers to identify tree nut species that should be included in food allergen labelling lists and ensure analytical methods for determination of allergens in foods are targeting appropriate molecules. Copyright © 2017. Published by Elsevier Ltd.

Heterogeneity of hypoxia in solid tumours and mechanochemical reactions with oxygen nanobubbles.

PubMed

Orel, V B; Zabolotny, M A; Orel, V E

2017-05-01

Tumour hypoxia leads to radio and chemotherapy resistance among cancer patients. The aim of this paper is to formulate a hypothesis on the heterogeneity of hypoxia in solid tumours. Tumour vasculature is known to be significantly variable. The great structural and functional abnormalities of tumour microcirculation cause spatial and temporal heterogeneity in its perfusion. Tumours have constantly been under the influence of pulsatile blood perfusion with variable pressure that initiates inhomogeneous erythrocyte deformation and following impact on oxygen disorder release from red blood cells into plasma within the blood vessel. Furthermore, stochastically released oxygen in tumour vessel, plasma and interstitial fluid may lead to heterogeneity of hypoxia. Under the influence of increased heterogeneity of hemodynamic force, the oxygen molecules dissolved in blood plasma are inclined to form nanobubbles (NBs) in tumour vessels. Considering the fact that tumour interstitial fluid pressure is increased compared to normal tissues, we assume that oxygen NBs may burst under the impact of shear stress. During the course of mechanochemical reaction, when a nanobubble (NB) bursts, both reactive oxygen species and ions form in various charged states. In consequence of a chain reaction, free radical oxygen molecules bind to proteins and lipids, thus reducing oxygen molecules in a chaotic manner within the tumour. The proposed hypothesis should be used as a methodical approach based on the simultaneous ultrasound imaging diagnostic techniques and therapy, regarding the mechanochemical effect on NB conglomerates with drugs in the tumour. Copyright © 2017 Elsevier Ltd. All rights reserved.

A novel small molecule, Rosline, inhibits growth and induces caspase-dependent apoptosis in human lung cancer cells A549 through a reactive oxygen species-dependent mechanism.

PubMed

Zhao, Ting; Feng, Yang; Jin, Wenling; Pan, Hui; Li, Haizhou; Zhao, Yang

2016-06-01

Chemical screening using synthetic small molecule libraries has provided a huge amount of novel active molecules. It generates lead compound for drug development and brings focus on molecules for mechanistic investigations on many otherwise intangible biological processes. In this study, using non-small cell lung cancer cell A549 to screen against a structurally novel and diverse synthetic small molecule library of 2,400 compounds, we identified a molecule named rosline that has strong anti-proliferation activity on A549 cells with a 50% cell growth inhibitory concentration (IC50 ) of 2.87 ± 0.39 µM. We showed that rosline treatment increased the number of Annexin V-positive staining cell, as well as G2/M arrest in their cell cycle progression. Further, we have demonstrated that rosline induces a decrease of mitochondrial membrane potential (Δφm ) and an increase of caspases 3/7 and 9 activities in A549 cells, although having no effect on the activity of caspase 8. Moreover, we found that rosline could induce the production of reactive oxygen species (ROS) and inhibit the phosphorylation of signaling molecule Akt in A549 cells. Alternatively, an antioxidant N-acetyl-L-cysteine (NAC) significantly attenuated rosline's effects on the mitochondrial membrane potential, caspases 3/7 and 9 activities, cell viabilities and the phosphorylation of Akt. Our results demonstrated that ROS played an important role in the apoptosis of A549 cells induced by rosline. © 2016 International Federation for Cell Biology.

The effects of hyperbaric oxygen therapy on oxidative stress, inflammation, and symptoms in children with autism: an open-label pilot study

PubMed Central

Rossignol, Daniel A; Rossignol, Lanier W; James, S Jill; Melnyk, Stepan; Mumper, Elizabeth

2007-01-01

Background Recently, hyperbaric oxygen therapy (HBOT) has increased in popularity as a treatment for autism. Numerous studies document oxidative stress and inflammation in individuals with autism; both of these conditions have demonstrated improvement with HBOT, along with enhancement of neurological function and cognitive performance. In this study, children with autism were treated with HBOT at atmospheric pressures and oxygen concentrations in current use for this condition. Changes in markers of oxidative stress and inflammation were measured. The children were evaluated to determine clinical effects and safety. Methods Eighteen children with autism, ages 3–16 years, underwent 40 hyperbaric sessions of 45 minutes duration each at either 1.5 atmospheres (atm) and 100% oxygen, or at 1.3 atm and 24% oxygen. Measurements of C-reactive protein (CRP) and markers of oxidative stress, including plasma oxidized glutathione (GSSG), were assessed by fasting blood draws collected before and after the 40 treatments. Changes in clinical symptoms, as rated by parents, were also assessed. The children were closely monitored for potential adverse effects. Results At the endpoint of 40 hyperbaric sessions, neither group demonstrated statistically significant changes in mean plasma GSSG levels, indicating intracellular oxidative stress appears unaffected by either regimen. A trend towards improvement in mean CRP was present in both groups; the largest improvements were observed in children with initially higher elevations in CRP. When all 18 children were pooled, a significant improvement in CRP was found (p = 0.021). Pre- and post-parental observations indicated statistically significant improvements in both groups, including motivation, speech, and cognitive awareness (p < 0.05). No major adverse events were observed. Conclusion In this prospective pilot study of children with autism, HBOT at a maximum pressure of 1.5 atm with up to 100% oxygen was safe and well tolerated

HaloTag technology for specific and covalent labeling of fusion proteins.

PubMed

Benink, Hélène A; Urh, Marjeta

2015-01-01

Appending proteins of interest to fluorescent protein tags such as GFP has revolutionized how proteins are studied in the cellular environment. Over the last few decades many varieties of fluorescent proteins have been generated, each bringing new capability to research. However, taking full advantage of standard fluorescent proteins with advanced and differential features requires significant effort on the part of the researcher. This approach necessitates that many genetic fusions be generated and confirmed to function properly in cells with the same protein of interest. To lessen this burden, a newer category of protein fusion tags termed "self-labeling protein tags" has been developed. This approach utilizes a single protein tag, the function of which can be altered by attaching various chemical moieties (fluorescent labels, affinity handles, etc.). In this way a single genetically encoded protein fusion can easily be given functional diversity and adaptability as supplied by synthetic chemistry. Here we present protein labeling methods using HaloTag technology; comprised of HaloTag protein and the collection of small molecules designed to bind it specifically and provide it with varied functionalities. For imaging purposes these small molecules, termed HaloTag ligands, contain distinct fluorophores. Due to covalent and rapid binding between HaloTag protein and its ligands, labeling is permanent and efficient. Many of these ligands have been optimized for permeability across cellular membranes allowing for live cell labeling and imaging analysis. Nonpermeable ligands have also been developed for specific labeling of surface proteins. Overall, HaloTag is a versatile technology that empowers the end user to label a protein of interest with the choice of different fluorophores while alleviating the need for generation of multiple genetic fusions.

Phosphatidylglycerol Synthesis in Spinach Chloroplasts: Characterization of the Newly Synthesized Molecule

PubMed Central

Sparace, Salvatore A.; Mudd, J. Brian

1982-01-01

Intact chloroplasts from spinach (Spinacia oleracea L., hybrid 424) readily incorporate [14C]glycerol-3-phosphate and [14C]acetate into diacylglycerol, monoacylglycerol, diacylglycrol, free fatty acids (only when acetate is the precursor), phosphatidic acid, phosphatidylcholine, and most notably phosphatidylglycerol. The fraction of phosphatidylglycerol synthesized is greatly increased by the presence of manganese chloride in the reaction mixture. Glycerol-3-phosphate-labeled phosphatidylglycerol is equally labeled in the two glycerol moieties of the molecule. Acetate-labeled phosphatidylglycerol is equally labeled in both acyl groups. Position one contains primarily oleate, linoleate and small amounts of palmitate. Position two contains primarily palmitate. No radioactive trans-Δ3-hexadecenoate was detected. The labeling patterns indicate that the radioactive phosphatidylglycerol is the product of de novo chloroplast lipid biosynthesis and furthermore, phosphatidylglycerol may be a substrate for fatty acid desaturation. Images Fig. 1 PMID:16662664

Direct single-molecule dynamic detection of chemical reactions.

PubMed

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N.; Zhang, Deqing; Guo, Xuefeng

2018-01-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry. PMID:29487914

Direct detection of free radicals and reactive oxygen species in thylakoids.

PubMed

Hideg, Eva; Kálai, Tamás; Hideg, Kálmán

2011-01-01

In plants, reactive oxygen species (ROS), also known as active oxygen species (AOS), are associated with normal, physiologic processes as well as with responses to adverse conditions. ROS are connected to stress in many ways: as primary elicitors, as products and propagators of oxidative damage, or as signal molecules initiating defense or adaptation. The photosynthetic electron transport is a major site of oxidative stress by visible or ultraviolet light, high or low temperature, pollutants or herbicides. ROS production can be presumed from detecting oxidatively damaged lipids, proteins, or pigments as well as from the alleviating effects of added antioxidants. On the contrary, measuring ROS by special sensor molecules provides more direct information. This chapter focuses on the application of spin trapping electron paramagnetic resonance (EPR) spectroscopy for detecting ROS: singlet oxygen and oxygen free radicals in thylakoid membrane preparations.

Pharmacogenomic Biomarkers: an FDA Perspective on Utilization in Biological Product Labeling.

PubMed

Schuck, Robert N; Grillo, Joseph A

2016-05-01

Precision medicine promises to improve both the efficacy and safety of therapeutic products by better informing why some patients respond well to a drug, and some experience adverse reactions, while others do not. Pharmacogenomics is a key component of precision medicine and can be utilized to select optimal doses for patients, more precisely identify individuals who will respond to a treatment and avoid serious drug-related toxicities. Since pharmacogenomic biomarker information can help inform drug dosing, efficacy, and safety, pharmacogenomic data are critically reviewed by FDA staff to ensure effective use of pharmacogenomic strategies in drug development and appropriate incorporation into product labels. Pharmacogenomic information may be provided in drug or biological product labeling to inform health care providers about the impact of genotype on response to a drug through description of relevant genomic markers, functional effects of genomic variants, dosing recommendations based on genotype, and other applicable genomic information. The format and content of labeling for biologic drugs will generally follow that of small molecule drugs; however, there are notable differences in pharmacogenomic information that might be considered useful for biologic drugs in comparison to small molecule drugs. Furthermore, the rapid entry of biologic drugs for treatment of rare genetic diseases and molecularly defined subsets of common diseases will likely lead to increased use of pharmacogenomic information in biologic drug labels in the near future. In this review, we outline the general principles of therapeutic product labeling and discuss the utilization of pharmacogenomic information in biologic drug labels.

Nucleic acid analysis using terminal-phosphate-labeled nucleotides

DOEpatents

Korlach, Jonas [Ithaca, NY; Webb, Watt W [Ithaca, NY; Levene, Michael [Ithaca, NY; Turner, Stephen [Ithaca, NY; Craighead, Harold G [Ithaca, NY; Foquet, Mathieu [Ithaca, NY

2008-04-22

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Comprehensive assessment of impaired peripheral and coronary artery endothelial functions in smokers using brachial artery ultrasound and oxygen-15-labeled water PET.

PubMed

Ochi, Noriki; Yoshinaga, Keiichiro; Ito, Yoichi M; Tomiyama, Yuuki; Inoue, Mamiko; Nishida, Mutsumi; Manabe, Osamu; Shibuya, Hitoshi; Shimizu, Chikara; Suzuki, Eriko; Fujii, Satoshi; Katoh, Chietsugu; Tamaki, Nagara

2016-10-01

Comprehensive evaluation of endothelium-dependent and endothelium-independent vascular functions in peripheral arteries and coronary arteries in smokers has never been performed previously. Through the use of brachial artery ultrasound and oxygen-15-labeled water positron emission tomography (PET), we sought to investigate peripheral and coronary vascular dysfunctions in smokers. Eight smokers and 10 healthy individuals underwent brachial artery ultrasound at rest, during reactive hyperemia [250mmHg cuff occlusion (flow-mediated dilatation (FMD)], and following sublingual nitroglycerin (NTG) administration. Myocardial blood flow (MBF) was assessed through O-15-labeled water PET at rest, during adenosine triphosphate (ATP) administration, and during a cold pressor test (CPT). Through ultrasound, smokers were shown to have significantly reduced %FMD compared to controls (6.62±2.28% vs. 11.29±2.75%, p=0.0014). As assessed by O-15-labeled water PET, smokers were shown to have a significantly lower CPT response than were controls (21.1±9.5% vs. 50.9±16.9%, p=0.0004). There was no relationship between %FMD and CPT response (r=0.40, p=0.097). Endothelium-independent vascular dilatation was similar for both groups in terms of coronary flow reserve with PET (p=0.19). Smokers tended to have lower %NTG in the brachial artery (p=0.055). Smokers exhibited impaired coronary endothelial function as well as peripheral brachial artery endothelial function. In addition, there was no correlation between PET and ultrasound measurements, possibly implying that while smokers may have systemic vascular endothelial dysfunction, the characteristics of that dysfunction may be different in peripheral arteries and coronary arteries. Copyright © 2016. Published by Elsevier Ltd.

Magnetic coupling of Fe-porphyrin molecules adsorbed on clean and c(2×2) oxygen-reconstructed Co(100) investigated by spin-polarized photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Weber, A. P.; Caruso, A. N.; Vescovo, E.; Ali, Md. E.; Tarafder, K.; Janjua, S. Z.; Sadowski, J. T.; Oppeneer, P. M.

2013-05-01

The spin-polarized electronic structure of iron octaethylporphyrin (FeOEP) molecules adsorbed on a pristine and on a c(2×2) oxygen-reconstructed Co(100) surface has been analyzed by means of spin-polarized photoemission spectroscopy (SPPES) and first-principles density functional theory with the on-site Coulomb repulsion U term (DFT+U) calculations with and without Van der Waals corrections. The aim is to examine the magnetic exchange mechanism between the FeOEP molecules and the Co(100) substrate in the presence or absence of the oxygen mediator. The results demonstrate that the magnetic coupling from the ferromagnetic substrate to the adsorbed FeOEP molecules is ferromagnetic, whereas, the coupling is antiferromagnetic for the FeOEP on the c(2×2)O/Co(100) system. Spin-resolved partial densities of states extracted from ab initio DFT+U modeling are in fairly good comparison with the electronic spectral densities seen in angle-integrated SPPES energy dispersion curves for submonolayer coverages of FeOEP. Through combined analysis of these spectra and theoretical results, we determine that hybridization of 2p orbitals of N and O with Co 3d orbitals facilitates indirect magnetic exchange interactions between Fe and Co, whereas, a direct Fe-Co interaction involving the Fe dz2 orbital is also found for FeOEP on Co. It is observed through SPPES that the spin polarization of the photoemission-visible molecular overlayers decreases to zero as coverage is increased beyond the submonolayer regime, indicating that only interfacial magnetic coupling is at work. Microspot low-energy electron diffraction and low-energy electron microscopy were performed to characterize the physical order of the molecular coverage, revealing that FeOEP structural domains are orders of magnitude greater in size on c(2×2)O/Co(100) than on clean Co(100), which coincides with reduced scattering from the disorder and sharper features seen in SPPES.

Gold Nanoparticle Labels Amplify Ellipsometric Signals

NASA Technical Reports Server (NTRS)

Venkatasubbarao, Srivatsa

2008-01-01

The ellipsometric method reported in the immediately preceding article was developed in conjunction with a method of using gold nanoparticles as labels on biomolecules that one seeks to detect. The purpose of the labeling is to exploit the optical properties of the gold nanoparticles in order to amplify the measurable ellipsometric effects and thereby to enable ultrasensitive detection of the labeled biomolecules without need to develop more-complex ellipsometric instrumentation. The colorimetric, polarization, light-scattering, and other optical properties of nanoparticles depend on their sizes and shapes. In the present method, these size-and-shape-dependent properties are used to magnify the polarization of scattered light and the diattenuation and retardance of signals derived from ellipsometry. The size-and-shape-dependent optical properties of the nanoparticles make it possible to interrogate the nanoparticles by use of light of various wavelengths, as appropriate, to optimally detect particles of a specific type at high sensitivity. Hence, by incorporating gold nanoparticles bound to biomolecules as primary or secondary labels, the performance of ellipsometry as a means of detecting the biomolecules can be improved. The use of gold nanoparticles as labels in ellipsometry has been found to afford sensitivity that equals or exceeds the sensitivity achieved by use of fluorescence-based methods. Potential applications for ellipsometric detection of gold nanoparticle-labeled biomolecules include monitoring molecules of interest in biological samples, in-vitro diagnostics, process monitoring, general environmental monitoring, and detection of biohazards.

Label-free probing of genes by time-domain terahertz sensing.

PubMed

Haring Bolivar, P; Brucherseifer, M; Nagel, M; Kurz, H; Bosserhoff, A; Büttner, R

2002-11-07

A label-free sensing approach for the label-free characterization of genetic material with terahertz (THz) electromagnetic waves is presented. Time-resolved THz analysis of polynucleotides demonstrates a strong dependence of the complex refractive index of DNA molecules in the THz frequency range on their hybridization state. By monitoring THz signals one can thus infer the binding state (hybridized or denatured) of oligo- and polynucleotides, enabling the label-free determination the genetic composition of unknown DNA sequences. A broadband experimental proof-of-principle in a freespace analytic configuration, as well as a higher-sensitivity approach using integrated THz sensors reaching femtomol detection levels and demonstrating the capability to detect single-base mutations, are presented. The potential application for next generation high-throughput label-free genetic analytic systems is discussed.

PROGRESS IN DETAILED KINETIC MODELING OF THE COMBUSTION OF OXYGENATED COMPONENTS OF BIOFUELS

PubMed Central

Sy Tran, Luc; Sirjean, Baptiste; Glaude, Pierre-Alexandre; Fournet, René; Battin-Leclerc, Frédérique

2013-01-01

Due to growing environmental concerns and diminishing petroleum reserves, a wide range of oxygenated species has been proposed as possible substitutes to fossil fuels: alcohols, methyl esters, acyclic and cyclic ethers. After a short review the major detailed kinetic models already proposed in the literature for the combustion of these molecules, the specific classes of reactions considered for modeling the oxidation of acyclic and cyclic oxygenated molecules respectively, are detailed. PMID:23700355

Computer simulation of gene detection without PCR by single molecule detection

NASA Astrophysics Data System (ADS)

Davis, Lloyd M.; Williams, John G.; Lamb, Don T.

1999-01-01

Pioneer Hi-Bred is developing a low-cost method for rapid screening of DNA, for use in research on elite crop seed genetics. Unamplified genomic DNA with the requisite base sequence is simultaneously labeled by two different colored fluorescent probes, which hybridize near the selected gene. Dual-channel single molecule detection (SMD) within a flow cell, then provides a sensitive and specific assay for the gene. The technique has been demonstrated using frequency- doubled Nd:YAG laser excitation of two visible-wavelength dyes. A prototype instrument employing infrared fluorophores and laser diodes for excitation has been developed. Here, we report results from a Monte Carlo simulation of the new instrument, in which experimentally determined photophysical parameters for candidate infrared dyes are used for parametric studies of experimental operating conditions. Fluorophore photostability is found to be a key factor in determining the instrument sensitivity. Most infrared dyes have poor photostability, resulting in inefficient SMD. However, the normalized cross-correlation function of the photon signals from each of the two channels can still yield a discernable peak, provided that the concentration of dual- labeled molecules is sufficiently high. Further, for low concentrations, processing of the two photon streams with Gaussian -weighted sliding sum digital filters and selection of simultaneously occurring peaks can also provide a sensitive indicator of the presence of dual-labeled molecules, although accidental coincidences must be considered in the interpretation of results.

Highly sensitive detection of target molecules using a new fluorescence-based bead assay

NASA Astrophysics Data System (ADS)

Scheffler, Silvia; Strauß, Denis; Sauer, Markus

2007-07-01

Development of immunoassays with improved sensitivity, specificity and reliability are of major interest in modern bioanalytical research. We describe the development of a new immunomagnetic fluorescence detection (IM-FD) assay based on specific antigen/antibody interactions and on accumulation of the fluorescence signal on superparamagnetic PE beads in combination with the use of extrinsic fluorescent labels. IM-FD can be easily modified by varying the order of coatings and assay conditions. Depending on the target molecule, antibodies (ABs), entire proteins, or small protein epitopes can be used as capture molecules. The presence of target molecules is detected by fluorescence microscopy using fluorescently labeled secondary or detection antibodies. Here, we demonstrate the potential of the new assay detecting the two tumor markers IGF-I and p53 antibodies in the clinically relevant concentration range. Our data show that the fluorescence-based bead assay exhibits a large dynamic range and a high sensitivity down to the subpicomolar level.

Studies related to the development of the Viking 1975 labeled release experiment

NASA Technical Reports Server (NTRS)

Devincenzi, D. L.; Deal, P. H.

1976-01-01

The labeled release life detection experiment on the Viking 1975 Mars mission is based on the concept that microorganisms will metabolize radioactive organic substrates in a nutrient medium and release radioactive carbon dioxide. Several experiments, using laboratory equipment, were carried out to evaluate various aspects of the concept. Results indicate: (1) label is released by sterilization-treated soil, (2) substantial quantities of label are retained in solution under basic conditions, (3) the substrate used, as well as position of label in the molecule, affect release of label, (4) label release is depressed by radiolytic decomposition of substrates, and (5) About 100,000 organisms are required to produce a detectable response. These results, suggest additional areas for testing, add to the data base for interpretation of flight results, and have significance for broader application of this technique for assessing microbial activity.

Quantitative single-molecule imaging by confocal laser scanning microscopy.

PubMed

Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

2008-11-25

A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

Gating capacitive field-effect sensors by the charge of nanoparticle/molecule hybrids.

PubMed

Poghossian, Arshak; Bäcker, Matthias; Mayer, Dirk; Schöning, Michael J

2015-01-21

The semiconductor field-effect platform is a powerful tool for chemical and biological sensing with direct electrical readout. In this work, the field-effect capacitive electrolyte-insulator-semiconductor (EIS) structure - the simplest field-effect (bio-)chemical sensor - modified with citrate-capped gold nanoparticles (AuNPs) has been applied for a label-free electrostatic detection of charged molecules by their intrinsic molecular charge. The EIS sensor detects the charge changes in AuNP/molecule inorganic/organic hybrids induced by the molecular adsorption or binding events. The feasibility of the proposed detection scheme has been exemplarily demonstrated by realizing capacitive EIS sensors consisting of an Al-p-Si-SiO2-silane-AuNP structure for the label-free detection of positively charged cytochrome c and poly-d-lysine molecules as well as for monitoring the layer-by-layer formation of polyelectrolyte multilayers of poly(allylamine hydrochloride)/poly(sodium 4-styrene sulfonate), representing typical model examples of detecting small proteins and macromolecules and the consecutive adsorption of positively/negatively charged polyelectrolytes, respectively. For comparison, EIS sensors without AuNPs have been investigated, too. The adsorption of molecules on the surface of AuNPs has been verified via the X-ray photoelectron spectroscopy method. In addition, a theoretical model of the functioning of the capacitive field-effect EIS sensor functionalized with AuNP/charged-molecule hybrids has been discussed.

Effects of oxygen toxicity on cuprolinic blue-stained proteoglycans in alveolar basement membranes.

PubMed

Ferrara, T B; Fox, R B

1992-02-01

Effects of oxygen toxicity on distribution and density of proteoglycans in basement membranes of newborn rat lungs were assessed by electron microscopic analysis of tissues processed with cuprolinic blue, a cationic label that characteristically labels these anionically charged macromolecules. Newborn rats placed in greater than 95% oxygen at birth were killed at weekly intervals for 4 wk, and lung tissues fixed in 2.5% glutaraldehyde with 0.2% cuprolinic blue were processed for electron microscopy. Alveolar basement membranes from oxygen-treated and control animals were compared for differences in thickness and proteoglycan concentration and distribution. Results showed progressive thickening of alveolar basement membranes with increased duration of oxygen exposure. The normal distribution of proteoglycans, which is predominantly in the lamina rara externa of alveolar basement membranes, was frequently lost in thickened membranes found in oxygen-treated animals. Density of proteoglycans in these membranes decreased to 56% of normal by 2 wk of age and remained low with continued oxygen administration. Proteoglycan concentration in basement membranes on the interstitial side of alveolar capillaries in both control and oxygen-treated animals was low compared with proteoglycan concentration in basement membranes that opposed the alveolar air space, and administration of oxygen diminished these differences. These results demonstrate a direct alteration of proteoglycan distribution and density in the developing lung as a result of oxygen toxicity. This could result in decreased cell adhesion, influence the cellular response to lung injury, and contribute to the increased permeability seen with this disorder.

Adsorption and Dissociation of Molecular Oxygen on the (0001) Surface of Double Hexagonal Close Packed Americium

NASA Astrophysics Data System (ADS)

Dholabhai, Pratik; Atta-Fynn, Raymond; Ray, Asok

2008-03-01

Oxygen molecule adsorption on (0001) surface of double hexagonal packed americium has been studied in detail within the framework of density functional theory using a full-potential all-electron linearized augmented plane wave plus local orbitals method. The most stable configuration corresponded to molecular dissociation with the oxygen atoms occupying neighboring three-fold hollow h3 sites. Chemisorption energies and adsorption geometries for the adsorbed species, and change in work functions, magnetic moments, partial charges inside muffin-tins, difference charge density distributions and density of states for the bare Am slab and the Am slab after adsorption of the oxygen molecule will be discussed. The effects of chemisorption on Am 5f electron localization-delocalization in the vicinity of the Fermi level and the reaction barrier calculation for the dissociation of oxygen molecule to the most stable h3 sites will be discussed.

Synergism of Saturn, Enceladus and Titan and Formation of HCNO Prebiotic Molecules

NASA Technical Reports Server (NTRS)

Sittler, Edward C.; Cooper, John F.

