Effector-triggered defence against apoplastic fungal pathogens

PubMed Central

Stotz, Henrik U.; Mitrousia, Georgia K.; de Wit, Pierre J.G.M.; Fitt, Bruce D.L.

2014-01-01

R gene-mediated host resistance against apoplastic fungal pathogens is not adequately explained by the terms pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) or effector-triggered immunity (ETI). Therefore, it is proposed that this type of resistance is termed ‘effector-triggered defence’ (ETD). Unlike PTI and ETI, ETD is mediated by R genes encoding cell surface-localised receptor-like proteins (RLPs) that engage the receptor-like kinase SOBIR1. In contrast to this extracellular recognition, ETI is initiated by intracellular detection of pathogen effectors. ETI is usually associated with fast, hypersensitive host cell death, whereas ETD often triggers host cell death only after an elapsed period of endophytic pathogen growth. In this opinion, we focus on ETD responses against foliar fungal pathogens of crops. PMID:24856287

EXPONENTIAL TIME DIFFERENCING FOR HODGKIN–HUXLEY-LIKE ODES

PubMed Central

Börgers, Christoph; Nectow, Alexander R.

2013-01-01

Several authors have proposed the use of exponential time differencing (ETD) for Hodgkin–Huxley-like partial and ordinary differential equations (PDEs and ODEs). For Hodgkin–Huxley-like PDEs, ETD is attractive because it can deal effectively with the stiffness issues that diffusion gives rise to. However, large neuronal networks are often simulated assuming “space-clamped” neurons, i.e., using the Hodgkin–Huxley ODEs, in which there are no diffusion terms. Our goal is to clarify whether ETD is a good idea even in that case. We present a numerical comparison of first- and second-order ETD with standard explicit time-stepping schemes (Euler’s method, the midpoint method, and the classical fourth-order Runge–Kutta method). We find that in the standard schemes, the stable computation of the very rapid rising phase of the action potential often forces time steps of a small fraction of a millisecond. This can result in an expensive calculation yielding greater overall accuracy than needed. Although it is tempting at first to try to address this issue with adaptive or fully implicit time-stepping, we argue that neither is effective here. The main advantage of ETD for Hodgkin–Huxley-like systems of ODEs is that it allows underresolution of the rising phase of the action potential without causing instability, using time steps on the order of one millisecond. When high quantitative accuracy is not necessary and perhaps, because of modeling inaccuracies, not even useful, ETD allows much faster simulations than standard explicit time-stepping schemes. The second-order ETD scheme is found to be substantially more accurate than the first-order one even for large values of Δt. PMID:24058276

Electron Transfer Ion/Ion Reactions in a Three-Dimensional Quadrupole Ion Trap: Reactions of Doubly and Triply Protonated Peptides with SO2·−

PubMed Central

Pitteri, Sharon J.; Chrisman, Paul A.; Hogan, Jason M.; McLuckey, Scott A.

2005-01-01

Ion–ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2·−. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2·− give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2·− shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide. PMID:15762593

Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.

PubMed

Saba, Julian; Dutta, Sucharita; Hemenway, Eric; Viner, Rosa

2012-01-01

Currently, glycans are attracting attention from the scientific community as potential biomarkers or as posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization of glycoproteins and glycopeptides remains analytically challenging. Here, we report on the implementation of a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) on a hybrid linear ion trap-orbitrap mass spectrometer. This acquisition strategy uses the complementary fragmentations of ETD and HCD for glycopeptides analysis in an intelligent fashion. Furthermore, the approach minimizes user input for optimizing instrumental parameters and enables straightforward detection of glycopeptides. ETD spectra are only acquired when glycan oxonium ions from MS/MS HCD are detected. The advantage of this approach is that it streamlines data analysis and improves dynamic range and duty cycle. Here, we present the benefits of HCD-PD-ETD relative to the traditional alternating HCD/ETD for a trainer set containing twelve-protein mixture with two glycoproteins: human serotransferrin, ovalbumin and contaminations of two other: bovine alpha 1 acid glycoprotein (bAGP) and bovine fetuin.

[GRADE Evidence to Decision (EtD) frameworks: a systematic and transparent approach to making well informed healthcare choices. 2: Clinical practice guidelines.

PubMed

Morgano, Gian Paolo; Parmelli, Elena; Amato, Laura; Iannone, Primiano; Marchetti, Marco; Moja, Lorenzo; Davoli, Marina; Schünemann, Holger

2018-05-01

In the first article in this series we described the GRADE (Grading of Recommendations Assessment, Development and Evaluation) Evidence to Decision (EtD) frameworks and their rationale for different types of decisions. In this second article, we describe the use of EtD frameworks for clinical recommendations and how it can help clinicians and patients who use those recommendations. EtD frameworks for clinical practice recommendations provide a structured and transparent approach for guideline panels. The framework helps ensure consideration of key criteria that determine whether an intervention should be recommended and that judgments are informed by the best available evidence. Frameworks are also a way for panels to make guideline users aware of the rationale (justification) for their recommendations.

Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods

PubMed Central

Shen, Yufeng; Tolić, Nikola; Xie, Fang; Zhao, Rui; Purvine, Samuel O.; Schepmoes, Athena A.; Ronald, J. Moore; Anderson, Gordon A.; Smith, Richard D.

2011-01-01

We report on the effectiveness of CID, HCD, and ETD for LC-FT MS/MS analysis of peptides using a tandem linear ion trap-Orbitrap mass spectrometer. A range of software tools and analysis parameters were employed to explore the use of CID, HCD, and ETD to identify peptides isolated from human blood plasma without the use of specific “enzyme rules”. In the evaluation of an FDR-controlled SEQUEST scoring method, the use of accurate masses for fragments increased the numbers of identified peptides (by ~50%) compared to the use of conventional low accuracy fragment mass information, and CID provided the largest contribution to the identified peptide datasets compared to HCD and ETD. The FDR-controlled Mascot scoring method provided significantly fewer peptide identifications than with SEQUEST (by 1.3–2.3 fold) at the same confidence levels, and CID, HCD, and ETD provided similar contributions to identified peptides. Evaluation of de novo sequencing and the UStags method for more intense fragment ions revealed that HCD afforded more sequence consecutive residues (e.g., ≥7 amino acids) than either CID or ETD. Both the FDR-controlled SEQUEST and Mascot scoring methods provided peptide datasets that were affected by the decoy database and mass tolerances applied (e.g., the identical peptides between the datasets could be limited to ~70%), while the UStags method provided the most consistent peptide datasets (>90% overlap) with extremely low (near zero) numbers of false positive identifications. The m/z ranges in which CID, HCD, and ETD contributed the largest number of peptide identifications were substantially overlapping. This work suggests that the three peptide ion fragmentation methods are complementary, and that maximizing the number of peptide identifications benefits significantly from a careful match with the informatics tools and methods applied. These results also suggest that the decoy strategy may inaccurately estimate identification FDRs. PMID:21678914

On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications.

PubMed

Wu, Shiaw-Lin; Hühmer, Andreas F R; Hao, Zhiqi; Karger, Barry L

2007-11-01

We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as the sequence of large peptide fragments (i.e., 2000-10,000 Da) from complex proteins, such as beta-casein, epidermal growth factor receptor (EGFR), and tissue plasminogen activator (t-PA) at the low femtomol level. The incorporation of an additional CID activation step for a charge-reduced species, isolated from ETD fragment ions, improved ETD fragmentation when precursor ions with high m/z (approximately >1000) were automatically selected for fragmentation. Specifically, the identification of the exact phosphorylation sites was strengthened by the extensive coverage of the peptide sequence with a near-continuous product ion series. The identification of N-linked glycosylation sites in EGFR and an O-linked glycosylation site in t-PA were also improved through the enhanced identification of the peptide backbone sequence of the glycosylated precursors. The new strategy is a good starting survey scan to characterize enzymatic peptide mixtures over a broad range of masses using LC-MS with data-dependent acquisition, as the three activation steps can provide complementary information to each other. In general, large peptides can be extensively characterized by the ETD and CRCID steps, including sites of modification from the generated, near-continuous product ion series, supplemented by the CID-MS2 step. At the same time, small peptides (e.g.,

International Energy: Subject Thesaurus. Revision 1

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

Not Available

The International Energy Agency: Subject Thesaurus contains the standard vocabulary of indexing terms (descriptors) developed and structured to build and maintain energy information databases. Involved in this cooperative task are (1) the technical staff of the USDOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the International Energy Agency`s Energy Technology Data Exchange (ETDE) and (2) the International Atomic Energy Agency`s International Nuclear Information System (INIS) staff representing the more than 100 countries and organizations that record and index information for the international nuclear information community. ETDE member countries are also members of INIS.more » Nuclear information prepared for INIS by ETDE member countries is included in the ETDE Energy Database, which contains the online equivalent of the printed INIS Atomindex. Indexing terminology is therefore cooperatively standardized for use in both information systems. This structured vocabulary reflects thscope of international energy research, development, and technological programs. The terminology of this thesaurus aids in subject searching on commercial systems, such as ``Energy Science & Technology`` by DIALOG Information Services, ``Energy`` by STN International and the ``ETDE Energy Database`` by SilverPlatter. It is also the thesaurus for the Integrated Technical Information System (ITIS) online databases of the US Department of Energy.« less

UniNovo: a universal tool for de novo peptide sequencing.

PubMed

Jeong, Kyowon; Kim, Sangtae; Pevzner, Pavel A

2013-08-15

Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function. The performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-02-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-05-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

Electron-Transfer Ion/Ion Reactions of Doubly Protonated Peptides: Effect of Elevated Bath Gas Temperature

PubMed Central

Pitteri, Sharon J.; Chrisman, Paul A.; McLuckey, Scott A.

2005-01-01

In this study, the electron-transfer dissociation (ETD) behavior of cations derived from 27 different peptides (22 of which are tryptic peptides) has been studied in a 3D quadrupole ion trap mass spectrometer. Ion/ion reactions between peptide cations and nitrobenzene anions have been examined at both room temperature and in an elevated temperature bath gas environment to form ETD product ions. From the peptides studied, the ETD sequence coverage tends to be inversely related to peptide size. At room temperature, very high sequence coverage (~100%) was observed for small peptides (≤7 amino acids). For medium-sized peptides composed of 8–11 amino acids, the average sequence coverage was 46%. Larger peptides with 14 or more amino acids yielded an average sequence coverage of 23%. Elevated-temperature ETD provided increased sequence coverage over room-temperature experiments for the peptides of greater than 7 residues, giving an average of 67% for medium-sized peptides and 63% for larger peptides. Percent ETD, a measure of the extent of electron transfer, has also been calculated for the peptides and also shows an inverse relation with peptide size. Bath gas temperature does not have a consistent effect on percent ETD, however. For the tryptic peptides, fragmentation is localized at the ends of the peptides suggesting that the distribution of charge within the peptide may play an important role in determining fragmentation sites. A triply protonated peptide has also been studied and shows behavior similar to the doubly charged peptides. These preliminary results suggest that for a given charge state there is a maximum size for which high sequence coverage is obtained and that increasing the bath gas temperature can increase this maximum. PMID:16131079

Design of integrated eye tracker-display device for head mounted systems

NASA Astrophysics Data System (ADS)

David, Y.; Apter, B.; Thirer, N.; Baal-Zedaka, I.; Efron, U.

2009-08-01

We propose an Eye Tracker/Display system, based on a novel, dual function device termed ETD, which allows sharing the optical paths of the Eye tracker and the display and on-chip processing. The proposed ETD design is based on a CMOS chip combining a Liquid-Crystal-on-Silicon (LCoS) micro-display technology with near infrared (NIR) Active Pixel Sensor imager. The ET operation allows capturing the Near IR (NIR) light, back-reflected from the eye's retina. The retinal image is then used for the detection of the current direction of eye's gaze. The design of the eye tracking imager is based on the "deep p-well" pixel technology, providing low crosstalk while shielding the active pixel circuitry, which serves the imaging and the display drivers, from the photo charges generated in the substrate. The use of the ETD in the HMD Design enables a very compact design suitable for Smart Goggle applications. A preliminary optical, electronic and digital design of the goggle and its associated ETD chip and digital control, are presented.

Surface modification of calcium hydroxyapatite by grafting of etidronic acid

NASA Astrophysics Data System (ADS)

Othmani, Masseoud; Aissa, Abdallah; Bac, Christophe Goze; Rachdi, Férid; Debbabi, Mongi

2013-06-01

The surface of prepared calcium hydroxyapatite CaHAp has been modified by grafting the etidronic acid (ETD). For that purpose, CaHAp powders have been suspended in an aqueous etidronate solution with different concentrations. The obtained composites CaHAp-(ETD) were characterized by TEM and AFM techniques to determinate morphological properties and were also characterized by XRD, IR, NMR and chemical and thermal analysis to determinate their physico-chemical properties and essentially the nature of the interaction between the inorganic support and the grafted organic ETD. After reaction with ETD, XRD powder analysis shows that the apatitic structure remains unchanged with slight affectation of its crystallinity. The presence of etidronate fragment bounded to hydroxyapatite was confirmed by IR and solid-state NMR spectroscopy. TEM and AFM techniques indicate that the presence of etidronate changes the morphology of the particles. Basing on the obtained results, a reactional mechanism was proposed to explain the formation of covalent Casbnd Osbnd Porg bonds on the hydroxyapatite surface between the superficial hydroxyl groups (tbnd Casbnd OH) of the apatite and phosphonate group (Psbnd OH) of etidronate.

Methodologies for Removing/Desorbing and Transporting Particles from Surfaces to Instrumentation

NASA Astrophysics Data System (ADS)

Miller, Carla J.; Cespedes, Ernesto R.

2012-12-01

Explosive trace detection (ETD) continues to be a key technology supporting the fight against terrorist bombing threats. Very selective and sensitive ETD instruments have been developed to detect explosive threats concealed on personnel, in vehicles, in luggage, and in cargo containers, as well as for forensic analysis (e.g. post blast inspection, bomb-maker identification, etc.) in a broad range of homeland security, law enforcement, and military applications. A number of recent studies have highlighted the fact that significant improvements in ETD systems' capabilities will be achieved, not by increasing the selectivity/sensitivity of the sensors, but by improved techniques for particle/vapor sampling, pre-concentration, and transport to the sensors. This review article represents a compilation of studies focused on characterizing the adhesive properties of explosive particles, the methodologies for removing/desorbing these particles from a range of surfaces, and approaches for transporting them to the instrument. The objectives of this review are to summarize fundamental work in explosive particle characterization, to describe experimental work performed in harvesting and transport of these particles, and to highlight those approaches that indicate high potential for improving ETD capabilities.

DRY–WET CYCLES INCREASE PESTICIDE RESIDUE RELEASE FROM SOIL

PubMed Central

Jablonowski, Nicolai David; Linden, Andreas; Köppchen, Stephan; Thiele, Björn; Hofmann, Diana; Burauel, Peter

2012-01-01

Soil drying and rewetting may alter the release and availability of aged pesticide residues in soils. A laboratory experiment was conducted to evaluate the influence of soil drying and wetting on the release of pesticide residues. Soil containing environmentally long-term aged (9–17 years) 14C-labeled residues of the herbicides ethidimuron (ETD) and methabenzthiazuron (MBT) and the fungicide anilazine (ANI) showed a significantly higher release of 14C activity in water extracts of previously dried soil compared to constantly moistened soil throughout all samples (ETD: p < 0.1, MBT and ANI: p < 0.01). The extracted 14C activity accounted for 44% (ETD), 15% (MBT), and 20% (ANI) of total residual 14C activity in the samples after 20 successive dry–wet cycles, in contrast to 15% (ETD), 5% (MBT), and 6% (ANI) in extracts of constantly moistened soils. In the dry–wet soils, the dissolved organic carbon (DOC) content correlated with the measured 14C activity in the aqueous liquids and indicated a potential association of DOC with the pesticide molecules. Liquid chromatography MS/MS analyses of the water extracts of dry–wet soils revealed ETD and MBT in detectable amounts, accounting for 1.83 and 0.01%, respectively, of total applied water-extractable parent compound per soil layer. These findings demonstrate a potential remobilization of environmentally aged pesticide residue fractions from soils due to abiotic stresses such as wet–dry cycles. Environ. Toxicol. Chem. 2012; 31: 1941–1947. © 2012 SETAC PMID:22782855

Sequence Elucidation of an Unknown Cyclic Peptide of High Doping Potential by ETD and CID Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Guan, Fuyu; Uboh, Cornelius E.; Soma, Lawrence R.; Rudy, Jeffrey

2011-04-01

Identification of an unknown substance without any information remains a daunting challenge despite advances in chemistry and mass spectrometry. However, an unknown cyclic peptide in a sample with very limited volume seized at a Pennsylvania racetrack has been successfully identified. The unknown sample was determined by accurate mass measurements to contain a small unknown peptide as the major component. Collision-induced dissociation (CID) of the unknown peptide revealed the presence of Lys (not Gln, by accurate mass), Phe, and Arg residues, and absence of any y-type product ion. The latter, together with the tryptic digestion results of the unusual deamidation and absence of any tryptic cleavage, suggests a cyclic structure for the peptide. Electron-transfer dissociation (ETD) of the unknown peptide indicated the presence of Gln (not Lys, by the unusual deamidation), Phe, and Arg residues and their connectivity. After all the results were pieced together, a cyclic tetrapeptide, cyclo[Arg-Lys-N(C6H9)Gln-Phe], is proposed for the unknown peptide. Observations of different amino acid residues from CID and ETD experiments for the peptide were interpreted by a fragmentation pathway proposed, as was preferential CID loss of a Lys residue from the peptide. ETD was used for the first time in sequencing of a cyclic peptide; product ions resulting from ETD of the peptide identified were categorized into two types and named pseudo-b and pseudo-z ions that are important for sequencing of cyclic peptides. The ETD product ions were interpreted by fragmentation pathways proposed. Additionally, multi-stage CID mass spectrometry cannot provide complete sequence information for cyclic peptides containing adjacent Arg and Lys residues. The identified cyclic peptide has not been documented in the literature, its pharmacological effects are unknown, but it might be a "designer" drug with athletic performance-enhancing effects.

Self-Paced Interactive Multimedia Courseware: A Learning Support Resource for Enhancing Electronic Theses and Dissertations Development

ERIC Educational Resources Information Center

Essel, Harry Barton; Osei-Poku, Patrick; Tachie-Menson, Akosua; Opoku-Asare, Nana Afia

2016-01-01

Submission of Electronic Theses and Dissertations (ETDs) by postgraduate students has become a common phenomenon in learning environments globally. The purpose of ETDs is to train postgraduate students as knowledge workers in online publishing and also extend their skills beyond word processing. The challenge however, is that many postgraduate…

Distinguishing aspartic and isoaspartic acids in peptides by several mass spectrometric fragmentation methods

PubMed Central

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-01-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post source decay (PSD), MALDI 157 nm photodissociation, TMPP charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. PMID:27613306

The Effects of Trivalent Lanthanide Cationization on the Electron Transfer Dissociation of Acidic Fibrinopeptide B and its Analogs

NASA Astrophysics Data System (ADS)

Commodore, Juliette J.; Cassady, Carolyn J.

2016-09-01

Electrospray ionization (ESI) on mixtures of acidic fibrinopeptide B and two peptide analogs with trivalent lanthanide salts generates [M + Met + H]4+, [M + Met]3+, and [M + Met -H]2+, where M = peptide and Met = metal (except radioactive promethium). These ions undergo extensive and highly efficient electron transfer dissociation (ETD) to form metallated and non-metallated c- and z-ions. All metal adducted product ions contain at least two acidic sites, which suggest attachment of the lanthanide cation at the side chains of one or more acidic residues. The three peptides undergo similar fragmentation. ETD on [M + Met + H]4+ leads to cleavage at every residue; the presence of both a metal ion and an extra proton is very effective in promoting sequence-informative fragmentation. Backbone dissociation of [M + Met]3+ is also extensive, although cleavage does not always occur between adjacent glutamic acid residues. For [M + Met - H ]2+, a more limited range of product ions form. All lanthanide metal peptide complexes display similar fragmentation except for europium (Eu). ETD on [M + Eu - H]2+ and [M + Eu]3+ yields a limited amount of peptide backbone cleavage; however, [M + Eu + H]4+ dissociates extensively with cleavage at every residue. With the exception of the results for Eu(III), metallated peptide ion formation by ESI, ETD fragmentation efficiencies, and product ion formation are unaffected by the identity of the lanthanide cation. Adduction with trivalent lanthanide metal ions is a promising tool for sequence analysis of acidic peptides by ETD.

Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs.

PubMed

Yan, Yan; Zhang, Kaizhong

2016-12-23

De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance of de novo sequencing is greatly improved. Currently, with large amount of spectra sequenced everyday, spectra libraries containing tens of thousands of annotated experimental MS/MS spectra become available. These libraries provide information of the spectra properties, thus have the potential to be used with de novo sequencing to improve its performance. In this study, an improved de novo sequencing method assisted with spectra library is proposed. It uses spectra libraries as training datasets and introduces significant scores of the features used in our previous de novo sequencing method for HCD and ETD spectra pairs. Two pairs of HCD and ETD spectral datasets were used to test the performance of the proposed method and our previous method. The results show that this proposed method achieves better sequencing accuracy with higher ranked correct sequences and less computational time. This paper proposed an advanced de novo sequencing method for HCD and ETD spectra pair and used information from spectra libraries and significant improved previous similar methods.

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

NASA Astrophysics Data System (ADS)

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

The GRADE Evidence to Decision (EtD) framework for health system and public health decisions.

PubMed

Moberg, Jenny; Oxman, Andrew D; Rosenbaum, Sarah; Schünemann, Holger J; Guyatt, Gordon; Flottorp, Signe; Glenton, Claire; Lewin, Simon; Morelli, Angela; Rada, Gabriel; Alonso-Coello, Pablo

2018-05-29

To describe a framework for people making and using evidence-informed health system and public health recommendations and decisions. We developed the GRADE Evidence to Decision (EtD) framework for health system and public health decisions as part of the DECIDE project, in which we simultaneously developed frameworks for these and other types of healthcare decisions, including clinical recommendations, coverage decisions and decisions about diagnostic tests. Building on GRADE EtD tables, we used an iterative approach, including brainstorming, consultation of the literature and with stakeholders, and an international survey of policy-makers. We applied the framework to diverse examples, conducted workshops and user testing with health system and public health guideline developers and policy-makers, and observed and tested its use in real-life guideline panels. All the GRADE EtD frameworks share the same basic structure, including sections for formulating the question, making an assessment and drawing conclusions. Criteria listed in the assessment section of the health system and public health framework cover the important factors for making these types of decisions; in addition to the effects and economic impact of an option, the priority of the problem, the impact of the option on equity, and its acceptability and feasibility are important considerations that can inform both whether and how to implement an option. Because health system and public health interventions are often complex, detailed implementation considerations should be made when making a decision. The certainty of the evidence is often low or very low, but decision-makers must still act. Monitoring and evaluation are therefore often important considerations for these types of decisions. We illustrate the different components of the EtD framework for health system and public health decisions by presenting their application in a framework adapted from a real-life guideline. This framework provides a structured and transparent approach to support policy-making informed by the best available research evidence, while making the basis for decisions accessible to those whom they will affect. The health system and public health EtD framework can also be used to facilitate dissemination of recommendations and enable decision-makers to adopt, and adapt, recommendations or decisions.

Intranasal fluticasone associated with delayed tympanostomy tube placement in children with eustachian tube dysfunction.