2011-01-01

Saturn as a system has two very exotic moons Titan and Enceladus. Titan, taking in energy from Saturn's magnetosphere, solar UV irradiation, and cosmic rays, can make HCN based molecules as discussed in earlier paper by Raulin and Owen. Space radiation effects at both moons, and as coupled by the Saturn magnetosphere, could cause an unexpected series of events potentially leading to prebiotic chemical evolution at Titan with HCNO from magnetospheric oxygen as the new ingredient. The "Old Faithful" model suggests that Enceladus, highly irradiated by Saturn magnetospheric electrons and thus having a source of chemical energy from radiolytic gas production, has episodic ejections of water vapor, carbon dioxide, and various hydrocarbons into Saturn's magnetosphere. The hydrocarbons do not survive transport through the plasma environment, but oxygen ions from Enceladus water molecules become the dominant ion species in the outer magnetosphere. At Titan, Cassini discovered that 1) keV oxygen ions, evidently from Enceladus, are bombarding Titan's upper atmosphere and 2) heavy positive and negative ions exist in significant abundances within Titan's upper atmosphere. Initial models of heavy ion formation in Titan's upper atmosphere invoked polymerization of aromatics such as benzenes and their radicals to make polycyclic aromatic hydrocarbons (PAH) , while a more recent model by Sittler et al., has raised the possibility of carbon chains forming from the polymerization of acetylene and its radicals to make fullerenes. Laboratory measurements indicate that fullerenes, which are hollow carbon shells, can trap keV oxygen ions. Clustering of the fullerenes with aerosol mixtures from PAHs and the dominant nitrogen molecules could form larger aerosols enriched in trapped oxygen. Aerosol precipitation could then convey these chemically complex structures deeper into the atmosphere and to the moon surface. Ionizing solar UV, magnetospheric electron, and galactic cosmic ray

Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts.

PubMed

Kardash, Maria E; Dzuba, Sergei A

2017-05-25

The clustering of molecules is an important feature of plasma membrane organization. It is challenging to develop methods for quantifying membrane heterogeneities because of their transient nature and small size. Here, we obtained evidence that transient membrane heterogeneities can be frozen at cryogenic temperatures which allows the application of solid-state experimental techniques sensitive to the nanoscale distance range. We employed the pulsed version of electron paramagnetic resonance (EPR) spectroscopy, the electron spin echo (ESE) technique, for spin-labeled molecules in multilamellar lipid bilayers. ESE decays were refined for pure contribution of spin-spin magnetic dipole-dipolar interaction between the labels; these interactions manifest themselves at a nanometer distance range. The bilayers were prepared from different types of saturated and unsaturated lipids and cholesterol (Chol); in all cases, a small amount of guest spin-labeled substances 5-doxyl-stearic-acid (5-DSA) or 3β-doxyl-5α-cholestane (DChl) was added. The local concentration found of 5-DSA and DChl molecules was remarkably higher than the mean concentration in the bilayer, evidencing the formation of lipid-mediated clusters of these molecules. To our knowledge, formation of nanoscale clusters of guest amphiphilic molecules in biological membranes is a new phenomenon suggested only recently. Two-dimensional 5-DSA molecular clusters were found, whereas flat DChl molecules were found to be clustered into stacked one-dimensional structures. These clusters disappear when the Chol content is varied between the boundaries known for lipid raft formation at room temperatures. The room temperature EPR evidenced entrapping of DChl molecules in the rafts.

A cost-effective approach to produce 15N-labelled amino acids employing Chlamydomonas reinhardtii CC503.

PubMed

Nicolás Carcelén, Jesús; Marchante-Gayón, Juan Manuel; González, Pablo Rodríguez; Valledor, Luis; Cañal, María Jesús; Alonso, José Ignacio García

2017-08-18

The use of enriched stable isotopes is of outstanding importance in chemical metrology as it allows the application of isotope dilution mass spectrometry (IDMS). Primary methods based on IDMS ensure the quality of the analytical measurements and traceability of the results to the international system of units. However, the synthesis of isotopically labelled molecules from enriched stable isotopes is an expensive and a difficult task. Either chemical and biochemical methods to produce labelled molecules have been proposed, but so far, few cost-effective methods have been described. The aim of this study was to use the microalgae Chlamydomonas reinhardtii to produce, at laboratory scale, 15 N-labelled amino acids with a high isotopic enrichment. To do that, a culture media containing 15 NH 4 Cl was used. No kinetic isotope effect (KIE) was observed. The labelled proteins biosynthesized by the microorganism were extracted from the biomass and the 15 N-labelled amino acids were obtained after a protein hydrolysis with HCl. The use of the wall deficient strain CC503 cw92 mt+ is fit for purpose, as it only assimilates ammonia as nitrogen source, avoiding isotope contamination with nitrogen from the atmosphere or the reagents used in the culture medium, and enhancing the protein extraction efficiency compared to cell-walled wild type Chlamydomonas. The isotopic enrichment of the labelled amino acids was calculated from their isotopic composition measured by gas chromatography mass spectrometry (GC-MS). The average isotopic enrichment for the 16 amino acids characterized was 99.56 ± 0.05% and the concentration of the amino acids in the hydrolysate ranged from 18 to 90 µg/mL. Previously reported biochemical methods to produce isotopically labelled proteins have been applied in the fields of proteomics and fluxomics. For these approaches, low amounts of products are required and the isotopic enrichment of the molecules has never been properly determined. So far, only 13

Doubly labeled water method: in vivo oxygen and hydrogen isotope fractionation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schoeller, D.A.; Leitch, C.A.; Brown, C.

The accuracy and precision of the doubly labeled water method for measuring energy expenditure are influenced by isotope fractionation during evaporative water loss and CO/sub 2/ excretion. To characterize in vivo isotope fractionation, we collected and isotopically analyzed physiological fluids and gases. Breath and transcutaneous water vapor were isotopically fractionated. The degree of fractionation indicated that the former was fractionated under equilibrium control at 37/sup 0/C, and the latter was kinetically fractionated. Sweat and urine were unfractionated. By use of isotopic balance models, the fraction of water lost via fractionating routes was estimated from the isotopic abundances of body water,more » local drinking water, and dietary solids. Fractionated water loss averaged 23% (SD = 10%) of water turnover, which agreed with our previous estimates based on metabolic rate, but there was a systematic difference between the results based on O/sub 2/ and hydrogen. Corrections for isotopic fractionation of water lost in breath and (nonsweat) transcutaneous loss should be made when using labeled water to measure water turnover or CO/sub 2/ production.« less

T2-prepared velocity selective labelling: A novel idea for full-brain mapping of oxygen saturation.

PubMed

Alderliesten, Thomas; De Vis, Jill B; Lemmers, Petra M A; van Bel, Frank; Benders, Manon J N L; Hendrikse, Jeroen; Petersen, Esben T

2016-10-01

Disturbances in cerebral oxygenation saturation (SO 2 ) have been linked to adverse outcome in adults, children, and neonates. In intensive care, the cerebral SO 2 is increasingly being monitored by Near-InfraRed Spectroscopy (NIRS). Unfortunately NIRS has a limited penetration depth. The "modified T 2 -prepared Blood Imaging of Oxygen Saturation" (T 2 -BIOS) MR sequence provides a step towards full brain SO 2 measurement. Tissue SO 2 , and venous SO 2 (S v O 2 ) were obtained simultaneously by T 2 -BIOS during a respiratory challenge in ten healthy volunteers. These two measures were compared to SO 2 that was obtained by a single probe MR-compatible NIRS setup, and to cerebral blood flow and venous SO 2 that were obtained by arterial spin labelling and T 2 -TRIR, respectively. SO 2-T2-BIOS and SO 2-NIRS had a mean bias of -4.0% (95% CI -21.3% to 13.3%). S v O 2-T2-BIOS correlated with SO 2-NIRS (R 2 =0.41, p=0.002) and S v O 2-T2-TRIR (R 2 =0.87, p=0.002). In addition, SO 2-NIRS correlated with S v O 2-T2-TRIR (R 2 =0.85, p=0.003) Frontal cerebral blood flow correlated with SO 2-T2-BIOS (R 2 =0.21, p=0.04), but was not significant in relation to SO 2-NIRS . Full brain SO 2 assessment by any technique may help validating NIRS and may prove useful in guiding the clinical management of patient populations with cerebral injury following hypoxic-ischaemic events. The agreement between NIRS and T 2 -BIOS provides confidence in measuring cerebral SO 2 by either technique. As it stands now, the T 2 -BIOS represents a novel idea and future work will focus on improvements to make it a reliable tool for SO 2 assessment. Copyright © 2016 Elsevier Inc. All rights reserved.

Photoaffinity Labeling Studies on a Promoter of Dendritic Spine Formation

NASA Astrophysics Data System (ADS)

Sibucao, Kevin Carlo Abril

The small molecule BTA-EG4 has been shown to be a promoter of dendritic spine formation. The mechanism behind this phenomenon, however, is not well understood. The work in this dissertation is motivated by this gap in knowledge. The first part of this dissertation focuses on photoaffinity labeling studies to identify the cellular targets of BTA-EG4. Chapter 1 provides a summary of Alzheimer's disease, the rational design of BTA-EG 4, and methods to determine targets of small molecules. In Chapter 2, the synthesis of a BTA-EG4-based photoaffinity labeling probe and photodegradation studies are presented. Kinetic studies demonstrate that the probe photolyzes rapidly under UV light. In Chapter 3, photoaffinity labeling studies and subsequent protein identification experiments are reported. Competition experiments with the photoaffinity labeling probe and BTA-EG4 demonstrate that the probe labels a 55-kDa protein specifically. Tandem mass spectrometry revealed that the 55-kDa protein is the actin binding protein fascin 1. The second part of this dissertation focuses on the major protein identified from photoaffinity labeling studies, fascin 1. Chapter 4 provides a brief survey of the structure and function of fascin 1. In Chapter 5, characterizations of the interaction between BTA-EG4 and fascin 1 are reported. Isothermal titration calorimetry confirms the physical binding between fascin 1 and BTA-EG6, a BTA-EG4 analog. Slow speed sedimentation assays reveal that BTA-EG4 does not affect the actin-bundling activity of fascin 1. However, GST pull-down experiments show that BTA-EG4 inhibits the binding of fascin 1 with the GTPase Rab35. In addition, this work demonstrates that BTA-EG4 may be mechanistically distinct from the known fascin inhibitor G2.

Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters.

PubMed

Alexandrino, M; Knief, C; Lipski, A

2001-10-01

Deuterated styrene ([(2)H(8)]styrene) was used as a tracer in combination with phospholipid fatty acid (PLFA) analysis for characterization of styrene-degrading microbial populations of biofilters used for treatment of waste gases. Deuterated fatty acids were detected and quantified by gas chromatography-mass spectrometry. The method was evaluated with pure cultures of styrene-degrading bacteria and defined mixed cultures of styrene degraders and non-styrene-degrading organisms. Incubation of styrene degraders for 3 days with [(2)H(8)]styrene led to fatty acids consisting of up to 90% deuterated molecules. Mixed-culture experiments showed that specific labeling of styrene-degrading strains and only weak labeling of fatty acids of non-styrene-degrading organisms occurred after incubation with [(2)H(8)]styrene for up to 7 days. Analysis of actively degrading filter material from an experimental biofilter and a full-scale biofilter by this method showed that there were differences in the patterns of labeled fatty acids. For the experimental biofilter the fatty acids with largest amounts of labeled molecules were palmitic acid (16:0), 9,10-methylenehexadecanoic acid (17:0 cyclo9-10), and vaccenic acid (18:1 cis11). These lipid markers indicated that styrene was degraded by organisms with a Pseudomonas-like fatty acid profile. In contrast, the most intensively labeled fatty acids of the full-scale biofilter sample were palmitic acid and cis-11-hexadecenoic acid (16:1 cis11), indicating that an unknown styrene-degrading taxon was present. Iso-, anteiso-, and 10-methyl-branched fatty acids showed no or weak labeling. Therefore, we found no indication that styrene was degraded by organisms with methyl-branched fatty fatty acids, such as Xanthomonas, Bacillus, Streptomyces, or Gordonia spp.

Titan's Oxygen Chemistry and its Impact on Haze Formation

NASA Astrophysics Data System (ADS)

Vuitton, Veronique; Carrasco, Nathalie; Flandinet, Laurene; Horst, Sarah; Klippenstein, Stephen; Lavvas, Panayotis; Orthous-Daunay, Francois-Regis; Thissen, Roland; Yelle, Roger

2016-06-01

Though Titan's atmosphere is reducing with its 98% N2, 2% CH4 and 0.1% H2, CO is the fourth most abundant molecule with a uniform mixing ratio of ˜50 ppm. Two other oxygen bearing molecules have also been observed in Titan's atmosphere: CO2 and H2O, with a mixing ratio of ˜15 and ˜1 ppb, respectively. The physical and chemical processes that determine the abundances of these species on Titan have been at the centre of a long-standing debate as they place constraints on the origin and evolution of its atmosphere [1]. Moreover, laboratory experiments have shown that oxygen can be incorporated into complex molecules, some of which are building blocks of life [2]. Finally, the presence of CO modifies the production rate and size of tholins [3,4], which transposed to Titan's haze may have some strong repercussions on the temperature structure and dynamics of the atmosphere. We present here our current understanding of Titan's oxygen chemistry and of its impact on the chemical composition of the haze. We base our discussion on a photochemical model that describes the first steps of the chemistry and on state-of-the-art laboratory experiments for the synthesis and chemical analysis of aerosol analogues. We used a very-high resolution mass spectrometer (LTQ-Orbitrap XL instrument) to characterize the soluble part of tholin samples generated from N2/CH4/CO mixtures at different mixing ratios and with two different laboratory set-ups. These composition measurements provide some understanding of the chemical mechanisms by which CO affects particle formation and growth. Our final objective is to obtain a global picture of the fate and impact of oxygen on Titan, from its origin to prebiotic molecules to haze particles to material deposited on the surface.

Cleaning Carbon Nanotubes by Use of Mild Oxygen Plasmas

NASA Technical Reports Server (NTRS)

Petkov, Mihail

2006-01-01

Experiments have shown that it is feasible to use oxygen radicals (specifically, monatomic oxygen) from mild oxygen plasmas to remove organic contaminants and chemical fabrication residues from the surfaces of carbon nanotubes (CNTs) and metal/CNT interfaces. A capability for such cleaning is essential to the manufacture of reproducible CNT-based electronic devices. The use of oxygen radicals to clean surfaces of other materials is fairly well established. However, previously, cleaning of CNTs and of graphite by use of oxygen plasmas had not been attempted because both of these forms of carbon were known to be vulnerable to destruction by oxygen plasmas. The key to success of the present technique is, apparently, to ensure that the plasma is mild . that is to say, that the kinetic and internal energies of the oxygen radicals in the plasma are as low as possible. The plasma oxygen-radical source used in the experiments was a commercial one marketed for use in removing hydrocarbons and other organic contaminants from vacuum systems and from electron microscopes and other objects placed inside vacuum systems. In use, the source is installed in a vacuum system and air is leaked into the system at such a rate as to maintain a background pressure of .0.56 torr (.75 Pa). In the source, oxygen from the air is decomposed into monatomic oxygen by radio-frequency excitation of a resonance of the O2 molecule (N2 is not affected). Hence, what is produced is a mild (non-energetic) oxygen plasma. The oxygen radicals are transported along with the air molecules in the flow created by the vacuum pump. In the experiments, exposure to the oxygen plasma in this system was shown to remove organic contaminants and chemical fabrication residues from several specimens. Many high-magnification scanning electron microscope (SEM) images of CNTs were taken before and after exposure to the oxygen plasma. As in the example shown in the figure, none of these images showed evidence of degradation

Evolution and Protein Packaging of Small Molecule RNA Aptamers

PubMed Central

Lau, Jolene L.; Baksh, Michael M.; Fiedler, Jason D.; Brown, Steven D.; Kussrow, Amanda; Bornhop, Darryl J.; Ordoukhanian, Phillip

2011-01-01

A high-affinity RNA aptamer (Kd = 50 nM) was efficiently identified by SELEX against a heteroaryl dihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (non-encapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique. PMID:21899290

Incorporation of oxygen into abscisic Acid and phaseic Acid from molecular oxygen.

PubMed

Creelman, R A; Zeevaart, J A

1984-05-01

Abscisic acid accumulates in detached, wilted leaves of Xanthium strumarium. When these leaves are subsequently rehydrated, phaseic acid, a catabolite of abscisic acid, accumulates. Analysis by gas chromatography-mass spectrometry of phaseic acid isolated from stressed and subsequently rehydrated leaves placed in an atmosphere containing 20% (18)O(2) and 80% N(2) indicates that one atom of (18)O is incorporated in the 6'-hydroxymethyl group of phaseic acid. This suggests that the enzyme that converts abscisic acid to phaseic acid is an oxygenase.Analysis by gas chromatography-mass spectrometry of abscisic acid isolated from stressed leaves kept in an atmosphere containing (18)O(2) indicates that one atom of (18)O is present in the carboxyl group of abscisic acid. Thus, when abscisic acid accumulates in water-stressed leaves, only one of the four oxygens present in the abscisic acid molecule is derived from molecular oxygen. This suggests that either (a) the oxygen present in the 1'-, 4'-, and one of the two oxygens at the 1-position of abscisic acid arise from water, or (b) there exists a stored precursor with oxygen atoms already present in the 1'- and 4'-positions of abscisic acid which is converted to abscisic acid under conditions of water stress.

Label-free photoacoustic nanoscopy

PubMed Central

Danielli, Amos; Maslov, Konstantin; Garcia-Uribe, Alejandro; Winkler, Amy M.; Li, Chiye; Wang, Lidai; Chen, Yun; Dorn, Gerald W.; Wang, Lihong V.

2014-01-01

Abstract. Super-resolution microscopy techniques—capable of overcoming the diffraction limit of light—have opened new opportunities to explore subcellular structures and dynamics not resolvable in conventional far-field microscopy. However, relying on staining with exogenous fluorescent markers, these techniques can sometimes introduce undesired artifacts to the image, mainly due to large tagging agent sizes and insufficient or variable labeling densities. By contrast, the use of endogenous pigments allows imaging of the intrinsic structures of biological samples with unaltered molecular constituents. Here, we report label-free photoacoustic (PA) nanoscopy, which is exquisitely sensitive to optical absorption, with an 88 nm resolution. At each scanning position, multiple PA signals are successively excited with increasing laser pulse energy. Because of optical saturation or nonlinear thermal expansion, the PA amplitude depends on the nonlinear incident optical fluence. The high-order dependence, quantified by polynomial fitting, provides super-resolution imaging with optical sectioning. PA nanoscopy is capable of super-resolution imaging of either fluorescent or nonfluorescent molecules. PMID:25104412

Wyman's equation and oxygen flux through the red cell.

PubMed

McCabe, Michael; Maguire, David J

2007-01-01

Wyman's equation of 1966 describes the facilitation of flux of a reversibly bound substrate such as oxygen, consequent on the translational diffusion of the binding protein (the carrier). While Wyman's equation, or some modification of it such as that by Murray 2, may provide a realistic description of the flux of oxygen through a dilute solution of haemoglobin (see also Wittenburg), it is unlikely to be the complete explanation, nor even the basis, for oxygen transport through the intact red cell. The mature erythrocyte contains approximately 350 g/l haemoglobin, and while this suggests that only 35% of the available water volume is actually occupied by the protein, the remaining 65% is unavailable for protein translational diffusion due to the mutual exclusion of the haemoglobin molecules. For this reason we have examined other possible mechanisms whereby haemoglobin may facilitate the translational diffusion of oxygen within the erythrocyte. Possible alternatives include rotational diffusion by the haemoglobins, intracellular shuffling of haemoglobins due to shape changes by the erythrocyte, and haemoglobin rotations and oxygen exchange consequent on the charge change which accompanies substration and desubstration of the haemoglobin molecule. Finally the dipole interactions are shown to generate significant intermolecular attractions between adjacent haemoglobins.

Energetic Metastable Oxygen and Nitrogen Atoms in the Terrestrial Atmosphere

NASA Technical Reports Server (NTRS)

Kharchenko, Vasili

2004-01-01

We have investigated the impact of hot metastable oxygen atoms on the product yields and rate coefficients of atmospheric reactions involving O( (sup 1)D). The contribution of the metastable oxygen atoms to the thermal balance of the terrestrial atmosphere between 50 and 200 km has been determined. We found that the presence of hot O((sup l)D) atoms in the mesosphere and lower thermosphere significantly increases the production rate of the rotationally-vibrationally excited NO molecules. The computed yield of the NO molecules in N2O+ O((sup 1)D) atmospheric collisions, involving non-Maxwellian distributions of the metastable oxygen atoms, is more than two times larger than the NO-yield at a thermal equilibrium. The calculated non-equilibrium rate and yield functions are important for ozone and nitrous oxide modeling in the stratosphere, mesosphere and lower thermosphere.

A matrix-assisted laser desorption/ionization mass spectroscopy method for the analysis of small molecules by integrating chemical labeling with the supramolecular chemistry of cucurbituril.

PubMed

Ding, Jun; Xiao, Hua-Ming; Liu, Simin; Wang, Chang; Liu, Xin; Feng, Yu-Qi

2018-10-05

Although several methods have realized the analysis of low molecular weight (LMW) compounds using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by overcoming the problem of interference with MS signals in the low mass region derived from conventional organic matrices, this emerging field still requires strategies to address the issue of analyzing complex samples containing LMW components in addition to the LMW compounds of interest, and solve the problem of lack of universality. The present study proposes an integrated strategy that combines chemical labeling with the supramolecular chemistry of cucurbit [n]uril (CB [n]) for the MALDI MS analysis of LMW compounds in complex samples. In this strategy, the target LMW compounds are first labeled by introducing a series of bifunctional reagents that selectively react with the target analytes and also form stable inclusion complexes with CB [n]. Then, the labeled products act as guest molecules that readily and selectively form stable inclusion complexes with CB [n]. This strategy relocates the MS signals of the LMW compounds of interest from the low mass region suffering high interference to the high mass region where interference with low mass components is absent. Experimental results demonstrate that a wide range of LMW compounds, including carboxylic acids, aldehydes, amines, thiol, and cis-diols, can be successfully detected using the proposed strategy, and the limits of detection were in the range of 0.01-1.76 nmol/mL. In addition, the high selectivity of the labeling reagents for the target analytes in conjunction with the high selectivity of the binding between the labeled products and CB [n] ensures an absence of signal interference with the non-targeted LMW components of complex samples. Finally, the feasibility of the proposed strategy for complex sample analysis is demonstrated by the accurate and rapid quantitative analysis of aldehydes in saliva and herbal

Appearance and distribution of surface proteins of the human erythrocyte membrane. An electron microscope and immunochemical labeling study

PubMed Central

Shotton, D.; Thompson, K.; Wofsy, L.; Branton, D.

1978-01-01

We have used freeze-etching, before and after immunoferritin labeling, to visualize spectrin molecules and other surface proteins of the human erythrocyte membrane. After intramembrane particle aggregation was induced, spectrin molecules, identified by labeling with ferritin-conjugated antispectrin, were clustered on the cytoplasmic surface of the membrane in patches directly underlying the particle clusters. This labeling pattern confirms the involvement of spectrin in such particle aggregates, as previously inferred from indirect evidence. Ferritin-conjugated antihapten molecules, directed against external and cytoplasmic surface proteins of the erythrocyte membrane which had been covalently labeled nonspecifically with the hapten p-diazoniumphenyl-beta-D-lactoside, were similarly found in direct association with such intramembrane particle aggregates. This indicates that when spectrin and the intramembrane particles are aggregated, all the major proteins of the erythrocyte membrane are constrained to coaggregate with them. Although giving no direct information concerning the freedom of translational movement of proteins in the unperturbed erythrocyte membrane, these experiments suggest that a close dynamic association may exist between the integral and peripheral protein components of the membrane, such that immobilization of one component can restrict the lateral mobility of others. PMID:10605454

Analysis of lipid raft molecules in the living brain slices.

PubMed

Kotani, Norihiro; Nakano, Takanari; Ida, Yui; Ito, Rina; Hashizume, Miki; Yamaguchi, Arisa; Seo, Makoto; Araki, Tomoyuki; Hojo, Yasushi; Honke, Koichi; Murakoshi, Takayuki

2017-08-24

Neuronal plasma membrane has been thought to retain a lot of lipid raft components which play important roles in the neural function. Although the biochemical analyses of lipid raft using brain tissues have been extensively carried out in the past 20 years, many of their experimental conditions do not coincide with those of standard neuroscience researches such as neurophysiology and neuropharmacology. Hence, the physiological methods for lipid raft analysis that can be compatible with general neuroscience have been required. Herein, we developed a system to physiologically analyze ganglioside GM1-enriched lipid rafts in brain tissues using the "Enzyme-Mediated Activation of Radical Sources (EMARS)" method that we reported (Kotani N. et al. Proc. Natl. Acad. Sci. U S A 105, 7405-7409 (2008)). The EMARS method was applied to acute brain slices prepared from mouse brains in aCSF solution using the EMARS probe, HRP-conjugated cholera toxin subunit B, which recognizes ganglioside GM1. The membrane molecules present in the GM1-enriched lipid rafts were then labeled with fluorescein under the physiological condition. The fluorescein-tagged lipid raft molecules called "EMARS products" distributed differentially among various parts of the brain. On the other hand, appreciable differences were not detected among segments along the longitudinal axis of the hippocampus. We further developed a device to label the lipid raft molecules in acute hippocampal slices under two different physiological conditions to detect dynamics of the lipid raft molecules during neural excitation. Using this device, several cell membrane molecules including Thy1, known as a lipid raft resident molecule in neurons, were confirmed by the EMARS method in living hippocampal slices. Copyright © 2017 Elsevier Ltd. All rights reserved.

Titan’s Oxygen Chemistry and its Impact on Haze Formation

NASA Astrophysics Data System (ADS)

Vuitton, Veronique; He, Chao; Moran, Sarah; Wolters, Cedric; Flandinet, Laurene; Orthous-Daunay, Francois-Regis; Thissen, Roland; Horst, Sarah

2018-06-01

Though Titan's atmosphere is reducing with its 98% N2, 2% CH4 and 0.1% H2, CO is the fourth most abundant molecule with a uniform mixing ratio of ~50 ppm. Two other oxygen bearing molecules have also been observed in Titan's atmosphere: CO2 and H2O, with a mixing ratio of ~15 and ~1 ppb, respectively. The physical and chemical processes that determine the abundances of these species on Titan have been at the centre of a long-standing debate as they place constraints on the origin and evolution of its atmosphere. Moreover, laboratory experiments have shown that oxygen can be incorporated into complex molecules, some of which are building blocks of life. Finally, the presence of CO modifies the production rate and size of tholins, which transposed to Titan's haze may have some strong repercussions on the temperature structure and dynamics of the atmosphere.We present here our current understanding of Titan's oxygen chemistry and of its impact on the chemical composition of the haze. We base our discussion on state-of-the-art laboratory experiments for the synthesis and chemical analysis of aerosol analogues. We used a very-high resolution mass spectrometer (LTQ-Orbitrap XL instrument) to characterize the soluble part of tholin samples generated from N2/CH4/CO mixtures at different mixing ratios. These composition measurements provide some understanding of the chemical mechanisms by which CO affects particle formation and growth. Our final objective is to obtain a global picture of the fate and impact of oxygen on Titan, from its origin to prebiotic molecules to haze particles to material deposited on the surface.

Sensitivity Analysis of Flux Determination in Heart by H2 18O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways

PubMed Central

Schryer, David W.; Peterson, Pearu; Illaste, Ardo; Vendelin, Marko

2012-01-01

To characterize intracellular energy transfer in the heart, two organ-level methods have frequently been employed: inversion and saturation transfer, and dynamic labeling. Creatine kinase (CK) fluxes obtained by following oxygen labeling have been considerably smaller than the fluxes determined by saturation transfer. It has been proposed that dynamic labeling determines net flux through CK shuttle, whereas saturation transfer measures total unidirectional flux. However, to our knowledge, no sensitivity analysis of flux determination by oxygen labeling has been performed, limiting our ability to compare flux distributions predicted by different methods. Here we analyze oxygen labeling in a physiological heart phosphotransfer network with active CK and adenylate kinase (AdK) shuttles and establish which fluxes determine the labeling state. A mathematical model consisting of a system of ordinary differential equations was composed describing enrichment in each phosphoryl group and inorganic phosphate. By varying flux distributions in the model and calculating the labeling, we analyzed labeling sensitivity to different fluxes in the heart. We observed that the labeling state is predominantly sensitive to total unidirectional CK and AdK fluxes and not to net fluxes. We conclude that measuring dynamic incorporation of into the high-energy phosphotransfer network in heart does not permit unambiguous determination of energetic fluxes with a higher magnitude than the ATP synthase rate when the bidirectionality of fluxes is taken into account. Our analysis suggests that the flux distributions obtained using dynamic labeling, after removing the net flux assumption, are comparable with those from inversion and saturation transfer. PMID:23236266

Longitudinal Assessment of Renal Perfusion and Oxygenation in Transplant Donor-Recipient Pairs Using Arterial Spin Labeling and Blood Oxygen Level-Dependent Magnetic Resonance Imaging.

PubMed

Niles, David J; Artz, Nathan S; Djamali, Arjang; Sadowski, Elizabeth A; Grist, Thomas M; Fain, Sean B

2016-02-01

The aims of this study were to assess renal function in kidney transplant recipients and their respective donors over 2 years using arterial spin labeling (ASL) and blood oxygen level-dependent (BOLD) magnetic resonance imaging (MRI) and to prospectively evaluate the effect of losartan on functional MRI measures in recipients. The study included 15 matched pairs of renal transplant donors and recipients. Arterial spin labeling and BOLD MRI of the kidneys were performed on donors before transplant surgery (baseline) and on both donors and recipients at 3 months, 1 year, and 2 years after transplant. After 3 months, 7 of the 15 recipients were prescribed 25 to 50 mg/d losartan for the remainder of the study. A linear mixed-effects model was used to evaluate perfusion, R2*, estimated glomerular filtration rate, and fractional excretion of sodium for changes across time or associated with losartan treatment. In donors, cortical perfusion in the remaining kidney decreased by 50 ± 19 mL/min per 100 g (11.8%) between baseline and 2 years (P < 0.05), while cortical R2* declined modestly by 0.7 ± 0.3 s-1 (5.6%; P < 0.05). In transplanted kidneys, cortical perfusion decreased markedly by 141 ± 21 mL/min per 100 g (34.2%) between baseline and 2 years (P < 0.001), while medullary R2* declined by 1.5 ± 0.8 s-1 (8.3%; P = 0.06). Single-kidney estimated glomerular filtration rate increased between baseline and 2 years by 17.7 ± 2.7 mL/min per 1.73 m (40.3%; P < 0.0001) in donors and to 14.6 ± 4.3 mL/min per 1.73 m (33.3%; P < 0.01) in recipients. Cortical perfusion at 1 and 2 years in recipients receiving 25 to 50 mg/d losartan was 62 ± 24 mL/min per 100 g higher than recipients not receiving the drug (P < 0.05). No significant effects of losartan were observed for any other markers of renal function. The results suggest an important role for noninvasive functional monitoring with ASL and BOLD MRI in kidney transplant recipients and donors, and they indicate a potentially

Macrofauna regulate heterotrophic bacterial carbon and nitrogen incorporation in low-oxygen sediments

PubMed Central

Hunter, William R; Veuger, Bart; Witte, Ursula

2012-01-01

Oxygen minimum zones (OMZs) currently impinge upon >1 million km2 of sea floor and are predicted to expand with climate change. We investigated how changes in oxygen availability, macrofaunal biomass and retention of labile organic matter (OM) regulate heterotrophic bacterial C and N incorporation in the sediments of the OMZ-impacted Indian continental margin (540–1100 m; [O2]=0.35–15 μmol l−1). In situ pulse-chase experiments traced 13C:15N-labelled phytodetritus into bulk sediment OM and hydrolysable amino acids, including the bacterial biomarker 𝒟-alanine. Where oxygen availability was lowest ([O2]=0.35 μmol l−1), metazoan macrofauna were absent and bacteria assimilated 30–90% of the labelled phytodetritus within the sediment. At higher oxygen levels ([O2]=2–15 μmol l−1) the macrofaunal presence and lower phytodetritus retention with the sediment occur concomitantly, and bacterial phytodetrital incorporation was reduced and retarded. Bacterial C and N incorporation exhibited a significant negative relationship with macrofaunal biomass across the OMZ. We hypothesise that fauna–bacterial interactions significantly influence OM recycling in low-oxygen sediments and need to be considered when assessing the consequences of global change on biogeochemical cycles. PMID:22592818

Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule.

PubMed

Feng, Chunjing; Zhu, Jing; Sun, Jiewei; Jiang, Wei; Wang, Lei

2015-10-01

Here, we developed an enzyme-free, label-free, and sensitive fluorescence cooperative amplification strategy based on a hairpin assembly circuit which coupled catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR) for small molecule adenosine. A double-strand DNA probe with aptamer-catalysis strand (Apt-C) and inhibit strand (Inh) was designed for adenosine recognition and signal transduction which was named as Apt-C/Inh. Hairpins H1 and H2 were employed for constructing the CHA, and hairpins H3 and H4 for the HCR. Through the binding of adenosine and the Apt-C, the Inh was released from the Apt-C/Inh. Then the free Apt-C initiated the CHA through successively opening H1 and H2, generating H1/H2 complex and recyclable Apt-C. Next, the released Apt-C entered another CHA cycle, and the H1/H2 complex further initiated the HCR of H3 and H4 which induced the formation of the concatemers of H3/H4 complex. Such a process brought the two ends of hairpins H3 into close proximity, yielding numerous integrated G-quadruplexes which were initially sequestered in the stem and two terminals of H3. Finally, N-methyl mesoporphyrin IX (NMM) was added to generate an enhanced fluorescence signal. In the proposed strategy, driven only by the energy from hybridization, one target could trigger multiple HCR events via CHA-based target-cycle, leading to a remarkable enzyme-free amplification for adenosine. The detection limit could achieve as low as 9.7 × 10(-7) mol L(-1). Furthermore, G-quadruplexes were applied to construct label-free hairpin assembly circuit, which made it more simple and cost-effective. The satisfactory recoveries were obtained when detecting adenosine in spiked human serum and urine samples, demonstrating the feasibility of this detection strategy in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Non-equilibrium kinetics of plasma-assisted combustion: the role of electronically excited atoms and molecules

NASA Astrophysics Data System (ADS)

Popov, Nikolay

2016-09-01

A review of experimental and theoretical investigations of the effect of electronically excited atoms and molecules on the induction delay time and on the shift of the ignition temperature threshold of combustible mixtures is presented. At relatively low initial gas temperature, the effect of excited O(1D) atoms on the oxidation and reforming of combustible mixtures is quite significant due to the high rates of reactions of O(1D) atoms with hydrogen and hydrocarbon molecules. The singlet oxygen molecules, O2(a1Δg) , participate both in chain initiation and chain branching reactions, but the effect of O2(a1Δg) in the ignition processes is generally less important compared to the oxygen atoms. To reduce the ignition delay time and decrease the temperature threshold of fuel-air mixtures, the use of gas discharges with relatively high E/N values is recommended. In this case the reactions of electronically excited N2(A3Σu+ , B3πg , C3πu , a'1Σu-) molecules, and atomic particles in ground and electronically excited states are extremely important. The energy stored in electronic excitation of atoms and molecules is spent on the additional dissociation of oxygen and fuel molecules, on the fast gas heating, and finally to the triggering of chain branching reactions. This work was partially supported by AOARD AFOSR, FA2386-13-1-4064 grant and Linked International Laboratory LIA KaPPA (France-Russia).

Current-voltage characteristics of double stranded versus single stranded DNA molecules

NASA Astrophysics Data System (ADS)

Hartzell, B.; Chen, Hong; Heremans, J. J.; McCord, B.; Soghomonian, V.

2004-03-01

Investigation of DNA conductivity has focused on the native, duplex structure, with controversial results. Here, we present the influence of the double-helical structure on charge transport through lambda DNA molecules. The current-voltage (I-V) characteristics of both disulfide-labeled double stranded DNA (dsDNA) and disulfide-labeled single stranded DNA (ssDNA) were measured. The ssDNA was formed from the dsDNA using two different methods for comparison purposes: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics of both the double stranded and single stranded samples were close-to-linear when measured at room temperature. However, the ssDNA samples consistently gave conductivity values about two orders of magnitude smaller in amplitude. Our results suggest an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to support charge transport.(NSF NIRT 0103034)

High-throughput, dual probe biological assays based on single molecule detection

DOEpatents

Hollars, Christopher W [Brentwood, CA; Huser, Thomas R [Livermore, CA; Lane, Stephen M [Oakland, CA; Balhorn, Rodney L [Livermore, CA; Bakajin, Olgica [San Leandro, CA; Darrow, Christopher [Pleasanton, CA; Satcher, Jr., Joe H.

2006-07-11

A method and apparatus with the sensitivity to detect and identify single target molecules through the localization of dual, fluorescently labeled probe molecules. This can be accomplished through specific attachment of the taget to a surface or in a two-dimensional (2D) flowing fluid sheet having approximate dimensions of 0.5 .mu.m.times.100 .mu.m.times.100 .mu.m. A device using these methods would have 10.sup.3 10.sup.4 greater throughput than previous one-dimensional (1D) micro-stream devices having 1 .mu.m.sup.3 interrogation volumes and would for the first time allow immuno- and DNA assays at ultra-low (femtomolar) concentrations to be performed in short time periods (.about.10 minutes). The use of novel labels (such as metal or semiconductor nanoparticles) may be incorporated to further extend the sensitivity possibly into the attomolar range.

Investigating rhodamine B-labeled peptoids: scopes and limitations of its applications.

PubMed

Birtalan, Esther; Rudat, Birgit; Kölmel, Dominik K; Fritz, Daniel; Vollrath, Sidonie B L; Schepers, Ute; Bräse, Stefan

2011-01-01

The fluorophore rhodamine B is often used in biological assays. It is inexpensive, robust under a variety of reaction conditions, can be covalently linked to bioactive molecules, and has suitable spectral properties in terms of absorption and fluorescence wavelength. Nonetheless, there are some drawbacks: it can readily form a spirolactam compound, which is nonfluorescent, and therefore may not be the dye of choice for all fluorescence microscopy applications. Herein this spirolactam formation was observed by purifying such a labeled peptoid with high performance liquid chromatography (HPLC) and monitored in detail by making a series of analytical HPLC runs over time. Additionally, a small library of eight peptoids with rhodamine B as label was synthesized. Analysis of the absorption properties of these molecules demonstrated that the problem of fluorescence loss can be overcome by coupling secondary amines with rhodamine B.

Organic Molecules in Oxygen-Rich Circumstellar Envelopes: Methanol and Hydrocarbons

NASA Technical Reports Server (NTRS)

Charnley, S. B.; Tielens, A. G. G. M.; Kress, M. E.

1995-01-01

The existence of anomalously high abundances of gaseous CH4 has been invoked to explain the unexpectedly high abundances of the carbon-bearing molecules HCN and H2CO in the outflows from O-rich red giants. We have modelled the chemistry that proceeds in the outer envelope when CH4 is injected from the inner envelope. We find that photolysis by the interstellar radiation field drives an ion-neutral chemistry which produces several organic molecules. The calculated abundances of CH3OH, C2H and C2 can be comparable to those calculated for H2CO and HCN. Species such as C2H4, C2H2 and CH3CN can also be abundant. A search for CH3OH and C2H in several O-rich outflows known to exhibit strong HCN emission is needed. As it derives entirely from the CH4 photochain, is insensitive to the envelope temperature distribution, and has accessible transitions at millimetre wavelengths, the detection of the C2H radical would provide further indirect support for the presence of the hypothesized methane.

LABELLING OF NUCLEIC ACID WITH RADIOACTIVE ISOTOPES AND THEIR APPLICATION (in Yugoslavian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becarevic, A.; Hudnik-Plevnik, T.; Glisin, V.

The DNA of the liver and spleen of rats was labeled with P/sup 32/. The specific activity obtained was high enough to be able to follow the fate of these acids after injection in irradiated and non-irradiated rats. The results show that, after injection in the rats, the labeled kids were degraded into small fragmnts, which were utilized as building blocks for the synthesis of the big molecules of the cells. (auth)

Synergism of Saturn, Enceladus and Titan and Formation of HCNO Exobiological Molecules

NASA Technical Reports Server (NTRS)

Sittler, Edward C., Jr.; Cooper, John F.

2010-01-01

Saturn as a system has two very exotic moons Titan and Enceladus. Titan with energy input from Saturn's magnetosphere, solar UV irradiation, and cosmic rays can make HCN based molecules as discussed in earlier paper by [1]. Space radiation effects at both moons, and as coupled by the Saturn magnetosphere could cause an unexpected series of events leading to the evolution of biological models at Titan composed of HCNO with oxygen as the new ingredient. The "Old Faithful" model by [2] suggests that Enceladus, highly irradiated by Saturn magnetospheric electrons, has episodic ejections of water vapor driven by radiolytic oxidation gas products into Saturn's magnetosphere. At Titan Cassini discovered 1) that keV oxygen ions, evidently from Enceladus, are bombarding Titan's upper atmosphere [3] and 2) the discovery of heavy positive and negative ions within Titan's upper atmosphere [4]. Initial models of heavy ion formation in Titan's upper atmosphere invoked polymerization of aromatics such as Benzenes and their radicals to make PAHs [5], while a more recent model by [6] has raised the possibility of carbon chains forming from the polymerization of acetylene and its radicals to eventually make fullerenes. Laboratory measurements indicate that fullerenes, which are hollow carbon shells, can trap the keV oxygen and with the clustering of fullerenes and possible mixture with PAHs, some with nitrogen molecules, can make the larger aerosols with oxygen within them. Then with further ionizing irradiation from cosmic rays deep in the atmosphere "tholin" molecules are produced with all the molecular components present from which organic molecules can form. Among the molecular components are amino acids, the fundamental building blocks of life as we know it. This process maybe a common chemical pathway, both at the system level and at the molecular level, to form prebiotic and perhaps even biotic molecules. Such processes can be occurring throughout our universe, such as

Theoretical analysis of ozone generation by pulsed dielectric barrier discharge in oxygen

NASA Astrophysics Data System (ADS)

Wei, L. S.; Zhou, J. H.; Wang, Z. H.; Cen, K. F.

2007-08-01

The use of very short high-voltage pulses combined with a dielectric layer results in high-energy electrons that dissociate oxygen molecules into atoms, which are a prerequisite for the subsequent production of ozone by collisions with oxygen molecules and third particles. The production of ozone depends on both the electrical and the physical parameters. For ozone generation by pulsed dielectric barrier discharge in oxygen, a mathematical model, which describes the relation between ozone concentration and these parameters that are of importance in its design, is developed according to dimensional analysis theory. A formula considering the ozone destruction factor is derived for predicting the characteristics of the ozone generation, within the range of the corona inception voltage to the gap breakdown voltage. The trend showing the dependence of the concentration of ozone in oxygen on these parameters generally agrees with the experimental results, thus confirming the validity of the mathematical model.

Quantum-Chemical Simulation of the Solvent Effect on Spontaneous Emission of Singlet Oxygen

NASA Astrophysics Data System (ADS)

Ivashin, N. V.; Shchupak, E. E.

2018-01-01

A molecular simulation of the solvent effect on radiative rate constant k r of singlet oxygen is carried out. This study included a search for the most probable conformations of the complexes of molecules of singlet oxygen and ten solvents and calculation of dipole moments M of transitions a 1Δ g -b1Σ g + ( M a-b ) and a 1Δ g - X 3Σ g - ( M a-X ) of the oxygen molecule for them. Averaging of M a-b by conformations, taking into account the probability of their formation for complexes without atoms with a large atomic number (Cl, S), yields values that, as a rule, correlate well with the behavior of k r in the experiment. Taking into account the possibility of decreasing the distance (compared to equilibrium) between molecules in a collision complex at room temperature made it possible to achieve satisfactory agreement of the calculated and experimental data also for complexes with CCl4, C2Cl4, and CS2. The obtained data indicate that a number of factors affect k r . The correlation of k r with molecular polarizability in a number of cases is due, on the one hand, to its effect on the strength of dispersion interactions in the complex and, on the other hand, to the fact that it to some extent reflects the position of the upper filled orbitals of the solvent molecule. Both factors affect the degree of mixing of the π orbitals of the singlet oxygen molecule with the orbitals of the solvent molecule, which, as was found earlier, facilitates the activation of the a 1Δ g -b1Σ g + transition and the borrowing of its intensity by the a 1Δ g - X 3Σ g - transition.

Atmospheric Oxygen Photoabsorption

NASA Technical Reports Server (NTRS)

Slanger, Tom G.

1996-01-01

The work conducted on this grant was devoted to various aspects of the photophysics and photochemistry of the oxygen molecule. Predissociation linewidths were measured for several vibrational levels in the O2(B3 Sigma(sub u)(sup -)) state, providing good agreement with other groups working on this important problem. Extensive measurements were made on the loss kinetics of vibrationally excited oxygen, where levels between v = 5 and v = 22 were investigated. Cavity ring-down spectroscopy was used to measure oscillator strengths in the oxygen Herzberg bands. The great sensitivity of this technique made it possible to extend the known absorption bands to the dissociation limit as well as providing many new absorption lines that seem to be associated with new O2 transitions. The literature concerning the Herzberg band strengths was evaluated in light of our new measurements, and we made recommendations for the appropriate Herzberg continuum cross sections to be used in stratospheric chemistry. The transition probabilities for all three Herzberg band systems were re-evaluated, and we are recommending a new set of values.

Ultrasensitive detection and characterization of molecules with infrared plasmonic metamaterials

PubMed Central

Cheng, Fei; Yang, Xiaodong; Gao, Jie

2015-01-01

Infrared vibrational spectroscopy is an effective technique which enables the direct probe of molecular fingerprints, and such detection can be further enhanced by the emerging engineered plasmonic metamaterials. Here we experimentally demonstrate ultrasensitive detection and characterization of polymer molecules based on an asymmetric infrared plasmonic metamaterial, and quantitatively analyze the molecule detection sensitivity and molecule-structure interactions. A sharp, non-radiative Fano resonance supported by the plasmonic metamaterial exhibits strongly enhanced near-field, and the resonance frequency is tailored to match the vibrational fingerprint of the target molecule. By utilizing the near-field nature of the plasmonic excitation, significantly enhanced absorption signal of molecules in the infrared spectroscopy are obtained, enabling ultrasensitive detection of only minute quantities of organic molecules. The enhancement of molecular absorption up to 105 fold is obtained, and sensitive detection of molecules at zeptomole levels (corresponding to a few tens of molecules within a unit cell) is achieved with high signal-to-noise ratio in our experiment. The demonstrated infrared plasmonic metamaterial sensing platform offers great potential for improving the specificity and sensitivity of label-free, biochemical detection. PMID:26388404

Singlet Oxygen at the Laundromat

NASA Astrophysics Data System (ADS)

Keeports, David

1995-09-01

Singlet molecular oxygen is an interesting molecule both visually and theoretically, since its red chemiluminescence can be analyzed by the application of simple molecular orbital theory. It can be produced from the reaction of hydrogen peroxide from either chlorine gas or hypochlorite ion from household bleach. Here we demostrate how to produce it using simple laundry cleansers.

Why is the partial oxygen pressure of human tissues a crucial parameter? Small molecules and hypoxia

PubMed Central

Carreau, Aude; Hafny-Rahbi, Bouchra El; Matejuk, Agata; Grillon, Catherine; Kieda, Claudine

2011-01-01

Abstract Oxygen supply and diffusion into tissues are necessary for survival. The oxygen partial pressure (pO2), which is a key component of the physiological state of an organ, results from the balance between oxygen delivery and its consumption. In mammals, oxygen is transported by red blood cells circulating in a well-organized vasculature. Oxygen delivery is dependent on the metabolic requirements and functional status of each organ. Consequently, in a physiological condition, organ and tissue are characterized by their own unique ‘tissue normoxia’ or ‘physioxia’ status. Tissue oxygenation is severely disturbed during pathological conditions such as cancer, diabetes, coronary heart disease, stroke, etc., which are associated with decrease in pO2, i.e. ‘hypoxia’. In this review, we present an array of methods currently used for assessing tissue oxygenation. We show that hypoxia is marked during tumour development and has strong consequences for oxygenation and its influence upon chemotherapy efficiency. Then we compare this to physiological pO2 values of human organs. Finally we evaluate consequences of physioxia on cell activity and its molecular modulations. More importantly we emphasize the discrepancy between in vivo and in vitro tissue and cells oxygen status which can have detrimental effects on experimental outcome. It appears that the values corresponding to the physioxia are ranging between 11% and 1% O2 whereas current in vitro experimentations are usually performed in 19.95% O2, an artificial context as far as oxygen balance is concerned. It is important to realize that most of the experiments performed in so-called normoxia might be dangerously misleading. PMID:21251211

Thermochemical analyses of the oxidative vaporization of metals and oxides by oxygen molecules and atoms

NASA Technical Reports Server (NTRS)

Kohl, F. J.; Leisz, D. M.; Fryburg, G. C.; Stearns, C. A.

1977-01-01

Equilibrium thermochemical analyses are employed to describe the vaporization processes of metals and metal oxides upon exposure to molecular and atomic oxygen. Specific analytic results for the chromium-, platinum-, aluminum-, and silicon-oxygen systems are presented. Maximum rates of oxidative vaporization predicted from the thermochemical considerations are compared with experimental results for chromium and platinum. The oxidative vaporization rates of chromium and platinum are considerably enhanced by oxygen atoms.

Carbon Electrode-Molecule Junctions: A Reliable Platform for Molecular Electronics.

PubMed

Jia, Chuancheng; Ma, Bangjun; Xin, Na; Guo, Xuefeng

2015-09-15

The development of reliable approaches to integrate individual or a small collection of molecules into electrical nanocircuits, often termed "molecular electronics", is currently a research focus because it can not only overcome the increasing difficulties and fundamental limitations of miniaturization of current silicon-based electronic devices, but can also enable us to probe and understand the intrinsic properties of materials at the atomic- and/or molecular-length scale. This development might also lead to direct observation of novel effects and fundamental discovery of physical phenomena that are not accessible by traditional materials or approaches. Therefore, researchers from a variety of backgrounds have been devoting great effort to this objective, which has started to move beyond simple descriptions of charge transport and branch out in different directions, reflecting the interdisciplinarity. This Account exemplifies our ongoing interest and great effort in developing efficient lithographic methodologies capable of creating molecular electronic devices through the combination of top-down micro/nanofabrication with bottom-up molecular assembly. These devices use nanogapped carbon nanomaterials (such as single-walled carbon nanotubes (SWCNTs) and graphene), with a particular focus on graphene, as point contacts formed by electron beam lithography and precise oxygen plasma etching. Through robust amide linkages, functional molecular bridges terminated with diamine moieties are covalently wired into the carboxylic acid-functionalized nanogaps to form stable carbon electrode-molecule junctions with desired functionalities. At the macroscopic level, to improve the contact interface between electrodes and organic semiconductors and lower Schottky barriers, we used SWCNTs and graphene as efficient electrodes to explore the intrinsic properties of organic thin films, and then build functional high-performance organic nanotransistors with ultrahigh responsivities

Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays.

PubMed

Hou, Sen; Sun, Lili; Wieczorek, Stefan A; Kalwarczyk, Tomasz; Kaminski, Tomasz S; Holyst, Robert

2014-01-15

Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3' or 5') end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye. Existing methods are insufficient to measure the percentage of the doubly-labeled dsDNA component in the fluorescent DNA sample and it is even difficult to distinguish the doubly-labeled DNA component from the singly-labeled component. Accurate measurement of the percentage of such doubly labeled dsDNA component is a critical prerequisite for quantitative biochemical measurements, which has puzzled scientists for decades. We established a fluorescence correlation spectroscopy (FCS) system to measure the percentage of doubly labeled dsDNA (PDL) in the total fluorescent dsDNA pool. The method is based on comparative analysis of the given sample and a reference dsDNA sample prepared by adding certain amount of unlabeled ssDNA into the original ssDNA solution. From FCS autocorrelation functions, we obtain the number of fluorescent dsDNA molecules in the focal volume of the confocal microscope and PDL. We also calculate the labeling efficiency of ssDNA. The method requires minimal amount of material. The samples have the concentration of DNA in the nano-molar/L range and the volume of tens of microliters. We verify our method by using restriction enzyme Hind III to cleave the fluorescent dsDNA. The kinetics of the reaction depends strongly on PDL, a critical parameter for quantitative biochemical measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

NASA Astrophysics Data System (ADS)

Reinhart, Wesley F.; Reifenberger, Jeff G.; Gupta, Damini; Muralidhar, Abhiram; Sheats, Julian; Cao, Han; Dorfman, Kevin D.