PubMed

Crowson, Matthew G; Ryan, Marisa A; Ramprasad, Vaibhav H; Choi, Kevin J; Raynor, Eileen

2017-03-01

Pediatric patient caregivers may prefer to avoid a surgical intervention and request a medical management option for eustachian tube dysfunction (ETD). However, there are limited published data evaluating the efficacy of intranasal fluticasone in the medical management of ETD as an alternative to tympanostomy tube placement. The objectives of this study were to: 1) determine if intranasal fluticasone (INF) prevented tympanostomy tube placement in children with ETD, and 2) describe differences in patient response to INF related to cleft lip and/or palate (CLP) and Down syndrome. Case series with planned chart review at a Tertiary academic hospital. We reviewed pediatric patients treated with INF for ETD. Inclusion criteria included ETD, no prior intranasal or oral steroid therapy, and no prior tympanostomy tube placement. Outcomes included time-to- tympanostomy tube placement with or without INF and therapy compliance. Kaplan-Meier survival analyses with log-rank tests and Fisher's exact tests were used to examine outcome variables. 676 fulfilled inclusion criteria. 393 (58.7%) were male, and 355 (52.5%) Caucasian with mean age of 27.1 months old. 92 (13.6%) had CLP and 46 (6.8%) had Down Syndrome. 266 (39.4%) received INF, and 202 (88.2%) were compliant at their next visit. 474 (70.1%) had tympanostomy tubes placed. Children treated with INF were less likely to have tympanostomy tubes placed than children not treated (52.6% vs. 81.5%; p < 0.0001). Using survival analyses, INF use was associated with significantly longer mean time-to-tympanostomy tube than no INF use (199.4 vs. 133.7 days; p < 0.0001). INF did not reduce time-to-tympanostomy tube in patients with CLP (p = 0.05) or Down Syndrome (p = 0.27). INF significantly reduces the number of children requiring tympanostomy tube placement for ETD. The CLP and Down Syndrome anatomical variants may attenuate INF efficacy. Further in vivo characterization of INF action on eustachian tube tissues will help further substantiate these observations. Copyright © 2017 Elsevier B.V. All rights reserved.

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

PubMed Central

Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

2014-01-01

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH3)2) and ‘heavy’ (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency. PMID:21952753

Cation Recombination Energy/Coulomb Repulsion Effects in ETD/ECD as Revealed by Variation of Charge per Residue at Fixed Total Charge

PubMed Central

Mentinova, Marija; Crizer, David M.; Baba, Takashi; McGee, William M.; Glish, Gary L.; McLuckey, Scott A.

2013-01-01

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) experiments in electrodynamic ion traps operated in the presence of a bath gas in the 1–10 mTorr range have been conducted on a common set of doubly protonated model peptides of the form X(AG)nX (X = lysine, arginine, or histidine, n=1, 2, or 4). The partitioning of reaction products was measured using thermal electrons, anions of azobenzene, and anions of 1,3-dinitrobenzene as reagents. Variation of n alters the charge per residue of the peptide cation, which affects recombination energy. The ECD experiments showed that H-atom loss is greatest for the n=1 peptides and decreases as n increases. Proton transfer in ETD, on the other hand, is expected to increase as charge per residue decreases (i.e., as n increases). These opposing tendencies were apparent in the data for the K(AG)nK peptides. H-atom loss appeared to be more prevalent in ECD than in ETD and is rationalized on the basis of either internal energy differences, differences in angular momentum transfer associated with the electron capture versus electron transfer processes, or a combination of the two. The histidine peptides showed the greatest extent of charge reduction without dissociation, the arginine peptides showed the greatest extent of side-chain cleavages, and the lysine peptides generally showed the greatest extent of partitioning into the c/z•-product ion channels. The fragmentation patterns for the complementary c- and z•-ions for ETD and ECD were found to be remarkably similar, particularly for the peptides with X = lysine. PMID:23568028

Progress in a selective method for the determination of the acetaldehyde-derived DNA adducts by using HILIC-ESI-MS/MS.

PubMed

Murakami, Hiroya; Horiba, Ruri; Iwata, Tomoko; Miki, Yuta; Uno, Bunji; Sakai, Tadao; Kaneko, Kazuhiro; Ishihama, Yasushi; Teshima, Norio; Esaka, Yukihiro

2018-01-15

Acetaldehyde (AA), which is present in tobacco smoke, automobile exhaust gases and alcohol beverage, is a mutagen and carcinogen. AA reacts with 2'-deoxyguanosine (dG) in DNA to form N 2 -ethyl-dG (EtdG) and cyclic, 1, N 2 -propano-dG (CPrdG), which are considered to have a critical role in carcinogenesis induced by AA. In this study, we have developed a highly sensitive method for the quantitation of the two AA-derived DNA adducts by using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) in which hydrophilic interaction chromatography (HILIC) employing mobile phases of high organic solvent concentration was selected to improve the ionization efficiency in the ESI process. Fourteen times and 11 times larger peak areas for EtdG and CPrdG, respectively, in HILIC-ESI-MS/MS were obtained compared with those in reversed phase (RP)-LC-ESI-MS/MS. Furthermore, 6.9 times (for EtdG) and 2.4 times (for CPrdG) larger peak areas were also obtained as additional enhancement by varying additive compounds in the HILIC mobile phases from ammonium acetate to ammonium bicarbonate. In total, the enhancements in detected MS signal intensities by exchanging from the RP-LC system to the HILIC system are 97 times for EtdG and 26 times for CPrdG, respectively. Three commercially available HILIC columns with different polar functional groups were examined and sufficient separation between normal 2'-deoxynucleosides and the AA-derived DNA adducts was achieved by a carbamoyl-bonded HILIC column. Finally, we applied the established method to quantify EtdG and CPrdG in the damaged calf thymus DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Electron Transfer Dissociation with Supplemental Activation to Differentiate Aspartic and Isoaspartic Residues in Doubly Charged Peptide Cations

PubMed Central

Chan, Wai Yi Kelly; Chan, T. W. Dominic; O’Connor, Peter B.

2011-01-01

Electron-transfer dissociation (ETD) with supplemental activation of the doubly charged deamidated tryptic digested peptide ions allows differentiation of isoaspartic acid and aspartic acid residues using c + 57 or z• − 57 peaks. The diagnostic peak clearly localizes and characterizes the isoaspartic acid residue. Supplemental activation in ETD of the doubly charged peptide ions involves resonant excitation of the charge reduced precursor radical cations and leads to further dissociation, including extra backbone cleavages and secondary fragmentation. Supplemental activation is essential to obtain a high quality ETD spectrum (especially for doubly charged peptide ions) with sequence information. Unfortunately, the low-resolution of the ion trap mass spectrometer makes detection of the diagnostic peak for the aspartic acid residue difficult due to interference with side-chain loss from arginine and glutamic acid residues. PMID:20304674

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods.

PubMed

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H 2 O, are present in PSD, photodissociation, and charge tagging. c • +57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.

Analyzing patient's waiting time in emergency & trauma department in public hospital - A case study

NASA Astrophysics Data System (ADS)

Roslan, Shazwa; Tahir, Herniza Md; Nordin, Noraimi Azlin Mohd; Zaharudin, Zati Aqmar

2014-09-01

Emergency and Trauma Department (ETD) is an important element for a hospital. It provides medical service, which operates 24 hours a day in most hospitals. However overcrowding is not exclusion for ETD. Overflowing occurs due to affordable services provided by public hospitals, since it is funded by the government. It is reported that a patient attending ETD must be treated within 90 minutes, in accordance to achieve the Key Performance Indicator (KPI). However, due to overcrowd situations, most patients have to wait longer than the KPI standard. In this paper, patient's average waiting time is analyzed. Using Chi-Square Test of Goodness, patient's inter arrival per hour is also investigated. As conclusion, Monday until Wednesday was identified as the days that exceed the KPI standard while Chi-Square Test of Goodness showed that the patient's inter arrival is independent and random.

Highly sensitive sites for guanine-O6 ethylation in rat brain DNA exposed to N-ethyl-N-nitrosourea in vivo.

PubMed Central

Nehls, P; Rajewsky, M F; Spiess, E; Werner, D

1984-01-01

Brain chromosomal DNA isolated from fetal BDIX-rats 1 h after i.v. administration of the ethylating N-nitroso carcinogen N-ethyl-N-nitrosourea (75 micrograms/g body weight), statistically contained one molecule of O6-ethyl-2'-deoxyguanosine (O6-EtdGuo) per 81 micron of DNA, as determined in enzymatic DNA hydrolysates by competitive radio-immunoassay using a high-affinity anti-(O6-EtdGuo) monoclonal antibody (ER-6). After fragmentation of the DNA by the restriction enzyme AluI (average fragment length, Lav = 0.28 micron = 970 bp; length range, Lr = 1.87-0.02 micron = 6540 - 60 bp), a small (approximately 2%) fraction of DNA enriched in specific polypeptides tightly associated with DNA was separated from the bulk DNA by a glass fiber binding technique. As analyzed by immune electron microscopy, approximately 1% of the DNA molecules in this fraction contained clusters of 2-10 (O6-EtdGuo)-antibody binding sites (ABS). On the cluster-bearing fragments (Lav, 0.85 micron +/- 0.50 micron S.D.; corresponding to 2970 +/- 1760 bp) the average ABS-ABS interspace distance was 110 nm (= 390 bp; range approximately 9-600 nm), indicating a highly non-random distribution of O6-EtdGuo in target cell DNA. Images Fig. 2. PMID:6370677

Determination of the DNA-binding characteristics of ethidium bromide, proflavine, and cisplatin by flow injection analysis: usefulness in studies on antitumor drugs.

PubMed

Alonso, A; Almendral, M J; Curto, Y; Criado, J J; Rodríguez, E; Manzano, J L

2006-08-15

Flow injection analysis was used to study the reactions occurring between DNA and certain compounds that bind to its double helix, deforming this and even breaking it, such that some of them (e.g., cisplatin) are endowed with antitumoral activity. Use of this technique in the merging zones and stopped-flow modes afforded data on the binding parameters and the kinetic characteristics of the process. The first compound studied was ethidium bromide (EtdBr), used as a fluorescent marker because its fluorescence is enhanced when it binds to DNA. The DNA-EtdBr binding parameters, the apparent intrinsic binding constant (0.31+/-0.02 microM(-1)), and the maximum number of binding sites per nucleotide (0.327+/-0.009) were determined. The modification introduced in these parameters by the presence of proflavine (Prf), a classic competitive inhibitor of the binding of EtdBr to the DNA double helix, was also studied, determining the value of the intrinsic binding constant of Prf (K(Prf) = 0.119+/-9x10(-3) microM(-1)). Finally, we determined the binding parameters between DNA and EtdBr in the presence of the antitumor agent cisplatin, a noncompetitive inhibitor of such binding. This provided information about the binding mechanism as well as the duration and activity of the binding of the compound in its pharmacological use.

International energy: Research organizations, 1988--1992. Revision 1

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

Hendricks, P.; Jordan, S.

This publication contains the standardized names of energy research organizations used in energy information databases. Involved in this cooperative task are (1) the technical staff of the US DOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the Energy Technology Data Exchange (ETDE) and (2) the International Nuclear Information System (INIS). ETDE member countries are also members of the International Nuclear Information System (INIS). Nuclear organization names recorded for INIS by these ETDE member countries are also included in the ETDE Energy Database. Therefore, these organization names are cooperatively standardized for use in bothmore » information systems. This publication identifies current organizations doing research in all energy fields, standardizes the format for recording these organization names in bibliographic citations, assigns a numeric code to facilitate data entry, and identifies report number prefixes assigned by these organizations. These research organization names may be used in searching the databases ``Energy Science & Technology`` on DIALOG and ``Energy`` on STN International. These organization names are also used in USDOE databases on the Integrated Technical Information System. Research organizations active in the past five years, as indicated by database records, were identified to form this publication. This directory includes approximately 31,000 organizations that reported energy-related literature from 1988 to 1992 and updates the DOE Energy Data Base: Corporate Author Entries.« less

Antagonistic interactions and production of halocin antimicrobial peptides among extremely halophilic prokaryotes isolated from the solar saltern of Sfax, Tunisia.

PubMed

Ghanmi, Fadoua; Carré-Mlouka, Alyssa; Vandervennet, Manon; Boujelben, Ines; Frikha, Doniez; Ayadi, Habib; Peduzzi, Jean; Rebuffat, Sylvie; Maalej, Sami

2016-05-01

Thirty-five extremely halophilic microbial strains isolated from crystallizer (TS18) and non-crystallizer (M1) ponds in the Sfax solar saltern in Tunisia were examined for their ability to exert antimicrobial activity. Antagonistic assays resulted in the selection of eleven strains that displayed such antimicrobial activity and they were further characterized. Three cases of cross-domain inhibition (archaea/bacteria or bacteria/archaea) were observed. Four archaeal strains exerted antimicrobial activity against several other strains. Three strains, for which several lines of evidence suggested the antimicrobial activity was, at least in part, due to peptide/protein agents (Halobacterium salinarum ETD5, Hbt. salinarum ETD8, and Haloterrigena thermotolerans SS1R12), were studied further. Optimal culture conditions for growth and antimicrobial production were determined. Using DNA amplification with specific primers, sequencing and RT-PCR analysis, Hbt. salinarum ETD5 and Hbt. salinarum ETD8 were shown to encode and express halocin S8, a hydrophobic antimicrobial peptide targeting halophilic archaea. Although the gene encoding halocin H4 was amplified from the genome of Htg. thermotolerans SS1R12, no transcript could be detected and the antimicrobial activity was most likely due to multiple antimicrobial compounds. This is also the first report that points to four different strains isolated from different geographical locations with the capacity to produce identical halocin S8 proteins.

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

Zhang, Qibin; Petyuk, Vladislav A.; Schepmoes, Athena A.

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycatedmore » peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.« less

Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis

NASA Astrophysics Data System (ADS)

Lyon, Yana A.; Beran, Gregory; Julian, Ryan R.

2017-07-01

Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers.

ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome

NASA Astrophysics Data System (ADS)

Porras-Yakushi, Tanya R.; Sweredoski, Michael J.; Hess, Sonja

2015-09-01

Comprehensive analysis of the ubiquitylome is a prerequisite to fully understand the regulatory role of ubiquitylation. However, the impact of key mass spectrometry parameters on ubiquitylome analyses has not been fully explored. In this study, we show that using electron transfer dissociation (ETD) fragmentation, either exclusively or as part of a decision tree method, leads to ca. 2-fold increase in ubiquitylation site identifications in K-ɛ-GG peptide-enriched samples over traditional collisional-induced dissociation (CID) or higher-energy collision dissociation (HCD) methods. Precursor ions were predominantly observed as 3+ charged species or higher and in a mass range 300-1200 m/z. N-ethylmaleimide was used as an alkylating agent to reduce false positive identifications resulting from overalkylation with halo-acetamides. These results demonstrate that the application of ETD fragmentation, in addition to narrowing the mass range and using N-ethylmaleimide yields more high-confidence ubiquitylation site identification than conventional CID and HCD analysis.

Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis

NASA Astrophysics Data System (ADS)

Weisbrod, Chad R.; Kaiser, Nathan K.; Syka, John E. P.; Early, Lee; Mullen, Christopher; Dunyach, Jean-Jacques; English, A. Michelle; Anderson, Lissa C.; Blakney, Greg T.; Shabanowitz, Jeffrey; Hendrickson, Christopher L.; Marshall, Alan G.; Hunt, Donald F.

2017-09-01

High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29 kDa, without the need for extensive spectral averaging (e.g., 60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. [Figure not available: see fulltext.

Quantitative relations between the eyeball, the optic nerve, and the optic canal important for intracranial pressure monitoring

PubMed Central

2014-01-01

Objective To find correlations between diameters of the optic nerve sheath (ONSD), the eyeball, and the optic canal that might be important for intracranial pressure monitoring. Methods In a prospective cohort study, the CT data of consecutive 400 adults (18+) with healthy eyes and optic nerves and absence of neurological diseases were collected and analyzed. When the CT scans were obtained, the diameters of the optic nerve sheath, the eyeball, and the optic canal were measured and statistically analyzed. The data obtained from the left and from the right eyeballs and optic nerves were compared. The correlation analysis was performed within these variables, with the gender, and the age. Results In healthy persons, the ONSD varies from 3.65 mm to 5.17 mm in different locations within the intraorbital space with no significant difference between sexes and age groups. There is a strong correlation between the eyeball transverse diameter (ETD) and ONSD that can be presented as ONSD/ETD index. In healthy subjects, the ONSD/ETD index equals 0.19. Conclusion The calculation of an index when ONSD is divided by the ETD of the eyeball presents precise normative database for ONSD intracranial pressure measurement technique. When the ONSD is measured for intracranial pressure monitoring, the most stable results can be obtained if the diameter is measured 10 mm from the globe. These data might serve as a normative database at emergency departments and in general neurological practice. PMID:25130267

Quantitative relations between the eyeball, the optic nerve, and the optic canal important for intracranial pressure monitoring.

PubMed

Vaiman, Michael; Gottlieb, Paul; Bekerman, Inessa

2014-08-17

To find correlations between diameters of the optic nerve sheath (ONSD), the eyeball, and the optic canal that might be important for intracranial pressure monitoring. In a prospective cohort study, the CT data of consecutive 400 adults (18+) with healthy eyes and optic nerves and absence of neurological diseases were collected and analyzed. When the CT scans were obtained, the diameters of the optic nerve sheath, the eyeball, and the optic canal were measured and statistically analyzed. The data obtained from the left and from the right eyeballs and optic nerves were compared. The correlation analysis was performed within these variables, with the gender, and the age. In healthy persons, the ONSD varies from 3.65 mm to 5.17 mm in different locations within the intraorbital space with no significant difference between sexes and age groups. There is a strong correlation between the eyeball transverse diameter (ETD) and ONSD that can be presented as ONSD/ETD index. In healthy subjects, the ONSD/ETD index equals 0.19. The calculation of an index when ONSD is divided by the ETD of the eyeball presents precise normative database for ONSD intracranial pressure measurement technique. When the ONSD is measured for intracranial pressure monitoring, the most stable results can be obtained if the diameter is measured 10 mm from the globe. These data might serve as a normative database at emergency departments and in general neurological practice.

Application of four watershed acidification models to Batchawana Watershed, Canada.

PubMed

Booty, W G; Bobba, A G; Lam, D C; Jeffries, D S

1992-01-01

Four watershed acidification models (TMWAM, ETD, ILWAS, and RAINS) are reviewed and a comparison of model performance is presented for a common watershed. The models have been used to simulate the dynamics of water quantity and quality at Batchawana Watershed, Canada, a sub-basin of the Turkey Lakes Watershed. The computed results are compared with observed data for a four-year period (Jan. 1981-Dec. 1984). The models exhibit a significant range in the ability to simulate the daily, monthly and seasonal changes present in the observed data. Monthly watershed outflows and lake chemistry predictions are compared to observed data. pH and ANC are the only two chemical parameters common to all four models. Coefficient of efficiency (E), linear (r) and rank (R) correlation coefficients, and regression slope (s) are used to compare the goodness of fit of the simulated with the observed data. The ILWAS, TMWAM and RAINS models performed very well in predicting the monthly flows, with values of r and R of approximately 0.98. The ETD model also showed strong correlations with linear (r) and rank (R) correlation coefficients of 0.896 and 0.892, respectively. The results of the analyses showed that TMWAM provided the best simulation of pH (E=0.264, r=0.648), which is slightly better than ETD (E=0.240, r=0.549), and much better than ILWAS (E=-2.965, r=0.293), and RAINS (E=-4.004, r=0.473). ETD was found to be superior in predicting ANC (E=0.608, r=0.781) as compared to TMWAM (E=0.340, r=0.598), ILWAS (E=0.275, r=0.442), and RAINS (E=-1.048, r=0.356). The TMWAM model adequately simulated SO4 over the four-year period (E=0.423, r=0.682) but the ETD (E=-0.904, r=0.274), ILWAS (E=-4.314, r=0.488), and RAINS (E=-6.479, r=0.126) models all performed poorer than the benchmark model (mean observed value).

Measurement of transverse energy at midrapidity in Pb-Pb collisions at √{sNN}=2.76 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Cabala, J.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; de, S.; de Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; De Marco, N.; de Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; Deplano, C.; Dhankher, P.; di Bari, D.; di Mauro, A.; di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, A. S.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbär, E.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lapidus, K.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; McDonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira de Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, D.; Pagano, P.; Paić, G.; Pal, S. K.; Pan, J.; Pandey, A. K.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Pereira da Costa, H.; Peresunko, D.; Pérez Lara, C. E.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ruzza, B. D.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarkar, N.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shahzad, M. I.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; de Souza, R. D.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Sumowidagdo, S.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thakur, D.; Thomas, D.; Tieulent, R.; Tikhonov, A.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Valencia Palomo, L.; Vallero, S.; van der Maarel, J.; van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vázquez Doce, O.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yang, P.; Yano, S.; Yasin, Z.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.; Alice Collaboration

2016-09-01

We report the transverse energy (ET) measured with ALICE at midrapidity in Pb-Pb collisions at √{sN N}=2.76 TeV as a function of centrality. The transverse energy was measured using identified single-particle tracks. The measurement was cross checked using the electromagnetic calorimeters and the transverse momentum distributions of identified particles previously reported by ALICE. The results are compared to theoretical models as well as to results from other experiments. The mean ET per unit pseudorapidity (η ), , in 0%-5% central collisions is 1737 ±6 (stat .)±97 (sys .) GeV. We find a similar centrality dependence of the shape of as a function of the number of participating nucleons to that seen at lower energies. The growth in at the LHC energies exceeds extrapolations of low-energy data. We observe a nearly linear scaling of with the number of quark participants. With the canonical assumption of a 1 fm/c formation time, we estimate that the energy density in 0%-5% central Pb-Pb collisions at √{sN N}=2.76 TeV is 12.3 ±1.0 GeV/fm 3 and that the energy density at the most central 80 fm2 of the collision is at least 21.5 ±1.7 GeV/fm 3 . This is roughly 2.3 times that observed in 0%-5% central Au-Au collisions at √{sN N}=200 GeV.

Stakeholders apply the GRADE evidence-to-decision framework to facilitate coverage decisions.

PubMed

Dahm, Philipp; Oxman, Andrew D; Djulbegovic, Benjamin; Guyatt, Gordon H; Murad, M Hassan; Amato, Laura; Parmelli, Elena; Davoli, Marina; Morgan, Rebecca L; Mustafa, Reem A; Sultan, Shahnaz; Falck-Ytter, Yngve; Akl, Elie A; Schünemann, Holger J

2017-06-01

Coverage decisions are complex and require the consideration of many factors. A well-defined, transparent process could improve decision-making and facilitate decision-maker accountability. We surveyed key US-based stakeholders regarding their current approaches for coverage decisions. Then, we held a workshop to test an evidence-to-decision (EtD) framework for coverage based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria. A total of 42 individuals (including 19 US stakeholders as well as international health policymakers and GRADE working group members) attended the workshop. Of the 19 stakeholders, 14 (74%) completed the survey before the workshop. Almost all of their organizations (13 of 14; 93%) used systematic reviews for coverage decision-making; few (2 of 14; 14%) developed their own evidence synthesis; a majority (9 of 14; 64%) rated the certainty of evidence (using various systems); almost all (13 of 14; 93%) denied formal consideration of resource use; and half (7 of 14; 50%) reported explicit criteria for decision-making. At the workshop, stakeholders successfully applied the EtD framework to four case studies and provided narrative feedback, which centered on contextual factors affecting coverage decisions in the United States, the need for reliable data on subgroups of patients, and the challenge of decision-making without formal consideration of resource use. Stakeholders successfully applied the EtD framework to four case studies and highlighted contextual factors affecting coverage decisions and affirmed its value. Their input informed the further development of a revised EtD framework, now publicly available (http://gradepro.org/). Published by Elsevier Inc.

Noninvasive assessment of the intracranial pressure in non-traumatic intracranial hemorrhage.