2015-02-01

We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.

Illumination of growth, division and secretion by metabolic labeling of the bacterial cell surface

PubMed Central

Siegrist, M. Sloan; Swarts, Benjamin M.; Fox, Douglas M.; Lim, Shion An; Bertozzi, Carolyn R.

2015-01-01

The cell surface is the essential interface between a bacterium and its surroundings. Composed primarily of molecules that are not directly genetically encoded, this highly dynamic structure accommodates the basic cellular processes of growth and division as well as the transport of molecules between the cytoplasm and the extracellular milieu. In this review, we describe aspects of bacterial growth, division and secretion that have recently been uncovered by metabolic labeling of the cell envelope. Metabolite derivatives can be used to label a variety of macromolecules, from proteins to non-genetically-encoded glycans and lipids. The embedded metabolite enables precise tracking in time and space, and the versatility of newer chemoselective detection methods offers the ability to execute multiple experiments concurrently. In addition to reviewing the discoveries enabled by metabolic labeling of the bacterial cell envelope, we also discuss the potential of these techniques for translational applications. Finally, we offer some guidelines for implementing this emerging technology. PMID:25725012

Performance limitations of label-free sensors in molecular diagnosis using complex samples

NASA Astrophysics Data System (ADS)

Varma, Manoj

2016-03-01

Label-free biosensors promised a paradigm involving direct detection of biomarkers from complex samples such as serum without requiring multistep sample processing typical of labelled methods such as ELISA or immunofluorescence assays. Label-free sensors have witnessed decades of development with a veritable zoo of techniques available today exploiting a multitude of physical effects. It is appropriate now to critically assess whether label-free technologies have succeeded in delivering their promise with respect to diagnostic applications, particularly, ambitious goals such as early cancer detection using serum biomarkers, which require low limits of detection (LoD). Comparison of nearly 120 limits of detection (LoD) values reported by labelled and label-free sensing approaches over a wide range of detection techniques and target molecules in serum revealed that labeled techniques achieve 2-3 orders of magnitude better LoDs. Data from experiments where labelled and label-free assays were performed simultaneously using the same assay parameters also confirm that the LoD achieved by labelled techniques is 2 to 3 orders of magnitude better than that by label-free techniques. Furthermore, label-free techniques required significant signal amplification, for e.g. using nanoparticle conjugated secondary antibodies, to achieve LoDs comparable to labelled methods substantially deviating from the original "direct detection" paradigm. This finding has important implications on the practical limits of applying label-free detection methods for molecular diagnosis.

Incorporation of Oxygen into Abscisic Acid and Phaseic Acid from Molecular Oxygen 1

PubMed Central

Creelman, Robert A.; Zeevaart, Jan A. D.

1984-01-01

Abscisic acid accumulates in detached, wilted leaves of Xanthium strumarium. When these leaves are subsequently rehydrated, phaseic acid, a catabolite of abscisic acid, accumulates. Analysis by gas chromatography-mass spectrometry of phaseic acid isolated from stressed and subsequently rehydrated leaves placed in an atmosphere containing 20% 18O2 and 80% N2 indicates that one atom of 18O is incorporated in the 6′-hydroxymethyl group of phaseic acid. This suggests that the enzyme that converts abscisic acid to phaseic acid is an oxygenase. Analysis by gas chromatography-mass spectrometry of abscisic acid isolated from stressed leaves kept in an atmosphere containing 18O2 indicates that one atom of 18O is present in the carboxyl group of abscisic acid. Thus, when abscisic acid accumulates in water-stressed leaves, only one of the four oxygens present in the abscisic acid molecule is derived from molecular oxygen. This suggests that either (a) the oxygen present in the 1′-, 4′-, and one of the two oxygens at the 1-position of abscisic acid arise from water, or (b) there exists a stored precursor with oxygen atoms already present in the 1′- and 4′-positions of abscisic acid which is converted to abscisic acid under conditions of water stress. PMID:16663564

A Freeze Substitution Fixation-Based Gold Enlarging Technique for EM Studies of Endocytosed Nanogold-Labeled Molecules

PubMed Central

He, Wanzhong; Kivork, Christine; Machinani, Suman; Morphew, Mary K.; Gail, Anna M.; Tesar, Devin B.; Tiangco, Noreen E.; McIntosh, J. Richard; Bjorkman, Pamela J.

2007-01-01

We have developed methods to locate individual ligands that can be used for electron microscopy studies of dynamic events during endocytosis and subsequent intracellular trafficking. The methods are based on enlargement of 1.4 nm Nanogold attached to an endocytosed ligand. Nanogold, a small label that does not induce misdirection of ligand-receptor complexes, is ideal for labeling ligands endocytosed by live cells, but is too small to be routinely located in cells by electron microscopy. Traditional pre-embedding enhancement protocols to enlarge Nanogold are not compatible with high pressure freezing/freeze substitution fixation (HPF/FSF), the most accurate method to preserve ultrastructure and dynamic events during trafficking. We have developed an improved enhancement procedure for chemically-fixed samples that reduced autonucleation, and a new pre-embedding gold-enlarging technique for HPF/FSF samples that preserved contrast and ultrastructure and can be used for high-resolution tomography. We evaluated our methods using labeled Fc as a ligand for the neonatal Fc receptor. Attachment of Nanogold to Fc did not interfere with receptor binding or uptake, and gold-labeled Fc could be specifically enlarged to allow identification in 2D projections and in tomograms. These methods should be broadly applicable to many endocytosis and transcytosis studies. PMID:17723309

Spin labeled antioxidants protect bacteria against the toxicity of alkylating antitumor drug CCNU.

PubMed

Gadjeva, Vesselina; Lazarova, Grozdanka; Zheleva, Antoaneta

2003-10-15

We have studied the toxic effect of the alkylating antitumor drug N'-cyclohexyl-N-(2-chloroethyl)-N-nitrosourea (lomustine, CCNU) on Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) strains, alone and in presence of oxygen radical-scavenging substances [Vitamin E, stable nitroxyl radical 2,2,6,6-tetramethylpiperidine-N-oxyl (TMPO), and spin labeled (nitroxyl free radical moiety containing) analogues of CCNU] and compared with that of the alkylating antitumor drug 5-(3,3-dimethyltriazene-1-yl)-imidazole-4-carboxamide (dacarbazine, DTIC). All spin labeled compounds tested were almost no toxic at doses of 50-500 microM/ml, whereas the alkylating antitumor drug CCNU showed toxicity in a dose dependent manner. Even low doses of spin labeled nitrosoureas provided protection against the toxicity caused by the antitumor drug CCNU alone. The lowest toxicity against E. coli and S. aureus were achieved when 500 microM/ml of CCNU was combined with 200 microM/ml of spin labeled nitrosourea N-[N'-(2-chloroethyl)-N'-nitrosocarbamoyl]-glycine amid of 2,2,6,6-tetramethyl-4-aminopiperidine-1-oxyl (SLCNUgly). A combination of TMPO with vitamin E completely abolished the toxicity of CCNU. Endogenous formation of oxygen radicals and their possible involvement in CCNU toxicity towards the bacteria strains tested have been also discussed.

Sequential ordering among multicolor fluorophores for protein labeling facility via aggregation-elimination based β-lactam probes.

PubMed

Sadhu, Kalyan K; Mizukami, Shin; Watanabe, Shuji; Kikuchi, Kazuya

2011-05-01

Development of protein labeling techniques with small molecules is enthralling because this method brings promises for triumph over the limitations of fluorescent proteins in live cell imaging. This technology deals with the functionalization of proteins with small molecules and is anticipated to facilitate the expansion of various protein assay methods. A new straightforward aggregation and elimination-based technique for a protein labeling system has been developed with a versatile emissive range of fluorophores. These fluorophores have been applied to show their efficiency for protein labeling by exploiting the same basic principle. A genetically modified version of class A type β-lactamase has been used as the tag protein (BL-tag). The strength of the aggregation interaction between a fluorophore and a quencher plays a governing role in the elimination step of the quencher from the probes, which ultimately controls the swiftness of the protein labeling strategy. Modulation in the elimination process can be accomplished by the variation in the nature of the fluorophore. This diversity facilitates the study of the competitive binding order among the synthesized probes toward the BL-tag labeling method. An aggregation and elimination-based BL-tag technique has been explored to develop an order of color labeling from the equimolar mixture of the labeling probe in solutions. The qualitative and quantitative determination of ordering within the probes toward labeling studies has been executed through SDS-PAGE and time-dependent fluorescence intensity enhancement measurements, respectively. The desirable multiple-wavelength fluorescence labeling probes for the BL-tag technology have been developed and demonstrate broad applicability of this labeling technology to live cell imaging with coumarin and fluorescein derivatives by using confocal microscopy.

Why is the partial oxygen pressure of human tissues a crucial parameter? Small molecules and hypoxia.

PubMed

Carreau, Aude; El Hafny-Rahbi, Bouchra; Matejuk, Agata; Grillon, Catherine; Kieda, Claudine

2011-06-01

Oxygen supply and diffusion into tissues are necessary for survival. The oxygen partial pressure (pO(2)), which is a key component of the physiological state of an organ, results from the balance between oxygen delivery and its consumption. In mammals, oxygen is transported by red blood cells circulating in a well-organized vasculature. Oxygen delivery is dependent on the metabolic requirements and functional status of each organ. Consequently, in a physiological condition, organ and tissue are characterized by their own unique 'tissue normoxia' or 'physioxia' status. Tissue oxygenation is severely disturbed during pathological conditions such as cancer, diabetes, coronary heart disease, stroke, etc., which are associated with decrease in pO(2), i.e. 'hypoxia'. In this review, we present an array of methods currently used for assessing tissue oxygenation. We show that hypoxia is marked during tumour development and has strong consequences for oxygenation and its influence upon chemotherapy efficiency. Then we compare this to physiological pO(2) values of human organs. Finally we evaluate consequences of physioxia on cell activity and its molecular modulations. More importantly we emphasize the discrepancy between in vivo and in vitro tissue and cells oxygen status which can have detrimental effects on experimental outcome. It appears that the values corresponding to the physioxia are ranging between 11% and 1% O(2) whereas current in vitro experimentations are usually performed in 19.95% O(2), an artificial context as far as oxygen balance is concerned. It is important to realize that most of the experiments performed in so-called normoxia might be dangerously misleading. © 2011 The Authors Journal of Cellular and Molecular Medicine © 2011 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

NMR studies of two spliced leader RNAs using isotope labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapham, J.; Crothers, D.M.

1994-12-01

Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions betweenmore » the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.« less

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

NASA Astrophysics Data System (ADS)

Chandra, Subhash

2004-06-01

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13C and 15N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13C15N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39K, 23Na and 40Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

Label free detection of phospholipids by infrared absorption spectroscopy

NASA Astrophysics Data System (ADS)

Ahmed, Tahsin; Foster, Erick; Vigil, Genevieve; Khan, Aamir A.; Bohn, Paul; Howard, Scott S.

2014-08-01

We present our study on compact, label-free dissolved lipid sensing by combining capillary electrophoresis separation in a PDMS microfluidic chip online with mid-infrared (MIR) absorption spectroscopy for biomarker detection. On-chip capillary electrophoresis is used to separate the biomarkers without introducing any extrinsic contrast agent, which reduces both cost and complexity. The label free biomarker detection could be done by interrogating separated biomarkers in the channel by MIR absorption spectroscopy. Phospholipids biomarkers of degenerative neurological, kidney, and bone diseases are detectable using this label free technique. These phospholipids exhibit strong absorption resonances in the MIR and are present in biofluids including urine, blood plasma, and cerebrospinal fluid. MIR spectroscopy of a 12-carbon chain phosphatidic acid (PA) (1,2-dilauroyl-snglycero- 3-phosphate (sodium salt)) dissolved in N-methylformamide, exhibits a strong amide peak near wavenumber 1660 cm-1 (wavelength 6 μm), arising from the phosphate headgroup vibrations within a low-loss window of the solvent. PA has a similar structure to many important phospholipids molecules like phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylserine (PS), making it an ideal molecule for initial proof-of-concept studies. This newly proposed detection technique can lead us to minimal sample preparation and is capable of identifying several biomarkers from the same sample simultaneously.

Single-Molecule Electrical Random Resequencing of DNA and RNA

NASA Astrophysics Data System (ADS)

Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

2012-07-01

Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Effects of myocardial infarction on the distribution and transport of nutrients and oxygen in porcine myocardium.

PubMed

Davis, Bryce H; Morimoto, Yoshihisa; Sample, Chris; Olbrich, Kevin; Leddy, Holly A; Guilak, Farshid; Taylor, Doris A

2012-10-01

One of the primary limitations of cell therapy for myocardial infarction is the low survival of transplanted cells, with a loss of up to 80% of cells within 3 days of delivery. The aims of this study were to investigate the distribution of nutrients and oxygen in infarcted myocardium and to quantify how macromolecular transport properties might affect cell survival. Transmural myocardial infarction was created by controlled cryoablation in pigs. At 30 days post-infarction, oxygen and metabolite levels were measured in the peripheral skeletal muscle, normal myocardium, the infarct border zone, and the infarct interior. The diffusion coefficients of fluorescein or FITC-labeled dextran (0.3-70 kD) were measured in these tissues using fluorescence recovery after photobleaching. The vascular density was measured via endogenous alkaline phosphatase staining. To examine the influence of these infarct conditions on cells therapeutically used in vivo, skeletal myoblast survival and differentiation were studied in vitro under the oxygen and glucose concentrations measured in the infarct tissue. Glucose and oxygen concentrations, along with vascular density were significantly reduced in infarct when compared to the uninjured myocardium and infarct border zone, although the degree of decrease differed. The diffusivity of molecules smaller than 40 kD was significantly higher in infarct center and border zone as compared to uninjured heart. Skeletal myoblast differentiation and survival were decreased stepwise from control to hypoxia, starvation, and ischemia conditions. Although oxygen, glucose, and vascular density were significantly reduced in infarcted myocardium, the rate of macromolecular diffusion was significantly increased, suggesting that diffusive transport may not be inhibited in infarct tissue, and thus the supply of nutrients to transplanted cells may be possible. in vitro studies mimicking infarct conditions suggest that increasing nutrients available to

Relative quantification of biomarkers using mixed-isotope labeling coupled with MS

PubMed Central

Chapman, Heidi M; Schutt, Katherine L; Dieter, Emily M; Lamos, Shane M

2013-01-01

The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers. PMID:23157360

Detecting RNA/DNA hybridization using double-labeled donor probes with enhanced fluorescence resonance energy transfer signals.

PubMed

Okamura, Yukio; Watanabe, Yuichiro

2006-01-01

Fluorescence resonance energy transfer (FRET) occurs when two fluorophores are in close proximity, and the emission energy of a donor fluorophore is transferred to excite an acceptor fluorophore. Using such fluorescently labeled oligonucleotides as FRET probes, makes possible specific detection of RNA molecules even if similar sequences are present in the environment. A higher ratio of signal to background fluorescence is required for more sensitive probe detection. We found that double-labeled donor probes labeled with BODIPY dye resulted in a remarkable increase in fluorescence intensity compared to single-labeled donor probes used in conventional FRET. Application of this double-labeled donor system can improve a variety of FRET techniques.

Choosing the right fluorophore for single-molecule fluorescence studies in a lipid environment.

PubMed

Zhang, Zhenfu; Yomo, Dan; Gradinaru, Claudiu

2017-07-01

Nonspecific interactions between lipids and fluorophores can alter the outcomes of single-molecule spectroscopy of membrane proteins in live cells, liposomes or lipid nanodiscs and of cytosolic proteins encapsulated in liposomes or tethered to supported lipid bilayers. To gain insight into these effects, we examined interactions between 9 dyes that are commonly used as labels for single-molecule fluorescence (SMF) and 6 standard lipids including cationic, zwitterionic and anionic types. The diffusion coefficients of dyes in the absence and presence of set amounts of lipid vesicles were measured by fluorescence correlation spectroscopy (FCS). The partition coefficients and the free energies of partitioning for different fluorophore-lipid pairs were obtained by global fitting of the titration FCS curves. Lipids with different charges, head groups and degrees of chain saturation were investigated, and interactions with dyes are discussed in terms of hydrophobic, electrostatic and steric contributions. Fluorescence imaging of individual fluorophores adsorbed on supported lipid bilayers provides visualization and additional quantification of the strength of dye-lipid interaction in the context of single-molecule measurements. By dissecting fluorophore-lipid interactions, our study provides new insights into setting up single-molecule fluorescence spectroscopy experiments with minimal interference from interactions between fluorescent labels and lipids in the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Single Lipid Molecule Dynamics on Supported Lipid Bilayers with Membrane Curvature.

PubMed

Cheney, Philip P; Weisgerber, Alan W; Feuerbach, Alec M; Knowles, Michelle K

2017-03-15

The plasma membrane is a highly compartmentalized, dynamic material and this organization is essential for a wide variety of cellular processes. Nanoscale domains allow proteins to organize for cell signaling, endo- and exocytosis, and other essential processes. Even in the absence of proteins, lipids have the ability to organize into domains as a result of a variety of chemical and physical interactions. One feature of membranes that affects lipid domain formation is membrane curvature. To directly test the role of curvature in lipid sorting, we measured the accumulation of two similar lipids, 1,2-Dihexadecanoyl- sn -glycero-3-phosphoethanolamine (DHPE) and hexadecanoic acid (HDA), using a supported lipid bilayer that was assembled over a nanopatterned surface to obtain regions of membrane curvature. Both lipids studied contain 16 carbon, saturated tails and a head group tag for fluorescence microscopy measurements. The accumulation of lipids at curvatures ranging from 28 nm to 55 nm radii was measured and fluorescein labeled DHPE accumulated more than fluorescein labeled HDA at regions of membrane curvature. We then tested whether single biotinylated DHPE molecules sense curvature using single particle tracking methods. Similar to groups of fluorescein labeled DHPE accumulating at curvature, the dynamics of single molecules of biotinylated DHPE was also affected by membrane curvature and highly confined motion was observed.

Antigen Binding and Site-Directed Labeling of Biosilica-Immobilized Fusion Proteins Expressed in Diatoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ford, Nicole R.; Hecht, Karen A.; Hu, Dehong

2016-01-08

The diatom Thalassiosira pseudonana was genetically modified to express biosilica-targeted fusion proteins incorporating a tetracysteine tag for site-directed labeling with biarsenical affinity probes and either EGFP or single chain antibody to test colocalization of probes with the EGFP-tagged recombinant protein or binding of biosilica-immobilized antibodies to large and small molecule antigens, respectively. Site-directed labeling with the biarsenical probes demonstrated colocalization with EGFP-encoded proteins in nascent and mature biosilica, supporting their use in studying biosilica maturation. Isolated biosilica transformed with a single chain antibody against either the Bacillus anthracis surface layer protein EA1 or small molecule explosive trinitrotoluene (TNT) effectively boundmore » the respective antigens. A marked increase in fluorescence lifetime of the TNT surrogate Alexa Fluor 555-trinitrobenzene reflected the high binding specificity of the transformed isolated biosilica. These results demonstrated the potential use of biosilica-immobilized single chain antibodies as binders for large and small molecule antigens in sensing and therapeutics.« less

Effects of 31 FDA approved small-molecule kinase inhibitors on isolated rat liver mitochondria.

PubMed

Zhang, Jun; Salminen, Alec; Yang, Xi; Luo, Yong; Wu, Qiangen; White, Matthew; Greenhaw, James; Ren, Lijun; Bryant, Matthew; Salminen, William; Papoian, Thomas; Mattes, William; Shi, Qiang

2017-08-01

The FDA has approved 31 small-molecule kinase inhibitors (KIs) for human use as of November 2016, with six having black box warnings for hepatotoxicity (BBW-H) in product labeling. The precise mechanisms and risk factors for KI-induced hepatotoxicity are poorly understood. Here, the 31 KIs were tested in isolated rat liver mitochondria, an in vitro system recently proposed to be a useful tool to predict drug-induced hepatotoxicity in humans. The KIs were incubated with mitochondria or submitochondrial particles at concentrations ranging from therapeutic maximal blood concentrations (Cmax) levels to 100-fold Cmax levels. Ten endpoints were measured, including oxygen consumption rate, inner membrane potential, cytochrome c release, swelling, reactive oxygen species, and individual respiratory chain complex (I-V) activities. Of the 31 KIs examined only three including sorafenib, regorafenib and pazopanib, all of which are hepatotoxic, caused significant mitochondrial toxicity at concentrations equal to the Cmax, indicating that mitochondrial toxicity likely contributes to the pathogenesis of hepatotoxicity associated with these KIs. At concentrations equal to 100-fold Cmax, 18 KIs were found to be toxic to mitochondria, and among six KIs with BBW-H, mitochondrial injury was induced by regorafenib, lapatinib, idelalisib, and pazopanib, but not ponatinib, or sunitinib. Mitochondrial liability at 100-fold Cmax had a positive predictive power (PPV) of 72% and negative predictive power (NPV) of 33% in predicting human KI hepatotoxicity as defined by product labeling, with the sensitivity and specificity being 62% and 44%, respectively. Similar predictive power was obtained using the criterion of Cmax ≥1.1 µM or daily dose ≥100 mg. Mitochondrial liability at 1-2.5-fold Cmax showed a 100% PPV and specificity, though the NPV and sensitivity were 32% and 14%, respectively. These data provide novel mechanistic insights into KI hepatotoxicity and indicate that

48-spot single-molecule FRET setup with periodic acceptor excitation

NASA Astrophysics Data System (ADS)

Ingargiola, Antonino; Segal, Maya; Gulinatti, Angelo; Rech, Ivan; Labanca, Ivan; Maccagnani, Piera; Ghioni, Massimo; Weiss, Shimon; Michalet, Xavier

2018-03-01

Single-molecule Förster resonance energy transfer (smFRET) allows measuring distances between donor and acceptor fluorophores on the 3-10 nm range. Solution-based smFRET allows measurement of binding-unbinding events or conformational changes of dye-labeled biomolecules without ensemble averaging and free from surface perturbations. When employing dual (or multi) laser excitation, smFRET allows resolving the number of fluorescent labels on each molecule, greatly enhancing the ability to study heterogeneous samples. A major drawback to solution-based smFRET is the low throughput, which renders repetitive measurements expensive and hinders the ability to study kinetic phenomena in real-time. Here we demonstrate a high-throughput smFRET system that multiplexes acquisition by using 48 excitation spots and two 48-pixel single-photon avalanche diode array detectors. The system employs two excitation lasers allowing separation of species with one or two active fluorophores. The performance of the system is demonstrated on a set of doubly labeled double-stranded DNA oligonucleotides with different distances between donor and acceptor dyes along the DNA duplex. We show that the acquisition time for accurate subpopulation identification is reduced from several minutes to seconds, opening the way to high-throughput screening applications and real-time kinetics studies of enzymatic reactions such as DNA transcription by bacterial RNA polymerase.

Simulation of the low earth orbital atomic oxygen interaction with materials by means of an oxygen ion beam

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Rutledge, Sharon K.; Paulsen, Phillip E.; Steuber, Thomas J.

1989-01-01

Atomic oxygen is the predominant species in low-Earth orbit between the altitudes of 180 and 650 km. These highly reactive atoms are a result of photodissociation of diatomic oxygen molecules from solar photons having a wavelength less than or equal to 2430A. Spacecraft in low-Earth orbit collide with atomic oxygen in the 3P ground state at impact energies of approximately 4.2 to 4.5 eV. As a consequence, organic materials previously used for high altitude geosynchronous spacecraft are severely oxidized in the low-Earth orbital environment. The evaluation of materials durability to atomic oxygen requires ground simulation of this environment to cost effectively screen materials for durability. Directed broad beam oxygen sources are necessary to evaluate potential spacecraft materials performance before and after exposure to the simulated low-Earth orbital environment. This paper presents a description of a low energy, broad oxygen ion beam source used to simulate the low-Earth orbital atomic oxygen environment. The results of materials interaction with this beam and comparison with actual in-space tests of the same meterials will be discussed. Resulting surface morphologies appear to closely replicate those observed in space tests.

Category labels versus feature labels: category labels polarize inferential predictions.

PubMed

Yamauchi, Takashi; Yu, Na-Yung

2008-04-01

What makes category labels different from feature labels in predictive inference? This study suggests that category labels tend to make inductive reasoning polarized and homogeneous. In two experiments, participants were shown two schematic pictures of insects side by side and predicted the value of a hidden feature of one insect on the basis of the other insect. Arbitrary verbal labels were shown above the two pictures, and the meanings of the labels were manipulated in the instructions. In one condition, the labels represented the category membership of the insects, and in the other conditions, the same labels represented attributes of the insects. When the labels represented category membership, participants' responses became substantially polarized and homogeneous, indicating that the mere reference to category membership can modify reasoning processes.

Oxygen induces mutation in a strict anaerobe, Prevotella melaninogenica.

PubMed

Takumi, Shota; Komatsu, Masaharu; Aoyama, Kohji; Watanabe, Kunitomo; Takeuchi, Toru

2008-05-15

Strict anaerobes are highly sensitive to oxygen, but the mutagenicity of oxygen in strict anaerobes has not been well understood. Prevotella melaninogenica, a strict anaerobe, is susceptible to oxygen and shows an increase in oxidative DNA damage upon exposure to oxygen. In this study, we have investigated the mutagenicity of oxygen and the types of mutations induced by oxygen. Exposure to oxygen decreased cell survival and increased the levels of 8-oxo-deoxyguanosine (8-oxodG). The frequency of rifampicin-resistant mutants was markedly increased after exposure to oxygen. After sequencing a 254-bp fragment of the rpoB gene, which encodes the beta subunit of bacterial RNA polymerase, a target molecule of rifampicin, we found that most mutants induced by oxygen had GC to TA transversions, a signature of 8-oxodG. In addition, all detected single-nucleotide changes would lead to amino acid changes that confer rifampicin resistance. These results indicate that oxygen is mutagenic in a strict anaerobe, P. melaninogenica, and its mutagenic characteristics could be analyzed with this experimental system.

Communication: Alamethicin can capture lipid-like molecules in the membrane

NASA Astrophysics Data System (ADS)

Afanasyeva, Ekaterina F.; Syryamina, Victoria N.; Dzuba, Sergei A.

2017-01-01

Alamethicin (Alm) is a 19-mer antimicrobial peptide produced by fungus Trichoderma viride. Above a threshold concentration, Alm forms pores across the membrane, providing a mechanism of its antimicrobial action. Here we show that at a small concentration which is below the threshold value, Alm participates in formation of nanoscale lipid-mediated clusters of guest lipid-like molecules in the membrane. These results are obtained by electron spin echo (ESE) technique—a pulsed version of electron paramagnetic resonance—on spin-labeled stearic acid in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer with Alm added at 1/200 peptide-to-lipid ratio. ESE decay measurements are interpreted assuming that stearic acid molecules in the membrane are assembling around the Alm molecule. One may suggest that this Alm capturing effect on the guest lipid-like molecules could be important for the peptide antimicrobial action.

Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as.

PubMed

Kocks, Christine; Boltengagen, Anastasiya; Piwecka, Monika; Rybak-Wolf, Agnieszka; Rajewsky, Nikolaus

2018-01-01

Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.

Simple, rapid method for the preparation of isotopically labeled formaldehyde

DOEpatents

Hooker, Jacob Matthew [Port Jefferson, NY; Schonberger, Matthias [Mains, DE; Schieferstein, Hanno [Aabergen, DE; Fowler, Joanna S [Bellport, NY

2011-10-04

Isotopically labeled formaldehyde (*C.sup..sctn.H.sub.2O) is prepared from labeled methyl iodide (*C.sup..sctn.H.sub.3I) by reaction with an oxygen nucleophile having a pendant leaving group. The mild and efficient reaction conditions result in good yields of *C.sup..sctn.H.sub.2O with little or no *C isotopic dilution. The simple, efficient production of .sup.11CH.sub.2O is described. The use of the .sup.11CH.sub.2O for the formation of positron emission tomography tracer compounds is described. The reaction can be incorporated into automated equipment available to radiochemistry laboratories. The isotopically labeled formaldehyde can be used in a variety of reactions to provide radiotracer compounds for imaging studies as well as for scintillation counting and autoradiography.

Molecular Beam Chemistry: Reactions of Oxygen Atoms with Halogen Molecules.

DTIC Science & Technology

1982-10-15

nonlinear one has s = 3, r = 1, and n = 3/2. In the "loose" complex the bending modes go over to free rotation of the product diatomit molecule; thus s...contains no adjustable parameters. All observable properties *l of the reaction may be predicted including product velocity and angular dis- tributions...example, P. R. Bevington, Data Reduction and Error Analysis for the Physical Sciences (McGraw-Hill Book Co., New York, 1969). 65. Equation (3) is strictly

Seasonal changes in background levels of deuterium and oxygen-18 prove water drinking by harp seals, which affects the use of the doubly labelled water method.

PubMed

Nordøy, Erling S; Lager, Anne R; Schots, Pauke C

2017-12-01

The aim of this study was to monitor seasonal changes in stable isotopes of pool freshwater and harp seal ( Phoca groenlandica ) body water, and to study whether these potential seasonal changes might bias results obtained using the doubly labelled water (DLW) method when measuring energy expenditure in animals with access to freshwater. Seasonal changes in the background levels of deuterium and oxygen-18 in the body water of four captive harp seals and in the freshwater pool in which they were kept were measured over a time period of 1 year. The seals were offered daily amounts of capelin and kept under a seasonal photoperiod of 69°N. Large seasonal variations of deuterium and oxygen-18 in the pool water were measured, and the isotope abundance in the body water showed similar seasonal changes to the pool water. This shows that the seals were continuously equilibrating with the surrounding water as a result of significant daily water drinking. Variations in background levels of deuterium and oxygen-18 in freshwater sources may be due to seasonal changes in physical processes such as precipitation and evaporation that cause fractionation of isotopes. Rapid and abrupt changes in the background levels of deuterium and oxygen-18 may complicate calculation of energy expenditure by use of the DLW method. It is therefore strongly recommended that analysis of seasonal changes in background levels of isotopes is performed before the DLW method is applied on (free-ranging) animals, and to use a control group in order to correct for changes in background levels. © 2017. Published by The Company of Biologists Ltd.

Nitrogen diffusion in hafnia and the impact of nitridation on oxygen and hydrogen diffusion: A first-principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sathiyanarayanan, Rajesh, E-mail: rajessat@in.ibm.com, E-mail: rajesh.sathiyanarayanan@gmail.com; Pandey, R. K.; Murali, K. V. R. M.

2015-01-21

Using first-principles simulations, we have computed incorporation energies and diffusion barriers of ammonia, the nitrogen molecule and atomic nitrogen in monoclinic hafnia (m-HfO{sub 2}). Our calculations show that ammonia is likely to dissociate into an NH{sub 2} molecular unit, whereas the nitrogen molecule remains as a molecule either in the interstitial space or at an oxygen lattice site. The lowest energy pathway for the diffusion of atomic nitrogen interstitials consists of the hopping of the nitrogen interstitial between neighboring three-coordinated lattice oxygen atoms that share a single Hf atom, and the barrier for such hops is determined by a switchingmore » mechanism. The substitutional nitrogen atom shows a preference for diffusion through the doubly positive oxygen vacancy-mediated mechanism. Furthermore, we have investigated the impact of nitrogen atoms on the diffusion barriers of oxygen and hydrogen interstitials in m-HfO{sub 2}. Our results show that nitrogen incorporation has a significant impact on the barriers for oxygen and hydrogen diffusion: nitrogen atoms attract oxygen and hydrogen interstitials diffusing in the vicinity, thereby slowing down (reducing) their diffusion (diffusion length)« less

Single-Molecule Spectroscopy and Imaging Over the Decades

PubMed Central

Moerner, W. E.; Shechtman, Yoav; Wang, Quan

2016-01-01

As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990's, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many

A Novel Method for Assigning R, S Labels to Enantiomers.

ERIC Educational Resources Information Center

Huheey, James E.

1986-01-01

Discusses ways of teaching students about how to assign R (rectus) and S (sinister) labels to enantiomers by using their hands as models. The chirality of the human hands follows the Cahn-Ingold-Prelog Rules for assigning enantiomers and infers the correct chirality of molecules shown in two-dimensional drawings. (TW)

Magnetic properties of solid oxygen under pressure (Review Article)

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.

2015-11-01

Solid oxygen is a unique crystal combining properties of a simple molecular solid and a magnet. Unlike ordinary magnets, the exchange interaction in solid oxygen acts on a background of weak Van der Waals forces, providing a significant part of the total lattice energy. Therefore, the magnetic and lattice properties of solid oxygen are very closely related. This manifests itself in a very rich phase diagram and numerous anomalies of thermal, magnetic and optical properties. Low-temperature low-pressure α-O2 is a two-sublattice collinear Neel antiferromagnet. At a pressure of ˜6 GPa, α-O2 is transformed into δ-O2, in which three different magnetic structures are realized upon increasing temperature. At ˜8 GPa δ-O2 is transformed into ɛ-O2. In this transition, O2 molecules combine into four-molecule clusters (O2)4. This transformation is accompanied by a magnetic collapse. This review describes the evolution of the magnetic structure with increasing pressure, and analyzes the causes behind this behavior.

Intranucleus Single-Molecule Imaging in Living Cells.

PubMed

Shao, Shipeng; Xue, Boxin; Sun, Yujie

2018-06-01

Many critical processes occurring in mammalian cells are stochastic and can be directly observed at the single-molecule level within their physiological environment, which would otherwise be obscured in an ensemble measurement. There are various fundamental processes in the nucleus, such as transcription, replication, and DNA repair, the study of which can greatly benefit from intranuclear single-molecule imaging. However, the number of such studies is relatively small mainly because of lack of proper labeling and imaging methods. In the past decade, tremendous efforts have been devoted to developing tools for intranuclear imaging. Here, we mainly describe the recent methodological developments of single-molecule imaging and their emerging applications in the live nucleus. We also discuss the remaining issues and provide a perspective on future developments and applications of this field. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

An Infrared Actin Probe for Deep-Cell Electroporation-Based Single-Molecule Speckle (eSiMS) Microscopy

PubMed Central

Yamashiro, Sawako; Watanabe, Naoki

2017-01-01

Single-molecule speckle (SiMS) microscopy is a powerful method to directly elucidate biochemical reactions in live cells. However, since the signal from an individual fluorophore is extremely faint, the observation area by epi-fluorescence microscopy is restricted to the thin cell periphery to reduce autofluorescence, or only molecules near the plasma membrane are visualized by total internal reflection fluorescence (TIRF) microscopy. Here, we introduce a new actin probe labeled with near infrared (NIR) emissive CF680R dye for easy-to-use, electroporation-based SiMS microscopy (eSiMS) for deep-cell observation. CF680R-labeled actin (CF680R-actin) incorporated into actin structures and showed excellent brightness and photostability suitable for single-molecule imaging. Importantly, the intensity of autofluorescence with respect to SiMS brightness was reduced to approximately 13% compared to DyLight 550-labeled actin (DL550-actin). CF680R-actin enabled the monitoring of actin SiMS in actomyosin bundles associated with adherens junctions (AJs) located at 3.5–4 µm above the basal surfaces of epithelial monolayers. These favorable properties of CF680R-actin extend the application of eSiMS to actin turnover and flow analyses in deep cellular structures. PMID:28671584

DFT study on the interaction of TiO2 (001) surface with HCHO molecules

NASA Astrophysics Data System (ADS)

Wu, Guofei; Zhao, Cuihua; Guo, Changqing; Chen, Jianhua; Zhang, Yibing; Li, Yuqiong

2018-01-01

The interactions of formaldehyde (HCHO) molecule with TiO2 (001) surface were studied using density functional theory calculations. HCHO molecules are dissociated by the cleavage of Csbnd H bonds after adsorption on TiO2 surface. The strong interactions between HCHO melecules and TiO2 surface are largely attributed to the bonding of hydrogen of HCHO and oxygen of TiO2 surface, which is mainly from the hybridization of the H 1s, O 2p and O 2s. The newly formed Hsbnd O bonds cause the structure changes of TiO2 surface, and lead to the cleavage of Osbnd Ti bond of TiO2 surface. The Csbnd O bond that the dissociated remains of HCHO and newly formed Hsbnd O bond can be oxidized to form carbon dioxide and water in subsequent action by oxygen from the atomosphere. The charges transfer from HCHO to TiO2 surface, and the sum amount of the charges transferred from four HCHO molecules to TiO2 surface is bigger than that from one HCHO molecule to TiO2 surface due to the combined interaction of four HCHO molecules with TiO2 surface.

High-throughput single-molecule telomere characterization.

PubMed

McCaffrey, Jennifer; Young, Eleanor; Lassahn, Katy; Sibert, Justin; Pastor, Steven; Riethman, Harold; Xiao, Ming

2017-11-01

We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment. The methodology also permits subtelomere and haplotype-resolved analyses of SRE organization and variation, providing a window into the population dynamics and potential functions of these complex and structurally variant telomere-adjacent DNA regions. At its current stage of development, the assay can be used to identify and characterize telomere length distributions of 30-35 discrete telomeres simultaneously and accurately. The assay's utility is demonstrated using early versus late passage and senescent human diploid fibroblasts, documenting the anticipated telomere attrition on a global telomere-by-telomere basis as well as identifying subtelomere-specific biases for critically short telomeres. Similarly, we present the first global single-telomere-resolved analyses of two cancer cell lines. © 2017 McCaffrey et al.; Published by Cold Spring Harbor Laboratory Press.

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones.

PubMed

Kalvelage, Tim; Lavik, Gaute; Jensen, Marlene M; Revsbech, Niels Peter; Löscher, Carolin; Schunck, Harald; Desai, Dhwani K; Hauss, Helena; Kiko, Rainer; Holtappels, Moritz; LaRoche, Julie; Schmitz, Ruth A; Graco, Michelle I; Kuypers, Marcel M M

2015-01-01

Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein.

Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells

PubMed Central

McQuilken, Molly; La Riviere, Patrick J.; Occhipinti, Patricia; Verma, Amitabh; Oldenbourg, Rudolf; Gladfelter, Amy S.; Tani, Tomomi

2016-01-01

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells. PMID:27679846

Singlet Oxygen Generation by Cyclometalated Complexes and Applications†

PubMed Central

Ashen-Garry, David; Selke, Matthias

2014-01-01

While cyclometalated complexes have been extensively studied for optoelectronic applications, these compounds also represent a relatively new class of photosensitizers for the production of singlet oxygen. Thus far, singlet oxygen generation from cyclometalated Ir and Pt complexes has been studied in detail. In this review, photophysical data for singlet oxygen generation from these complexes is presented, and the mechanism of 1O2 generation is discussed, including evidence for singlet oxygen generation via an electron transfer mechanism for some of cyclometalated Ir complexes. The period from the first report of singlet oxygen generation by a cyclometalated Ir complex in 2002 through August 2013 is covered in this review. This new class of singlet oxygen photosensitizers may prove to be rather versatile due to the ease of substitution of ancillary ligands without loss of activity. Several cyclometalated complexes have been tethered to zeolites, polystyrene, or quantum dots. Applications for photooxygenation of organic molecules, including “traditional” singlet oxygen reactions (ene reaction, [4+2] and [2+2] cycloadditions) as well as oxidative coupling of amines are presented. Potential biomedical applications are also reviewed. PMID:24344628

Method of Stamping Surface-Enhance Raman Spectroscopy for Label-Free, Multiplexed, Molecular Sensing and Imaging

NASA Technical Reports Server (NTRS)

Shih, Wei-Chuan (Inventor)

2017-01-01

The present disclosure relates the use of a stamping surface enhanced Raman scattering (S-SERS) technique with nanoporous gold disk (NPGD) plasmonic substrates to produce a label-free, multiplexed molecular sensing and imaging technique. A NPGD SERS substrate is stamped onto a surface containing one or more target molecules, followed by SERS measurement of the target molecules located between the surface and SERS substrate. The target molecules may be deposited on the surface, which may be a carrier substrate such as polydimethylsiloxane (PDMS).

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

1995-01-01

Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

Visualizing water molecules in transmembrane proteins using radiolytic labeling methods†

PubMed Central

Orban, Tivadar; Gupta, Sayan; Palczewski, Krzysztof; Chance, Mark R.

2010-01-01

Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often co-localize with strategically placed polar or charged groups critical for protein function. Yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of ‘ordered’ waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern and thus the observed waters likely represent a subset of tightly-bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, owing to advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins. PMID:20047303

Frequency-domain photoacoustic and fluorescence microscopy: application on labeled and unlabeled cells

NASA Astrophysics Data System (ADS)

Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Pfeffer, Karoline; Wohlfarth, Sven; Hannesschläger, Günther; Klar, Thomas A.; Berer, Thomas

2018-02-01

In this paper, multimodal optical-resolution frequency-domain photoacoustic and fluorescence scanning microscopy is presented on labeled and unlabeled cells. In many molecules, excited electrons relax radiatively and non-radiatively, leading to fluorescence and photoacoustic signals, respectively. Both signals can then be detected simultaneously. There also exist molecules, e.g. hemoglobin, which do not exhibit fluorescence, but provide photoacoustic signals solely. Other molecules, especially fluorescent dyes, preferentially exhibit fluorescence. The fluorescence quantum yield of a molecule and with it the strength of photoacoustic and fluorescence signals depends on the local environment, e.g. on the pH. Therefore, the local distribution of the simultaneously recorded photoacoustic and fluorescence signals may be used in order to obtain information about the local chemistry.

IRMS detection of testosterone manipulated with 13C labeled standards in human urine by removing the labeled 13C.

PubMed

Wang, Jingzhu; Yang, Rui; Yang, Wenning; Liu, Xin; Xing, Yanyi; Xu, Youxuan

2014-12-10

Isotope ratio mass spectrometry (IRMS) is applied to confirm testosterone (T) abuse by determining the carbon isotope ratios (δ(13)C value). However, (13)C labeled standards can be used to control the δ(13)C value and produce manipulated T which cannot be detected by the current method. A method was explored to remove the (13)C labeled atom at C-3 from the molecule of androsterone (Andro), the metabolite of T in urine, to produce the resultant (A-nor-5α-androstane-2,17-dione, ANAD). The difference in δ(13)C values between Andro and ANAD (Δδ(13)CAndro-ANAD, ‰) would change significantly in case manipulated T is abused. Twenty-one volunteers administered T manipulated with different (13)C labeled standards. The collected urine samples were analyzed with the established method, and the maximum value of Δδ(13)CAndro-ANAD post ingestion ranged from 3.0‰ to 8.8‰. Based on the population reference, the cut-off value of Δδ(13)CAndro-ANAD for positive result was suggested as 1.2‰. The developed method could be used to detect T manipulated with 3-(13)C labeled standards. Copyright © 2014 Elsevier B.V. All rights reserved.

Heavy isotope labeling study of the turnover of forskolin-stimulated adenylate cyclase in BC/sup 3/H1 cell line

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bouhelal, R.; Bockaert, J.; Mermet-Bouvier, R.

1987-06-25

We have used the method of heavy isotope labeling to study the metabolic turnover of adenylate cyclase in a nonfusing muscle cell line, the BC/sup 3/H1 cells. These cells contains an adenylate cyclase coupled to beta-adrenergic receptors and highly stimulated by forskolin, a potent activator of the enzyme. After transfer of the cells from normal medium to heavy medium (a medium containing heavy labeled amino acids, /sup 3/H, /sup 13/C, /sup 15/N), heavy isotope-labeled adenylate cyclase molecules progressively replace pre-existing light molecules. In sucrose gradient differential sedimentation, after a 5-day switch in heavy medium, the enzyme exhibited a higher massmore » (s = 8.40 +/- 0.03 S, n = 13) compared to the control enzyme. Indeed, the increase in the sedimentation coefficient of the heavy molecules was due to the synthesis of new molecules of adenylate cyclase labeled with heavy isotope amino acids since in the presence of cycloheximide, an inhibitor of protein synthesis, no change in the sedimentation pattern of the forskolin-stimulated adenylate cyclase occurred. After incorporation of heavy isotope amino acids in the adenylate cyclase molecules, the kinetics parameters of the enzyme did not change. However, adenylate cyclase from cells incubated with heavy medium exhibits an activity about 2-fold lower than control. After switching the cells to the heavy medium, the decrease of the activity of the enzyme occurred during the first 24 h and thereafter remained at a steady state for at least 4 days. In contrast, 24 h after the switch, the sedimentation coefficient of forskolin-stimulated adenylate cyclase was progressively shifted to a higher value.« less

Oxygen regulates molecular mechanisms of cancer progression and metastasis.

PubMed

Gupta, Kartik; Madan, Esha; Sayyid, Muzzammil; Arias-Pulido, Hugo; Moreno, Eduardo; Kuppusamy, Periannan; Gogna, Rajan

2014-03-01

Oxygen is the basic molecule which supports life and it truly is "god's gift to life." Despite its immense importance, research on "oxygen biology" has never received the light of the day and has been limited to physiological and biochemical studies. It seems that in modern day biology, oxygen research is summarized in one word "hypoxia." Scientists have focused on hypoxia-induced transcriptomics and molecular-cellular alterations exclusively in disease models. Interestingly, the potential of oxygen to control the basic principles of biology like homeostatic maintenance, transcription, replication, and protein folding among many others, at the molecular level, has been completely ignored. Here, we present a perspective on the crucial role played by oxygen in regulation of basic biological phenomena. Our conclusion highlights the importance of establishing novel research areas like oxygen biology, as there is great potential in this field for basic science discoveries and clinical benefits to the society.

Exotic Metal Molecules in Oxygen-Rich Envelopes: Detection of AlOH (X1Σ^+) in VY Canis Majoris

NASA Astrophysics Data System (ADS)

Tenenbaum, E. D.; Ziurys, L. M.

2010-06-01

A new interstellar molecule, AlOH, has been detected toward the envelope of VY Canis Majoris, an oxygen-rich red supergiant. Three rotational transitions of AlOH were observed using the facilities of the Arizona Radio Observatory (ARO). The J = 9 → 8 and J = 7 → 6 lines at 1 mm were measured with the ARO Submillimeter Telescope (SMT), while the J = 5 → 4 transition at 2 mm was observed with the ARO 12 m antenna on Kitt Peak. The AlOH spectra exhibit quite narrow line widths, indicating that the emission arises from within the dust acceleration zone of the central circumstellar outflow. From a radiative transfer analysis, the abundance of AlOH relative to H_2 was found to be 1x10-7 for a source size of 0.26'' or 22 R_*. AlOH is likely formed just beyond the photosphere via thermodynamic equilibrium chemistry, and then disappears due to dust condensation. The AlOH/AlO abundance ratio found in VY CMa is ˜17. LTE calculations predict the monohydroxides should be the major carriers of Al, Ca, and Mg in O-rich envelopes, as opposed to the oxides or halides.

Slags in a Large Variation Range of Oxygen Potential Based on the Ion and Molecule Coexistence Theory

NASA Astrophysics Data System (ADS)

Yang, Xue-Min; Li, Jin-Yan; Zhang, Meng; Chai, Guo-Min; Zhang, Jian

2014-12-01

A thermodynamic model for predicting sulfide capacity of CaO-FeO-Fe2O3-Al2O3-P2O5 slags in a large variation range of oxygen potential corresponding to mass percentage of FetO from 1.88 to 55.50 pct, i.e., IMCT- model, has been developed by coupling with the deduced desulfurization mechanism of the slags based on the ion and molecule coexistence theory (IMCT). The developed IMCT- model has been verified through comparing the determined sulfide capacity after Ban-ya et al.[20] with the calculated by the developed IMCT- model and the calculated by the reported sulfide capacity models such as the KTH model. Mass percentage of FetO as 6.75 pct corresponding to the mass action concentration of FetO as 0.0637 or oxygen partial as 2.27 × 10-6 Pa is the criterion for distinguishing reducing and oxidizing zones for the slags. Sulfide capacity of the slags in reducing zone is controlled by reaction ability of CaO regardless of slag oxidization ability. However, sulfide capacity of the slags in oxidizing zone shows an obvious increase tendency with the increasing of slag oxidization ability. Sulfide capacity of the slags in reducing zone keeps almost constant with variation of the simplified complex basicity (pct CaO)/((pct Al2O3) + (pct P2O5)), or optical basicity, or the mass action concentration ratios of N FeO/ N CaO, , , and . Sulfide capacity of the slags in oxidizing zone shows an obvious increase with the increasing of the simplified complex basicity (pct CaO)/((pct Al2O3) + (pct P2O5)) or optical basicity, or the aforementioned mass action concentration ratios. Thus, the aforementioned mass action concentration ratios and the corresponding mass percentage ratios of various iron oxides to basic oxide CaO are recommended to represent the comprehensive effect of various iron oxides and basic oxide CaO on sulfide capacity of the slags.

Two-colour dip spectroscopy of jet-cooled molecules

NASA Astrophysics Data System (ADS)

Ito, Mitsuo

In optical-optical double resonance spectroscopy, the resonance transition from an intermediate state to a final state can be detected by a dip of the signal (fluorescence or ion) associated with the intermediate state. This method probing the signal of the intermediate state may be called `two-colour dip spectroscopy'. Various kinds of two-colour dip spectroscopy such as two-colour fluorescence/ion dip spectroscopy, two-colour ionization dip spectroscopy employing stimulated emission, population labelling spectroscopy and mass-selected ion dip spectroscopy with dissociation were briefly described, paying special attention to their characteristics in excitation, detection and application. They were extensively and successfully applied to jet-cooled large molecules and provided us with new useful information on the energy and dynamics of excited molecules.

CdS nanowires formed by chemical synthesis using conjugated single-stranded DNA molecules

NASA Astrophysics Data System (ADS)

Sarangi, S. N.; Sahu, S. N.; Nozaki, S.

2018-03-01

CdS nanowires were successfully grown by chemical synthesis using two conjugated single-stranded (ss) DNA molecules, poly G (30) and poly C (30), as templates. During the early stage of the synthesis with the DNA molecules, the Cd 2+ interacts with Poly G and Poly C and produces the (Cd 2+)-Poly GC complex. As the growth proceeds, it results in nanowires. The structural analysis by grazing angle x-ray diffraction and transmission electron microscopy confirmed the zinc-blende CdS nanowires with the growth direction of <220>. Although the nanowires are well surface-passivated with the DNA molecules, the photoluminescence quenching was caused by the electron transfer from the nanowires to the DNA molecules. The quenching can be used to detect and label the DNAs.

Stereochemistry of silicon in oxygen-containing compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serezhkin, V. N., E-mail: Serezhkin@samsu.ru; Urusov, V. S.

2017-01-15

Specific stereochemical features of silicon in oxygen-containing compounds, including hybrid silicates with all oxygen atoms of SiO{sub n} groups ({sub n} = 4, 5, or 6) entering into the composition of organic anions or molecules, are described by characteristics of Voronoi—Dirichlet polyhedra. It is found that in rutile-like stishovite and post-stishovite phases with the structures similar to those of СаСl{sub 2}, α-PbO{sub 2}, or pyrite FeS{sub 2}, the volume of Voronoi—Dirichlet polyhedra of silicon and oxygen atoms decreases linearly with pressure increasing to 268 GPa. Based on these results, the possibility of formation of new post-stishovite phases is shown, namely,more » the fluorite-like structure (transition predicted at ~400 GPa) and a body-centered cubic lattice with statistical arrangement of silicon and oxygen atoms (~900 GPa).« less

Group Additivity Determination for Oxygenates, Oxonium Ions, and Oxygen-Containing Carbenium Ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dellon, Lauren D.; Sung, Chun-Yi; Robichaud, David J.