PubMed

Vaiman, Michael; Sigal, Tal; Kimiagar, Itzhak; Bekerman, Inessa

2016-12-01

The article describes the modified technique of measuring the diameters of the optic nerve sheath (ONSD) for assessment of the intracranial pressure (ICP) in patients with intracerebral or subarachnoid hemorrhage (SAH). The CT scans of 443 patients were analyzed retrospectively. The ONSDs were measured at 3mm behind the globe and at the point where the ophthalmic artery crosses the optic nerve. The ONSD/eyeball transverse diameter (ETD) ratio was calculated. The correlation analysis was performed with the Glasgow Coma Scale score, Hemispheric Stroke Scale score, Glasgow Outcome Score, and invasive ICP readings. ONSD was enlarged in 95% of patients with intracerebral hemorrhage or SAH. Pathological ONSDs were 6.6±0.8mm (cut-off value >5.5mm; p<0.05). ONSD/ETD ratio was 0.29±0.05 against normative 0.19±0.02 (p<0.01) with no correlation with initial Glasgow Coma Scale score or Hemispheric Stroke Scale score. There was an inverse correlation between ONSD/ETD ratio and Glasgow Outcome Score (r=-0.7) and direct correlation with invasive ICP readings. This study provides further evidence that in patients with intracranial hemorrhage and SAH, the presence of ONSD greater than a threshold of 5.5mm is significantly predictive of invasively measured elevated ICP. The prediction of raised ICP can be further refined by measuring ONSD at the point where the optic nerve and the ophthalmic artery cross, and by determining the ratio between the ONSD and ETD. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Early Tech Development Course: Experiential Commercialization Education for the Medical Academician.

PubMed

Servoss, Jonathan; Chang, Connie; Fay, Jonathan; Ward, Kevin

2017-04-01

Research produced by medical academicians holds promise for developing into biomedical innovations in therapeutics, devices, diagnostics, and health care information technology; however, the road to biomedical innovation is fraught with risk, including the challenge of moving from basic research insight onto a viable commercialization path. Compounding this challenge is the growing demand on medical academicians to be more productive in their clinical, teaching, and research duties within a resource-constrained environment. In 2014, the University of Michigan (UM) Medical School and College of Engineering codesigned and implemented an accelerated, biomedical-focused version of the National Science Foundation (NSF) Innovation Corps (I-Corps) program. The UM Early Tech Development (ETD) Course, designed for medical academicians exploring the commercial potential of early-stage ideas, covers the NSF I-Corps concept; supports the formation of teams of faculty, graduate, and medical students; and accommodates medical academicians' schedules. From 2014 to 2015, the ETD Course graduated 39 project teams from UM and other institutions. One-third of the teams have continued to pursue their projects, receiving additional funding, engaging industry partners, or enrolling in the NSF I-Corps program. The ETD Course, a potential pipeline to the NSF I-Corps program, captures a target audience of medical academicians and others in academic medicine. To better understand the long-term effects of the course and its relationship to the NSF I-Corps program, the authors will conduct a study on the careers of all ETD Course graduates, including those who have enrolled in NSF I-Corps versus those who have not.

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics.

PubMed

Tsiatsiani, Liana; Giansanti, Piero; Scheltema, Richard A; van den Toorn, Henk; Overall, Christopher M; Altelaar, A F Maarten; Heck, Albert J R

2017-02-03

A key step in shotgun proteomics is the digestion of proteins into peptides amenable for mass spectrometry. Tryptic peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) because the fragmentation rules are well-understood. Here, we investigate LysargiNase, a perfect trypsin mirror protease, because it cleaves equally specific at arginine and lysine residues, albeit at the N-terminal end. LysargiNase peptides are therefore practically tryptic-like in length and sequence except that following ESI, the two protons are now both positioned at the N-terminus. Here, we compare side-by-side the chromatographic separation properties, gas-phase fragmentation characteristics, and (phospho)proteome sequence coverage of tryptic (i.e., (X) n K/R) and LysargiNase (i.e., K/R(X) n ) peptides using primarily electron-transfer dissociation (ETD) and, for comparison, HCD. We find that tryptic and LysargiNase peptides fragment nearly as mirror images. For LysargiNase predominantly N-terminal peptide ions (c-ions (ETD) and b-ions (HCD)) are formed, whereas for trypsin, C-terminal fragment ions dominate (z-ions (ETD) and y-ions (HCD)) in a homologous mixture of complementary ions. Especially during ETD, LysargiNase peptides fragment into low-complexity but information-rich sequence ladders. Trypsin and LysargiNase chart distinct parts of the proteome, and therefore, the combined use of these enzymes will benefit a more in-depth and reliable analysis of (phospho)proteomes.

The Early Tech Development Course: Experiential Commercialization Education for the Medical Academician

PubMed Central

Chang, Connie; Fay, Jonathan; Ward, Kevin

2017-01-01

Problem Research produced by medical academicians holds promise for developing into biomedical innovations in therapeutics, devices, diagnostics, and health care information technology; however, the road to biomedical innovation is fraught with risk, including the challenge of moving from basic research insight onto a viable commercialization path. Compounding this challenge is the growing demand on medical academicians to be more productive in their clinical, teaching, and research duties within a resource-constrained environment. Approach In 2014, the University of Michigan (UM) Medical School and College of Engineering codesigned and implemented an accelerated, biomedical-focused version of the National Science Foundation (NSF) Innovation Corps (I-Corps) program. The UM Early Tech Development (ETD) Course, designed for medical academicians exploring the commercial potential of early-stage ideas, covers the NSF I-Corps concept; supports the formation of teams of faculty, graduate, and medical students; and accommodates medical academicians’ schedules. Outcomes From 2014 to 2015, the ETD Course graduated 39 project teams from UM and other institutions. One-third of the teams have continued to pursue their projects, receiving additional funding, engaging industry partners, or enrolling in the NSF I-Corps program. Next Steps The ETD Course, a potential pipeline to the NSF I-Corps program, captures a target audience of medical academicians and others in academic medicine. To better understand the long-term effects of the course and its relationship to the NSF I-Corps program, the authors will conduct a study on the careers of all ETD Course graduates, including those who have enrolled in NSF I-Corps versus those who have not. PMID:28351064

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

Zhang, Qibin; Tang, Ning; Brock, Jonathan W.

Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resultedmore » in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.« less

Enrichment and Analysis of Non-enzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron Transfer Dissociation Mass Spectrometry

PubMed Central

Zhang, Qibin; Tang, Ning; Brock, Jonathan W. C.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

2008-01-01

Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus. PMID:17488106

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin

NASA Astrophysics Data System (ADS)

Lermyte, Frederik; Łącki, Mateusz Krzysztof; Valkenborg, Dirk; Gambin, Anna; Sobott, Frank

2017-01-01

Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions—primarily different forms of charge reduction—occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/ z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are `preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction.

Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides

PubMed Central

Liu, Jian; McLuckey, Scott A.

2012-01-01

The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation. PMID:23264749

The quantitative evaluation of intracranial pressure by optic nerve sheath diameter/eye diameter CT measurement.

PubMed

Bekerman, Inessa; Sigal, Tal; Kimiagar, Itzhak; Ben Ely, Anna; Vaiman, Michael

2016-12-01

The changes of the optic nerve sheath diameter (ONSD) have been used to assess changes of the intracranial pressure for 20 years. The aim of this research was to further quantify the technique of measuring the ONSD for this purpose. Retrospective study of computed tomographic (CT) data of 1766 adult patients with intracranial hypotension (n=134) or hypertension (n=1632) were analyzed. The eyeball transverse diameter (ETD) and ONSD were obtained bilaterally, and the ONSD/ETD ratio was calculated. The ratio was used to calculate the normal ONSD for patients and to estimate the intracranial pressure of the patients before and after the onset of the pathology. Correlation analysis was performed with invasively measured intracranial pressure, the presence or absence of papilledema, sex, and age. In hypotension cases, the ONSD by CT was 3.4±0.7 mm (P=.03 against normative 4.4±0.8 mm). In cases with hypertension, the diameter was 6.9±1.3 (P=.02, with a cutoff value ˃5.5 mm). The ONSD/ETD ratio was 0.29±0.04 against 0.19±0.02 in healthy adults (P=.01). The ONSD and the ONSD/ETD ratio can indicate low intracranial pressure, but quantification is impossible at intracranial pressure less than 13 mm Hg. In elevated intracranial pressure, the ONSD and the ratio provide readings that correspond to readings in millimeters of mercury. The ONSD method, reinforced with additional calculations, may help to indicate a raised intracranial pressure, evaluate its severity quantitatively, and establish quantitative goals for treatment of intracranial hypertension, but the limitations of the method are to be taken into account. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of chemosensory function in patients with chronic Eustachian tube dysfunction prior to and after balloon dilatation.

PubMed

Ute, Walliczek-Dworschak; Lisa, Schmierer; Brandon, Greene; Robert, Pellegrino; Philipp, Dworschak; Stuck, Boris Alexander; Christian, Güldner

2018-10-01

Eustachian tube dysfunction (ETD) affects approximately 1% of adults in the general population. Non treated Eustachian tube dysfunction can result in chronic middle ear diseases, which have been shown to significantly affect taste sensitivity. A promising treatment is balloon dilatation of the Eustachian tube. The primary aim of the present study was to investigate whether individuals with ETD had impairment in chemosensory functions, and the changes of the chemosensory function after balloon dilatation of the Eustachian tube. 26 patients (17 female, 9 male) (=56 ears) suffering from ETD with a mean age of 39±15years were included in the present study. 20 patients (76%) returned to be evaluated at the follow up (=40 ears) 51±22days after balloon dilatation. For pre- and post operation, gustatory function was measured with a lateralized gustatory test with the taste strips and olfactory function was tested by means of the Sniffin' Sticks test battery (threshold, discrimination and identification (ID)). Patients' baseline taste function (summed taste score 9.8±3.5 (mean±SD)) was significantly impaired compared to normative data (summed taste score 12.4±2.3; p=0.002). After balloon dilatation of the Eustachian tube, the taste function remained stable (summed taste score 9.4±4.3; p=0.814). Olfactory function (odor ID, summed score (TDI)) improved postoperatively (TDI 32.4±3.6) compared to pre-operative scores (TDI 33.6±4.0; p=0.012), but not to a clinically relevant extent. This study suggests, that patients suffering from ETD exhibit reduced taste scores. Balloon dilatation of the Eustachian tube does not seem to influence gustatory function, but olfactory function showed improvement. Copyright © 2018 Elsevier B.V. All rights reserved.

Using Unconstrained Tongue Motion as an Alternative Control Mechanism for Wheeled Mobility

PubMed Central

Huo, Xueliang; Ghovanloo, Maysam

2015-01-01

Tongue drive system (TDS) is a tongue-operated, minimally invasive, unobtrusive, noncontact, and wireless assistive technology that infers users’ intentions by detecting and classifying their voluntary tongue motions, and translating them to user-defined commands. We have developed customized interface circuitry between an external TDS (eTDS) prototype and a commercial powered wheelchair (PWC) as well as three control strategies to evaluate the tongue motion as an alternative control input for wheeled mobility. We tested the eTDS performance in driving PWCs on 12 able-bodied human subjects, of which 11 were novice. The results showed that all subjects could complete navigation tasks by operating the PWC using their tongue motions. Despite little prior experience, the average time using the eTDS and the tongue was only approximately three times longer than using a joystick and the fingers. Navigation time was strongly dependant on the number of issued commands, which reduced by gaining experience. Particularly, the unintended issued commands (the Midas touch problem) were rare, demonstrating the effectiveness of the tongue tracking and external magnetic field cancellation algorithms as well as the safety of the TDS for wheeled mobility. PMID:19362901

Using unconstrained tongue motion as an alternative control mechanism for wheeled mobility.

PubMed

Huo, Xueliang; Ghovanloo, Maysam

2009-06-01

Tongue drive system (TDS) is a tongue-operated, minimally invasive, unobtrusive, noncontact, and wireless assistive technology that infers users' intentions by detecting and classifying their voluntary tongue motions, and translating them to user-defined commands. We have developed customized interface circuitry between an external TDS (eTDS) prototype and a commercial powered wheelchair (PWC) as well as three control strategies to evaluate the tongue motion as an alternative control input for wheeled mobility. We tested the eTDS performance in driving PWCs on 12 able-bodied human subjects, of which 11 were novice. The results showed that all subjects could complete navigation tasks by operating the PWC using their tongue motions. Despite little prior experience, the average time using the eTDS and the tongue was only approximately three times longer than using a joystick and the fingers. Navigation time was strongly dependant on the number of issued commands, which reduced by gaining experience. Particularly, the unintended issued commands (the Midas touch problem) were rare, demonstrating the effectiveness of the tongue tracking and external magnetic field cancellation algorithms as well as the safety of the TDS for wheeled mobility.

Technology Base Research Project for electrochemical energy storage

NASA Astrophysics Data System (ADS)

Kinoshita, K.

1985-06-01

The DOE Electrochemical Energy Storage Program is divided into two projects: (1) the exploratory technology development and testing (ETD) project and (2) the technology base research (TBR) project. The role of the TBR Project is to perform supporting research for the advanced battery systems under development by the ETD Project, and to evaluate new systems with potentially superior performance, durability and/or cost characteristics. The specific goal of the TBR Project is to identify the most promising electrochemical technologies and transfer them to industry and/or the ETD Project for further development and scale-up. This report summarizes the research, financial, and management activities relevant to the TBR Project in CY 1984. General problem areas addressed by the project include identification of new electrochemical couples for advanced batteries, determination of technical feasibility of the new couples, improvements in battery components and materials, establishment of engineering principles applicable to electrochemical energy storage and conversion, and the assessment of fuel-cell technology for transportation applications. Major emphasis is given to applied research which will lead to superior performance and lower life-cycle costs. The TBR Project is divided into three major project elements: exploratory research, applied science research, and air systems research.

Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS3 versus multi-stage activation tandem mass spectrometry

PubMed Central

Zhang, Qibin; Petyuk, Vladislav A.; Schepmoes, Athena A.; Orton, Daniel J.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Metz, Thomas O.

2009-01-01

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet widely available and often suffers from significantly lower sensitivity than CID. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss-triggered MS3 and multi-stage activation) during liquid chromatography/multi-stage mass spectrometric (LC/MSn) analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss-triggered MS3 experiments, MS3 scans triggered by neutral losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss-triggered MS3 approach resulted in much higher specificity. Both techniques are viable alternatives to ETD for identifying glycated peptides. PMID:18763275

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

NASA Astrophysics Data System (ADS)

Viglino, Emilie; Lai, Cheuk Kuen; Mu, Xiaoyan; Chu, Ivan K.; Tureček, František

2016-09-01

We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in CuII(2,2 ':6 ',2 ″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates.

Efficacy and Safety of Cannabidiol and Tetrahydrocannabivarin on Glycemic and Lipid Parameters in Patients With Type 2 Diabetes: A Randomized, Double-Blind, Placebo-Controlled, Parallel Group Pilot Study.

PubMed

Jadoon, Khalid A; Ratcliffe, Stuart H; Barrett, David A; Thomas, E Louise; Stott, Colin; Bell, Jimmy D; O'Sullivan, Saoirse E; Tan, Garry D

2016-10-01

Cannabidiol (CBD) and Δ(9)-tetrahydrocannabivarin (THCV) are nonpsychoactive phytocannabinoids affecting lipid and glucose metabolism in animal models. This study set out to examine the effects of these compounds in patients with type 2 diabetes. In this randomized, double-blind, placebo-controlled study, 62 subjects with noninsulin-treated type 2 diabetes were randomized to five treatment arms: CBD (100 mg twice daily), THCV (5 mg twice daily), 1:1 ratio of CBD and THCV (5 mg/5 mg, twice daily), 20:1 ratio of CBD and THCV (100 mg/5 mg, twice daily), or matched placebo for 13 weeks. The primary end point was a change in HDL-cholesterol concentrations from baseline. Secondary/tertiary end points included changes in glycemic control, lipid profile, insulin sensitivity, body weight, liver triglyceride content, adipose tissue distribution, appetite, markers of inflammation, markers of vascular function, gut hormones, circulating endocannabinoids, and adipokine concentrations. Safety and tolerability end points were also evaluated. Compared with placebo, THCV significantly decreased fasting plasma glucose (estimated treatment difference [ETD] = -1.2 mmol/L; P < 0.05) and improved pancreatic β-cell function (HOMA2 β-cell function [ETD = -44.51 points; P < 0.01]), adiponectin (ETD = -5.9 × 10(6) pg/mL; P < 0.01), and apolipoprotein A (ETD = -6.02 μmol/L; P < 0.05), although plasma HDL was unaffected. Compared with baseline (but not placebo), CBD decreased resistin (-898 pg/ml; P < 0.05) and increased glucose-dependent insulinotropic peptide (21.9 pg/ml; P < 0.05). None of the combination treatments had a significant impact on end points. CBD and THCV were well tolerated. THCV could represent a new therapeutic agent in glycemic control in subjects with type 2 diabetes. © 2016 by the American Diabetes Association.

Sensitivity and specificity of eustachian tube function tests in adults.

PubMed

Doyle, William J; Swarts, J Douglas; Banks, Julianne; Casselbrant, Margaretha L; Mandel, Ellen M; Alper, Cuneyt M

2013-07-01

The study demonstrates the utility of eustachian tube (ET) function (ETF) test results for accurately assigning ears to disease state. To determine if ETF tests can identify ears with physician-diagnosed ET dysfunction (ETD) in a mixed population at high sensitivity and specificity and to define the interrelatedness of ETF test parameters. Through use of the forced-response, inflation-deflation, Valsalva, and sniffing tests, ETF was evaluated in 15 control ears of adult subjects after unilateral myringotomy (group 1) and in 23 ears of 19 adult subjects with ventilation tubes inserted for ETD (group 2). Data were analyzed using logistic regression including each parameter independently and then a step-down discriminant analysis including all ETF test parameters to predict group assignment. Factor analysis operating over all parameters was used to explore relatedness. ETF testing. ETF parameters for the forced response, inflation-deflation, Valsalva, and sniffing tests measured in 15 control ears of adult subjects after unilateral myringotomy (group 1) and in 23 ears of 19 adult subjects with ventilation tubes inserted for ETD (group 2). The discriminant analysis identified 4 ETF test parameters (Valsalva, ET opening pressure, dilatory efficiency, and percentage of positive pressure equilibrated) that together correctly assigned ears to group 2 at a sensitivity of 95% and a specificity of 83%. Individual parameters representing the efficiency of ET opening during swallowing showed moderately accurate assignments of ears to their respective groups. Three factors captured approximately 98% of the variance among parameters: the first had negative loadings of the ETF structural parameters; the second had positive loadings of the muscle-assisted ET opening parameters; and the third had negative loadings of the muscle-assisted ET opening parameters and positive loadings of the structural parameters. These results show that ETF tests can correctly assign individual ears to physician-diagnosed ETD with high sensitivity and specificity and that ETF test parameters can be grouped into structural-functional categories.

Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni*

PubMed Central

Scott, Nichollas E.; Parker, Benjamin L.; Connolly, Angela M.; Paulech, Jana; Edwards, Alistair V. G.; Crossett, Ben; Falconer, Linda; Kolarich, Daniel; Djordjevic, Steven P.; Højrup, Peter; Packer, Nicolle H.; Larsen, Martin R.; Cordwell, Stuart J.

2011-01-01

Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence. PMID:20360033

Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni.

PubMed

Scott, Nichollas E; Parker, Benjamin L; Connolly, Angela M; Paulech, Jana; Edwards, Alistair V G; Crossett, Ben; Falconer, Linda; Kolarich, Daniel; Djordjevic, Steven P; Højrup, Peter; Packer, Nicolle H; Larsen, Martin R; Cordwell, Stuart J

2011-02-01

Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence.

Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information

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

Shen, Yufeng; Tolic, Nikola; Purvine, Samuel O.

2011-11-07

The peptidome (i.e. processed and degraded forms of proteins) of e.g. blood can potentially provide insights into disease processes, as well as a source of candidate biomarkers that are unobtainable using conventional bottom-up proteomics approaches. MS dissociation methods, including CID, HCD, and ETD, can each contribute distinct identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant analysis and informatics challenges. In this work, we explored a simple approach for better utilization of high accuracy fragment ion mass measurements provided e.g. by FT MS/MS and demonstrate significant improvements relative to conventionalmore » descriptive and probabilistic scores methods. For example, at the same FDR level we identified 20-40% more peptides than SEQUEST and Mascot scoring methods using high accuracy fragment ion information (e.g., <10 mass errors) from CID, HCD, and ETD spectra. Species identified covered >90% of all those identified from SEQUEST, Mascot, and MS-GF scoring methods. Additionally, we found that the merging the different fragment spectra provided >60% more species using the UStags method than achieved previously, and enabled >1000 peptidome components to be identified from a single human blood plasma sample with a 0.6% peptide-level FDR, and providing an improved basis for investigation of potentially disease-related peptidome components.« less

On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin

NASA Astrophysics Data System (ADS)

Nicolardi, Simone; Giera, Martin; Kooijman, Pieter; Kraj, Agnieszka; Chervet, Jean-Pierre; Deelder, André M.; van der Burgt, Yuri E. M.

2013-12-01

Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80 % (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.

Highly Enhanced Electromechanical Stability of Large-Area Graphene with Increased Interfacial Adhesion Energy by Electrothermal-Direct Transfer for Transparent Electrodes.

PubMed

Kim, Jangheon; Kim, Gi Gyu; Kim, Soohyun; Jung, Wonsuk

2016-09-07

Graphene, a two-dimensional sheet of carbon atoms in a hexagonal lattice structure, has been extensively investigated for research and industrial applications as a promising material with outstanding electrical, mechanical, and chemical properties. To fabricate graphene-based devices, graphene transfer to the target substrate with a clean and minimally defective surface is the first step. However, graphene transfer technologies require improvement in terms of uniform transfer with a clean, nonfolded and nontorn area, amount of defects, and electromechanical reliability of the transferred graphene. More specifically, uniform transfer of a large area is a key challenge when graphene is repetitively transferred onto pretransferred layers because the adhesion energy between graphene layers is too low to ensure uniform transfer, although uniform multilayers of graphene have exhibited enhanced electrical and optical properties. In this work, we developed a newly suggested electrothermal-direct (ETD) transfer method for large-area high quality monolayer graphene with less defects and an absence of folding or tearing of the area at the surface. This method delivers uniform multilayer transfer of graphene by repetitive monolayer transfer steps based on high adhesion energy between graphene layers and the target substrate. To investigate the highly enhanced electromechanical stability, we conducted mechanical elastic bending experiments and reliability tests in a highly humid environment. This ETD-transferred graphene is expected to replace commercial transparent electrodes with ETD graphene-based transparent electrodes and devices such as a touch panels with outstanding electromechanical stability.

Optimizing Travel Time to Outpatient Interventional Radiology Procedures in a Multi-Site Hospital System Using a Google Maps Application.

PubMed

Mandel, Jacob E; Morel-Ovalle, Louis; Boas, Franz E; Ziv, Etay; Yarmohammadi, Hooman; Deipolyi, Amy; Mohabir, Heeralall R; Erinjeri, Joseph P

2018-02-20

The purpose of this study is to determine whether a custom Google Maps application can optimize site selection when scheduling outpatient interventional radiology (IR) procedures within a multi-site hospital system. The Google Maps for Business Application Programming Interface (API) was used to develop an internal web application that uses real-time traffic data to determine estimated travel time (ETT; minutes) and estimated travel distance (ETD; miles) from a patient's home to each a nearby IR facility in our hospital system. Hypothetical patient home addresses based on the 33 cities comprising our institution's catchment area were used to determine the optimal IR site for hypothetical patients traveling from each city based on real-time traffic conditions. For 10/33 (30%) cities, there was discordance between the optimal IR site based on ETT and the optimal IR site based on ETD at non-rush hour time or rush hour time. By choosing to travel to an IR site based on ETT rather than ETD, patients from discordant cities were predicted to save an average of 7.29 min during non-rush hour (p = 0.03), and 28.80 min during rush hour (p < 0.001). Using a custom Google Maps application to schedule outpatients for IR procedures can effectively reduce patient travel time when more than one location providing IR procedures is available within the same hospital system.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy.