Bio-oil produced from biomass fast pyrolysis often requires catalytic upgrading to remove oxygen and acidic species over zeolite catalysts. The elementary reactions in the mechanism for this process involve carbenium and oxonium ions. In order to develop a detailed kinetic model for the catalytic upgrading of biomass, rate constants are required for these elementary reactions. The parameters in the Arrhenius equation can be related to thermodynamic properties through structure-reactivity relationships, such as the Evans-Polanyi relationship. For this relationship, enthalpies of formation of each species are required, which can be reasonably estimated using group additivity. However, the literature previously lacked groupmore » additivity values for oxygenates, oxonium ions, and oxygen-containing carbenium ions. In this work, 71 group additivity values for these types of groups were regressed, 65 of which had not been reported previously and six of which were newly estimated based on regression in the context of the 65 new groups. Heats of formation based on atomization enthalpy calculations for a set of reference molecules and isodesmic reactions for a small set of larger species for which experimental data was available were used to demonstrate the accuracy of the Gaussian-4 quantum mechanical method in estimating enthalpies of formation for species involving the moieties of interest. Isodesmic reactions for a total of 195 species were constructed from the reference molecules to calculate enthalpies of formation that were used to regress the group additivity values. The results showed an average deviation of 1.95 kcal/mol between the values calculated from Gaussian-4 and isodesmic reactions versus those calculated from the group additivity values that were newly regressed. Importantly, the new groups enhance the database for group additivity values, especially those involving oxonium ions.« less

Calcium phosphate nanoparticles as versatile carrier for small and large molecules across cell membranes

NASA Astrophysics Data System (ADS)

Sokolova, Viktoriya; Rotan, Olga; Klesing, Jan; Nalbant, Perihan; Buer, Jan; Knuschke, Torben; Westendorf, Astrid M.; Epple, Matthias

2012-06-01

The successful transport of molecules across the cell membrane is a key point in biology and medicine. In most cases, molecules alone cannot penetrate the cell membrane, therefore an efficient carrier is needed. Calcium phosphate nanoparticles (diameter: 100-250 nm, depending on the functionalization) were loaded with fluorescent oligonucleotides, peptide, proteins, antibodies, polymers or porphyrins and characterized by dynamic light scattering, nanoparticle tracking analysis and scanning electron microscopy. Any excess of molecules was removed by ultracentrifugation, and the dissolved molecules at the same concentration were used as control. The uptake of such fluorescence-labeled nanoparticles into HeLa cells was monitored by fluorescence microscopy and confocal laser scanning microscopy. Calcium phosphate nanoparticles were able to transport all molecules across the cell membrane, whereas the dissolved molecules alone were taken up only to a very small extent or even not at all.

No-carrier-added labeling of the neuroprotective Ebselen with selenium-73 and selenium-75.

PubMed

Helfer, Andreas; Ermert, Johannes; Humpert, Sven; Coenen, Heinz H

2015-03-01

Selenium-73 is a positron emitting non-standard radionuclide, which is suitable for positron emission tomography. A copper-catalyzed reaction allowed no-carrier-added labeling of the anti-inflammatory seleno-organic compound Ebselen with (73) Se and (75) Se under addition of sulfur carrier in a one-step reaction. The new authentically labeled radioselenium molecule is thus available for preclinical evaluation and positron emission tomography studies. Copyright © 2015 John Wiley & Sons, Ltd.

Evaluation of genotoxicity testing of FDA approved large molecule therapeutics.

PubMed

Sawant, Satin G; Fielden, Mark R; Black, Kurt A

2014-10-01

Large molecule therapeutics (MW>1000daltons) are not expected to enter the cell and thus have reduced potential to interact directly with DNA or related physiological processes. Genotoxicity studies are therefore not relevant and typically not required for large molecule therapeutic candidates. Regulatory guidance supports this approach; however there are examples of marketed large molecule therapeutics where sponsors have conducted genotoxicity studies. A retrospective analysis was performed on genotoxicity studies of United States FDA approved large molecule therapeutics since 1998 identified through the Drugs@FDA website. This information was used to provide a data-driven rationale for genotoxicity evaluations of large molecule therapeutics. Fifty-three of the 99 therapeutics identified were tested for genotoxic potential. None of the therapeutics tested showed a positive outcome in any study except the peptide glucagon (GlucaGen®) showing equivocal in vitro results, as stated in the product labeling. Scientific rationale and data from this review indicate that testing of a majority of large molecule modalities do not add value to risk assessment and support current regulatory guidance. Similarly, the data do not support testing of peptides containing only natural amino acids. Peptides containing non-natural amino acids and small molecules in conjugated products may need to be tested. Copyright © 2014 Elsevier Inc. All rights reserved.

Doubly labelled water assessment of energy expenditure: principle, practice, and promise.

PubMed

Westerterp, Klaas R

2017-07-01

The doubly labelled water method for the assessment of energy expenditure was first published in 1955, application in humans started in 1982, and it has become the gold standard for human energy requirement under daily living conditions. The method involves enriching the body water of a subject with heavy hydrogen ( 2 H) and heavy oxygen ( 18 O), and then determining the difference in washout kinetics between both isotopes, being a function of carbon dioxide production. In practice, subjects get a measured amount of doubly labelled water ( 2 H 2 18 O) to increase background enrichment of body water for 18 O of 2000 ppm with at least 180 ppm and background enrichment of body water for 2 H of 150 ppm with 120 ppm. Subsequently, the difference between the apparent turnover rates of the hydrogen and oxygen of body water is assessed from blood-, saliva-, or urine samples, collected at the start and end of the observation interval of 1-3 weeks. Samples are analyzed for 18 O and 2 H with isotope ratio mass spectrometry. The doubly labelled water method is the indicated method to measure energy expenditure in any environment, especially with regard to activity energy expenditure, without interference with the behavior of the subjects. Applications include the assessment of energy requirement from total energy expenditure, validation of dietary assessment methods and validation of physical activity assessment methods with doubly labelled water measured energy expenditure as reference, and studies on body mass regulation with energy expenditure as a determinant of energy balance.

Steroids, triterpenoids and molecular oxygen

PubMed Central

Summons, Roger E; Bradley, Alexander S; Jahnke, Linda L; Waldbauer, Jacob R

2006-01-01

There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions

SISGR: Room Temperature Single-Molecule Detection and Imaging by Stimulated Emission Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Xiaoliang Sunney

molecular specificity than absorption and fluorescence. Current sensitivity limit of SRS microscopy has not yet reached single molecule detection. We proposed to capitalize on our state-of-the-art SRS microscopy and develop near-resonance enhanced SRS for single molecule detection of carotenoids and heme proteins. The specific aims we pursued are: (1) building the next SRS generation microscope that utilizes near resonance enhancement to allow detection and imaging of single molecules with undetectable fluorescence, such as -carotene. (2) using near-resonance SRS as a contrast mechanism to study dye-sensitize semiconductor interface, elucidating the heterogeneous electron ejection kinetics with high spatial and temporal resolution. (3) studying the binding and unbinding of oxygen in single hemoglobin molecules in order to gain molecular level understanding of the long-standing issue of cooperativity. The new methods developed in the fund period of this grant have advanced the detection sensitivity in many aspects. Near-resonance SRS improved the signal by using shorter wavelengths for SRS microscopy. Frequency modulation and multi-color SRS target the reduction of background to improve the chemical specificity of SRS while maintaining the high imaging speed. Time-domain coherent Raman scattering microscopy targets to reduce the noise floor of coherent Raman microscopy. These methods have already demonstrated first-of-a-kind new applications in biology and medical research. However, we are still one order of magnitude away from single molecule limit. It is important to continue to improve the laser specification and develop new imaging methods to finally achieve label-free single molecule microscopy.« less

Proximity labeling of cis-ligands of CD22/Siglec-2 reveals stepwise α2,6 sialic acid-dependent and -independent interactions.

PubMed

Alborzian Deh Sheikh, Amin; Akatsu, Chizuru; Imamura, Akihiro; Abdu-Allah, Hajjaj H M; Takematsu, Hiromu; Ando, Hiromune; Ishida, Hideharu; Tsubata, Takeshi

2018-01-01

Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22. Here we labeled molecules in the proximity of CD22 in situ on B cell surface using biotin-tyramide. Molecules including CD22, CD45 and IgM were labeled in wild-type but not ST6GalI -/- B cells that lack α2,6 sialic acids, indicating that these molecules associate with CD22 by lectin-glycan interaction, and are therefore cis-ligands. In ST6GalI -/- B cells, these cis-ligands are located in a slightly more distance from CD22. Thus, the lectin-glycan interaction recruits cis-ligands already located in the relative proximity of CD22 through non-lectin-glycan interaction to the close proximity. Moreover, cis-ligands are labeled in Cmah -/- B cells that lack Neu5Gc preferred by mouse CD22 as efficiently as in wild-type B cells, indicating that very low affinity lectin-glycan interaction is sufficient for recruiting cis-ligands, and can be detected by proximity labeling. Thus, proximity labeling with tyramide appears to be a useful method to identify cis-ligands and to analyze their interaction with the lectins. Copyright © 2017 Elsevier Inc. All rights reserved.

Titan's Oxygen Chemistry and its Impact on Haze Formation

NASA Astrophysics Data System (ADS)

Vuitton, Veronique; Carrasco, Nathalie; Flandinet, Laurene; Horst, Sarah; Klippenstein, Stephen; Lavvas, Panayotis; Orthous-Daunay, Francois-Regis; Quirico, Eric; Thissen, Roland; Yelle, Roger V.

2016-10-01

Though Titan's atmosphere is reducing with its 98% N2, 2% CH4 and 0.1% H2, CO is the fourth most abundant molecule with a uniform mixing ratio of ~50 ppm. Two other oxygen bearing molecules have also been observed in Titan's atmosphere: CO2 and H2O, with a mixing ratio of ~15 and ~1 ppb, respectively. The physical and chemical processes that determine the abundances of these species on Titan have been at the centre of a long-standing debate as they place constraints on the origin and evolution of its atmosphere [1]. Moreover, laboratory experiments have shown that oxygen can be incorporated into complex molecules, some of which are building blocks of life [2]. Finally, the presence of CO modifies the production rate and size of tholins [3, 4], which transposed to Titan's haze may have some strong repercussions on the temperature structure and dynamics of the atmosphere.We present here our current understanding of Titan's oxygen chemistry and of its impact on the chemical composition of the haze. We base our discussion on a photochemical model that describes the first steps of the chemistry and on state-of-the-art laboratory experiments for the synthesis and chemical analysis of aerosol analogues. We used a very-high resolution mass spectrometer (LTQ-Orbitrap XL instrument) to characterize the soluble part of tholin samples generated from N2/CH4/CO mixtures at different mixing ratios and with two different laboratory set-ups. These composition measurements provide some understanding of the chemical mechanisms by which CO affects particle formation and growth. Our final objective is to obtain a global picture of the fate and impact of oxygen on Titan, from its origin to prebiotic molecules to haze particles to material deposited on the surface.[1] S.M. Hörst et al., The origin of oxygen species in Titan's atmosphere, J. Geophys. Res., 113, E10006 (2008).[2] S.M. Hörst et al., Formation of amino acids and nucleotide bases in a Titan atmosphere simulation experiment

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

1995-04-11

A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

The effect of oxygen fugacity on the solubility of carbon-oxygen fluids in basaltic melt

NASA Technical Reports Server (NTRS)

Pawley, Alison R.; Holloway, John R.; Mcmillan, Paul F.

1992-01-01

The solubility of CO2-CO fluids in a midocean ridge basalt have been measured at 1200 C, 500-1500 bar, and oxygen fugacities between NNO and NNO-4. In agreement with results of previous studies, the results reported here imply that, at least at low pressures, CO2 dissolves in basaltic melt only in the form of carbonate groups. The dissolution reaction is heterogeneous, with CO2 molecules in the fluid reacting directly with reactive oxygens in the melt to produce CO3(2-). CO, on the other hand, is insoluble, dissolving neither as carbon, molecular CO, nor CO3(2-). It is shown that, for a given pressure and temperature, the concentration of dissolved carbon-bearing species in basaltic melt in equilibrium with a carbon-oxygen fluid is proportional to the mole fraction of CO2 in the fluid, which is a function of fO2. At low pressures CO2 solubility is a linear function of CO2 fugacity at constant temperatures.

Atomic scale observation of oxygen delivery during silver–oxygen nanoparticle catalysed oxidation of carbon nanotubes

PubMed Central

Yue, Yonghai; Yuchi, Datong; Guan, Pengfei; Xu, Jia; Guo, Lin; Liu, Jingyue

2016-01-01

To probe the nature of metal-catalysed processes and to design better metal-based catalysts, atomic scale understanding of catalytic processes is highly desirable. Here we use aberration-corrected environmental transmission electron microscopy to investigate the atomic scale processes of silver-based nanoparticles, which catalyse the oxidation of multi-wall carbon nanotubes. A direct semi-quantitative estimate of the oxidized carbon atoms by silver-based nanoparticles is achieved. A mechanism similar to the Mars–van Krevelen process is invoked to explain the catalytic oxidation process. Theoretical calculations, together with the experimental data, suggest that the oxygen molecules dissociate on the surface of silver nanoparticles and diffuse through the silver nanoparticles to reach the silver/carbon interfaces and subsequently oxidize the carbon. The lattice distortion caused by oxygen concentration gradient within the silver nanoparticles provides the direct evidence for oxygen diffusion. Such direct observation of atomic scale dynamics provides an important general methodology for investigations of catalytic processes. PMID:27406595

Carbon nanotubes-based chemiresistive immunosensor for small molecules: detection of nitroaromatic explosives.

PubMed

Park, Miso; Cella, Lakshmi N; Chen, Wilfred; Myung, Nosang V; Mulchandani, Ashok

2010-12-15

In recent years, there has been a growing focus on use of one-dimensional (1-D) nanostructures, such as carbon nanotubes and nanowires, as transducer elements for label-free chemiresistive/field-effect transistor biosensors as they provide label-free and high sensitivity detection. While research to-date has elucidated the power of carbon nanotubes- and other 1-D nanostructure-based field effect transistors immunosensors for large charged macromolecules such as proteins and viruses, their application to small uncharged or charged molecules has not been demonstrated. In this paper we report a single-walled carbon nanotubes (SWNTs)-based chemiresistive immunosensor for label-free, rapid, sensitive and selective detection of 2,4,6-trinitrotoluene (TNT), a small molecule. The newly developed immunosensor employed a displacement mode/format in which SWNTs network forming conduction channel of the sensor was first modified with trinitrophenyl (TNP), an analog of TNT, and then ligated with the anti-TNP single chain antibody. Upon exposure to TNT or its derivatives the bound antibodies were displaced producing a large change, several folds higher than the noise, in the resistance/conductance of SWNTs giving excellent limit of detection, sensitivity and selectivity. The sensor detected between 0.5 ppb and 5000 ppb TNT with good selectivity to other nitroaromatic explosives and demonstrated good accuracy for monitoring TNT in untreated environmental water matrix. We believe this new displacement format can be easily generalized to other one-dimensional nanostructure-based chemiresistive immuno/affinity-sensors for detecting small and/or uncharged molecules of interest in environmental monitoring and health care. Copyright © 2010 Elsevier B.V. All rights reserved.

Oxygen and Metastasis: A Conversation with Dr. Nick Restifo

Cancer.gov

Dr. Nick Restifo, a senior investigator in NCI’s Center for Cancer Research, discusses his recently published study finding that Oxygen, a molecule necessary for life, paradoxically aids cancer metastasis to the lung by impairing cancer-killing immune cells.

Nanofiber Based Optical Sensors for Oxygen Determination

NASA Astrophysics Data System (ADS)

Xue, Ruipeng

Oxygen sensors based on luminescent quenching of nanofibers were developed for measurement of both gaseous and dissolved oxygen concentrations. Electrospinning was used to fabricate "core-shell" fiber configurations in which oxygen-sensitive transition metal complexes are embedded into a polymer 'core' while a synthetic biocompatible polymer provides a protective 'shell.' Various matrix polymers and luminescent probes were studied in terms of their sensitivity, linear calibration, reversibility, response time, stability and probe-matrix interactions. Due to the small size and high surface area of these nanofibers, all samples showed rapid response and a highly linear response to oxygen. The sensitivity and photostability of the sensors were controlled by the identity of both the probe molecule and the polymer matrix. Such nanofiber sensor forms are particularly suitable in biological applications due to the fact that they do not consume oxygen, are biocompatible and biomimetic and can be easily incorporated into cell culture. Applications of these fibers in cancer cell research, wound healing, breath analysis and waste water treatment were explored.

Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation.

PubMed

Lee, Taehyung C; Moran, Crystal R; Cistrone, Philip A; Dawson, Philip E; Deniz, Ashok A

2018-04-12

Single-molecule fluorescence is widely used to study conformational complexity in proteins, and has proven especially valuable with intrinsically disordered proteins (IDPs). Protein studies using dual-color single-molecule Förster resonance energy transfer (smFRET) are now quite common, but many could benefit from simultaneous measurement of multiple distances through multi-color labeling. Such studies, however, have suffered from limitations in site-specific incorporation of more than two dyes per polypeptide. Here we present a fully site-specific three-color labeling scheme for α-synuclein, an IDP with important putative functions and links to Parkinson disease. The convergent synthesis combines native chemical ligation with regiospecific cysteine protection of expressed protein fragments to permit highly controlled labeling via standard cysteine-maleimide chemistry, enabling more global smFRET studies. Furthermore, this modular approach is generally compatible with recombinant proteins and expandable to accommodate even more complex experiments, such as by labeling with additional colors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Molecules-in-molecules fragment-based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides.

PubMed

Jose, K V Jovan; Raghavachari, Krishnan

2016-12-01

The molecules-in-molecules (MIM) fragment-based method has recently been adapted to evaluate the chiroptical (vibrational circular dichroism [VCD] and Raman optical activity [ROA]) spectra of large molecules such as peptides. In the MIM-VCD and MIM-ROA methods, the relevant higher energy derivatives of the parent molecule are assembled from the corresponding derivatives of smaller fragment subsystems. In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 3 10 -helix, α-helix, β-hairpin, γ-turn, and β-extended conformers of gas phase polyalanine (chain length n = 6-14). The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size. For a better understanding the site-specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled 13 C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two-step-MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets. The chiroptical spectra of α-(alanine) 20 polypeptide obtained using the two-step-MIM model, including continuum solvation effects, show good agreement with the full calculations and experiment. This benchmark study suggests that the MIM-fragment approach can assist in predicting and interpreting chiroptical spectra of large polypeptides. © 2016 Wiley Periodicals, Inc.

Single cell systems biology by super-resolution imaging and combinatorial labeling

PubMed Central

Lubeck, Eric; Cai, Long

2012-01-01

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using Fluorescence in situ Hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells provides a natural approach to bring systems biology into single cells. PMID:22660740

Synthesis of {111} Facet-Exposed MgO with Surface Oxygen Vacancies for Reactive Oxygen Species Generation in the Dark.

PubMed

Hao, Ying-Juan; Liu, Bing; Tian, Li-Gang; Li, Fa-Tang; Ren, Jie; Liu, Shao-Jia; Liu, Ying; Zhao, Jun; Wang, Xiao-Jing

2017-04-12

Seeking a simple and moderate route to generate reactive oxygen species (ROS) for antibiosis is of great interest and challenge. This work demonstrates that molecule transition and electron rearrangement processes can directly occur only through chemisorption interaction between the adsorbed O 2 and high-energy {111} facet-exposed MgO with abundant surface oxygen vacancies (SOVs), hence producing singlet oxygen and superoxide anion radicals without light irradiation. These ROS were confirmed by electron paramagnetic resonance, in situ Raman, and scavenger experiments. Furthermore, heat plays a crucial role for the electron transfer process to accelerate the formation of ·O 2 - , which is verified by temperature kinetic experiments of nitro blue tetrazolium reduction in the dark. Therefore, the presence of oxygen vacancy can be considered as an intensification of the activation process. The designed MgO is acquired in one step via constructing a reduction atmosphere during the combustion reaction process, which has an ability similar to that of noble metal Pd to activate molecular oxygen and can be used as an effective bacteriocide in the dark.

Metastable Oxygen Production by Electron-Impact of Oxygen

NASA Astrophysics Data System (ADS)

Hein, J. D.; Malone, C. P.; Johnson, P. V.; Kanik, I.

2014-12-01

Electron-impact excitation processes involving atomic and molecular oxygen are important in atmospheric interactions. The production of long-lived metastable O(1S) and O(1D) through electron impact of oxygen-containing molecules plays a significant role in the dynamics of planetary atmospheres (Earth, Mars, Europa, Io, Enceladus) and cometary bodies (Hale-Bopp). The electron-impact excitation channels to O(1S) and O(1D) are important for determining energy partitioning and dynamics. To reliably model natural phenomena and interpret observational data, the accurate determination of underlying collision processes (cross sections, dissociation dynamics) through fundamental experimental studies is essential. The detection of metastable species in laboratory experiments requires a novel approach. Typical radiative de-excitation detection techniques cannot be performed due to the long-lived nature of excited species, and conventional particle detectors are insensitive to the low internal energies O(1S) and O(1D). We have recently constructed an apparatus to detect and characterize metastable oxygen production by electron impact using the "rare gas conversion technique." Recent results will be presented, including absolute excitation functions for target gases O2, CO, CO2, and N2O. This work was performed at the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with the National Aeronautics and Space Administration (NASA). Financial support through NASA's OPR, PATM, and MFRP programs, as well as the NASA Postdoctoral Program (NPP) are gratefully acknowledged.

Exposure of vitamins to UVB and UVA radiation generates singlet oxygen.

PubMed

Knak, Alena; Regensburger, Johannes; Maisch, Tim; Bäumler, Wolfgang

2014-05-01

Deleterious effects of UV radiation in tissue are usually attributed to different mechanisms. Absorption of UVB radiation in cell constituents like DNA causes photochemical reactions. Absorption of UVA radiation in endogenous photosensitizers like vitamins generates singlet oxygen via photosensitized reactions. We investigated two further mechanisms that might be involved in UV mediated cell tissue damage. Firstly, UVB radiation and vitamins also generate singlet oxygen. Secondly, UVB radiation may change the chemical structure of vitamins that may change the role of such endogenous photosensitizers in UVA mediated mechanisms. Vitamins were irradiated in solution using monochromatic UVB (308 nm) or UVA (330, 355, or 370 nm) radiation. Singlet oxygen was directly detected and quantified by its luminescence at 1270 nm. All investigated molecules generated singlet oxygen with a quantum yield ranging from 0.007 (vitamin D3) to 0.64 (nicotinamide) independent of the excitation wavelength. Moreover, pre-irradiation of vitamins with UVB changed their absorption in the UVB and UVA spectral range. Subsequently, molecules such as vitamin E and vitamin K1, which normally exhibit no singlet oxygen generation in the UVA, now produce singlet oxygen when exposed to UVA at 355 nm. This interplay of different UV sources is inevitable when applying serial or parallel irradiation with UVA and UVB in experiments in vitro. These results should be of particular importance for parallel irradiation with UVA and UVB in vivo, e.g. when exposing the skin to solar radiation.

Approaching the evolutionary advantage of ancillary types of haemoglobin in Daphnia magna by simulation of oxygen supply.

PubMed

Moenickes, S; Richter, O; Pirow, R

2010-02-01

The planktonic crustacean Daphnia magna synthesizes haemoglobin (Hb) macromolecules of variant subunit composition and oxygen affinity. This is one of the strategies by which the animals cope with variations in environmental conditions such as ambient oxygen tension. The enrichment of high-affinity Hb molecules in the haemolymph of hypoxia-exposed animals is thought to reduce Hb synthesis costs due to an enhanced transport efficiency of these molecules in comparison to the low-affinity Hb molecules. How great this economic advantage is, and under which conditions this benefit disappears, is still not fully understood. Here we implemented a rigorously simplified model of the daphnid body and described the transport of oxygen from the environment via the haemolymph to the tissues in terms of the convection-diffusion-reaction equation. The model was validated by comparing various model predictions with experimental data. A sensitivity analysis was used to evaluate the influence of parameter uncertainties on the model predictions. Cost-benefit analysis revealed in which way at the system's level the increase in Hb oxygen affinity improves the oxygen loading at the respiratory surfaces and impairs the release of oxygen to the tissues. The benefit arising from the improved oxygen loading exceeds the disadvantage of impaired unloading only under conditions where the ambient oxygen tension is critically low and the Hb concentration is high. The low-affinity Hb, on the other hand, provides an advantage given that the Hb concentration is low and the ambient oxygen tension is well above the critical level. Computer-aided modelling and simulation therefore provide valuable mechanistic insights into the driving forces that could have shaped the evolution of globin genes in daphnids.

Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging

PubMed Central

Xiong, Hanqing; Zhou, Zhenqiao; Zhu, Mingqiang; Lv, Xiaohua; Li, Anan; Li, Shiwei; Li, Longhui; Yang, Tao; Wang, Siming; Yang, Zhongqin; Xu, Tonghui; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

2014-01-01

Resin embedding is a well-established technique to prepare biological specimens for microscopic imaging. However, it is not compatible with modern green-fluorescent protein (GFP) fluorescent-labelling technique because it significantly quenches the fluorescence of GFP and its variants. Previous empirical optimization efforts are good for thin tissue but not successful on macroscopic tissue blocks as the quenching mechanism remains uncertain. Here we show most of the quenched GFP molecules are structurally preserved and not denatured after routine embedding in resin, and can be chemically reactivated to a fluorescent state by alkaline buffer during imaging. We observe up to 98% preservation in yellow-fluorescent protein case, and improve the fluorescence intensity 11.8-fold compared with unprocessed samples. We demonstrate fluorescence microimaging of resin-embedded EGFP/EYFP-labelled tissue block without noticeable loss of labelled structures. This work provides a turning point for the imaging of fluorescent protein-labelled specimens after resin embedding. PMID:24886825

Correlative Single-Molecule Localization Microscopy and Confocal Microscopy.

PubMed

Soeller, Christian; Hou, Yufeng; Jayasinghe, Isuru D; Baddeley, David; Crossman, David

2017-01-01

Single-molecule localization microscopy allows the ability to image fluorescence labeled molecular targets at nanoscale resolution. However, for many biological questions the ability to provide tissue and cellular context in addition to these high resolution data is eminently informative. Here, we describe a procedure to achieve this aim by correlatively imaging human cardiac tissue first at the nanoscale with direct stochastic optical reconstruction microscopy (dSTORM) and then at the diffraction limit with conventional confocal microscopy.