PubMed

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P; Nguyen, Huong T H; Dang, Andy; Tureček, František

2018-01-16

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z 4 + H] +● fragment ion-radicals of the R-C ● H-CONH- type, initially formed by N-C α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [ ● DAAR + H] + isomers and used to assign structures to the action spectra. The potential energy surface of [ ● DAAR + H] + isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [ ● XAAR + H] + ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H] ● -ETD fragments containing Asp, Asn, Glu, and Gln residues. Graphical Abstract ᅟ.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P.; Nguyen, Huong T. H.; Dang, Andy; Tureček, František

2018-01-01

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z4 + H]+● fragment ion-radicals of the R-C●H-CONH- type, initially formed by N-Cα bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [●DAAR + H]+ isomers and used to assign structures to the action spectra. The potential energy surface of [●DAAR + H]+ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [●XAAR + H]+ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone Cα positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]●-ETD fragments containing Asp, Asn, Glu, and Gln residues. [Figure not available: see fulltext.

Morphology and Structure of High-redshift Massive Galaxies in the CANDELS Fields

NASA Astrophysics Data System (ADS)

Guan-wen, Fang; Ze-sen, Lin; Xu, Kong

2018-01-01

Using the multi-band photometric data of all five CANDELS (Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey) fields and the near-infrared (F125W and F160W) high-resolution images of HST WFC3 (Hubble Space Telescope Wide Field Camera 3), a quantitative study of morphology and structure of mass-selected galaxies is presented. The sample includes 8002 galaxies with a redshift 1 < z < 3 and stellar mass M*> 1010M⊙. Based on the Convolutional Neural Network (ConvNet) criteria, we classify the sample galaxies into SPHeroids (SPH), Early-Type Disks (ETD), Late-Type Disks (LTD), and IRRegulars (IRR) in different redshift bins. The findings indicate that the galaxy morphology and structure evolve with redshift up to z ∼ 3, from irregular galaxies in the high-redshift universe to the formation of the Hubble sequence dominated by disks and spheroids. For the same redshift interval, the median values of effective radii (re) of different morphological types are in a descending order: IRR, LTD, ETD, and SPH. But for the Sérsic index (n), the order is reversed (SPH, ETD, LTD, and IRR). In the meantime, the evolution of galaxy size (re) with the redshift is explored for the galaxies of different morphological types, and it is confirmed that their size will enlarge with time. However, such a phenomenon is not found in the relations between the redshift (1 < z < 3) and the mean axis ratio (b/a), as well as the Sérsic index (n).

Smooth pursuit eye movements in 1,087 men: effects of schizotypy, anxiety, and depression.

PubMed

Smyrnis, Nikolaos; Evdokimidis, Ioannis; Mantas, Asimakis; Kattoulas, Emmanouil; Stefanis, Nicholas C; Constantinidis, Theodoros S; Avramopoulos, Dimitrios; Stefanis, Costas N

2007-05-01

Individuals with schizotypal personality disorder or high scores in questionnaires measuring schizotypy are at high risk for the development of schizophrenia and they also share some of the same phenotypic characteristics such as eye-tracking dysfunction (ETD). The question arises whether these individuals form a distinct high-risk group in the general population or whether schizotypy and ETD co-vary in the general population with no distinct cutoff point for a high-risk group. A large sample of military conscripts aged 18-25 were screened using oculomotor, cognitive and psychometric tools for the purposes of a prospective study on predisposing factors for the development of psychosis. Schizotypy measured using the perceptual aberration scale (PAS) and the schizotypal personality questionnaire (SPQ), anxiety and depression, measured using the Symptom Checklist 90-R, had no effect on pursuit performance in the total sample. Small groups of individuals with very high scores in schizotypy questionnaires were then identified. These groups were not mutually exclusive. The high PAS group had higher root-mean-square error scores (a quantitative measure for pursuit quality) than the total sample, and the high disorganized factor of SPQ group had lower gain and higher saccade frequencies in pursuit than the total sample. The presence of significant differences in pursuit performance only for predefined high schizotypy groups favors the hypothesis that individuals with high schizotypy might present one or more high-risk groups, distinct from the general population, that are prone to ETD as that observed in schizophrenia.

High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples*

PubMed Central

Madsen, James A.; Xu, Hua; Robinson, Michelle R.; Horton, Andrew P.; Shaw, Jared B.; Giles, David K.; Kaoud, Tamer S.; Dalby, Kevin N.; Trent, M. Stephen; Brodbelt, Jennifer S.

2013-01-01

The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS1 and MS2 data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collision-induced dissociation of peptide cations, and when these methods were combined into a single search, an increase of up to 13% sequence coverage was observed for the kinases. The ability to sequence peptide anions and cations in alternating scans in the same chromatographic run was also demonstrated. Because ETD has a significant bias toward identifying highly basic peptides, negative UVPD was used to improve the identification of the more acidic peptides in conjunction with positive ETD for the more basic species. In this case, tryptic peptides from the cytosolic section of HeLa cells were analyzed by polarity switching nanoLC-MS/MS utilizing ETD for cation sequencing and UVPD for anion sequencing. Relative to searching using ETD alone, positive/negative polarity switching significantly improved sequence coverages across identified proteins, resulting in a 33% increase in unique peptide identifications and more than twice the number of peptide spectral matches. PMID:23695934

Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

NASA Astrophysics Data System (ADS)

Medzihradszky, Katalin F.; Bohlen, Christopher J.

2012-05-01

A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

Deflection Analysis of the Space Shuttle External Tank Door Drive Mechanism

NASA Technical Reports Server (NTRS)

Tosto, Michael A.; Trieu, Bo C.; Evernden, Brent A.; Hope, Drew J.; Wong, Kenneth A.; Lindberg, Robert E.

2008-01-01

Upon observing an abnormal closure of the Space Shuttle s External Tank Doors (ETD), a dynamic model was created in MSC/ADAMS to conduct deflection analyses for assessing whether the Door Drive Mechanism (DDM) was subjected to excessive additional stress, and more importantly, to evaluate the magnitude of the induced step or gap with respect to shuttle s body tiles. To model the flexibility of the DDM, a lumped parameter approximation was used to capture the compliance of individual parts within the drive linkage. These stiffness approximations were then validated using FEA and iteratively updated in the model to converge on the actual distributed parameter equivalent stiffnesses. The goal of the analyses is to determine the deflections in the mechanism and whether or not the deflections are in the region of elastic or plastic deformation. Plastic deformation may affect proper closure of the ETD and would impact aero-heating during re-entry.

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.

PubMed

Swaney, Danielle L; Wenger, Craig D; Thomson, James A; Coon, Joshua J

2009-01-27

Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology--collision-activated dissociation (CAD)--and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors--OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD (8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved.

Artistic drawing as a mnemonic device

NASA Astrophysics Data System (ADS)

Baker Christensen, Leslie

Despite art-based learning being widely used, existing data are primarily qualitative, and most research has not isolated particular variables such as memory for empirical study. The few experiments that have been conducted demonstrated that drawing improves free recall of unpaired words, and retention improves after lessons integrated with drawing, drama, and narrative exercises. To help fill the gap in the current literature, the present study compared the effectiveness of encoding and the rate of memory decay between a drawing mnemonic and note taking on a paired associates task. Using a within-subjects experimental design, participants were presented with word pairs and asked to complete either a drawing mnemonic (DM) or note taking (NT) to assist memorization. Participants were tested immediately after the word pair presentation and after a 20-minute delay. Results supported the hypothesis that the DM condition would produce superior encoding, as evidenced by greater retention on the immediate test. However, no memory decay was observed in the experiment, and therefore results on the delayed test were inconclusive. In fact, scores for the NT condition improved over time whereas the scores for the DM condition did not, which might imply that note taking results in a different consolidation process than drawing. Findings from this study suggested that arts integration can be an effective method to support memory for learned information. Future studies that examine the effect of rehearsal and the long-term effectiveness of a drawing mnemonic are warranted. This dissertation is available in open access at AURA, http://aura.antioch.edu/ and Ohio Link ETD Center, https://etd.ohiolink.edu/etd.

Sensitivity and Specificity of Eustachian Tube Function Tests in Adults

PubMed Central

Doyle, William J.; Swarts, J. Douglas; Banks, Julianne; Casselbrant, Margaretha L; Mandel, Ellen M; Alper, Cuneyt M.

2013-01-01

Objective Determine if Eustachian Tube (ET) function (ETF) tests can identify ears with physician-diagnosed ET dysfunction (ETD) in a mixed population at high sensitivity and specificity and define the inter-relatedness of ETF test parameters. Methods ETF was evaluated using the Forced-Response, Inflation-Deflation, Valsalva and Sniffing tests in 15 control ears of adult subjects after unilateral myringotomy (Group I) and in 23 ears of 19 adult subjects with ventilation tubes inserted for ETD (Group II). Data were analyzed using logistic regression including each parameter independently and then a step-down Discriminant Analysis including all ETF test parameters to predict group assignment. Factor Analysis operating over all parameters was used to explore relatedness. Results The Discriminant Analysis identified 4 ETF test parameters (Valsalva, ET opening pressure, dilatory efficiency and % positive pressure equilibrated) that together correctly assigned ears to Group II at a sensitivity of 95% and a specificity of 83%. Individual parameters representing the efficiency of ET opening during swallowing showed moderately accurate assignments of ears to their respective groups. Three factors captured approximately 98% of the variance among parameters, the first had negative loadings of the ETF structural parameters, the second had positive loadings of the muscle-assisted ET opening parameters and the third had negative loadings of the muscle-assisted ET opening parameters and positive loadings of the structural parameters. Discussion These results show that ETF tests can correctly assign individual ears to physician-diagnosed ETD with high sensitivity and specificity and that ETF test parameters can be grouped into structural-functional categories. PMID:23868429

Age: An effect modifier of the association between allergic rhinitis and Otitis media with effusion.

PubMed

Roditi, Rachel E; Veling, Maria; Shin, Jennifer J

2016-07-01

1) To determine whether there is a significant relationship between allergic rhinitis and otitis media with effusion (OME), Eustachian tube dysfunction (ETD), or tympanic membrane retraction (TMR) in children in a nationally representative population; and 2) to determine whether age is an effect modifier of any such association because this hypothesis has yet to be tested. Retrospective analysis of cross-sectional national databases with limited potential for referral bias. National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey, 2005-2010. Univariate, multivariate, stratified, and subgroup analyses were performed as defined a priori. The primary outcomes were OME, ETD, or TMR; the primary predictor variable was allergic rhinitis, with age evaluated as an effect modifier. Data representing 1,491,045,375 pediatric visits were examined and demonstrated that age was an effect modifier of the assessed association. More specifically, in children 6 years of age or older, the presence of allergic rhinitis significantly increased the odds of OME, ETD, or TMR (odds ratio [OR] 4.20; 95% confidence interval [CI] 2.17, 8.09; P < 0.001), whereas in children less than 6 years of age there was no significant association (OR 1.13; 95% CI 0.53, 2.46; P = 0.745). Age is an effect modifier of the association between allergic rhinitis and OME; a significant relationship is observed in children 6 years of age and older, whereas there is no significant association in younger children. 2c. Laryngoscope, 126:1687-1692, 2016. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

Staphylococcus aureus nasal carriage in Ukraine: antibacterial resistance and virulence factor encoding genes.

PubMed

Netsvyetayeva, Irina; Fraczek, Mariusz; Piskorska, Katarzyna; Golas, Marlena; Sikora, Magdalena; Mlynarczyk, Andrzej; Swoboda-Kopec, Ewa; Marusza, Wojciech; Palmieri, Beniamino; Iannitti, Tommaso

2014-03-05

The number of studies regarding the incidence of multidrug resistant strains and distribution of genes encoding virulence factors, which have colonized the post-Soviet states, is considerably limited. The aim of the study was (1) to assess the Staphylococcus (S.) aureus nasal carriage rate, including Methicillin Resistant S. aureus (MRSA) strains in adult Ukrainian population, (2) to determine antibiotic resistant pattern and (3) the occurrence of Panton Valentine Leukocidine (PVL)-, Fibronectin-Binding Protein A (FnBPA)- and Exfoliative Toxin (ET)-encoding genes. Nasal samples for S. aureus culture were obtained from 245 adults. The susceptibility pattern for several classes of antibiotics was determined by disk diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The virulence factor encoding genes, mecA, lukS-lukF, eta, etb, etd, fnbA, were detected by Polymerase Chain Reaction (PCR). The S. aureus nasal carriage rate was 40%. The prevalence of nasal MRSA carriage in adults was 3.7%. LukS-lukF genes were detected in over 58% of the strains. ET-encoding genes were detected in over 39% of the strains and the most prevalent was etd. The fnbA gene was detected in over 59% of the strains. All MRSA isolates tested were positive for the mecA gene. LukS-lukF genes and the etd gene were commonly co-present in MRSA, while lukS-lukF genes and the fnbA gene were commonly co-present in Methicillin Sensitive S. aureus (MSSA) isolates. No significant difference was detected between the occurrence of lukS-lukF genes (P > 0.05) and the etd gene (P > 0.05) when comparing MRSA and MSSA. The occurrence of the fnbA gene was significantly more frequent in MSSA strains (P < 0.05). In Ukraine, S. aureus is a common cause of infection. The prevalence of S. aureus nasal carriage in our cohort of patients from Ukraine was 40.4%. We found that 9.1% of the strains were classified as MRSA and all MRSA isolates tested positive for the mecA gene. We also observed a high prevalence of PVL- and ET- encoding genes among S. aureus nasal carriage strains. A systematic surveillance system can help prevent transmission and spread of drug resistant toxin producing S. aureus strains.

GENETIC SUSCEPTIBILITY AND EXPERIMENTAL INDUCTION OF PULMONARY DISEASE

EPA Science Inventory

Genetic Susceptibility and Experimental Induction of Pulmonary Disease. UP Kodavanti, MC Schladweiler, AD Ledbetter, PS Gilmour, P Evansky, KR Smith*, WP Watkinson, DL Costa, KE Pinkerton*. ETD, NHEERL, ORD, US EPA, RTP, NC; *Univ California, Davis, CA, USA.
Conventional la...

The ETD-like fragmentation for small molecules

USDA-ARS?s Scientific Manuscript database

Introduction (137) Flavonoids are a class of plant and fungus secondary metabolites (three-ring structure C6-C3-C6 with various substitutions) involved in many functions such as pigmentation, UV filtration, symbiotic nitrogen fixation, cell cycle inhibitors, and defense mechanisms. These polyphenoli...

New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets.

PubMed

Zhu, Zhikai; Su, Xiaomeng; Go, Eden P; Desaire, Heather

2014-09-16

Glycoproteins are biologically significant large molecules that participate in numerous cellular activities. In order to obtain site-specific protein glycosylation information, intact glycopeptides, with the glycan attached to the peptide sequence, are characterized by tandem mass spectrometry (MS/MS) methods such as collision-induced dissociation (CID) and electron transfer dissociation (ETD). While several emerging automated tools are developed, no consensus is present in the field about the best way to determine the reliability of the tools and/or provide the false discovery rate (FDR). A common approach to calculate FDRs for glycopeptide analysis, adopted from the target-decoy strategy in proteomics, employs a decoy database that is created based on the target protein sequence database. Nonetheless, this approach is not optimal in measuring the confidence of N-linked glycopeptide matches, because the glycopeptide data set is considerably smaller compared to that of peptides, and the requirement of a consensus sequence for N-glycosylation further limits the number of possible decoy glycopeptides tested in a database search. To address the need to accurately determine FDRs for automated glycopeptide assignments, we developed GlycoPep Evaluator (GPE), a tool that helps to measure FDRs in identifying glycopeptides without using a decoy database. GPE generates decoy glycopeptides de novo for every target glycopeptide, in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides, are scored against the ETD data, from which FDRs can be calculated accurately based on the number of decoy matches and the ratio of the number of targets to decoys, for small data sets. GPE is freely accessible for download and can work with any search engine that interprets ETD data of N-linked glycopeptides. The software is provided at https://desairegroup.ku.edu/research.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data

NASA Astrophysics Data System (ADS)

Hamuro, Yoshitomo; E, Sook Yen

2018-05-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. [Figure not available: see fulltext.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data.

PubMed

Hamuro, Yoshitomo; E, Sook Yen

2018-05-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. Graphical Abstract ᅟ.

Free visual exploration of natural movies in schizophrenia.

PubMed

Silberg, Johanna Elisa; Agtzidis, Ioannis; Startsev, Mikhail; Fasshauer, Teresa; Silling, Karen; Sprenger, Andreas; Dorr, Michael; Lencer, Rebekka

2018-01-05

Eye tracking dysfunction (ETD) observed with standard pursuit stimuli represents a well-established biomarker for schizophrenia. How ETD may manifest during free visual exploration of real-life movies is unclear. Eye movements were recorded (EyeLink®1000) while 26 schizophrenia patients and 25 healthy age-matched controls freely explored nine uncut movies and nine pictures of real-life situations for 20 s each. Subsequently, participants were shown still shots of these scenes to decide whether they had explored them as movies or pictures. Participants were additionally assessed on standard eye-tracking tasks. Patients made smaller saccades (movies (p = 0.003), pictures (p = 0.002)) and had a stronger central bias (movies and pictures (p < 0.001)) than controls. In movies, patients' exploration behavior was less driven by image-defined, bottom-up stimulus saliency than controls (p < 0.05). Proportions of pursuit tracking on movies differed between groups depending on the individual movie (group*movie p = 0.011, movie p < 0.001). Eye velocity on standard pursuit stimuli was reduced in patients (p = 0.029) but did not correlate with pursuit behavior on movies. Additionally, patients obtained lower rates of correctly identified still shots as movies or pictures (p = 0.046). Our results suggest a restricted centrally focused visual exploration behavior in patients not only on pictures, but also on movies of real-life scenes. While ETD observed in the laboratory cannot be directly transferred to natural viewing conditions, these alterations support a model of impairments in motion information processing in patients resulting in a reduced ability to perceive moving objects and less saliency driven exploration behavior presumably contributing to alterations in the perception of the natural environment.

Toward a suitable structural analysis of gene delivery carrier based on polycationic carbohydrates by electron transfer dissociation tandem mass spectrometry.

PubMed

Przybylski, Cédric; Benito, Juan M; Bonnet, Véronique; Mellet, Carmen Ortiz; García Fernández, José M

2016-12-15

Polycationic carbohydrates represent an attractive class of biomolecules for several applications and particularly as non viral gene delivery vectors. In this case, the establishment of structure-biological activity relationship requires sensitive and accurate characterization tools to both control and achieve fine structural deciphering. Electrospray-tandem mass spectrometry (ESI-MS/MS) appears as a suitable approach to address these questions. In the study herein, we have investigated the usefulness of electron transfer dissociation (ETD) to get structural data about five polycationic carbohydrates demonstrated as promising gene delivery agents. A particular attention was paid to determine the influence of charge states as well as both fluoranthene reaction time and supplementary activation (SA) on production of charge reduced species, fragmentation yield, varying from 2 to 62%, as well as to obtain the most higher both diversity and intensity of fragments, according to charge states and targeted compounds. ETD fragmentation appeared to be mainly directed toward pending group rather than carbohydrate cyclic scaffold leading to a partial sequencing for building blocks when amino groups are close to carbohydrate core, but allowing to complete structural deciphering of some of them, such as those including dithioureidocysteaminyl group which was not possible with CID only. Such findings clearly highlight the potential to help the rational choice of the suitable analytical conditions, according to the nature of the gene delivery molecules exhibiting polycationic features. Moreover, our ETD-MS/MS approach open the way to a fine sequencing/identification of grafted groups carried on various sets of oligo-/polysaccharides in various fields such as glycobiology or nanomaterials, even with unknown or questionable extraction, synthesis or modification steps. Copyright © 2016 Elsevier B.V. All rights reserved.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data

NASA Astrophysics Data System (ADS)

Hamuro, Yoshitomo; E, Sook Yen

2018-03-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. [Figure not available: see fulltext.

Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization.

PubMed

Wiese, Heike; Kuhlmann, Katja; Wiese, Sebastian; Stoepel, Nadine S; Pawlas, Magdalena; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin; Drepper, Friedel; Warscheid, Bettina

2014-02-07

Over the past years, phosphoproteomics has advanced to a prime tool in signaling research. Since then, an enormous amount of information about in vivo protein phosphorylation events has been collected providing a treasure trove for gaining a better understanding of the molecular processes involved in cell signaling. Yet, we still face the problem of how to achieve correct modification site localization. Here we use alternative fragmentation and different bioinformatics approaches for the identification and confident localization of phosphorylation sites. Phosphopeptide-enriched fractions were analyzed by multistage activation, collision-induced dissociation and electron transfer dissociation (ETD), yielding complementary phosphopeptide identifications. We further found that MASCOT, OMSSA and Andromeda each identified a distinct set of phosphopeptides allowing the number of site assignments to be increased. The postsearch engine SLoMo provided confident phosphorylation site localization, whereas different versions of PTM-Score integrated in MaxQuant differed in performance. Based on high-resolution ETD and higher collisional dissociation (HCD) data sets from a large synthetic peptide and phosphopeptide reference library reported by Marx et al. [Nat. Biotechnol. 2013, 31 (6), 557-564], we show that an Andromeda/PTM-Score probability of 1 is required to provide an false localization rate (FLR) of 1% for HCD data, while 0.55 is sufficient for high-resolution ETD spectra. Additional analyses of HCD data demonstrated that for phosphotyrosine peptides and phosphopeptides containing two potential phosphorylation sites, PTM-Score probability cutoff values of <1 can be applied to ensure an FLR of 1%. Proper adjustment of localization probability cutoffs allowed us to significantly increase the number of confident sites with an FLR of <1%.Our findings underscore the need for the systematic assessment of FLRs for different score values to report confident modification site localization.

SPONTANEOUSLY HYPERTENSIVE RATS ARE SUSCEPTIBLE TO MICROVASCULAR THROMBOSIS IN RESPONSE TO PARTICULATE MATTER EXPOSURE

EPA Science Inventory

SPONTANEOUSLY HYPERTENSIVE RATS ARE SUSCEPTIBLE TO MICROVASCULAR THROMBOSIS IN RESPONSE TO PARTICULATE MATTER EXPOSURE.
PS Gilmour, MC Schladweiler, AD Ledbetter, and UP Kodavanti. US EPA, ORD, NHEERL, ETD, PTB, Research Triangle Park, NC USA.
Environmental particles (PM...

TARGETED DELIVERY OF INHALED PROTEINS

EPA Science Inventory

ETD-02-047 (Martonen) GPRA # 10108

TARGETED DELIVERY OF INHALED PROTEINS
T. B. Martonen1, J. Schroeter2, Z. Zhang3, D. Hwang4, and J. S. Fleming5
1Experimental Toxicology Division, National Health and Environmental Effects Research Laboratory, Research Triangle Park...

A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom

PubMed Central

Trevisan-Silva, Dilza; Bednaski, Aline V.; Fischer, Juliana S.G.; Veiga, Silvio S.; Bandeira, Nuno; Guthals, Adrian; Marchini, Fabricio K.; Leprevost, Felipe V.; Barbosa, Valmir C.; Senff-Ribeiro, Andrea; Carvalho, Paulo C.

2017-01-01

Venoms are a rich source for the discovery of molecules with biotechnological applications, but their analysis is challenging even for state-of-the-art proteomics. Here we report on a large-scale proteomic assessment of the venom of Loxosceles intermedia, the so-called brown spider. Venom was extracted from 200 spiders and fractioned into two aliquots relative to a 10 kDa cutoff mass. Each of these was further fractioned and digested with trypsin (4 h), trypsin (18 h), pepsin (18 h), and chymotrypsin (18 h), then analyzed by MudPIT on an LTQ-Orbitrap XL ETD mass spectrometer fragmenting precursors by CID, HCD, and ETD. Aliquots of undigested samples were also analyzed. Our experimental design allowed us to apply spectral networks, thus enabling us to obtain meta-contig assemblies, and consequently de novo sequencing of practically complete proteins, culminating in a deep proteome assessment of the venom. Data are available via ProteomeXchange, with identifier PXD005523. PMID:28696408

A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics.