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones

PubMed Central

Kalvelage, Tim; Lavik, Gaute; Jensen, Marlene M.; Revsbech, Niels Peter; Löscher, Carolin; Schunck, Harald; Desai, Dhwani K.; Hauss, Helena; Kiko, Rainer; Holtappels, Moritz; LaRoche, Julie; Schmitz, Ruth A.; Graco, Michelle I.; Kuypers, Marcel M. M.

2015-01-01

Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein. PMID:26192623

Singlet oxygen generation by cyclometalated complexes and applications.

PubMed

Ashen-Garry, David; Selke, Matthias

2014-01-01

While cyclometalated complexes have been extensively studied for optoelectronic applications, these compounds also represent a relatively new class of photosensitizers for the production of singlet oxygen. Thus far, singlet oxygen generation from cyclometalated Ir and Pt complexes has been studied in detail. In this review, photophysical data for singlet oxygen generation from these complexes are presented, and the mechanism of (1) O2 generation is discussed, including evidence for singlet oxygen generation via an electron-transfer mechanism for some of cyclometalated Ir complexes. The period from the first report of singlet oxygen generation by a cyclometalated Ir complex in 2002 through August 2013 is covered in this review. This new class of singlet oxygen photosensitizers may prove to be rather versatile due to the ease of substitution of ancillary ligands without loss of activity. Several cyclometalated complexes have been tethered to zeolites, polystyrene, or quantum dots. Applications for photooxygenation of organic molecules, including "traditional" singlet oxygen reactions (ene reaction, [4 + 2] and [2 + 2] cycloadditions) as well as oxidative coupling of amines are presented. Potential biomedical applications are also reviewed. © 2013 The American Society of Photobiology.

Novel image processing method study for a label-free optical biosensor

NASA Astrophysics Data System (ADS)

Yang, Chenhao; Wei, Li'an; Yang, Rusong; Feng, Ying

2015-10-01

Optical biosensor is generally divided into labeled type and label-free type, the former mainly contains fluorescence labeled method and radioactive-labeled method, while fluorescence-labeled method is more mature in the application. The mainly image processing methods of fluorescent-labeled biosensor includes smooth filtering, artificial gridding and constant thresholding. Since some fluorescent molecules may influence the biological reaction, label-free methods have been the main developing direction of optical biosensors nowadays. The using of wider field of view and larger angle of incidence light path which could effectively improve the sensitivity of the label-free biosensor also brought more difficulties in image processing, comparing with the fluorescent-labeled biosensor. Otsu's method is widely applied in machine vision, etc, which choose the threshold to minimize the intraclass variance of the thresholded black and white pixels. It's capacity-constrained with the asymmetrical distribution of images as a global threshold segmentation. In order to solve the irregularity of light intensity on the transducer, we improved the algorithm. In this paper, we present a new image processing algorithm based on a reflectance modulation biosensor platform, which mainly comprises the design of sliding normalization algorithm for image rectification and utilizing the improved otsu's method for image segmentation, in order to implement automatic recognition of target areas. Finally we used adaptive gridding method extracting the target parameters for analysis. Those methods could improve the efficiency of image processing, reduce human intervention, enhance the reliability of experiments and laid the foundation for the realization of high throughput of label-free optical biosensors.

Detailed analysis of complex single molecule FRET data with the software MASH

NASA Astrophysics Data System (ADS)

Hadzic, Mélodie C. A. S.; Kowerko, Danny; Börner, Richard; Zelger-Paulus, Susann; Sigel, Roland K. O.

2016-04-01

The processing and analysis of surface-immobilized single molecule FRET (Förster resonance energy transfer) data follows systematic steps (e.g. single molecule localization, clearance of different sources of noise, selection of the conformational and kinetic model, etc.) that require a solid knowledge in optics, photophysics, signal processing and statistics. The present proceeding aims at standardizing and facilitating procedures for single molecule detection by guiding the reader through an optimization protocol for a particular experimental data set. Relevant features were determined from single molecule movies (SMM) imaging Cy3- and Cy5-labeled Sc.ai5γ group II intron molecules synthetically recreated, to test the performances of four different detection algorithms. Up to 120 different parameterizations per method were routinely evaluated to finally establish an optimum detection procedure. The present protocol is adaptable to any movie displaying surface-immobilized molecules, and can be easily reproduced with our home-written software MASH (multifunctional analysis software for heterogeneous data) and script routines (both available in the download section of www.chem.uzh.ch/rna).

Rapid protein concentration, efficient fluorescence labeling and purification on a micro/nanofluidics chip.

PubMed

Wang, Chen; Ouyang, Jun; Ye, De-Kai; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua

2012-08-07

Fluorescence analysis has proved to be a powerful detection technique for achieving single molecule analysis. However, it usually requires the labeling of targets with bright fluorescent tags since most chemicals and biomolecules lack fluorescence. Conventional fluorescence labeling methods require a considerable quantity of biomolecule samples, long reaction times and extensive chromatographic purification procedures. Herein, a micro/nanofluidics device integrating a nanochannel in a microfluidics chip has been designed and fabricated, which achieves rapid protein concentration, fluorescence labeling, and efficient purification of product in a miniaturized and continuous manner. As a demonstration, labeling of the proteins bovine serum albumin (BSA) and IgG with fluorescein isothiocyanate (FITC) is presented. Compared to conventional methods, the present micro/nanofluidics device performs about 10(4)-10(6) times faster BSA labeling with 1.6 times higher yields due to the efficient nanoconfinement effect, improved mass, and heat transfer in the chip device. The results demonstrate that the present micro/nanofluidics device promises rapid and facile fluorescence labeling of small amount of reagents such as proteins, nucleic acids and other biomolecules with high efficiency.

Nitric oxide is a versatile sensor of low oxygen stress in plants

PubMed Central

Borisjuk, Ljudmilla

2008-01-01

The plant response to low levels of oxygen involves an interplay of transcriptional, translational and post-translational signaling. However, in plants, the sensing mechanism itself remains obscure. The role of nitric oxide (NO) in oxygen sensing and balancing has been extensively explored in our laboratory. We suggest that NO is generated within the mitochondria from nitrite in response to hypoxia, and that this small gaseous molecule can reversibly modify both the respiratory oxygen consumption and the oxygen availability within the seed. We further propose that hemoglobins play a central role in the detoxification of excess NO. PMID:19704575

Thermochemical Modeling of Nonequilibrium Oxygen Flows

NASA Astrophysics Data System (ADS)

Neitzel, Kevin Joseph

The development of hypersonic vehicles leans heavily on computational simulation due to the high enthalpy flow conditions that are expensive and technically challenging to replicate experimentally. The accuracy of the nonequilibrium modeling in the computer simulations dictates the design margin that is required for the thermal protection system and flight dynamics. Previous hypersonic vehicles, such as Apollo and the Space Shuttle, were primarily concerned with re-entry TPS design. The strong flow conditions of re-entry, involving Mach numbers of 25, quickly dissociate the oxygen molecules in air. Sustained flight, hypersonic vehicles will be designed to operate in Mach number ranges of 5 to 10. The oxygen molecules will not quickly dissociate and will play an important role in the flow field behavior. The development of nonequilibrium models of oxygen is crucial for limiting modeling uncertainty. Thermochemical nonequilibrium modeling is investigated for oxygen flows. Specifically, the vibrational relaxation and dissociation behavior that dominate the nonequilibrium physics in this flight regime are studied in detail. The widely used two-temperature (2T) approach is compared to the higher fidelity and more computationally expensive state-to-state (STS) approach. This dissertation utilizes a wide range of rate sources, including newly available STS rates, to conduct a comprehensive study of modeling approaches for hypersonic nonequilibrium thermochemical modeling. Additionally, the physical accuracy of the computational methods are assessed by comparing the numerical results with available experimental data. The numerical results and experimental measurements present strong nonequilibrium, and even non-Boltzmann behavior in the vibrational energy mode for the sustained hypersonic flight regime. The STS approach is able to better capture the behavior observed in the experimental data, especially for stronger nonequilibrium conditions. Additionally, a reduced order

Disintegration of Carbon Dioxide Molecules in a Microwave Plasma Torch.

PubMed

Kwak, Hyoung S; Uhm, Han S; Hong, Yong C; Choi, Eun H

2015-12-17

A pure carbon dioxide torch is generated by making use of 2.45 GHz microwave. Carbon dioxide gas becomes the working gas and produces a stable carbon dioxide torch. The torch volume is almost linearly proportional to the microwave power. Temperature of the torch flame is measured by making use of optical spectroscopy and thermocouple. Two distinctive regions are exhibited, a bright, whitish region of high-temperature zone and a bluish, dimmer region of relatively low-temperature zone. Study of carbon dioxide disintegration and gas temperature effects on the molecular fraction characteristics in the carbon dioxide plasma of a microwave plasma torch under atmospheric pressure is carried out. An analytical investigation of carbon dioxide disintegration indicates that substantial fraction of carbon dioxide molecules disintegrate and form other compounds in the torch. For example, the normalized particle densities at center of plasma are given by nCO2/nN = 6.12 × 10(-3), nCO/nN = 0.13, nC/nN = 0.24, nO/nN = 0.61, nC2/nN = 8.32 × 10(-7), nO2/nN = 5.39 × 10(-5), where nCO2, nCO, nC, nO, nC2, and nO2 are carbon dioxide, carbon monoxide, carbon and oxygen atom, carbon and oxygen molecule densities, respectively. nN is the neutral particle density. Emission profiles of the oxygen and carbon atom radicals and the carbon monoxide molecules confirm the theoretical predictions of carbon dioxide disintegration in the torch.

Disintegration of Carbon Dioxide Molecules in a Microwave Plasma Torch

PubMed Central

Kwak, Hyoung S.; Uhm, Han S.; Hong, Yong C.; Choi, Eun H.

2015-01-01

A pure carbon dioxide torch is generated by making use of 2.45 GHz microwave. Carbon dioxide gas becomes the working gas and produces a stable carbon dioxide torch. The torch volume is almost linearly proportional to the microwave power. Temperature of the torch flame is measured by making use of optical spectroscopy and thermocouple. Two distinctive regions are exhibited, a bright, whitish region of high-temperature zone and a bluish, dimmer region of relatively low-temperature zone. Study of carbon dioxide disintegration and gas temperature effects on the molecular fraction characteristics in the carbon dioxide plasma of a microwave plasma torch under atmospheric pressure is carried out. An analytical investigation of carbon dioxide disintegration indicates that substantial fraction of carbon dioxide molecules disintegrate and form other compounds in the torch. For example, the normalized particle densities at center of plasma are given by nCO2/nN = 6.12 × 10−3, nCO/nN = 0.13, nC/nN = 0.24, nO/nN = 0.61, nC2/nN = 8.32 × 10−7, nO2/nN = 5.39 × 10−5, where nCO2, nCO, nC, nO, nC2, and nO2 are carbon dioxide, carbon monoxide, carbon and oxygen atom, carbon and oxygen molecule densities, respectively. nN is the neutral particle density. Emission profiles of the oxygen and carbon atom radicals and the carbon monoxide molecules confirm the theoretical predictions of carbon dioxide disintegration in the torch. PMID:26674957

Label-free optical resonant sensors for biochemical applications

NASA Astrophysics Data System (ADS)

Ciminelli, Caterina; Campanella, Clarissa Martina; Dell'Olio, Francesco; Campanella, Carlo Edoardo; Armenise, Mario Nicola

2013-03-01

For a number of years, the scientific community has been paying growing attention to the monitoring and enhancement of public health and the quality of life through the detection of all dangerous agents for the human body, including gases, proteins, virus, and bacterial agents. When these agents are detected through label-free biochemical sensors, the molecules are not modified structurally or functionally by adding fluorescent or radioactive dyes. This work focuses on label-free optical ring resonator-based configurations suited for bio-chemical sensing, highlighting their physical aspects and specific applications. Resonant wavelength shift and the modal splitting occurring when the analyte interacts with microresonant structures are the two major physical aspects analyzed in this paper. Competitive optical platforms proposed in the literature are also illustrated together with their properties and performance.

Oxygen K edge scattering from bulk comb diblock copolymer reveals extended, ordered backbones above lamellar order-disorder transition

DOE PAGES

Kortright, Jeffrey Barrett; Sun, Jing; Spencer, Ryan K.; ...

2016-12-14

The evolution of molecular morphology in bulk samples of comb diblock copolymer pNdc 12-b-pNte 21 across the lamellar order-disorder transition (ODT) is studied using resonant x-ray scattering at the oxygen K edge, with the goal of determining whether the molecules remain extended or collapse above the ODT. The distinct spectral resonances of carbonyl oxygen on the backbone and ether oxygen in the pNte side chains combine with their different site symmetry within the molecule to yield strong differences in bulk structural sensitivity at all temperatures. Comparison with simple models for the disordered phase clearly reveals that disordering at the ODTmore » corresponds to loss of positional order of molecules with extended backbones that retain orientational order, rather than backbone collapse into a locally isotropic disordered phase. This conclusion is facilitated directly by the distinct structural sensitivity at the two resonances. Lastly, we discuss the roles of depolarized scattering in enhancing this sensitivity, and background fluorescence in limiting dynamic range, in oxygen resonant scattering.« less

Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation.

PubMed

Zhang, Hui; Guo, Peixuan

2014-05-15

Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described. Copyright © 2014 Elsevier Inc. All rights reserved.

Oxygen detection using the laser diode absorption technique

NASA Technical Reports Server (NTRS)

Disimile, P. J.; Fox, C. W.

1991-01-01

Accurate measurement of the concentration and flow rate of gaseous oxygen is becoming of greater importance. The detection technique presented is based on the principal of light absorption by the Oxygen A-Band. Oxygen molecules have characteristics which attenuate radiation in the 759-770 nm wavelength range. With an ability to measure changes in the relative light transmission to less than 0.01 percent, a sensitive optical gas detection system was configured. This system is smaller in size and light in weight, has low energy requirements and has a rapid response time. In this research program, the application of temperature tuning laser diodes and their ability to be wavelength shifted to a selected absorption spectral peak has allowed concentrations as low as 1300 ppm to be detected.

[Relationship among the Oxygen Concentration, Reactive Oxygen Species and the Biological Characteristics of Mouse Bone Marrow Hematopoietic Stem Cells].

PubMed

Ren, Si-Hua; He, Yu-Xin; Ma, Yi-Ran; Jin, Jing-Chun; Kang, Dan

2016-02-01

To investigate the effects of oxygen concentration and reactive oxygen species (ROS) on the biological characteristics of hematopoietic stem cells (HSC) and to analyzed the relationship among the oxygen concentration, ROS and the biological characteristics of mouse HSC through simulation of oxygen environment experienced by PB HSC during transplantation. The detection of reactive oxygen species (ROS), in vitro amplification, directional differentiation (BFU-E, CFU-GM, CFU-Mix), homing of adhesion molecules (CXCR4, CD44, VLA4, VLA5, P-selectin), migration rate, CFU-S of NOD/SCID mice irradiated with sublethal dose were performed to study the effect of oxgen concentration and reactive oxygen species on the biological characteristics of mouse BM-HSC and the relationship among them. The oxygen concentrations lower than normal oxygen concentration (especially hypoxic oxygen environment) could reduce ROS level and amplify more Lin(-) c-kit(+) Sca-1(+) BM HSC, which was more helpful to the growth of various colonies (BFU-E, CFU-GM, CFU-Mix) and to maintain the migratory ability of HSC, thus promoting CFU-S growth significantly after the transplantation of HSC in NOD/SCID mice irradiated by a sublethal dose. BM HSC exposed to oxygen environments of normal, inconstant oxygen level and strenuously thanging of oxygen concentration could result in higher level of ROS, at the same time, the above-mentioned features and functional indicators were relatively lower. The ROS levels of BM HSC in PB HSCT are closely related to the concentrations and stability of oxygen surrounding the cells. High oxygen concentration results in an high level of ROS, which is not helpful to maintain the biological characteristics of BM HSC. Before transplantation and in vitro amplification, the application of antioxidancs and constant oxygen level environments may be beneficial for transplantation of BMMSC.

On the Several Molecules and Nanostructures of Water

PubMed Central

Whitney, Cynthia Kolb

2012-01-01

This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion. PMID:22312305

On the several molecules and nanostructures of water.

PubMed

Whitney, Cynthia Kolb

2012-01-01

This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called 'Algebraic Chemistry'. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown's gas, and cold fusion.

A wearable conformal bandage for non-invasive two-dimensional imaging of skin oxygenation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Li, Zongxi; Roussakis, Emmanuel; Keeley, Emily; Apiou-Sbirlea, Gabriela; Birngruber, Reginald; Huang, Christene; Evans, Conor L.

2016-03-01

The complex surface topology and soft mechanics of the skin poses a considerable challenge to the development of wearable, conformal sensors. As a results, current clinical assessments of healing-related skin parameters often rely on bulky and expensive optical systems that are difficult to deploy at the point of care. Here, using a rapid-drying, liquid bandage containing oxygen-sensing molecules, we created a wearable sensor bandage that conforms the surface geometry of skin and wounds, and provides two-dimensional maps of cutaneous oxygenation in a non-disruptive fashion. Custom oxygen sensing phosphors have been developed in house that are at least five times brighter than the commercial sensing molecules, enabling the visualization of oxygen concentration using a simple color camera or even by eye under ambient lighting conditions. The oxygen-sensing bandage has been applied to monitor tissue ischemia, graft integration, as well as the progression of burn in animal models. Recent studies have demonstrated its ability to track and quantify skin inflammation induced by complete Freund's adjuvant in an in vivo porcine model.

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast*

PubMed Central

Burr, Risa; Stewart, Emerson V.; Shao, Wei; Zhao, Shan; Hannibal-Bach, Hans Kristian; Ejsing, Christer S.; Espenshade, Peter J.

2016-01-01

Eukaryotic lipid synthesis is oxygen-dependent with cholesterol synthesis requiring 11 oxygen molecules and fatty acid desaturation requiring 1 oxygen molecule per double bond. Accordingly, organisms evaluate oxygen availability to control lipid homeostasis. The sterol regulatory element-binding protein (SREBP) transcription factors regulate lipid homeostasis. In mammals, SREBP-2 controls cholesterol biosynthesis, whereas SREBP-1 controls triacylglycerol and glycerophospholipid biosynthesis. In the fission yeast Schizosaccharomyces pombe, the SREBP-2 homolog Sre1 regulates sterol homeostasis in response to changing sterol and oxygen levels. However, notably missing is an SREBP-1 analog that regulates triacylglycerol and glycerophospholipid homeostasis in response to low oxygen. Consistent with this, studies have shown that the Sre1 transcription factor regulates only a fraction of all genes up-regulated under low oxygen. To identify new regulators of low oxygen adaptation, we screened the S. pombe nonessential haploid deletion collection and identified 27 gene deletions sensitive to both low oxygen and cobalt chloride, a hypoxia mimetic. One of these genes, mga2, is a putative transcriptional activator. In the absence of mga2, fission yeast exhibited growth defects under both normoxia and low oxygen conditions. Mga2 transcriptional targets were enriched for lipid metabolism genes, and mga2Δ cells showed disrupted triacylglycerol and glycerophospholipid homeostasis, most notably with an increase in fatty acid saturation. Indeed, addition of exogenous oleic acid to mga2Δ cells rescued the observed growth defects. Together, these results establish Mga2 as a transcriptional regulator of triacylglycerol and glycerophospholipid homeostasis in S. pombe, analogous to mammalian SREBP-1. PMID:27053105

Aluminum nanostructures with strong visible-range SERS activity for versatile micropatterning of molecular security labels.

PubMed

Lay, Chee Leng; Koh, Charlynn Sher Lin; Wang, Jing; Lee, Yih Hong; Jiang, Ruibin; Yang, Yijie; Yang, Zhe; Phang, In Yee; Ling, Xing Yi

2018-01-03

The application of aluminum (Al)-based nanostructures for visible-range plasmonics, especially for surface-enhanced Raman scattering (SERS), currently suffers from inconsistent local electromagnetic field distributions and/or inhomogeneous distribution of probe molecules. Herein, we lithographically fabricate structurally uniform Al nanostructures which enable homogeneous adsorption of various probe molecules. Individual Al nanostructures exhibit strong local electromagnetic field enhancements, in turn leading to intense SERS activity. The average SERS enhancement factor (EF) for individual nanostructures exceeds 10 4 for non-resonant probe molecules in the visible spectrum. These Al nanostructures also retain more than 70% of their original SERS intensities after one-month storage, displaying superb stability under ambient conditions. We further achieve tunable polarization-dependent SERS responses using anisotropic Al nanostructures, facilitating the design of sophisticated SERS-based security labels. Our micron-sized security label comprises two-tier security features, including a machine-readable hybrid quick-response (QR) code overlaid with a set of ciphertexts. Our work demonstrates the versatility of Al-based structures in low-cost modern chemical nano-analytics and forgery protection.

Diffusive shunting of gases and other molecules in the renal vasculature: physiological and evolutionary significance.

PubMed

Ngo, Jennifer P; Ow, Connie P C; Gardiner, Bruce S; Kar, Saptarshi; Pearson, James T; Smith, David W; Evans, Roger G

2016-11-01

Countercurrent systems have evolved in a variety of biological systems that allow transfer of heat, gases, and solutes. For example, in the renal medulla, the countercurrent arrangement of vascular and tubular elements facilitates the trapping of urea and other solutes in the inner medulla, which in turn enables the formation of concentrated urine. Arteries and veins in the cortex are also arranged in a countercurrent fashion, as are descending and ascending vasa recta in the medulla. For countercurrent diffusion to occur, barriers to diffusion must be small. This appears to be characteristic of larger vessels in the renal cortex. There must also be gradients in the concentration of molecules between afferent and efferent vessels, with the transport of molecules possible in either direction. Such gradients exist for oxygen in both the cortex and medulla, but there is little evidence that large gradients exist for other molecules such as carbon dioxide, nitric oxide, superoxide, hydrogen sulfide, and ammonia. There is some experimental evidence for arterial-to-venous (AV) oxygen shunting. Mathematical models also provide evidence for oxygen shunting in both the cortex and medulla. However, the quantitative significance of AV oxygen shunting remains a matter of controversy. Thus, whereas the countercurrent arrangement of vasa recta in the medulla appears to have evolved as a consequence of the evolution of Henle's loop, the evolutionary significance of the intimate countercurrent arrangement of blood vessels in the renal cortex remains an enigma. Copyright © 2016 the American Physiological Society.

Correction for intravascular activity in the oxygen-15 steady-state technique is independent of the regional hematocrit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lammertsma, A.A.; Baron, J.C.; Jones, T.

1987-06-01

The oxygen-15 steady-state technique to measure the regional cerebral metabolic rate for oxygen requires a correction for the nonextracted intravascular molecular oxygen-15. To perform this correction, an additional procedure is carried out using RBCs labeled with /sup 11/CO or C/sup 15/O. The previously reported correction method, however, required knowledge of the regional cerebral to large vessel hematocrit ratio. A closer examination of the underlying model eliminated this ratio. Both molecular oxygen and carbon monoxide are carried by RBCs and are therefore similarly affected by a change in hematocrit.

Lessons from single-cell transcriptome analysis of oxygen-sensing cells.

PubMed

Zhou, Ting; Matsunami, Hiroaki

2018-05-01

The advent of single-cell RNA-sequencing (RNA-Seq) technology has enabled transcriptome profiling of individual cells. Comprehensive gene expression analysis at the single-cell level has proven to be effective in characterizing the most fundamental aspects of cellular function and identity. This unbiased approach is revolutionary for small and/or heterogeneous tissues like oxygen-sensing cells in identifying key molecules. Here, we review the major methods of current single-cell RNA-Seq technology. We discuss how this technology has advanced the understanding of oxygen-sensing glomus cells in the carotid body and helped uncover novel oxygen-sensing cells and mechanisms in the mice olfactory system. We conclude by providing our perspective on future single-cell RNA-Seq research directed at oxygen-sensing cells.

Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

Fluorine-18 labeled tracers for PET studies in the neurosciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Yu-Shin; Fowler, J.S.

This chapter focuses on fluorine-18, the positron emitter with the longest half-life, the lowest positron energy and probably, the most challenging chemistry. The incorporation of F-18 into organic compounds presents many challenges, including: the need to synthesize and purify the compound within a 2--3 hour time frame; the limited number of labeled precursor molecules; the need to work on a microscale; and the need to produce radiotracers which are chemically and radiochemically pure, sterile and pyrogen-free, and suitable for intravenous injection. The PET method and F-18 labeling of organic molecules are described followed by highlights of the applications of F-18more » labeled compounds in the neurosciences and neuropharmacology. It is important to emphasize the essential and pivotal role that organic synthesis has played in the progression of the PET field over the past twenty years from one in which only a handful of institutions possessed the instrumentation and staff to carry out research to the present-day situation where there are more than 200 PET centers worldwide. During this period PET has become an important scientific tool in the neurosciences, cardiology and oncology. It is important to point out that PET is by no means a mature field. The fact that a hundreds of different F-18 labeled compounds have been developed but only a few possess the necessary selectivity and sensitivity in vivo to track a specific biochemical process illustrates this and underscores a major difficulty in radiotracer development, namely the selection of priority structures for synthesis and the complexities of the interactions between chemical compounds and living systems. New developments in rapid organic synthesis are needed in order to investigate new molecular targets and to improve the quantitative nature of PET experiments.« less

Interaction of Spin-Labeled Lipid Membranes with Transition Metal Ions

PubMed Central

2015-01-01

The large values of spin relaxation enhancement (RE) for PC spin-labels in the phospholipid membrane induced by paramagnetic metal salts dissolved in the aqueous phase can be explained by Heisenberg spin exchange due to conformational fluctuations of the nitroxide group as a result of membrane fluidity, flexibility of lipid chains, and, possibly, amphiphilic nature of the nitroxide label. Whether the magnetic interaction occurs predominantly via Heisenberg spin exchange (Ni) or by the dipole–dipole (Gd) mechanism, it is essential for the paramagnetic ion to get into close proximity to the nitroxide moiety for efficient RE. For different salts of Ni the RE in phosphatidylcholine membranes follows the anionic Hofmeister series and reflects anion adsorption followed by anion-driven attraction of paramagnetic cations on the choline groups. This adsorption is higher for chaotropic ions, e.g., perchlorate. (A chaotropic agent is a molecule in water solution that can disrupt the hydrogen bonding network between water molecules.) However, there is no anionic dependence of RE for model membranes made from negatively charged lipids devoid of choline groups. We used Ni-induced RE to study the thermodynamics and electrostatics of ion/membrane interactions. We also studied the effect of membrane composition and the phase state on the RE values. In membranes with cholesterol a significant difference is observed between PC labels with nitroxide tethers long enough vs not long enough to reach deep into the membrane hydrophobic core behind the area of fused cholesterol rings. This study indicates one must be cautious in interpreting data obtained by PC labels in fluid membranes in terms of probing membrane properties at different immersion depths when it can be affected by paramagnetic species at the membrane surface. PMID:26490692

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

The reduction and oxidation of ceria: A natural abundance triple oxygen isotope perspective

NASA Astrophysics Data System (ADS)

Hayles, Justin; Bao, Huiming

2015-06-01

Ceria (CeO2) is a heavily studied material in catalytic chemistry for use as an oxygen storage medium, oxygen partial pressure regulator, fuel additive, and for the production of syngas, among other applications. Ceria powders are readily reduced and lose structural oxygen when subjected to low pO2 and/or high temperature conditions. Such dis-stoichiometric ceria can then re-oxidize under higher pO2 and/or lower temperature by incorporating new oxygen into the previously formed oxygen site vacancies. Despite extensive studies on ceria, the mechanisms for oxygen adsorption-desorption, dissociation-association, and diffusion of oxygen species on ceria surface and within the crystal structure are not well known. We predict that a large kinetic oxygen isotope effect should accompany the release and incorporation of ceria oxygen. As the first attempt to determine the existence and the degree of the isotope effect, this study focuses on a set of simple room-temperature re-oxidation experiments that are also relevant to a laboratory procedure using ceria to measure the triple oxygen isotope composition of CO2. Triple-oxygen-isotope labeled ceria powders are heated at 700 °C and cooled under vacuum prior to exposure to air. By combining results from independent experimental sets with different initial oxygen isotope labels and using a combined mass-balance and triangulation approach, we have determined the isotope fractionation factors for both high temperature reduction in vacuum (⩽10-4 mbar) and room temperature re-oxidation in air. Results indicate that there is a 1.5‰ ± 0.8‰ increase in the δ18O value of ceria after being heated in vacuum at 700 °C for 1 h. When the vacuum is broken at room temperature, the previously heated ceria incorporates 3-19% of its final structural oxygen from air, with a δ18O value of 2.1-4.1+7.7 ‰ for the incorporated oxygen. The substantial incorporation of oxygen from air supports that oxygen mobility is high in vacancy

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: An optical boiler generating singlet oxygen O2 (a1Δg)

NASA Astrophysics Data System (ADS)

Lipatov, N. I.; Biryukov, A. S.; Gulyamova, E. S.

2008-12-01

An ecologically perfect generator of singlet oxygen O2 (a1Δg) is proposed which fundamentally differs from existing singlet-oxygen generators. Excited O2 (a1Δg) molecules are generated due to interaction of the O2 (X3Σ-g) molecules with a quasi-monochromatic field, which is supplied from an external source to a closed volume — an optical boiler containing oxygen. It is shown that, by pumping continuously the optical boiler by the light field of power ~3×105 W, it is possible to accumulate up to 40% of singlet oxygen (O2(b1Σ+g)) + (O2 (a1Δg)) in the boiler volume during ~10-2 s.

Horseradish peroxidase-labeled oligonucleotides and fluorescent tyramides for rapid detection of chromosome-specific repeat sequences.

PubMed

van Gijlswijk, R P; Wiegant, J; Vervenne, R; Lasan, R; Tanke, H J; Raap, A K

1996-01-01

We present a sensitive and rapid fluorescence in situ hybridization (FISH) strategy for detecting chromosome-specific repeat sequences. It uses horseradish peroxidase (HRP)-labeled oligonucleotide sequences in combination with fluorescent tyramide-based detection. After in situ hybridization, the HRP conjugated to the oligonucleotide probe is used to deposit fluorescently labeled tyramide molecules at the site of hybridization. The method features full chemical synthesis of probes, strong FISH signals, and short processing periods, as well as multicolor capabilities.

Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler.

PubMed

Zhu, Peizhi; Clamme, Jean-Pierre; Deniz, Ashok A

2005-11-01

A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10-30 A range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules.

Fluorescence Quenching by TEMPO: A Sub-30 Å Single-Molecule Ruler

PubMed Central

Zhu, Peizhi; Clamme, Jean-Pierre; Deniz, Ashok A.

2005-01-01

A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10–30 Å range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules. PMID:16199509

Method for preparing radionuclide-labeled chelating agent-ligand complexes

DOEpatents

Meares, Claude F.; Li, Min; DeNardo, Sally J.

1999-01-01

Radionuclide-labeled chelating agent-ligand complexes that are useful in medical diagnosis or therapy are prepared by reacting a radionuclide, such as .sup.90 Y or .sup.111 In, with a polyfunctional chelating agent to form a radionuclide chelate that is electrically neutral; purifying the chelate by anion exchange chromatography; and reacting the purified chelate with a targeting molecule, such as a monoclonal antibody, to form the complex.

Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments

PubMed Central

2017-01-01

Caged organic fluorophores are established tools for localization-based super-resolution imaging. Their use relies on reversible deactivation of standard organic fluorophores by chemical reduction or commercially available caged dyes with ON switching of the fluorescent signal by ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores and caged rhodamine dyes, i.e., chemical deactivation of fluorescence, for single-molecule Förster resonance energy transfer (smFRET) experiments with freely diffusing molecules. They allow temporal separation and sorting of multiple intramolecular donor–acceptor pairs during solution-based smFRET. We use this “caged FRET” methodology for the study of complex biochemical species such as multisubunit proteins or nucleic acids containing more than two fluorescent labels. Proof-of-principle experiments and a characterization of the uncaging process in the confocal volume are presented. These reveal that chemical caging and UV reactivation allow temporal uncoupling of convoluted fluorescence signals from, e.g., multiple spectrally similar donor or acceptor molecules on nucleic acids. We also use caging without UV reactivation to remove unwanted overlabeled species in experiments with the homotrimeric membrane transporter BetP. We finally outline further possible applications of the caged FRET methodology, such as the study of weak biochemical interactions, which are otherwise impossible with diffusion-based smFRET techniques because of the required low concentrations of fluorescently labeled biomolecules. PMID:28362086

Trace fluorescent labeling for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pusey, Marc, E-mail: marc.pusey@ixpressgenes.com; Barcena, Jorge; Morris, Michelle

2015-06-27

The presence of a covalently bound fluorescent probe at a concentration of <0.5% does not affect the outcome of macromolecule crystallization screening experiments. Additionally, the fluorescence can be used to determine new, not immediately apparent, lead crystallization conditions. Fluorescence can be a powerful tool to aid in the crystallization of proteins. In the trace-labeling approach, the protein is covalently derivatized with a high-quantum-yield visible-wavelength fluorescent probe. The final probe concentration typically labels ≤0.20% of the protein molecules, which has been shown to not affect the crystal nucleation or diffraction quality. The labeled protein is then used in a plate-screening experimentmore » in the usual manner. As the most densely packed state of the protein is the crystalline form, then crystals show as the brightest objects in the well under fluorescent illumination. A study has been carried out on the effects of trace fluorescent labeling on the screening results obtained compared with nonlabeled protein, and it was found that considering the stochastic nature of the crystal nucleation process the presence of the probe did not affect the outcomes obtained. Other effects are realised when using fluorescence. Crystals are clearly seen even when buried in precipitate. This approach also finds ‘hidden’ leads, in the form of bright spots, with ∼30% of the leads found being optimized to crystals in a single-pass optimization trial. The use of visible fluorescence also enables the selection of colors that bypass interfering substances, and the screening materials do not have to be UV-transparent.« less

An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore.

PubMed

Liu, Jiaquan; Hanne, Jeungphill; Britton, Brooke M; Shoffner, Matthew; Albers, Aaron E; Bennett, Jared; Zatezalo, Rachel; Barfield, Robyn; Rabuka, David; Lee, Jong-Bong; Fishel, Richard

2015-11-19

Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.

Reactive oxygen species generation and signaling in plants

PubMed Central

Tripathy, Baishnab Charan; Oelmüller, Ralf

2012-01-01

The introduction of molecular oxygen into the atmosphere was accompanied by the generation of reactive oxygen species (ROS) as side products of many biochemical reactions. ROS are permanently generated in plastids, peroxisomes, mitochiondria, the cytosol and the apoplast. Imbalance between ROS generation and safe detoxification generates oxidative stress and the accumulating ROS are harmful for the plants. On the other hand, specific ROS function as signaling molecules and activate signal transduction processes in response to various stresses. Here, we summarize the generation of ROS in the different cellular compartments and the signaling processes which are induced by ROS. PMID:23072988

Ovalbumin labeling with p-hydroxymercurybenzoate: The effect of different denaturing agents and the kinetics of reaction.

PubMed

Campanella, Beatrice; Onor, Massimo; Biancalana, Lorenzo; D'Ulivo, Alessandro; Bramanti, Emilia

2015-08-15

The aim of our study was to investigate how denaturing agents commonly used in protein analysis influence the labeling between a reactive molecule and proteins. For this reason, we investigated the labeling of ovalbumin (OVA) as a globular model protein with p-hydroxymercurybenzoate (pHMB) in its native state (phosphate buffer solution) and in different denaturing conditions (8 molL(-1) urea, 3 molL(-1) guanidinium thiocyanate, 6 molL(-1) guanidinium chloride, 0.2% sodium dodecyl sulfate, and 20% methanol). In addition to chemical denaturation, thermal denaturation was also tested. The protein was pre-column simultaneously denatured and derivatized, and the pHMB-labeled denatured OVA complexes were analyzed by size exclusion chromatography (SEC) coupled online with chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS). The number of -SH groups titrated greatly depends on the protein structure in solution. Indeed, we found that, depending on the adopted denaturing conditions, OVA gave different aggregate species that influence the complexation process. The results were compared with those obtained by a common alternative procedure for the titration of -SH groups that employs monobromobimane (mBBr) as tagging molecule and molecular fluorescence spectroscopy as detection technique. We also investigated the labeling kinetics for denatured OVA and pHMB, finding that the 4 thiolic groups of OVA have a very different reactivity toward mercury labeling, in agreement with previous studies. Copyright © 2015 Elsevier Inc. All rights reserved.

EPR oxygen imaging and hyperpolarized 13C MRI of pyruvate metabolism as noninvasive biomarkers of tumor treatment response to a glycolysis inhibitor 3-bromopyruvate.

PubMed

Matsumoto, Shingo; Saito, Keita; Yasui, Hironobu; Morris, H Douglas; Munasinghe, Jeeva P; Lizak, Martin; Merkle, Hellmut; Ardenkjaer-Larsen, Jan Henrik; Choudhuri, Rajani; Devasahayam, Nallathamby; Subramanian, Sankaran; Koretsky, Alan P; Mitchell, James B; Krishna, Murali C

2013-05-01

The hypoxic nature of tumors results in treatment resistance and poor prognosis. To spare limited oxygen for more crucial pathways, hypoxic cancerous cells suppress mitochondrial oxidative phosphorylation and promote glycolysis for energy production. Thereby, inhibition of glycolysis has the potential to overcome treatment resistance of hypoxic tumors. Here, EPR imaging was used to evaluate oxygen dependent efficacy on hypoxia-sensitive drug. The small molecule 3-bromopyruvate blocks glycolysis pathway by inhibiting hypoxia inducible enzymes and enhanced cytotoxicity of 3-bromopyruvate under hypoxic conditions has been reported in vitro. However, the efficacy of 3-bromopyruvate was substantially attenuated in hypoxic tumor regions (pO2<10 mmHg) in vivo using squamous cell carcinoma (SCCVII)-bearing mouse model. Metabolic MRI studies using hyperpolarized 13C-labeled pyruvate showed that monocarboxylate transporter-1 is the major transporter for pyruvate and the analog 3-bromopyruvate in SCCVII tumor. The discrepant results between in vitro and in vivo data were attributed to biphasic oxygen dependent expression of monocarboxylate transporter-1 in vivo. Expression of monocarboxylate transporter-1 was enhanced in moderately hypoxic (8-15 mmHg) tumor regions but down regulated in severely hypoxic (<5 mmHg) tumor regions. These results emphasize the importance of noninvasive imaging biomarkers to confirm the action of hypoxia-activated drugs. Copyright © 2012 Wiley Periodicals, Inc.

Towards monitoring conformational changes of the GPCR neurotensin receptor 1 by single-molecule FRET

NASA Astrophysics Data System (ADS)

Heitkamp, Thomas; Grisshammer, Reinhard; Börsch, Michael

2018-02-01

Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular side to NTSR1 and induces conformational changes that trigger intracellular signaling processes. Our goal is to monitor the conformational dynamics of single fluorescently labeled NTSR1. For this, we fused the fluorescent protein mNeonGreen to the C terminus of NTSR1, purified the receptor fusion protein from E. coli membranes, and reconstituted NTSR1 into liposomes with E. coli polar lipids. Using single-molecule anisotropy measurements, NTSR1 was found to be monomeric in liposomes, with a small fraction being dimeric and oligomeric, showing homoFRET. Similar results were obtained for NTSR1 in detergent solution. Furthermore, we demonstrated agonist binding to NTSR1 by time-resolved single-molecule Förster resonance energy transfer (smFRET), using neurotensin labeled with the fluorophore ATTO594.

In vivo biotinylation and incorporation of a photo-inducible unnatural amino acid to an antibody-binding domain improve site-specific labeling of antibodies.

PubMed

Kanje, Sara; Hober, Sophia

2015-04-01

Antibodies are important molecules in many research fields, where they play a key role in various assays. Antibody labeling is therefore of great importance. Currently, most labeling techniques take advantage of certain amino acid side chains that commonly appear throughout proteins. This makes it hard to control the position and exact degree of labeling of each antibody. Hence, labeling of the antibody may affect the antibody-binding site. This paper presents a novel protein domain based on the IgG-binding domain C2 of streptococcal protein G, containing the unnatural amino acid BPA, that can cross-link other molecules. This novel domain can, with improved efficiency compared to previously reported similar domains, site-specifically cross-link to IgG at the Fc region. An efficient method for simultaneous in vivo incorporation of BPA and specific biotinylation in a flask cultivation of Escherichia coli is described. In comparison to a traditionally labeled antibody sample, the C2-labeled counterpart proved to have a higher proportion of functional antibodies when immobilized on a solid surface and the same limit of detection in an ELISA. This method of labeling is, due to its efficiency and simplicity, of high interest for all antibody-based assays where it is important that labeling does not interfere with the antibody-binding site. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals

NASA Astrophysics Data System (ADS)

Liu, Chuang; Xie, Liping; Zhang, Rongqing

2015-12-01

Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.

Crossed beam studies of ion-molecule reactions in methane and ammonia

NASA Technical Reports Server (NTRS)

Smith, G. P. K.; Saunders, M.; Cross, R. J., Jr.

1976-01-01

A crossed-beam apparatus is used to measure the product ion velocity and angular distributions for the following ion-molecule reactions in the relative energy range from 2 to 9 eV: CH4(+) + NH3 yields NH4(+) + CH3; CH4(+) + NH3 yields CNH5(+) + H2; NH2(+) + CH4 yields CNH4(+) + H2 (or 2H); and CH3(+) + NH3 yields CNH4(+) + H2 (or 2H). These reactions are also studied by means of deuterium labeling as a further probe of the detailed reaction dynamics. Probability contour plots for the four reactions are constructed in Cartesian velocity space, and product peaks in the plots are discussed. Relative cross sections and Q values are computed for two of the reactions as well as for the corresponding deuterium-labelled reactions. The results show that the present ion-neutral condensation reactions are highly exothermic with a deep well for the internal complex, that little hydrogen scrambling occurs, and that the energy of the reactions is released mainly as internal energy, even to the extent of producing two hydrogen atoms in some cases rather than one hydrogen atom or molecule.

Convergent synthesis of 13N-labelled Peptidic structures using aqueous [13N]NH3.

PubMed

Blower, Julia E; Cousin, Samuel F; Gee, Antony D

2017-01-01

Nitrogen-13 has a 10-min half-life which places time constraints on the complexity of viable synthetic methods for its incorporation into PET imaging agents. In exploring ways to overcome this limitation, we have used the Ugi reaction to develop a rapid one-pot method for radiolabelling peptidic molecules using [ 13 N]NH 3 as a synthetic precursor. Carrier-added [ 13 N]NH 3 (50 μL) was added to a solution of carboxylic acid, aldehyde, and isocyanide in 2,2,2-TFE (200 μL). The mixture was heated in a microwave synthesiser at 120 °C for 10 min. Reactions were analysed by radio-HPLC and radio-LCMS. Isolation of the target 13 N-labelled peptidic Ugi compound was achieved via semi-preparative radio-HPLC as demonstrated for Ugi 1. Radio-HPLC analysis of each reaction confirmed the formation of radioactive products co-eluting with their respective reference standards with radiochemical yields of the crude products ranging from 11% to 23%. Two cyclic γ-lactam structures were also achieved via intra-molecular reactions. Additional radioactive by-products observed in the radio-chromatogram were identified as 13 N-labelled di-imines formed from the reaction of [ 13 N]NH 3 with two isocyanide molecules. The desired 13 N-labelled Ugi product was isolated using semi-preparative HPLC. We have developed a one-pot method that opens up new routes to radiolabel complex, peptidic molecules with 13 N using aqueous [ 13 N]NH 3 as a synthetic precursor.

The Properties of Oxygen Investigated with Easily Accessible Instrumentation: The "One-Photon-Two-Molecule" Mechanism Revisited

ERIC Educational Resources Information Center

Adelhelm, Manfred; Aristov, Natasha; Habekost, Achim

2010-01-01

The physical properties of oxygen, in particular, the blue color of the liquid phase, the red glow of its chemiluminescence, and its paramagnetism as shown by the entrapment or deflection of liquid oxygen by a magnetic field, can be investigated in a regular school setting with hand-held spectrophotometers and digital cameras. In college-level…

Nitrogen and Oxygen Photochemistry following SL9

NASA Technical Reports Server (NTRS)

Moses, Julianne I.; Allen, Mark; Gladstone, G. Randall

1995-01-01

The collision of Shoemaker Levy 9 (SL9) with Jupiter caused many new molecular species to be deposited in the Jovian stratosphere. We use a photochemical model to follow the evolution of the impact derived species. Our results regarding the nitrogen and oxygen compounds are presented here. NH3 photolysis initiates the nitrogen photochemistry. Much of the nitrogen ends up in N2, nitrogen-sulfur compounds, and HCN, but NH3 and nitriles such as C2H3CN may also exist in observable quantities for a year or so after the impacts. Oxygen species survive for a long time in the Jovian stratosphere. The only major oxygen containing compounds that exhibit dramatic changes in the lower stratosphere in the first year following the impacts are SO, SO2, and OCS - H2O, CO2, and CO are comparatively stable. We discuss the important photochemical processes operating on the nitrogen and oxygen species in the Jovian stratosphere, make prediction concerning the temporal variation of the major species, and identify molecules that might act as good tracers for atmospheric dynamics.

Carbon stars with oxygen-rich circumstellar material

NASA Technical Reports Server (NTRS)

Jura, Michael; Hawkins, I.

1991-01-01

The IUE satellite was used to search for companions to two carbon-rich stars with oxygen-rich circumstellar envelopes, EU And and V778 Cyg. Depending upon the amount of interstellar extinction and distances (probably between 1 and 2 kpc from the Sun) to these two stars, upper limits were placed between approx. 1.5 and 6 solar mass to the mass of any main sequence companions. For the 'near' distance of 1 kpc, it seems unlikely that there are white dwarf companions because the detection would be expected of ultraviolet emission from accretion of red giant wind material onto the white dwarf. A new model is proposed to explain the oxygen-rich envelopes. If these stars have a high nitrogen abundance, the carbon that is in excess of the oxygen may be carried in the circumstellar envelopes in HCN rather than C2H2 which is a likely key seed molecule for the formation of carbon grains. Consequently, carbon particles may not form; instead, oxygen-rich silicate dust may nucleate from the SiO present in the outflow.

Controlled enzymatic cutting of DNA molecules adsorbed on surfaces using soft lithography

NASA Astrophysics Data System (ADS)

Auerbach, Alyssa; Budassi, Julia; Shea, Emily; Zhu, Ke; Sokolov, Jonathan

2013-03-01

The enzyme DNase I was applied to adsorbed and aligned DNA molecules (Lamda, 48.5 kilobase pairs (kbp), and T4, 165.6 kbp), stretched linearly on a surface, by stamping with a polydimethylsiloxane (PDMS) grating. The DNAs were cut by the enzyme into separated, micron-sized segments along the length of the molecules at positions determined by the grating dimensions (3-20 microns). Ozone-treated PDMS stamps were coated with DNase I solutions and placed in contact with surface-adsorbed DNA molecules deposited on a 750 polymethylmethacrylate (PMMA) film spun-cast onto a silicon substrate. The stamps were applied under pressure for times up to 15 minutes at 37 C. The cutting was observed by fluorescence microscopy imaging of DNA labeled with YOYO dye. Cutting was found to be efficient despite the steric hindrance due to surface attachment of the molecules. Methods for detaching and separating the cut segments for sequencing applications will be discussed. Supported by NSF-DMR program.

Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

PubMed Central

Boujday, Souhir; Lamy de la Chapelle, Marc; Srajer, Johannes; Knoll, Wolfgang

2015-01-01

In this short summary we summarize some of the latest developments in vibrational spectroscopic tools applied for the sensing of (small) molecules and biomolecules in a label-free mode of operation. We first introduce various concepts for the enhancement of InfraRed spectroscopic techniques, including the principles of Attenuated Total Reflection InfraRed (ATR-IR), (phase-modulated) InfraRed Reflection Absorption Spectroscopy (IRRAS/PM-IRRAS), and Surface Enhanced Infrared Reflection Absorption Spectroscopy (SEIRAS). Particular attention is put on the use of novel nanostructured substrates that allow for the excitation of propagating and localized surface plasmon modes aimed at operating additional enhancement mechanisms. This is then be complemented by the description of the latest development in Surface- and Tip-Enhanced Raman Spectroscopies, again with an emphasis on the detection of small molecules or bioanalytes. PMID:26343666

Experimental and clinical experience with iodine 123-labeled iodophenylpentadecanoic acid in cardiology.

PubMed

Reske, S N

1994-01-01

Iodine 123-labeled iodophenylpentadecanoic acid (IPPA) has been synthesized for investigating myocardial free fatty acid (FFA) metabolism. The diagnostic application of labeled FFA in heart disease may be important, because FFA is the preferred substrate of cardiac energy metabolism at rest in the fasting state. In addition, regional myocardial FFA uptake and regional myocardial blood flow are tightly coupled in normal myocardium with beta-oxidation, which is extremely sensitive to oxygen deprivation. This article outlines basic physiologic pathways of cardiac IPPA metabolism in normal, acutely ischemic, and reperfused viable myocardium and summarizes the results of experimental studies in animals, validating the application of IPPA as an 123I-labeled fatty acid analog. In addition, the most important clinical studies indicating the clinical use of IPPA for diagnosis of coronary heart disease and myocardial viability are presented.

Control of root growth and development by reactive oxygen species.

PubMed

Tsukagoshi, Hironaka

2016-02-01

Reactive oxygen species (ROS) are relatively simple molecules that exist within cells growing in aerobic conditions. ROS were originally associated with oxidative stress and seen as highly reactive molecules that are injurious to many cell components. More recently, however, the function of ROS as signal molecules in many plant cellular processes has become more evident. One of the most important functions of ROS is their role as a plant growth regulator. For example, ROS are key molecules in regulating plant root development, and as such, are comparable to plant hormones. In this review, the molecular mechanisms of ROS that are mainly associated with plant root growth are discussed. The molecular links between root growth regulation by ROS and other signals will also be briefly discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observation of an electrical signal from a single molecule

NASA Astrophysics Data System (ADS)

Aslan, Arooj; Shaheen, Noor; Dobiszewski, Kyle; Kanwal, Alokik; Farrow, Reginald; Thomas, Gordon

We have attached a folded protein molecule to the tip of a carbon nanotube using electrophoresis. We have then measured the electrons produced when the protein catalyzes a series of reactions. As an initial example of the reactions, we have used the catalysis by glucose-oxidase of glucose. We can show that the characteristic dynamic signals from the molecule scale with the glucose concentration. The molecule on the carbon nanotube tip is stable with respect to time under controlled conditions. The signals also indicate the glucose diffusion as its concentration is locally depleted at the nanotube by the catalysis. We use a second carbon nanotube with a laccase molecule on its tip to complete the circuit with an oxygen reaction. In a previous stage of this process, the other end of the nanotube is attached with a low-impedance electrical connection to a Ti thin film and the measuring circuitry. This work is an early step toward investigating the feasibility of an implantable glucose monitor to help treat diabetes.

Carotenoids, versatile components of oxygenic photosynthesis.

PubMed

Domonkos, Ildikó; Kis, Mihály; Gombos, Zoltán; Ughy, Bettina

2013-10-01

Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evaluation of the performance of high temperature conversion reactors for compound-specific oxygen stable isotope analysis.

PubMed

Hitzfeld, Kristina L; Gehre, Matthias; Richnow, Hans-Hermann

2017-05-01

In this study conversion conditions for oxygen gas chromatography high temperature conversion (HTC) isotope ratio mass spectrometry (IRMS) are characterised using qualitative mass spectrometry (IonTrap). It is shown that physical and chemical properties of a given reactor design impact HTC and thus the ability to accurately measure oxygen isotope ratios. Commercially available and custom-built tube-in-tube reactors were used to elucidate (i) by-product formation (carbon dioxide, water, small organic molecules), (ii) 2nd sources of oxygen (leakage, metal oxides, ceramic material), and (iii) required reactor conditions (conditioning, reduction, stability). The suitability of the available HTC approach for compound-specific isotope analysis of oxygen in volatile organic molecules like methyl tert-butyl ether is assessed. Main problems impeding accurate analysis are non-quantitative HTC and significant carbon dioxide by-product formation. An evaluation strategy combining mass spectrometric analysis of HTC products and IRMS 18 O/ 16 O monitoring for future method development is proposed.