PubMed

Marx, Harald; Lemeer, Simone; Schliep, Jan Erik; Matheron, Lucrece; Mohammed, Shabaz; Cox, Jürgen; Mann, Matthias; Heck, Albert J R; Kuster, Bernhard

2013-06-01

We present a peptide library and data resource of >100,000 synthetic, unmodified peptides and their phosphorylated counterparts with known sequences and phosphorylation sites. Analysis of the library by mass spectrometry yielded a data set that we used to evaluate the merits of different search engines (Mascot and Andromeda) and fragmentation methods (beam-type collision-induced dissociation (HCD) and electron transfer dissociation (ETD)) for peptide identification. We also compared the sensitivities and accuracies of phosphorylation-site localization tools (Mascot Delta Score, PTM score and phosphoRS), and we characterized the chromatographic behavior of peptides in the library. We found that HCD identified more peptides and phosphopeptides than did ETD, that phosphopeptides generally eluted later from reversed-phase columns and were easier to identify than unmodified peptides and that current computational tools for proteomics can still be substantially improved. These peptides and spectra will facilitate the development, evaluation and improvement of experimental and computational proteomic strategies, such as separation techniques and the prediction of retention times and fragmentation patterns.

Eye Tracking Dysfunction in Schizophrenia: Characterization and Pathophysiology

PubMed Central

Sereno, Anne B.; Gooding, Diane C.; O’Driscoll, Gilllian A.

2011-01-01

Eye tracking dysfunction (ETD) is one of the most widely replicated behavioral deficits in schizophrenia and is over-represented in clinically unaffected first-degree relatives of schizophrenia patients. Here, we provide an overview of research relevant to the characterization and pathophysiology of this impairment. Deficits are most robust in the maintenance phase of pursuit, particularly during the tracking of predictable target movement. Impairments are also found in pursuit initiation and correlate with performance on tests of motion processing, implicating early sensory processing of motion signals. Taken together, the evidence suggests that ETD involves higher-order structures, including the frontal eye fields, which adjust the gain of the pursuit response to visual and anticipated target movement, as well as early parts of the pursuit pathway, including motion areas (the middle temporal area and the adjacent medial superior temporal area). Broader application of localizing behavioral paradigms in patient and family studies would be advantageous for refining the eye tracking phenotype for genetic studies. PMID:21312405

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry

PubMed Central

Swaney, Danielle L.; Wenger, Craig D.; Thomson, James A.; Coon, Joshua J.

2009-01-01

Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology—collision-activated dissociation (CAD)—and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors—OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD (8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved. PMID:19144917

A Location Aware Middleware Framework for Collaborative Visual Information Discovery and Retrieval

DTIC Science & Technology

2017-09-14

Information Discovery and Retrieval Andrew J.M. Compton Follow this and additional works at: https://scholar.afit.edu/etd Part of the Digital...and Dissertations by an authorized administrator of AFIT Scholar. For more information , please contact richard.mansfield@afit.edu. Recommended Citation...

How Can Biologically-Based Modeling of Arsenic Kinetics and Dynamics Inform the Risk Assessment Process? -- ETD

EPA Science Inventory

Quantitative biologically-based models describing key events in the continuum from arsenic exposure to the development of adverse health effects provide a framework to integrate information obtained across diverse research areas. For example, genetic polymorphisms in arsenic me...

CARDIOPULMONARY GENE EXPRESSION PROFILES IN NORMO- AND SPONTANEOUSLY HYPERSENSITIVE (SH) RATS: IMPACT OF PARTICULATE MATTER (PM) EXPOSURE

EPA Science Inventory

CARDIOPULMONARY GENE EXPRESSION PROFILES IN NORMO- AND SPONTANEOUSLY HYPERTENSIVE (SH) RATS: IMPACT OF PARTICULATE MATTER (PM) EXPOSURE. SS Nadadur UP Kodavanti, Pulmonary Toxicology Branch, ETD, ORD, NHEERL, US Environmental Protection Agency, Research Triangle Park, NC 27711.

QUALITY CONTROL FOR RESEARCH STUDIES: A CRITICAL PART OF THE QUALITY SYSTEM AT THE U. S. EPA

EPA Science Inventory

QUALITY CONTROL FOR RESEARCH STUDIES: A CRITICAL PART OF THE QUALITY SYSTEM AT THE U.S. EPA Mette C.J. Schladweiler, Scientist, and Thomas J. Hughes, QA and Records Manager, Experimental Toxicology Division (ETD), National Health and Environmental Effects Research Laboratory (NHE...

Evaluation of Interoperability Protocols in Repositories of Electronic Theses and Dissertations

ERIC Educational Resources Information Center

Hakimjavadi, Hesamedin; Masrek, Mohamad Noorman

2013-01-01

Purpose: The purpose of this study is to evaluate the status of eight interoperability protocols within repositories of electronic theses and dissertations (ETDs) as an introduction to further studies on feasibility of deploying these protocols in upcoming areas of interoperability. Design/methodology/approach: Three surveys of 266 ETD…

Dissertation Genre Change as a Result of Electronic Theses and Dissertation Programs

ERIC Educational Resources Information Center

Pantelides, Kate

2015-01-01

The increasing prevalence of mandatory Electronic Theses and Dissertations (ETDs) policies has ushered in rather dramatic dissertation genre change. The affordances of the medium offer expanded access and audience, availability of new compositional tools, and alternate formats, the implications of which are just beginning to appear in…

Electronic Theses and Dissertations at the University of Virginia.

ERIC Educational Resources Information Center

Sharretts, Christina W.; Shieh, Jackie; French, James C.

1999-01-01

Describes the electronic theses and dissertations (ETD) program at the University of Virginia (UVA). The system is designed to be easy and self-explanatory. Submission instructions guide the student step-by-step. Screen messages, such as errors, are generated automatically when appropriate, while email messages, regarding the status of the…

ARE MACROPHAGES ACTIVATED AND INDUCE PULMONARY INJURY BY INTRACELLULARLY BIOAVAILABLE IRON?

EPA Science Inventory

ARE MACROPHAGES ACTIVATED AND INDUCE PULMONARY INJURY BY INTRACELLULARLY BIOAVAILABLE IRON? UP Kodavanti1, MCJ Schladweiler1, S Becker2, DL Costa1, P Mayer3, A Ziesenis3, WG Kreyling3, 1ETD, 2HSDivision, NHEERL, USEPA, Research Triangle Park, NC, USA, and 3GSF, Inhalation Biology...

PREDICTIVE SIMULATION MODELING FOR ANTIANDROGEN IMPACTS ON RODENT PROSTATE

EPA Science Inventory

Predictive simulation modeling for antiandrogen impacts on rodent prostate
HA Barton1, RW Setzer1, LK Potter1,2
1US EPA, ORD, NHEERL, ETD, PKB, Research Triangle Park, NC and 2Curriculum in Toxicology, UNC, Chapel Hill, NC

Changes in rodent prostate weight and functi...

RESIDUAL OIL FLY ASH (ROFA) AND VANADIUM-INDUCED GENE EXPRESSION PROFILES IN HUMAN VASCULAR ENDOTHELIAL CELLS

EPA Science Inventory

Residual oil fly ash (ROFA) and vanadium-induced gene expression profiles in human vascular endothelial cells.
Srikanth S. Nadadur, Urmila P. Kodavanti, Mary Jane Selgrade and Daniel L. Costa, Pulmonary Toxicology Branch, ETD, NHEERL, ORD, US EPA, Research Triangle Park, N...

The Long and Winding Road: Duties of an NHEERL QA Manager from 1999 to 2008

EPA Science Inventory

My career as a US EPA Quality Assurance Manager (QAM) started on September 26, 1999 when I was appointed the QA and Records Manager for the Experimental Toxicology Division (ETD) in NHEERL, in the Office of Research and Development (ORD), on the Research Triangle Campus in RTP, N...

COMPARISON OF DETOXIFICATION AND BIOACTIVATION PATHWAYS FOR BROMODICHLOROMETHANE IN THE RAT

EPA Science Inventory

Comparison of Detoxification and Bioactivation pathways FOR Bromodichloromethane in the Rat
M.K. Ross1, C.R. Eklund2, and R.A. Pegram2
1Curriculum in Toxicology, UNC-CH, Chapel Hill, NC
2ETD, NHEERL/ORD, USEPA, Research Triangle Park, NC

Bromodichloromethane (BDCM...

POSTNATAL DISPOSITION OF TCDD IN LONG EVANS RATS FOLLOWING GESTATIONAL EXPOSURE

EPA Science Inventory

POSTNATAL DISPOSITION OF TCDD IN LONG EVANS RATS FOLLOWING GESTATIONAL EXPOSURE.
J J Diliberto', J T Hamm'.2, F McQuaid', and L S Birnbaum'. 'US EPA, ORD/NHEERL/ETD, RTP, NC; 2Curriculum in Toxicology, University of North Carolina, Chapel Hill, NC.
2,3,7,8-Tetrachlorodibenz...

EFFECTS OF SUBCHRONIC EXPOSURE TO CONCENTRATED AMBIENT PARTICULATES IN SPONTANEOUSLY HYPERTENSIVE RATS

EPA Science Inventory

EFFECTS OF SUBCHRONIC EXPOSURE TO CONCENTRATED AMBIENT PARTICULATES IN SPONTANEOUSLY HYPERTENSIVE RATS. WP Watkinson1, LB Wichers2, JP Nolan1, DW Winsett1, UP Kodavanti1, MCJ Schladweiler1, and DL Costa1 1US EPA, ORD/NHEERL/ETD/PTB, RTP, NC; 2UNC SPH and Curriculum in Toxic...

Large-Scale Campus Computer Technology Implementation: Lessons from the First Year.

ERIC Educational Resources Information Center

Nichols, Todd; Frazer, Linda H.

The purpose of the Elementary Technology Demonstration Schools (ETDS) Project, funded by IBM and Apple, Inc., was to demonstrate the effectiveness of technology in accelerating the learning of low achieving at-risk students and enhancing the education of high achieving students. The paper begins by giving background information on the district,…

Early Childhood Development Cultural Considerations--Commonalities, Variables, and Local Community Determinants for Program Modules.

ERIC Educational Resources Information Center

Taylor, Anne P.; Warren, Dave

The paper discusses cultural commonality and variability considerations of the Native American populations served by the Federation of Rocky Mountain States Educational Technical Development (ETD) Project. Section I explores important factors to consider when setting up an Early Childhood Development program module for Indian people, such as…

IN VITRO METABOLISM OF PYRETHROIDS IN RAT LIVER MICROSOMES

EPA Science Inventory

IN VITRO METABOLISM OF PYRETHROIDS IN RAT LIVER MICROSOMES

SJ Godin1, RA Harrison2 MF. Hughes 2, MJ DeVito2; 1Curriculum In Toxicology, UNC-CH, Chapel Hill NC, USA; 2ETD, NHEERL, ORD, US EPA, RTP, NC, 27711, USA.

Pyrethroids are neurotoxic pesticides that bin...

METABOLISM OF VINCLOZOLIN AND ITS METABOLITES IN RATS

EPA Science Inventory

ETD-04-008

METABOLISM OF VINCLOZOLIN AND ITS METABOLITES IN RAT. A Sierra-Santoyo1, R Harrison2, H A Barton2 and M F Hughes2. 1Toxicology Section, CINVESTAV-IPN, Mexico City, Mexico; 2USEPA, ORD, NHEERL, RTP, NC.

Vinclozolin (V) is a fungicide used in agricultural...

Facing Future Users--The Challenge of Transforming a Traditional Online Database into a Web Service.

ERIC Educational Resources Information Center

Tolonen, Eva

The Energy Technology Data Exchange (ETDE) agreement included 19 member countries spanning four continents: Japan and the Republic of Korea; Belgium, Denmark, Finland, France, Germany, Italy, The Netherlands, Norway, Poland, Spain, Sweden, Switzerland, and the United Kingdom; Canada, Mexico, and the United States; and Brazil. The participating…

HPLC ANALYSIS OF VINCLOZOLIN AND ITS METABOLITES IN SERUM

EPA Science Inventory

HPLC ANALYSIS OF VINCLOZOLIN AND ITS METABOLITES IN SERUM. A Sierra-Santoyo1,2, H A Barton1 and M F Hughes1. 1US EPA, ORD, NHEERL, ETD, RTP, NC; 2Toxicology Section, CINVESTAV-IPN, Mexico City, Mexico.

The fungicide vinclozolin (V) is used predominantly for treatment...

INCORPORATION OF LABELED NITRIC OXIDE INTO RESPIRATORY TRACT LINING FLUIDS AND BLOOD PLASMA DURING LUNG INFLAMMATION

EPA Science Inventory

Incorporation of labeled nitric oxide (N18O) into respiratory tract lining fluids and blood plasma during lung inflammation. Slade, R., Norwood, J., Crissman, K., McKee, J., Hatch, G. PTB, ETD, NHEERL, ORD, USEPA, Res. Tri. Pk., NC

Our earlier studies have demonstrated t...

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...

NEUTROPHILS PLAY A CRITICAL ROLE IN THE DEVELOPMENT OF LPS-INDUCED AIRWAY DISEASE

EPA Science Inventory

ETD-02-045 (GAVETT) GPRA # 10108

Neutrophils Play a Critical Role in the Development of LPS-Induced Airway Disease.
Jordan D. Savov, Stephen H. Gavett*, David M. Brass, Daniel L. Costa*, and David A. Schwartz

ABSTRACT
We investigated the role of neutrophils...

Electronic Thesis Initiative: Pilot Project of McGill University, Montreal

ERIC Educational Resources Information Center

Park, Eun G.; Zou, Qing; McKnight, David

2007-01-01

Purpose: To set up a protocol for electronic thesis and dissertation (ETD) submission for the electronic thesis initiative pilot project at McGill University in Montreal, Canada. Design/methodology/approach: An electronic thesis and dissertation submission protocol was implemented and tested. To test authoring tools, we had 50 students submit…

APPLICATIONS OF A MODEL FOR THE HORMONAL REGULATION OF THE MENSTRUAL CYCLE

EPA Science Inventory

APPLICATIONS OF A MODEL FOR THE HORMONAL REGULATION OF THE MENSTRUAL CYCLE. Leona H. Clark1, Paul M. Schlosser2, and James F. Selgrade3. 1US Environmental Protection Agency, ORD, NHEERL, ETD, Research Triangle Park, NC; 2CIIT, Research Triangle Park, NC; 3North Carolina State Un...

DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROOVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

EPA Science Inventory

DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

Jeffry D. Schroeter, Curriculum in Toxicology, University of North Carolina, Chapel Hill, NC 27599; Ted B. Martonen, ETD, NHEERL, USEPA, RTP, NC 27711; Do...

DEVELOPING A PREDICTIVE SIMULATION MODEL FOR ANTIANDROGEN IMPACTS ON RODENT PROSTATE

EPA Science Inventory

Developing a predictive simulation model for antiandrogen impacts on rodent prostate
HA Barton1, RW Setzer1, LK Potter1,2
1US EPA, ORD, NHEERL, ETD, PKB, Research Triangle Park, NC and 2Curriculum in Toxicology, UNC, Chapel Hill, NC

Alterations in rodent prostate wei...

Czanderna Receives Research Award

Science.gov Websites

., May 5, 1999 — A scientist at the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) was recognized for his contributions to the science and technology of energy-related research . The Energy Technology Division (ETD) of The Electrochemical Society selected Dr. Al Czanderna for its

COMPARING ENVIRONMENTALLY RELEVANT PCBS TO TCDD

EPA Science Inventory

COMPARING ENVIRONMENTALLY RELEVANT PCBS TO TCDD. D E Burgin1, J J Diliberto2 and L S Birnbaum3.1UNC, Chapel Hill, NC, USA; 2USEPA/ORD/NHEERL, ETD, RTP, NC, USA

Environmental exposures to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) always occur as part of a complex mixture. ...

De novo peptide sequencing using CID and HCD spectra pairs.

PubMed

Yan, Yan; Kusalik, Anthony J; Wu, Fang-Xiang

2016-10-01

In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision-induced dissociation (CID) higher energy collisional dissociation (HCD), electron-capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full-length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry

NASA Astrophysics Data System (ADS)

Chen, Guangming; Zhang, Yixiang; Trinidad, Jonathan C.; Dann, Charles

2018-03-01

Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides. Multiple fragmentation techniques, namely HCD, CID, ETD, ETciD, and EThcD, have been used to compare the different fragmentation behaviors between peptides modified with these species. Sulfotyrosine undergoes neutral loss using HCD and CID, but the sulfuryl moiety is largely stable under ETD. In contrast, phosphotyrosine is stable during fragmentation using all these methods. This differential stability provides a mechanism to distinguish sulfopeptides from phosphopeptides. Based on the rigorous characterization presented herein, this work serves as a model for accurate identification of phosphotyrosine and, more challenging, sulfotyrosine, in complex proteomic samples. [Figure not available: see fulltext.

Effects of hypoglycaemia on working memory and regional cerebral blood flow in type 1 diabetes: a randomised, crossover trial.

PubMed

Gejl, Michael; Gjedde, Albert; Brock, Birgitte; Møller, Arne; van Duinkerken, Eelco; Haahr, Hanne L; Hansen, Charlotte T; Chu, Pei-Ling; Stender-Petersen, Kirstine L; Rungby, Jørgen

2018-03-01

The aim of this randomised, crossover trial was to compare cognitive functioning and associated brain activation patterns during hypoglycaemia (plasma glucose [PG] just below 3.1 mmol/l) and euglycaemia in individuals with type 1 diabetes mellitus. In this patient-blinded, crossover study, 26 participants with type 1 diabetes mellitus attended two randomised experimental visits: one hypoglycaemic clamp (PG 2.8 ± 0.2 mmol/l, approximate duration 55 min) and one euglycaemic clamp (PG 5.5 mmol/l ± 10%). PG levels were maintained by hyperinsulinaemic glucose clamping. Cognitive functioning was assessed during hypoglycaemia and euglycaemia conditions using a modified version of the digit symbol substitution test (mDSST) and control DSST (cDSST). Simultaneously, regional cerebral blood flow (rCBF) was measured in pre-specified brain regions by six H 2 15 O-positron emission tomographies (PET) per session. Working memory was impaired during hypoglycaemia as indicated by a statistically significantly lower mDSST score (estimated treatment difference [ETD] -0.63 [95% CI -1.13, -0.14], p = 0.014) and a statistically significantly longer response time (ETD 2.86 s [7%] [95% CI 0.67, 5.05], p = 0.013) compared with euglycaemia. During hypoglycaemia, mDSST task performance was associated with increased activity in the frontal lobe regions, superior parietal lobe and thalamus, and decreased activity in the temporal lobe regions (p < 0.05). Working memory activation (mDSST - cDSST) statistically significantly increased blood flow in the striatum during hypoglycaemia (ETD 0.0374% [95% CI 0.0157, 0.0590], p = 0.002). During hypoglycaemia (mean PG 2.9 mmol/l), working memory performance was impaired. Altered performance was associated with significantly increased blood flow in the striatum, a part of the basal ganglia implicated in regulating motor functions, memory, language and emotion. NCT01789593, clinicaltrials.gov FUNDING: This study was funded by Novo Nordisk.

Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry.

PubMed

Wang, Hao; Straubinger, Robert M; Aletta, John M; Cao, Jin; Duan, Xiaotao; Yu, Haoying; Qu, Jun

2009-03-01

Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z = 2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.

Accurate Localization and Relative Quantification of Arginine Methylation Using Nanoflow Liquid Chromatography Coupled to Electron Transfer Dissociation and Orbitrap Mass Spectrometry

PubMed Central

Wang, Hao; Straubinger, Robert M.; Aletta, John M.; Cao, Jin; Duan, Xiaotao; Yu, Haoying; Qu, Jun

2012-01-01

Protein arginine (Arg) methylation serves an important functional role in eukaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly-charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z=2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns. PMID:19110445

Be Creative, Determined, and Wise: Open Library Publishing and the Global South

ERIC Educational Resources Information Center

Baker, Matthew

2009-01-01

Libraries throughout the world are increasingly involved in the production of scholarly publications. Much of this has been thanks to the growth of open access (OA) publishing in all its forms, from peer-reviewed "gold" journals to "green" self-archiving, and electronic theses and dissertation (ETD) repositories. As a result, more and more of the…

Do Open Access Electronic Theses and Dissertations Diminish Publishing Opportunities in the Sciences?

ERIC Educational Resources Information Center

Ramírez, Marisa L.; McMillan, Gail; Dalton, Joan T.; Hanlon, Ann; Smith, Heather S.; Kern, Chelsea

2014-01-01

In academia, there is a growing acceptance of sharing the final electronic version of graduate work, such as a thesis or dissertation, in an online university repository. Though previous studies have shown that journal editors are willing to consider manuscripts derived from electronic theses and dissertations (ETDs), faculty advisors and graduate…

DIFFERENTIAL TRANSCRIPTION FACTOR ACTIVATION AD GENE EXPRESSION PROFILES IN HUMAN VASCULAR ENDOTHELIAL CELLS ON EXPOSURE TO RESIDUAL OIL FLY ASH (ROFA) AND VANADIUM

EPA Science Inventory

Differential transcription factor activation and gene expression profiles in human vascular endothelial cells on exposure to residual oil fly ash (ROFA) and vanadium.
Srikanth S. Nadadur and Daniel L. Costa, US EPA, ORD, NHEERL (ETD, Pulmonary Toxicology Branch), Research ...

COMPARING MIXTURES OF DIOXIN-LIKE AND NON DIOXIN-LIKE PCBS TO TCDD

EPA Science Inventory

COMPARING MIXTURES OF DIOXIN-LIKE AND NON DIOXIN-LIKE PCBS TO TCDD. D E Burgin1, J J Diliberto2 and L S Birnbaum3.1University of North Carolina/Toxicology, Chapel Hill, NC, USA; 2USEPA/ORD/NHEERL, ETD, Research Triangle Park, NC, USA; 3USEPA/ORD/NHEERL, HSD, Chapel Hill, NC, USA....

METABOLISM AND TISSUE DOSIMETRY OF PENTAVALENT AND TRIVALENT MONOMETHYLATED ARSENIC AFTER ORAL

EPA Science Inventory

METABOLISM AND TISSUE DOSIMETRY OF PENTAVALENT AND TRIVALENT MONOMETHYLATED ARSENIC AFTER ORAL ADMINISTRATION IN MICE
M F Hughes1, V Devesa2, B M Adair1, M Styblo2, E M Kenyon1, and D J Thomas1. 1US EPA, ORD, NHEERL, ETD, Research Triangle Park, NC; 2UNC-CH, CEMALB, Chapel Hi...

USE OF SENSITIVITY ANALYSIS ON A PHYSIOLOGICALLY-BASED PHARMACOKINETIC (PBPK) MODEL FOR CHLOROFORM IN RATS TO DETERMINE AGE-RELATED TOXICITY

EPA Science Inventory

USE OF SENSITIVITY ANALYSIS ON A PHYSIOLOGICALLY BASED PHARMACOKINETIC (PBPK) MODEL FOR CHLOROFORM IN RATS TO DETERMINE AGE-RELATED TOXICITY.
CR Eklund, MV Evans, and JE Simmons. US EPA, ORD, NHEERL, ETD,PKB, Research Triangle Park, NC.

Chloroform (CHCl3) is a disinfec...

PERINATAL EXPOSURE TO THE PESTICIDE HEPTACHLOR PRODUCES ALTERATIONS IN IMMUNE FUNCTION PARAMETERS IN SPRAGUE DAWLEY RATS

EPA Science Inventory

PERINATAL EXPOSURE TO THE PESTICIDE HEPTACHLOR PRODUCES ALTERATIONS IN IMMUNE FUNCTION PARAMETERS IN SPRAGUE DAWLEY RATS. R A Matulka1, AA Rooney3, W Williams2, CB Copeland2, and R J Smialowicz2. 1Curriculum in Toxicology, UNC, Chapel Hill, NC, USA; 2US EPA, ITB, ETD, NHEERL, RT...

GENE EXPRESSION PROFILES IN HUMAN AND RAT VASCULAR ENDOTHELIAL CELLS EXPOSED TO RESIDUAL OIL FLY ASH (ROFA) AND VANADIUM (V)

EPA Science Inventory

Gene expression profiles in human and rat vascular endothelial cells exposed to residual oil fly ash (ROFA) or vanadium (V).
Srikanth S. Nadadur, Darrell W. Winsett and Daniel L. Costa, US EPA, ORD, NHEERL (ETD, Pulmonary Toxicology Branch), Research Triangle Park, NC 27711.

CONCENTRATED AMBIENT PARTICULATE STUDIES IN HEALTHY AND COMPROMISED RODENTS

EPA Science Inventory

CONCENTRATED AMBIENT PARTICULATE STUDIES IN HEALTHY AND COMPROMISED RODENTS. WP Watkinson1, LB Wichers2, JP Nolan1, DW Winsett1, UP Kodavanti1, MCJ Schladweiler1, LC Walsh1, ER Lappi1, D Terrell1, R Slade1, AD Ledbetter1, and DL Costa1. 1USEPA, ORD/NHEERL/ETD/PTB, RTP, NC, US...

THE INFLUENCE OF SERUM BINDING PROTEINS AND CLEARANCE ON THE COMPARATIVE RECEPTOR BINDING POTENCY OF ENDOCRINE ACTIVE COMPOUNDS

EPA Science Inventory

THE INFLUENCE OF SERUM BINDING PROTEINS AND CLEARANCE ON THE COMPARATIVE RECEPTOR BINDING POTENCY OF ENDOCRINE ACTIVE COMPOUNDS. JG Teeguarden1 and HA Barton2. 1ENVIRON International, Ruston LA; 2US EPA, ORD, NHEERL, ETD, Pharmacokinetics Branch, RTP, NC.

One measure of th...

THE INFLUENCE OF SERUM BINDING PROTEINS AND FEEDBACK CONTROL OF SERUM ESTRADIOL LEVELS ON THE COMPARATIVE POTENCY OF ENDOCRINE ACTIVE COMPOUNDS

EPA Science Inventory

THE INFLUENCE OF SERUM BINDING PROTEINS ON THE COMPARATIVE RECEPTOR BINDING POTENCY OF ENDOCRINE ACTIVE COMPOUNDS. JG Teeguarden1 and HA Barton2. 1ICF Consulting, Research Triangle Park NC; 2US EPA, ORD, NHEERL, ETD, Pharmacokinetics Branch, RTP, NC.

Accurate comparison of...

INHIBITION OF TOBACCO SMOKE-INDUCED LUNG INFLAMMATION BY A CATALYTIC ANTIOXIDANT

EPA Science Inventory

AMathematical Model for the Kinetics of the Male Reproductive Endocrine System

Laura K. Potter1,2, H.A. Barton2 and R.W. Setzer2
1Curriculum in Toxicology, UNC-Chapel Hill, NC; 2US EPA, ORD, NHEERL, ETD, RTP, NC

In this presentation a model for the hormonal regul...

INFLUENCE OF TYPE II DIABETES AND OBESITY ON THE DISPOSITION AND ELIMINATION OF TCDD IN MICE

EPA Science Inventory

INFLUENCE OF TYPE II DIABETES AND OBESITY ON THE DISPOSTION AND ELIMINATION OF TCDD IN MICE. MJ DeVito', JJ Diliberto', DG Ross', C Emond2, VM Richardson', and LS Birnbaum', 'ETD, NHEERL, ORD, US EPA, RTP, NC, 27711, USA, 2National Research Council.
One possible explanation fo...

EFFECTS OF INDUCED RESPIRATORY CHANGES ON CARDIAC, VENTILATORY, AND THERMOREGULATORY PARAMETERS IN HEALTHY SPRAGUE-DAWLEY RATS

EPA Science Inventory

EFFECTS OF INDUCED RESPIRATORY CHANGES ON CARDIAC, VENTILATORY, AND THERMOREGULATORY PARAMETERS IN HEALTHY SPRAGUE-DAWLEY RATS. LB Wichers1, WH Rowan2, DL Costa2, MJ Campen3 and WP Watkinson2 1UNC SPH, Chapel Hill, NC, USA; 2USEPA, ORD/NHEERL/ETD/PTB, RTP, NC, USA; 3LRRI, A...

PERSISTENCE OF PULMONARY INJURY FOLLOWING INSTILLATION OF RESIDUAL OIL FLY ASH (ROFA) IN SPONTANEOUSLY HYPERTENSIVE (SH) RATS

EPA Science Inventory

PERSISTENCE OF PULMONARY INJURY FOLLOWING INSTILLATION OF RESIDUAL OIL FLY ASH (ROFA) IN SPONTANEOUSLY HYPERTENSIVE (SH) RATS. WP Watkinson1, LB Wichers2, JP Nolan1, UP Kodavanti1, MC Schladweiler1, R Hauser3, DW Winsett1, AD Ledbetter1, and DL Costa1. 1USEPA, ORD/NHEERL/ETD/PTB...

COMPARATIVE METABOLISM OF ARSENIC IN MICE AFTER A SINGLE OR REPEATED ORAL ADMINISTRATION OF ARSENATE

EPA Science Inventory

COMPARATIVE METABOLISM OF ARSENIC IN MICE AFTER A SINGLE OR REPEATED ORAL ADMINISTRATION OF ARSENATE
Michael F. Hughes*1, Elaina M. Kenyon1, Brenda C. Edwards1, Carol T. Mitchell1, Luz Maria Del Razo2 and David J. Thomas1
1US EPA, ORD, NHEERL, ETD, PKB, Research Triangle Pa...

DIFFERENTIAL GENE EXPRESSION PROFILES IN RAT TRACHAEL EPITHELIAL (RTE) CELLS IN RESPONSE TO COMBUSTION-SOURCE PARTICULATE MATTER (PM) AND VANADIUM (V) A PRIMARY METAL CONSTITUENT

EPA Science Inventory

Differential gene expression profiles in rat tracheal epithelial (RTE) cells in response to combustion-source particulate matter (PM) and vanadium (V) a primary metal constituent
Srikanth S. Nadadur, Janice A. Dye and Daniel L. Costa, US EPA, ORD, NHEERL (ETD, Pulmonary Toxico...

USING IN VIVO GAS UPDATE STUDIES TO ESTIMATE METABOLIC RATE CONSTANTS FOR CCL CHEMICALS: 1,1-DICHLOROPROPANE AND 2,2-DICHLOROPROPANE

EPA Science Inventory

USING IN VIVO GAS UPTAKE STUDIES TO ESTIMATE METABOLIC RATE CONSTANTS FOR CCL CHEMICALS: 1,1-DICHLOROPROPENE AND 2,2-DICHLOROPROPANE.
Mitchell, C T, Evans, M V, Kenyon, E M. NHEERL, U.S. EPA, ORD, ETD, RTP, NC

The Safe Drinking Water Act Amendments of 1996 required ...

A DYNAMIC PHYSIOLOGICALLY-BASED TOXICOKINETIC (DPBTK) MODEL FOR SIMULATION OF COMPLEX TOLUENE EXPOSURE SCENARIOS IN HUMANS

EPA Science Inventory

A GENERAL PHYSIOLOGICAL AND TOXICOKINETIC (GPAT) MODEL FOR SIMULATION OF COMPLEX TOLUENE EXPOSURE SCENARIOS IN HUMANS. E M Kenyon1, T Colemen2, C R Eklund1 and V A Benignus3. 1U.S. EPA, ORD, NHEERL, ETD, PKB, RTP, NC, USA; 2Biological Simulators, Inc., Jackson MS, USA, 3U.S. EP...

COMPARISON OF PULMONARY RESPONSES TO AUTOMOBILE-GENERATED AND NIST STANDARD REFERENCE MATERIAL DIESEL PARTICULATE EMISSIONS IN MICE

EPA Science Inventory

COMPARISON OF PULMONARY RESPONSES TO AUTOMOBILE-GENERATED AND NIST STANDARD REFERENCE MATERIAL DIESEL PARTICULATE EMISSIONS IN MICE. P. Singh1, C.A.J. Dick2, J. Richards3, M.J. Daniels3, and M.I. Gilmour3. 1NCSU, Raleigh, NC, 2UNC, Chapel Hill, NC and 3 USEPA, ORD, NHEERL, (ETD,...

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

PubMed

Brodie, Nicholas I; Huguet, Romain; Zhang, Terry; Viner, Rosa; Zabrouskov, Vlad; Pan, Jingxi; Petrotchenko, Evgeniy V; Borchers, Christoph H

2018-03-06

Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.

Characterization of Tyrosine Nitration and Cysteine Nitrosylation Modifications by Metastable Atom-Activation Dissociation Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-02-01

The fragmentation behavior of nitrated and S-nitrosylated peptides were studied using collision induced dissociation (CID) and metastable atom-activated dissociation mass spectrometry (MAD-MS). Various charge states, such as 1+, 2+, 3+, 2-, of modified and unmodified peptides were exposed to a beam of high kinetic energy helium (He) metastable atoms resulting in extensive backbone fragmentation with significant retention of the post-translation modifications (PTMs). Whereas the high electron affinity of the nitrotyrosine moiety quenches radical chemistry and fragmentation in electron capture dissociation (ECD) and electron transfer dissociation (ETD), MAD does produce numerous backbone cleavages in the vicinity of the modification. Fragment ions of nitrosylated cysteine modifications typically exhibit more abundant neutral losses than nitrated tyrosine modifications because of the extremely labile nature of the nitrosylated cysteine residues. However, compared with CID, MAD produced between 66% and 86% more fragment ions, which preserved the labile -NO modification. MAD was also able to differentiate I/L residues in the modified peptides. MAD is able to induce radical ion chemistry even in the presence of strong radical traps and therefore offers unique advantages to ECD, ETD, and CID for determination of PTMs such as nitrated and S-nitrosylated peptides.

Modes of orogen-parallel stretching and extensional exhumation in response to microplate indentation and roll-back subduction (Tauern Window, Eastern Alps)

NASA Astrophysics Data System (ADS)

Scharf, A.; Handy, M. R.; Favaro, S.; Schmid, S. M.; Bertrand, A.

2013-09-01

The Tauern Window exposes a Paleogene nappe stack consisting of highly metamorphosed oceanic (Alpine Tethys) and continental (distal European margin) thrust sheets. In the eastern part of this window, this nappe stack (Eastern Tauern Subdome, ETD) is bounded by a Neogene system of shear (the Katschberg Shear Zone System, KSZS) that accommodated orogen-parallel stretching, orogen-normal shortening, and exhumation with respect to the structurally overlying Austroalpine units (Adriatic margin). The KSZS comprises a ≤5-km-thick belt of retrograde mylonite, the central segment of which is a southeast-dipping, low-angle extensional shear zone with a brittle overprint (Katschberg Normal Fault, KNF). At the northern and southern ends of this central segment, the KSZS loses its brittle overprint and swings around both corners of the ETD to become subvertical, dextral, and sinistral strike-slip faults. The latter represent stretching faults whose displacements decrease westward to near zero. The kinematic continuity of top-east to top-southeast ductile shearing along the central, low-angle extensional part of the KSZS with strike-slip shearing along its steep ends, combined with maximum tectonic omission of nappes of the ETD in the footwall of the KNF, indicates that north-south shortening, orogen-parallel stretching, and normal faulting were coeval. Stratigraphic and radiometric ages constrain exhumation of the folded nappe complex in the footwall of the KSZS to have begun at 23-21 Ma, leading to rapid cooling between 21 and 16 Ma. This exhumation involved a combination of tectonic unroofing by extensional shearing, upright folding, and erosional denudation. The contribution of tectonic unroofing is greatest along the central segment of the KSZS and decreases westward to the central part of the Tauern Window. The KSZS formed in response to the indentation of wedge-shaped blocks of semi-rigid Austroalpine basement located in front of the South-Alpine indenter that was part of the Adriatic microplate. Northward motion of this indenter along the sinistral Giudicarie Belt offsets the Periadriatic Fault and triggered rapid exhumation of orogenic crust within the entire Tauern Window. Exhumation involved strike-slip and normal faulting that accommodated about 100 km of orogen-parallel extension and was contemporaneous with about 30 km of orogen-perpendicular, north-south shortening of the ETD. Extension of the Pannonian Basin related to roll-back subduction in the Carpathians began at 20 Ma, but did not affect the Eastern Alps before about 17 Ma. The effect of this extension was to reduce the lateral resistance to eastward crustal flow away from the zone of greatest thickening in the Tauern Window area. Therefore, we propose that roll-back subduction temporarily enhanced rather than triggered exhumation and orogen-parallel motion in the Eastern Alps. Lateral extrusion and orogen-parallel extension in the Eastern Alps have continued from 12 to 10 Ma to the present and are driven by northward push of Adria.

EFFECTS OF 2,2',4,4'-TETRABROMODIPHENYL ETHER ON CAR AND PXR REGULATED GENE EXPRESSION IN WEANLING FEMALE RATS

EPA Science Inventory

EFFECTS OF 2,2',4,4,'-TETRABROMODIPHENYL ETHER ON CAR AND PXR REGULATED GENE EXPRESSION IN WEANLING FEMALE RATS. V M RICHARDSON1, K M CROFTON2, AND M J DEVITO1. USEPA, ORD/NHEERL/ETD1/NTD2,RTP, NC, USA. The polybrominated diphenyl ether (PBDEs) mixture DE-71 (PBDEs) cause endo...

2018 Military Retirement Options: An Expected Net Present Value Decision Analysis Model

DTIC Science & Technology

2017-03-23

Decision Analysis Model Bret N. Witham Follow this and additional works at: https://scholar.afit.edu/etd Part of the Benefits and Compensation Commons...FORCE INSTITUTE OF TECHNOLOGY Wright-Patterson Air Force Base, Ohio DISTRIBUTION STATEMENT A. APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED...Science in Operations Research Bret N. Witham, BS Captain, USAF March 2017 DISTRIBUTION STATEMENT A. APPROVED FOR PUBLIC RELEASE; DISTRIBUTION

EFFECT OF DOSE ON THE EXCRETION AND METABOLISM OF MONOMETHYLARSONIC ACID IN THE MOUSE

EPA Science Inventory

EFFECT OF DOSE ON THE EXCRETION AND METABOLISM OF MONOMETHYLARSONIC ACID IN THE MOUSE
M F Hughes1, V Devesa2, B C Edwards1, C T Mitchell1, E M Kenyon1, and D J Thomas1. 1US EPA, ORD, NHEERL, ETD, Research Triangle Park, NC; 2UNC-CH, CEMALB, Chapel Hill, NC

Monomethylar...

Methodology to Improve Aviation Security With Terrorist Using Aircraft as a Weapon

DTIC Science & Technology

2013-09-01

STATEMENT Approval for public release;distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words ) The aviation industry... Electronic Baggage Screening Program EDS Explosive Detection System EMMI Energy, Matter, Material wealth, and Information ETD Explosives Trace...12 All checked baggage in the United States has been subjected to 100% screening since December 2003 under TSA’s Electronic Baggage Screening

COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (IAS) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (ASV) AND ARSENITE (ASIII)

EPA Science Inventory

COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (iAs) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (AsV) AND ARSENITE (AsIII). E M Kenyon, L M Del Razo and M F Hughes. U.S. EPA, ORD, NHEERL, ETD, PKB, RTP, NC, USA; ...

REAL-TIME MEASUREMENT OF AIRWAY RESPONSES TO SULOFUR DIOXIDE (SO2) IN AN INTACT, AWAKE GUINEA PIG MODEL

EPA Science Inventory

Real-time measurment of airway responses to Sulfur Dioxide (SO2) in an intact, awake guinea pig model. J Stanek1,2, Q Krantz2, J Nolan2, D Winsett2, W Watkinson2, and D Costa2. 1College of Veterinary Medicine, NCSU, Raleigh, NC, USA; 2Pulmonary Toxicology Branch, ETD, NHEERL, US...

Do Open Access Electronic Theses and Dissertations Diminish Publishing Opportunities in the Social Sciences and Humanities? Findings from a 2011 Survey of Academic Publishers

ERIC Educational Resources Information Center

Ramirez, Marisa L.; Dalton, Joan T.; McMillan, Gail; Read, Max; Seamans, Nancy H.

2013-01-01

An increasing number of higher education institutions worldwide are requiring submission of electronic theses and dissertations (ETDs) by graduate students and are subsequently providing open access to these works in online repositories. Faculty advisors and graduate students are concerned that such unfettered access to their work could diminish…

A mass spectrometer based explosives trace detector

NASA Astrophysics Data System (ADS)

Vilkov, Andrey; Jorabchi, Kaveh; Hanold, Karl; Syage, Jack A.

2011-05-01

In this paper we describe the application of mass spectrometry (MS) to the detection of trace explosives. We begin by reviewing the issue of explosives trace detection (ETD) and describe the method of mass spectrometry (MS) as an alternative to existing technologies. Effective security screening devices must be accurate (high detection and low false positive rate), fast and cost effective (upfront and operating costs). Ion mobility spectrometry (IMS) is the most commonly deployed method for ETD devices. Its advantages are compact size and relatively low price. For applications requiring a handheld detector, IMS is an excellent choice. For applications that are more stationary (e.g., checkpoint and alternatives to IMS are available. MS is recognized for its superior performance with regard to sensitivity and specificity, which translate to lower false negative and false positive rates. In almost all applications outside of security where accurate chemical analysis is needed, MS is usually the method of choice and is often referred to as the gold standard for chemical analysis. There are many review articles and proceedings that describe detection technologies for explosives. 1,2,3,4 Here we compare MS and IMS and identify the strengths and weaknesses of each method. - Mass spectrometry (MS): MS offers high levels of sensitivity and specificity compared to other technologies for chemical detection. Its traditional disadvantages have been high cost and complexity. Over the last few years, however, the economics have greatly improved and MS is now capable of routine and automated operation. Here we compare MS and IMS and identify the strengths and weaknesses of each method. - Ion mobility spectrometry (IMS): 5 MS-ETD Screening System IMS is similar in concept to MS except that the ions are dispersed by gas-phase viscosity and not by molecular weight. The main advantage of IMS is that it does not use a vacuum system, which greatly reduces the size, cost, and complexity relative to MS. However, the trade-off is that the measurement accuracy is considerably less than MS. This is especially true for complex samples or when screening for a large number of target compounds simultaneously.

UTILIZATION OF A PBPK MODEL TO PREDICT THE DISTRIBUTION OF 2, 3, 7-8 TETRACHLORODIBENZO-P-DIOXIN (TCDD) IN HUMANS DURING CRITICAL WINDOWS OF DEVELOPMENT

EPA Science Inventory

Utilization of A PBPK model to predict the distribution of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) in humans during critical windows of development.
C Emond1, MJ DeVito2 and LS Birnbaum2
1National Research Council, US EPA, ORD, NHEERL, (ETD, PK), RTP, NC, 27711, USA 2 US...

APPLICATION OF THE EXPOSURE DOSE ESTIMATING MODEL (ERDEM) TO ASSESSMENT OF DERMAL EXPOSURE IN THE RAT TO MALATHION

EPA Science Inventory

APPLICATION OF THE EXPOSURE DOSE ESTIMATING MODEL (ERDEM) TO ASSESSMENT OF DERMAL EXPOSURE IN THE RAT TO MALATHION.
Evans, M.V1., Power, F.W2., Dary, C.C2., Tornero-Velez, R2., and Blancato, J.N2.
1 NHEERL, US EPA, ORD, ETD, RTP, NC; 2 NERL, US EPA, ORD, EDRB, LV, NV
Re...

Predicting Dishonorable Discharge Among Military Recruits

DTIC Science & Technology

2013-03-01

train its members to give them the highest chance possible at a successful career. Jacob Rodriquez’s study, “Predicting the Military Career Success of...society as a whole. To improve the enlistment process and attract recruits with the highest probability of future career success , based on our...00036840801964450 Rodriguez, John J. (2008, January 1). Predicting the career success of air force academy cadets (Paper AAI3309209). ETD collection for

Application of Enlisted Force Retention Levels and Career Field Stability

DTIC Science & Technology

2017-03-23

a priority. This research focuses on modeling the enlisted force retention behavior. Specifically, this research examines a statistically based ...and must be manually corrected. Air Force Manpower , Personnel and Services (AF/A1PF) supplied the data used in this research . The data was...Stability Jamie T. Zimmerman Follow this and additional works at: https://scholar.afit.edu/etd Part of the Operational Research Commons This Thesis is

Parameter estimation of a three-axis spacecraft simulator using recursive least-squares approach with tracking differentiator and Extended Kalman Filter

NASA Astrophysics Data System (ADS)

Xu, Zheyao; Qi, Naiming; Chen, Yukun

2015-12-01

Spacecraft simulators are widely used to study the dynamics, guidance, navigation, and control of a spacecraft on the ground. A spacecraft simulator can have three rotational degrees of freedom by using a spherical air-bearing to simulate a frictionless and micro-gravity space environment. The moment of inertia and center of mass are essential for control system design of ground-based three-axis spacecraft simulators. Unfortunately, they cannot be known precisely. This paper presents two approaches, i.e. a recursive least-squares (RLS) approach with tracking differentiator (TD) and Extended Kalman Filter (EKF) method, to estimate inertia parameters. The tracking differentiator (TD) filter the noise coupled with the measured signals and generate derivate of the measured signals. Combination of two TD filters in series obtains the angular accelerations that are required in RLS (TD-TD-RLS). Another method that does not need to estimate the angular accelerations is using the integrated form of dynamics equation. An extended TD (ETD) filter which can also generate the integration of the function of signals is presented for RLS (denoted as ETD-RLS). States and inertia parameters are estimated simultaneously using EKF. The observability is analyzed. All proposed methods are illustrated by simulations and experiments.

Evaluation of a wireless wearable tongue–computer interface by individuals with high-level spinal cord injuries

PubMed Central

Huo, Xueliang; Ghovanloo, Maysam

2010-01-01

The tongue drive system (TDS) is an unobtrusive, minimally invasive, wearable and wireless tongue–computer interface (TCI), which can infer its users' intentions, represented in their volitional tongue movements, by detecting the position of a small permanent magnetic tracer attached to the users' tongues. Any specific tongue movements can be translated into user-defined commands and used to access and control various devices in the users' environments. The latest external TDS (eTDS) prototype is built on a wireless headphone and interfaced to a laptop PC and a powered wheelchair. Using customized sensor signal processing algorithms and graphical user interface, the eTDS performance was evaluated by 13 naive subjects with high-level spinal cord injuries (C2–C5) at the Shepherd Center in Atlanta, GA. Results of the human trial show that an average information transfer rate of 95 bits/min was achieved for computer access with 82% accuracy. This information transfer rate is about two times higher than the EEG-based BCIs that are tested on human subjects. It was also demonstrated that the subjects had immediate and full control over the powered wheelchair to the extent that they were able to perform complex wheelchair navigation tasks, such as driving through an obstacle course. PMID:20332552

3D-measurement using a scanning electron microscope with four Everhart-Thornley detectors

NASA Astrophysics Data System (ADS)

Vynnyk, Taras; Scheuer, Renke; Reithmeier, Eduard

2011-06-01

Due to the emerging degree of miniaturization in microstructures, Scanning-Electron-Microscopes (SEM) have become important instruments in the quality assurance of chip manufacturing. With a two- or multiple detector system for secondary electrons, a SEM can be used for the reconstruction of three dimensional surface profiles. Although there are several projects dealing with the reconstruction of three dimensional surfaces using electron microscopes with multiple Everhart-Thornley detectors (ETD), there is no profound knowledge of the behaviour of emitted electrons. Hence, several values, which are used for reconstruction algorithms, such as the photometric method, are only estimates; for instance, the exact collection efficiency of the ETD, which is still unknown. This paper deals with the simulation of electron trajectories in a one-, two- and four-detector system with varying working distances and varying grid currents. For each detector, the collection efficiency is determined by taking the working distance and grid current into account. Based on the gathered information, a new collection grid, which provides a homogenous emission signal for each detector of a multiple detector system, is developed. Finally, the results of the preceding tests are utilized for a reconstruction of a three dimensional surface using the photometric method with a non-lambert intensity distribution.

What Hinders Electron Transfer Dissociation (ETD) of DNA Cations?

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Leumann, Christian J.; Schürch, Stefan

2017-12-01

Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/ w or d/ z• ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS3 experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π-π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer. [Figure not available: see fulltext.

N- and O-Glycosylation in the Murine Synaptosome*

PubMed Central

Trinidad, Jonathan C.; Schoepfer, Ralf; Burlingame, Alma L.; Medzihradszky, Katalin F.

2013-01-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues. PMID:23816992

N- and O-glycosylation in the murine synaptosome.

PubMed

Trinidad, Jonathan C; Schoepfer, Ralf; Burlingame, Alma L; Medzihradszky, Katalin F

2013-12-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues.

Forecasting Traditional vs Blended Retirement System for Individual Service Members

DTIC Science & Technology

2017-03-23

Service (IRS) puts retirement plan options offered to employees into four categories: profit-sharing plans, defined benefit plans, money purchase...Retirement System to allow the continuation pay to be offered at no less than eight years of service and no more than 12 years of service . The acceptance... Service Members Kevin M. Dwyer Follow this and additional works at: https://scholar.afit.edu/etd Part of the Business Administration, Management, and

Investigation of the Mechanism of Electron Capture and Electron Transfer Dissociation of Peptides with a Covalently Attached Free Radical Hydrogen Atom Scavenger.

PubMed

Sohn, Chang Ho; Yin, Sheng; Peng, Ivory; Loo, Joseph A; Beauchamp, J L

2015-11-15

The mechanisms of electron capture and electron transfer dissociation (ECD and ETD) are investigated by covalently attaching a free-radical hydrogen atom scavenger to a peptide. The 2,2,6,6-tetramethylpiperidin-l-oxyl (TEMPO) radical was chosen as the scavenger due to its high hydrogen atom affinity (ca. 280 kJ/mol) and low electron affinity (ca. 0.45 ev), and was derivatized to the model peptide, FQX TEMPO EEQQQTEDELQDK. The X TEMPO residue represents a cysteinyl residue derivatized with an acetamido-TEMPO group. The acetamide group without TEMPO was also examined as a control. The gas phase proton affinity (882 kJ/mol) of TEMPO is similar to backbone amide carbonyls (889 kJ/mol), minimizing perturbation to internal solvation and sites of protonation of the derivatized peptides. Collision induced dissociation (CID) of the TEMPO tagged peptide dication generated stable odd-electron b and y type ions without indication of any TEMPO radical induced fragmentation initiated by hydrogen abstraction. The type and abundance of fragment ions observed in the CID spectra of the TEMPO and acetamide tagged peptides are very similar. However, ECD of the TEMPO labeled peptide dication yielded no backbone cleavage. We propose that a labile hydrogen atom in the charge reduced radical ions is scavenged by the TEMPO radical moiety, resulting in inhibition of N-C α backbone cleavage processes. Supplemental activation after electron attachment (ETcaD) and CID of the charge-reduced precursor ion generated by electron transfer of the TEMPO tagged peptide dication produced a series of b + H (b H ) and y + H (y H ) ions along with some c ions having suppressed intensities, consistent with stable O-H bond formation at the TEMPO group. In summary, the results indicate that ECD and ETD backbone cleavage processes are inhibited by scavenging of a labile hydrogen atom by the localized TEMPO radical moiety. This observation supports the conjecture that ECD and ETD processes involve long-lived intermediates formed by electron capture/transfer in which a labile hydrogen atom is present and plays a key role with low energy processes leading to c and z ion formation. Ab initio and density functional calculations are performed to support our conclusion, which depends most importantly on the proton affinity, electron affinity and hydrogen atom affinity of the TEMPO moiety.

Examining Regionalization Efforts to Develop Lessons Learned and Consideration for Department of Defense Medical Facilities

DTIC Science & Technology

2017-03-23

Consideration for Department of Defense Medical Facilities Erik B. Schuh Follow this and additional works at: https://scholar.afit.edu/etd Part of the...Citation Schuh, Erik B., "Examining Regionalization Efforts to Develop Lessons Learned and Consideration for Department of Defense Medical Facilities...Consideration for Department of Defense Medical Facilities THESIS Erik B. Schuh, 2Lt, USAF AFIT-ENS-MS-17-M-156 DEPARTMENT OF THE AIR FORCE AIR UNIVERSITY AIR

Advancing Air Force Scheduling through Modeling Problem Topologies

DTIC Science & Technology

2006-08-03

Merrill on August 23, 2005 and corresponded with Major David Van Veldhuizen in Fall 2005 about obtaining data. 3.4.3 Transitions Analytical Graphics and...observation satellite orbit. Technical Report CRT-2003-27, Centre de recherche sur les transports, July 2003. [5] Van -Dat Cung. ROADEF 2003: Results of the...collaborateurs/etd/default.htm. January, 2004. [15] P.J.M van Laarhoven, E.H.L. Aarts, and J.K. Lenstra. Job shop scheduling by simulated annealing

The Nexus of Extremism and Trafficking: Scourge of the World or So Much Hype?

DTIC Science & Technology

2013-10-01

in AML / CFT ,” International Monetary Fund. Available at: www. imf.org/external/np/leg/amlcft/eng/aml1.htm (accessed April 6, 2012). 19. “Money...tional Law Enforcement Organizations’ Interdiction Again Human Traffick- ing,” thesis presented to the Graduate Council of Texas State University-San...Marcos, December 2011, 18-21. Available at: http://repositories.tdl.org/txstate- ir/bitstream/handle/10529/ETD-TXSTATE-2011-12-299/BAILEY- THESIS . pdf

Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

PubMed Central

Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

2010-01-01

Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

Transverse energy production and charged-particle multiplicity at midrapidity in various systems from √{sN N}=7.7 to 200 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Afanasiev, S.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Al-Bataineh, H.; Alexander, J.; Alfred, M.; Al-Jamel, A.; Al-Ta'Ani, H.; Angerami, A.; Aoki, K.; Apadula, N.; Aphecetche, L.; Aramaki, Y.; Armendariz, R.; Aronson, S. H.; Asai, J.; Asano, H.; Aschenauer, E. C.; Atomssa, E. T.; Averbeck, R.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bai, X.; Baksay, G.; Baksay, L.; Baldisseri, A.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Barnes, P. D.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Batsouli, S.; Baublis, V.; Bauer, F.; Baumann, C.; Baumgart, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belikov, S.; Belmont, R.; Bennett, R.; Berdnikov, A.; Berdnikov, Y.; Bhom, J. H.; Bickley, A. A.; Bjorndal, M. T.; Black, D.; Blau, D. S.; Boissevain, J. G.; Bok, J. S.; Borel, H.; Boyle, K.; Brooks, M. L.; Brown, D. S.; Bryslawskyj, J.; Bucher, D.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Burward-Hoy, J. M.; Butsyk, S.; Campbell, S.; Caringi, A.; Castera, P.; Chai, J.-S.; Chang, B. S.; Charvet, J.-L.; Chen, C.-H.; Chernichenko, S.; Chi, C. Y.; Chiba, J.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choi, S.; Choudhury, R. K.; Christiansen, P.; Chujo, T.; Chung, P.; Churyn, A.; Chvala, O.; Cianciolo, V.; Citron, Z.; Cleven, C. R.; Cobigo, Y.; Cole, B. A.; Comets, M. P.; Conesa Del Valle, Z.; Connors, M.; Constantin, P.; Cronin, N.; Crossette, N.; Csanád, M.; Csörgő, T.; Dahms, T.; Dairaku, S.; Danchev, I.; Danley, T. W.; Das, K.; Datta, A.; Daugherity, M. S.; David, G.; Dayananda, M. K.; Deaton, M. B.; Deblasio, K.; Dehmelt, K.; Delagrange, H.; Denisov, A.; D'Enterria, D.; Deshpande, A.; Desmond, E. J.; Dharmawardane, K. V.; Dietzsch, O.; Ding, L.; Dion, A.; Diss, P. B.; Do, J. H.; Donadelli, M.; D'Orazio, L.; Drachenberg, J. L.; Drapier, O.; Drees, A.; Drees, K. A.; Dubey, A. K.; Durham, J. M.; Durum, A.; Dutta, D.; Dzhordzhadze, V.; Edwards, S.; Efremenko, Y. V.; Egdemir, J.; Ellinghaus, F.; Emam, W. S.; Engelmore, T.; Enokizono, A.; En'yo, H.; Espagnon, B.; Esumi, S.; Eyser, K. O.; Fadem, B.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Forestier, B.; Fraenkel, Z.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fujiwara, K.; Fukao, Y.; Fung, S.-Y.; Fusayasu, T.; Gadrat, S.; Gainey, K.; Gal, C.; Gallus, P.; Garg, P.; Garishvili, A.; Garishvili, I.; Gastineau, F.; Ge, H.; Germain, M.; Giordano, F.; Glenn, A.; Gong, H.; Gong, X.; Gonin, M.; Gosset, J.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grim, G.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guo, L.; Guragain, H.; Gustafsson, H.-Å.; Hachiya, T.; Hadj Henni, A.; Haegemann, C.; Haggerty, J. S.; Hagiwara, M. N.; Hahn, K. I.; Hamagaki, H.; Hamblen, J.; Hamilton, H. F.; Han, R.; Han, S. Y.; Hanks, J.; Harada, H.; Hartouni, E. P.; Haruna, K.; Harvey, M.; Hasegawa, S.; Haseler, T. O. S.; Hashimoto, K.; Haslum, E.; Hasuko, K.; Hayano, R.; Hayashi, S.; He, X.; Heffner, M.; Hemmick, T. K.; Hester, T.; Heuser, J. M.; Hiejima, H.; Hill, J. C.; Hobbs, R.; Hohlmann, M.; Hollis, R. S.; Holmes, M.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hori, Y.; Hornback, D.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Hur, M. G.; Ichihara, T.; Ichimiya, R.; Iinuma, H.; Ikeda, Y.; Imai, K.; Imazu, Y.; Imrek, J.; Inaba, M.; Inoue, Y.; Iordanova, A.; Isenhower, D.; Isenhower, L.; Ishihara, M.; Isinhue, A.; Isobe, T.; Issah, M.; Isupov, A.; Ivanishchev, D.; Iwanaga, Y.; Jacak, B. V.; Javani, M.; Jeon, S. J.; Jezghani, M.; Jia, J.; Jiang, X.; Jin, J.; Jinnouchi, O.; Johnson, B. M.; Jones, T.; Joo, K. S.; Jouan, D.; Jumper, D. S.; Kajihara, F.; Kametani, S.; Kamihara, N.; Kamin, J.; Kanda, S.; Kaneta, M.; Kaneti, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kanou, H.; Kapustinsky, J.; Karatsu, K.; Kasai, M.; Kawagishi, T.; Kawall, D.; Kawashima, M.; Kazantsev, A. V.; Kelly, S.; Kempel, T.; Key, J. A.; Khachatryan, V.; Khandai, P. K.; Khanzadeev, A.; Kijima, K. M.; Kikuchi, J.; Kim, A.; Kim, B. I.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.; Kim, E.-J.; Kim, G. W.; Kim, H. J.; Kim, K.-B.; Kim, M.; Kim, Y.-J.; Kim, Y. K.; Kim, Y.-S.; Kimelman, B.; Kinney, E.; Kiss, Á.; Kistenev, E.; Kitamura, R.; Kiyomichi, A.; Klatsky, J.; Klay, J.; Klein-Boesing, C.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kochenda, L.; Kochetkov, V.; Kofarago, M.; Komatsu, Y.; Komkov, B.; Konno, M.; Koster, J.; Kotchetkov, D.; Kotov, D.; Kozlov, A.; Král, A.; Kravitz, A.; Krizek, F.; Kroon, P. J.; Kubart, J.; Kunde, G. J.; Kurihara, N.; Kurita, K.; Kurosawa, M.; Kweon, M. J.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Le Bornec, Y.; Leckey, S.; Lee, B.; Lee, D. M.; Lee, G. H.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, M. K.; Lee, S.; Lee, S. H.; Lee, S. R.; Lee, T.; Leitch, M. J.; Leite, M. A. L.; Leitgab, M.; Lenzi, B.; Lewis, B.; Li, X.; Li, X. H.; Lichtenwalner, P.; Liebing, P.; Lim, H.; Lim, S. H.; Linden Levy, L. A.; Liška, T.; Litvinenko, A.; Liu, H.; Liu, M. X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Makek, M.; Malakhov, A.; Malik, M. D.; Manion, A.; Manko, V. I.; Mannel, E.; Mao, Y.; Maruyama, T.; Mašek, L.; Masui, H.; Masumoto, S.; Matathias, F.; McCain, M. C.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Means, N.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Midori, J.; Mignerey, A. C.; Mikeš, P.; Miki, K.; Miller, T. E.; Milov, A.; Mioduszewski, S.; Mishra, D. K.; Mishra, G. C.; Mishra, M.; Mitchell, J. T.; Mitrovski, M.; Miyachi, Y.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Mohapatra, S.; Montuenga, P.; Moon, H. J.; Moon, T.; Morino, Y.; Morreale, A.; Morrison, D. P.; Moskowitz, M.; Moss, J. M.; Motschwiller, S.; Moukhanova, T. V.; Mukhopadhyay, D.; Murakami, T.; Murata, J.; Mwai, A.; Nagae, T.; Nagamiya, S.; Nagashima, K.; Nagata, Y.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nam, S.; Nattrass, C.; Nederlof, A.; Netrakanti, P. K.; Newby, J.; Nguyen, M.; Nihashi, M.; Niida, T.; Nishimura, S.; Norman, B. E.; Nouicer, R.; Novák, T.; Novitzky, N.; Nukariya, A.; Nyanin, A. S.; Nystrand, J.; Oakley, C.; Obayashi, H.; O'Brien, E.; Oda, S. X.; Ogilvie, C. A.; Ohnishi, H.; Oide, H.; Ojha, I. D.; Oka, M.; Okada, K.; Omiwade, O. O.; Onuki, Y.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Otterlund, I.; Ouchida, M.; Ozawa, K.; Pak, R.; Pal, D.; Palounek, A. P. T.; Pantuev, V.; Papavassiliou, V.; Park, B. H.; Park, I. H.; Park, J.; Park, J. S.; Park, S.; Park, S. K.; Park, W. J.; Pate, S. F.; Patel, L.; Patel, M.; Pei, H.; Peng, J.-C.; Pereira, H.; Perepelitsa, D. V.; Perera, G. D. N.; Peresedov, V.; Peressounko, D. Yu.; Perry, J.; Petti, R.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Proissl, M.; Purschke, M. L.; Purwar, A. K.; Qu, H.; Rak, J.; Rakotozafindrabe, A.; Ramson, B. J.; Ravinovich, I.; Read, K. F.; Rembeczki, S.; Reuter, M.; Reygers, K.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richardson, E.; Rinn, T.; Riveli, N.; Roach, D.; Roche, G.; Rolnick, S. D.; Romana, A.; Rosati, M.; Rosen, C. A.; Rosendahl, S. S. E.; Rosnet, P.; Rowan, Z.; Rubin, J. G.; Rukoyatkin, P.; Ružička, P.; Rykov, V. L.; Ryu, M. S.; Ryu, S. S.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sakai, S.; Sakashita, K.; Sakata, H.; Sako, H.; Samsonov, V.; Sano, M.; Sano, S.; Sarsour, M.; Sato, H. D.; Sato, S.; Sato, T.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sekiguchi, Y.; Semenov, V.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shaver, A.; Shea, T. K.; Shein, I.; Shevel, A.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shohjoh, T.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Silvestre, C.; Sim, K. S.; Singh, B. K.; Singh, C. P.; Singh, V.; Skolnik, M.; Skutnik, S.; Slunečka, M.; Smith, W. C.; Snowball, M.; Solano, S.; Soldatov, A.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Staley, F.; Stankus, P. W.; Steinberg, P.; Stenlund, E.; Stepanov, M.; Ster, A.; Stoll, S. P.; Stone, M. R.; Sugitate, T.; Suire, C.; Sukhanov, A.; Sullivan, J. P.; Sumita, T.; Sun, J.; Sziklai, J.; Tabaru, T.; Takagi, S.; Takagui, E. M.; Takahara, A.; Taketani, A.; Tanabe, R.; Tanaka, K. H.; Tanaka, Y.; Taneja, S.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tarján, P.; Tennant, E.; Themann, H.; Thomas, D.; Thomas, T. L.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Togawa, M.; Toia, A.; Tojo, J.; Tomášek, L.; Tomášek, M.; Torii, H.; Towell, C. L.; Towell, R.; Towell, R. S.; Tram, V.-N.; Tserruya, I.; Tsuchimoto, Y.; Tsuji, T.; Tuli, S. K.; Tydesjö, H.; Tyurin, N.; Vale, C.; Valle, H.; van Hecke, H. W.; Vargyas, M.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Vinogradov, A. A.; Virius, M.; Voas, B.; Vossen, A.; Vrba, V.; Vznuzdaev, E.; Wagner, M.; Walker, D.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Wei, R.; Wessels, J.; Whitaker, S.; White, A. S.; White, S. N.; Willis, N.; Winter, D.; Wolin, S.; Woody, C. L.; Wright, R. M.; Wysocki, M.; Xia, B.; Xie, W.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yamaura, K.; Yang, R.; Yanovich, A.; Yasin, Z.; Ying, J.; Yokkaichi, S.; Yoo, J. H.; Yoon, I.; You, Z.; Young, G. R.; Younus, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zaudtke, O.; Zelenski, A.; Zhang, C.; Zhou, S.; Zimamyi, J.; Zolin, L.; Zou, L.; Phenix Collaboration

2016-02-01

Measurements of midrapidity charged-particle multiplicity distributions, d Nch/d η , and midrapidity transverse-energy distributions, d ET/d η , are presented for a variety of collision systems and energies. Included are distributions for Au +Au collisions at √{sNN}=200 , 130, 62.4, 39, 27, 19.6, 14.5, and 7.7 GeV, Cu +Cu collisions at √{sNN}=200 and 62.4 GeV, Cu +Au collisions at √{sNN}=200 GeV, U +U collisions at √{sNN}=193 GeV, d +Au collisions at √{sNN}=200 GeV, 3He+Au collisions at √{sNN}=200 GeV, and p +p collisions at √{sNN}=200 GeV. Centrality-dependent distributions at midrapidity are presented in terms of the number of nucleon participants, Npart, and the number of constituent quark participants, Nqp. For all A +A collisions down to √{sNN}=7.7 GeV, it is observed that the midrapidity data are better described by scaling with Nqp than scaling with Npart. Also presented are estimates of the Bjorken energy density, ɛBJ, and the ratio of d ET/d η to d Nch/d η , the latter of which is seen to be constant as a function of centrality for all systems.

Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

PubMed

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

2017-05-01

Gas-phase hydrogen/deuterium exchange (HDX) using D 2 O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

RAND Research Brief: Improving the Quality of DoD’s Civilian Workforce. Guidance for the Office of the Chancellor for Education and Professional Development

DTIC Science & Technology

2001-01-01

the Office of the Chancellor for Education and Professional Development to serve as the principal advocate for the academic quality and cost...provide ET&D services to DoD civilians. To carry out its mission the office needs to develop a strategic performance and planning process....effectiveness of all institutions, programs, and courses of instruction that serve DoD civilian workers. The Chancellor’s office, which operates within the

USE OF CYP1A2(-/-) KNOCKOUT AND CYP1A2(+/+) C57BL/6N PARENTAL STRAINS OF MICE TO COMPARE METABOLISM OF 2,3,7,8-TETRACHLORODIBENZO-P-DIOXIN (TCDD)

EPA Science Inventory

USE OF CYP1A2 (-/-) KNOCKOUT AND CYP1A2 (+/+) C57BL/6N PARENTAL STRAINS OF MICE TO COMPARE METABOLISM OF 2,3,7,8-TETRACHLORODIBENZO-P-DIOXIN (TCDD). J J Diliberto1 and H Hakk2. 1USEPA ORD, NHEERL, ETD, PKB, Research Triangle Park, NC, USA; 2USDA-ARS, BRL, Fargo, ND, USA. Spons...

Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS).

PubMed

Smith, Scott A; Kalcic, Christine L; Safran, Kyle A; Stemmer, Paul M; Dantus, Marcos; Reid, Gavin E

2010-12-01

To develop an improved understanding of the regulatory role that post-translational modifications (PTMs) involving phosphorylation play in the maintenance of normal cellular function, tandem mass spectrometry (MS/MS) strategies coupled with ion activation techniques such as collision-induced dissociation (CID) and electron-transfer dissociation (ETD) are typically employed to identify the presence and site-specific locations of the phosphate moieties within a given phosphoprotein of interest. However, the ability of these techniques to obtain sufficient structural information for unambiguous phosphopeptide identification and characterization is highly dependent on the ion activation method employed and the properties of the precursor ion that is subjected to dissociation. Herein, we describe the application of a recently developed alternative ion activation technique for phosphopeptide analysis, termed femtosecond laser-induced ionization/dissociation (fs-LID). In contrast to CID and ETD, fs-LID is shown to be particularly suited to the analysis of singly protonated phosphopeptide ions, yielding a wide range of product ions including a, b, c, x, y, and z sequence ions, as well as ions that are potentially diagnostic of the positions of phosphorylation (e.g., 'a(n)+1-98'). Importantly, the lack of phosphate moiety losses or phosphate group 'scrambling' provides unambiguous information for sequence identification and phosphorylation site characterization. Therefore, fs-LID-MS/MS can serve as a complementary technique to established methodologies for phosphoproteomic analysis. Copyright © 2010. Published by Elsevier Inc.

Large scale study of multiple-molecule queries

PubMed Central

2009-01-01

Background In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a single molecule lead. However, in some case, multiple molecules from the same family are available to seed the query and search for other members of the same family. Multiple-molecule query methods have been less studied than single-molecule query methods. Furthermore, the previous studies have relied on proprietary data and sometimes have not used proper cross-validation methods to assess the results. In contrast, here we develop and compare multiple-molecule query methods using several large publicly available data sets and background. We also create a framework based on a strict cross-validation protocol to allow unbiased benchmarking for direct comparison in future studies across several performance metrics. Results Fourteen different multiple-molecule query methods were defined and benchmarked using: (1) 41 publicly available data sets of related molecules with similar biological activity; and (2) publicly available background data sets consisting of up to 175,000 molecules randomly extracted from the ChemDB database and other sources. Eight of the fourteen methods were parameter free, and six of them fit one or two free parameters to the data using a careful cross-validation protocol. All the methods were assessed and compared for their ability to retrieve members of the same family against the background data set by using several performance metrics including the Area Under the Accumulation Curve (AUAC), Area Under the Curve (AUC), F1-measure, and BEDROC metrics. Consistent with the previous literature, the best parameter-free methods are the MAX-SIM and MIN-RANK methods, which score a molecule to a family by the maximum similarity, or minimum ranking, obtained across the family. One new parameterized method introduced in this study and two previously defined methods, the Exponential Tanimoto Discriminant (ETD), the Tanimoto Power Discriminant (TPD), and the Binary Kernel Discriminant (BKD), outperform most other methods but are more complex, requiring one or two parameters to be fit to the data. Conclusion Fourteen methods for multiple-molecule querying of chemical databases, including novel methods, (ETD) and (TPD), are validated using publicly available data sets, standard cross-validation protocols, and established metrics. The best results are obtained with ETD, TPD, BKD, MAX-SIM, and MIN-RANK. These results can be replicated and compared with the results of future studies using data freely downloadable from http://cdb.ics.uci.edu/. PMID:20298525

Analyses of some exoplanets' transits and transit timing variations

NASA Astrophysics Data System (ADS)

Püsküllü, ćaǧlar; Soydugan, Faruk

2017-02-01

We present solutions of the transit light curves and transit timing variations (TTVs) analyses of the exoplanets HAT-P-5b, HAT-P-9b and HAT-P-25b. Transit light curves were collected at Çanakkale Onsekiz Mart University Observatory and TUBITAK National Observatory. The models were produced by WINFITTER program and stellar, planetary and orbital properties were obtained and discussed. We gave new transit times and generated TTVs with them by appending additional data based on Exoplanet Transit Database (ETD). Significant signals at the TTVs were also investigated.

A New Optical Technique for Rapid Determination of Creep and Fatigue Thresholds at High Temperature.

DTIC Science & Technology

1984-04-01

measurements, made far away from the crack tip, produced much smoother and more sensible results. Measurements by Macha et al (16) agree very well with...dependent upon the measurement positin. It becomes independent of position far enough away from the tip; this is consistent with the results of Macha , et...D. E. Macha , W. N. Sharpe, Jr., and A. P. ’ral(11, ’.., "A Laser Interferometry Method for ,xp.rim,-rit;a1 Stress Intensity Factor Calibration", AST

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

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

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.

We report development of an approach providing high-resolution RPLC of proteins and its utility for mass spectrometry-based top-down proteomics. A chromatographic peak capacity of ~450 was achieved for proteins and large polypeptides having MWs up to 43 kDa in the context of proteomics applications. RPLC column lengths from 20 to 200 cm, particle sizes from 1.5 to 5 m, bonding alkyl chains from C1 to C2, C4, C8, and C18, and particle surface structures that spanned porous, superficially porous (porous shell, core-shell), and nonporous were investigated at pressures up to14K psi. Column length was found as the most important factormore » for >20 kDa proteins in gradient RPLC, and shortening column length degraded RPLC resolution and sensitivity regardless of the size and surface structure of the packing particles used. The alkyl chains bonded to the silica particle surface significantly affected the RPLC recovery and efficiency, and short alkyl C1-C4 phases provided higher sensitivity and resolution than C8 and C18 phases. Long gradient separations (e.g., >10 hours) with long columns (e.g., 100 cm) were particularly effective in conjunction with use of high accuracy mass spectrometers (e.g., the Orbitrap Elite) for top-down proteomics with improved proteoform coverage by allowing multiple HCD, CID, and ETD dissociation modes. It was also found that HCD produced small fragments useful for proteoform identification, while low energy CID and ETD often complemented HCD by providing large fragments.« less

Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

NASA Astrophysics Data System (ADS)

Zhang, Yun; Zhang, Hao; Cui, Weidong; Chen, Hao

2011-09-01

Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen ( m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae *

PubMed Central

Neubert, Patrick; Halim, Adnan; Zauser, Martin; Essig, Andreas; Joshi, Hiren J.; Zatorska, Ewa; Larsen, Ida Signe Bohse; Loibl, Martin; Castells-Ballester, Joan; Aebi, Markus; Clausen, Henrik; Strahl, Sabine

2016-01-01

O-Mannosylation is a vital protein modification conserved from fungi to humans. Yeast is a perfect model to study this post-translational modification, because in contrast to mammals O-mannosylation is the only type of O-glycosylation. In an essential step toward the full understanding of protein O-mannosylation we mapped the O-mannose glycoproteome in baker's yeast. Taking advantage of an O-glycan elongation deficient yeast strain to simplify sample complexity, we identified over 500 O-glycoproteins from all subcellular compartments for which over 2300 O-mannosylation sites were mapped by electron-transfer dissociation (ETD)-based MS/MS. In this study, we focus on the 293 O-glycoproteins (over 1900 glycosylation sites identified by ETD-MS/MS) that enter the secretory pathway and are targets of ER-localized protein O-mannosyltransferases. We find that O-mannosylation is not only a prominent modification of cell wall and plasma membrane proteins, but also of a large number of proteins from the secretory pathway with crucial functions in protein glycosylation, folding, quality control, and trafficking. The analysis of glycosylation sites revealed that O-mannosylation is favored in unstructured regions and β-strands. Furthermore, O-mannosylation is impeded in the proximity of N-glycosylation sites suggesting the interplay of these types of post-translational modifications. The detailed knowledge of the target proteins and their O-mannosylation sites opens for discovery of new roles of this essential modification in eukaryotes, and for a first glance on the evolution of different types of O-glycosylation from yeast to mammals. PMID:26764011

Hazard Assessment Computer System HACS/UIM Users’ Operation Manual. Volume II.

DTIC Science & Technology

1981-09-01

AMMONIUM OXALATE FAS FERROUS AMMONIUM SULFATE FCL FERRIC CHLORIDE FCP FERRIC GLYCEROPHOSPHATE FEC FERROUS CHLORIDE FFA FURFURAL FFB FERROUS FLUOROBORATE...FAL FFA FFBi FMA FNS FSA FSL FXX BAK GAT SAY SCM GCR GCS SOC SOS SPL SRF GSR STA J-2 HAC HAI HAL HEIR HCC HCL HCN HDC HE’S HDZ HFA HFX HMD HMI HPA...ENP EOEI EOP EOT EPC ETA ETC ETD ETf3 ETI FAL FFA FFB FMA FMS VSL OCR GOS GIA MAC HAI HCL Ht’Z HFA HMD HMI HPA HPdkt HPO HSS HXG IAA IAC IAL IAN IBR

Conference Proceedings on Vortex Flow Aerodynamics Held in Scheveningen, The Netherlands on 1-4 October 1990

DTIC Science & Technology

1991-07-01

example, caracterises par l’existence d’une pointe de survitesse importante, c’est le nombre de Reynolds qui r~git It "caract~re transitionnel’" de... caracterisation d’un Ecoulement cisaillC tridimensionnel autour d’une aile en fl~che. Une precedente Etude avait Etd nen~e qui avait pour but de qualifier I...su.vant iea configi-rations Attdi4es. 4 -m CARACTERISATION DE L ECLKTEg2NT Ii eat admis. anlon [22), que i𔄀clatement tourbiiionna~re est caravteris6

Understanding the Effects of NaCl, NaBr and Their Mixtures on Silver Nanowire Nucleation and Growth in Terms of the Distribution of Electron Traps in Silver Halide Crystals

PubMed Central

Rui, Yunjun; Zhao, Weiliang; Zhu, Dewei; Wang, Hengyu; Song, Guangliang; Swihart, Mark T.; Wan, Neng; Gu, Dawei; Tang, Xiaobing; Yang, Ying; Zhang, Tianyou

2018-01-01

In recent years, many research groups have synthesized ultra-thin silver nanowires (AgNWs) with diameters below 30 nm by employing Cl− and Br− simultaneously in the polyol process. However, the yield of AgNWs in this method was low, due to the production of Ag nanoparticles (AgNPs) as an unwanted byproduct, especially in the case of high Br− concentration. Here, we investigated the roles of Cl− and Br− in the preparation of AgNWs and then synthesized high aspect ratio (up to 2100) AgNWs in high yield (>85% AgNWs) using a Cl− and Br− co-mediated method. We found that multiply-twinned particles (MTPs) with different critical sizes were formed and grew into AgNWs, accompanied by a small and large amount of AgNPs for the NaCl and NaBr additives, respectively. For the first time, we propose that the growth of AgNWs of different diameters and yields can be understood based on the electron trap distribution (ETD) of the silver halide crystals. For the case of Cl− and Br− co-additives, a mixed silver halide crystal of AgBr1−xClx was formed, rather than the AgBr/AgCl mixture reported previously. In this type of crystal, the ETD is uniform, which is beneficial for the synthesis of AgNWs with small diameter (30~40 nm) and high aspect ratio. AgNW transparent electrodes were prepared in air by rod coating. A sheet resistance of 48 Ω/sq and transmittance of 95% at 550 nm were obtained without any post-treatment. PMID:29538281

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond

NASA Astrophysics Data System (ADS)

Samgina, Tatiana Yu; Kovalev, Sergey V.; Tolpina, Miriam D.; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T.

2018-05-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. [Figure not available: see fulltext.

Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2)

NASA Astrophysics Data System (ADS)

Anderson, Lissa C.; Håkansson, Maria; Walse, Björn; Nilsson, Carol L.

2017-09-01

Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a 45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. [Figure not available: see fulltext.

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond.

PubMed

Samgina, Tatiana Yu; Kovalev, Sergey V; Tolpina, Miriam D; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T

2018-05-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS 3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. Graphical Abstract ᅟ.

Evaluation of HIFU-induced lesion region using temperature threshold and equivalent thermal dose methods

NASA Astrophysics Data System (ADS)

Chang, Shihui; Xue, Fanfan; Zhou, Wenzheng; Zhang, Ji; Jian, Xiqi

2017-03-01

Usually, numerical simulation is used to predict the acoustic filed and temperature distribution of high intensity focused ultrasound (HIFU). In this paper, the simulated lesion volumes obtained by temperature threshold (TRT) 60 °C and equivalent thermal dose (ETD) 240 min were compared with the experimental results which were obtained by animal tissue experiment in vitro. In the simulation, the calculated model was established according to the vitro tissue experiment, and the Finite Difference Time Domain (FDTD) method was used to calculate the acoustic field and temperature distribution in bovine liver by the Westervelt formula and Pennes bio-heat transfer equation, and the non-linear characteristics of the ultrasound was considered. In the experiment, the fresh bovine liver was exposed for 8s, 10s, 12s under different power conditions (150W, 170W, 190W, 210W), and the exposure was repeated 6 times under the same dose. After the exposures, the liver was sliced and photographed every 0.2mm, and the area of the lesion region in every photo was calculated. Then, every value of the areas was multiplied by 0.2mm, and summed to get the approximation volume of the lesion region. The comparison result shows that the lesion volume of the region calculated by TRT 60 °C in simulation was much closer to the lesion volume obtained in experiment, and the volume of the region above 60 °C was larger than the experimental results, but the volume deviation was not exceed 10%. The volume of the lesion region calculated by ETD 240 min was larger than that calculated by TRT 60 °C in simulation, and the volume deviations were ranged from 4.9% to 23.7%.

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond

NASA Astrophysics Data System (ADS)

Samgina, Tatiana Yu; Kovalev, Sergey V.; Tolpina, Miriam D.; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T.

2018-01-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops.

The ATP required for potentiation of skeletal muscle contraction is released via pannexin hemichannels.

PubMed

Riquelme, Manuel A; Cea, Luis A; Vega, José L; Boric, Mauricio P; Monyer, Hannah; Bennett, Michael V L; Frank, Marina; Willecke, Klaus; Sáez, Juan C

2013-12-01

During repetitive stimulation of skeletal muscle, extracellular ATP levels raise, activating purinergic receptors, increasing Ca2+ influx, and enhancing contractile force, a response called potentiation. We found that ATP appears to be released through pannexin1 hemichannels (Panx1 HCs). Immunocytochemical analyses and function were consistent with pannexin1 localization to T-tubules intercalated with dihydropyridine and ryanodine receptors in slow (soleus) and fast (extensor digitorum longus, EDL) muscles. Isolated myofibers took up ethidium (Etd+) and released small molecules (as ATP) during electrical stimulation. Consistent with two glucose uptake pathways, induced uptake of 2-NBDG, a fluorescent glucose derivative, was decreased by inhibition of HCs or glucose transporter (GLUT4), and blocked by dual blockade. Adult skeletal muscles apparently do not express connexins, making it unlikely that connexin hemichannels contribute to the uptake and release of small molecules. ATP release, Etd+ uptake, and potentiation induced by repetitive electrical stimulation were blocked by HC blockers and did not occur in muscles of pannexin1 knockout mice. MRS2179, a P2Y1R blocker, prevented potentiation in EDL, but not soleus muscles, suggesting that in fast muscles ATP activates P2Y1 but not P2X receptors. Phosphorylation on Ser and Thr residues of pannexin1 was increased during potentiation, possibly mediating HC opening. Opening of Panx1 HCs during repetitive activation allows efflux of ATP, influx of glucose and possibly Ca2+ too, which are required for potentiation of contraction. This article is part of the Special Issue Section entitled 'Current Pharmacology of Gap Junction Channels and Hemichannels'. Copyright © 2013 Elsevier Ltd. All rights reserved.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

N-Glycopeptide Profiling in Arabidopsis Inflorescence

DOE PAGES

Xu, Shou-Ling; Medzihradszky, Katalin F.; Wang, Zhi-Yong; ...

2016-04-11

This study presents the first large scale analysis of plant intact glycopeptides. Using wheat germ agglutinin lectin weak affinity chromatography to enrich modified peptides, followed by ETD fragmentation tandem mass spectrometry, glycan compositions on over 1100 glycopeptides from 270 proteins found in Arabidopsis inflorescence tissue were characterized. While some sites were only detected with a single glycan attached, others displayed up to 16 different glycoforms. Among the identified glycopeptides were four modified in non-consensus glycosylation motifs. Finally, while most of the modified proteins are secreted, membrane, ER or Golgi localized proteins, surprisingly N-linked sugars were detected on a protein predictedmore » to be cytosolic or nuclear.« less

Localization accuracy of compact binary coalescences detected by the third-generation gravitational-wave detectors and implication for cosmology

NASA Astrophysics Data System (ADS)

Zhao, Wen; Wen, Linqing

2018-03-01

We use the Fisher information matrix to investigate the angular resolution and luminosity distance uncertainty for coalescing binary neutron stars (BNSs) and neutron star-black hole binaries (NSBHs) detected by the third-generation (3G) gravitational-wave (GW) detectors. Our study focuses on an individual 3G detector and a network of up to four 3G detectors at different locations including the United States, Europe, China, and Australia for the proposed Einstein Telescope (ET) and Cosmic Explorer (CE) detectors. In particular, we examine the effect of the Earth's rotation, as GW signals from BNS and low-mass NSBH systems could be hours long for 3G detectors. In this case, an individual detector can be effectively treated as a detector network with long baselines formed by the trajectory of the detector as it rotates with the Earth. Therefore, a single detector or two-detector networks could also be used to localize the GW sources effectively. We find that a time-dependent antenna beam-pattern function can help better localize BNS and NSBH sources, especially edge-on ones. The medium angular resolution for one ET-D detector is around 150 deg2 for BNSs at a redshift of z =0.1 , which improves rapidly with a decreasing low-frequency cutoff flow in sensitivity. The medium angular resolution for a network of two CE detectors in the United States and Europe, respectively, is around 20 deg2 at z =0.2 for the simulated BNS and NSBH samples. While for a network of two ET-D detectors, the similar angular resolution can be achieved at a much higher redshift of z =0.5 . The angular resolution of a network of three detectors is mainly determined by the baselines between detectors regardless of the CE or ET detector type. The medium angular resolution of BNS for a network of three detectors of the ET-D or CE type in the United States, Europe, and Australia is around 10 deg2 at z =2 . We discuss the implications of our results for multimessenger astronomy and, in particular, for using GW sources as independent tools to constrain the Hubble constant H0, the deceleration parameter q0, and the equation-of-state (EoS) of dark energy. We find that, in general, if 10 BNSs or NSBHs at z =0.1 with known redshifts are detected by 3G networks consisting of two ET-like detectors, H0 can be measured with an accuracy of 0.9%. If 1000 face-on BNSs at z <2 are detected with known redshifts, we are able to achieve Δ q0=0.002 for the deceleration parameter, or Δ w0=0.03 and Δ wa=0.2 for EoS of dark energy, respectively.

Improvements in health‐related quality of life over 3 years with liraglutide 3.0 mg compared with placebo in participants with overweight or obesity

PubMed Central

Gabriel Smolarz, B.; Meincke, H. H.; Fujioka, K.

2017-01-01

Summary Previously in the SCALE Obesity and Prediabetes trial, at 1 year, participants with obesity (or overweight with comorbidities) and prediabetes receiving liraglutide 3.0 mg experienced greater improvements in health‐related quality of life (HRQoL) than those receiving placebo. The current study extends these findings by examining 3‐year changes in HRQoL. HRQoL was assessed using the obesity‐specific Impact of Weight on Quality of Life‐Lite (IWQOL‐Lite) questionnaire, as well as the Short‐Form 36 v2 (SF‐36) health survey. At 3 years, mean change (±standard deviation) in IWQOL‐Lite total score from baseline for liraglutide (n = 1472) was 11.0 ± 14.2, vs. 8.1 ± 14.7 for placebo (n = 738) (estimated treatment difference [ETD] 3.4 [95% confidence interval (CI): 2.0, 4.7], P < 0.0001). Mean change in SF‐36 physical component summary (PCS) score from baseline for liraglutide was 3.1 ± 7.3, vs. 2.6 ± 7.6 for placebo (ETD 0.87 [95% CI: 0.17, 1.6], P = 0.0156). Mean change in SF‐36 mental component summary score did not significantly differ between groups. Both IWQOL‐Lite total score and PCS score demonstrated an association between greater HRQoL improvement with higher weight loss. Liraglutide 3.0 mg was also associated with improved health utility (Short‐Form‐6D and EuroQol‐5D, mapped from IWQOL‐Lite and/or SF‐36) vs. placebo. Liraglutide 3.0 mg, plus diet and exercise, is associated with long‐term improvements in HRQoL with obesity or overweight with comorbidity vs. placebo. PMID:29045079

Improvements in health-related quality of life over 3 years with liraglutide 3.0 mg compared with placebo in participants with overweight or obesity.

PubMed

Kolotkin, R L; Gabriel Smolarz, B; Meincke, H H; Fujioka, K

2018-02-01

Previously in the SCALE Obesity and Prediabetes trial, at 1 year, participants with obesity (or overweight with comorbidities) and prediabetes receiving liraglutide 3.0 mg experienced greater improvements in health-related quality of life (HRQoL) than those receiving placebo. The current study extends these findings by examining 3-year changes in HRQoL. HRQoL was assessed using the obesity-specific Impact of Weight on Quality of Life-Lite (IWQOL-Lite) questionnaire, as well as the Short-Form 36 v2 (SF-36) health survey. At 3 years, mean change (±standard deviation) in IWQOL-Lite total score from baseline for liraglutide (n = 1472) was 11.0 ± 14.2, vs. 8.1 ± 14.7 for placebo (n = 738) (estimated treatment difference [ETD] 3.4 [95% confidence interval (CI): 2.0, 4.7], P < 0.0001). Mean change in SF-36 physical component summary (PCS) score from baseline for liraglutide was 3.1 ± 7.3, vs. 2.6 ± 7.6 for placebo (ETD 0.87 [95% CI: 0.17, 1.6], P = 0.0156). Mean change in SF-36 mental component summary score did not significantly differ between groups. Both IWQOL-Lite total score and PCS score demonstrated an association between greater HRQoL improvement with higher weight loss. Liraglutide 3.0 mg was also associated with improved health utility (Short-Form-6D and EuroQol-5D, mapped from IWQOL-Lite and/or SF-36) vs. placebo. Liraglutide 3.0 mg, plus diet and exercise, is associated with long-term improvements in HRQoL with obesity or overweight with comorbidity vs. placebo. © 2017 The Authors. Clinical Obesity published by John Wiley & Sons Ltd on behalf of World Obesity Federation.

Comparative safety and efficacy of insulin degludec with insulin glargine in type 2 and type 1 diabetes: a meta-analysis of randomized controlled trials.

PubMed

Zhang, Xiao-Wen; Zhang, Xin-Lin; Xu, Biao; Kang, Li-Na

2018-05-01

To determine the safety and efficacy of insulin degludec versus glargine in patients with type 1 (T1D) and type 2 (T2D) diabetes mellitus. Databases were searched until July 5, 2017. We included randomized controlled trials comparing degludec with glargine in diabetic patients, each with a minimum of 16 weeks of follow-up. Eighteen trials with 16,791 patients were included. Degludec was associated with a statistically significant reduction in risk for all confirmed hypoglycemia at the maintenance treatment period [estimated rate ratio (ERR) 0.81; 95% confidence interval (CI) 0.72‒0.92; P = 0.001], nocturnal confirmed hypoglycemia at the entire (ERR 0.71; 95% CI 0.63‒0.80; P < 0.001) and maintenance treatment period (ERR 0.65; 95% CI 0.59‒0.71; P < 0.001), all irrespective of the pooled diabetic populations and follow-up durations. The differences in the rate of hypoglycemia were more pronounced in nocturnal period and maintenance period and in T2D than T1D patients. Degludec reduced the incidence of severe hypoglycemia in T2D [ERR 0.65; (0.52; 0.89); P = 0.005] but not T1D patients. HbA1c concentration was slightly higher in degludec over glargine but was not clinically relevant [estimated treatment difference (ETD) 0.03; 95% CI - 0.00 to 0.06%; P = 0.06]. Fasting plasma glucose level was lower in degludec-treated patients (ETD - 0.28 mmol/L; 95% CI - 0.44 to - 0.11 mmol/L; P = 0.001). Several subgroup analyses showed largely consistent findings. The rates of adverse events including total mortality and cardiovascular events were not significantly different between two treatment strategies. Insulin degludec appears to have better safety in reducing hypoglycemic events with similar efficacy compared with insulin glargine.

Medical waste treatment and disposal methods used by hospitals in Oregon, Washington, and Idaho.

PubMed

Klangsin, P; Harding, A K

1998-06-01

This study investigated medical waste practices used by hospitals in Oregon, Washington, and Idaho, which includes the majority of hospitals in the U.S. Environmental Protection Agency's (EPA) Region 10. During the fall of 1993, 225 hospitals were surveyed with a response rate of 72.5%. The results reported here focus on infectious waste segregation practices, medical waste treatment and disposal practices, and the operating status of hospital incinerators in these three states. Hospitals were provided a definition of medical waste in the survey, but were queried about how they define infectious waste. The results implied that there was no consensus about which agency or organization's definition of infectious waste should be used in their waste management programs. Confusion around the definition of infectious waste may also have contributed to the finding that almost half of the hospitals are not segregating infectious waste from other medical waste. The most frequently used practice of treating and disposing of medical waste was the use of private haulers that transport medical waste to treatment facilities (61.5%). The next most frequently reported techniques were pouring into municipal sewage (46.6%), depositing in landfills (41.6%), and autoclaving (32.3%). Other methods adopted by hospitals included Electro-Thermal-Deactivation (ETD), hydropulping, microwaving, and grinding before pouring into the municipal sewer. Hospitals were asked to identify all methods they used in the treatment and disposal of medical waste. Percentages, therefore, add up to greater than 100% because the majority chose more than one method. Hospitals in Oregon and Washington used microwaving and ETD methods to treat medical waste, while those in Idaho did not. No hospitals in any of the states reported using irradiation as a treatment technique. Most hospitals in Oregon and Washington no longer operate their incinerators due to more stringent regulations regarding air pollution emissions. Hospitals in Idaho, however, were still operating incinerators in the absence of state regulations specific to these types of facilities.

GRADE: Assessing the quality of evidence in environmental and occupational health.

PubMed

Morgan, Rebecca L; Thayer, Kristina A; Bero, Lisa; Bruce, Nigel; Falck-Ytter, Yngve; Ghersi, Davina; Guyatt, Gordon; Hooijmans, Carlijn; Langendam, Miranda; Mandrioli, Daniele; Mustafa, Reem A; Rehfuess, Eva A; Rooney, Andrew A; Shea, Beverley; Silbergeld, Ellen K; Sutton, Patrice; Wolfe, Mary S; Woodruff, Tracey J; Verbeek, Jos H; Holloway, Alison C; Santesso, Nancy; Schünemann, Holger J

2016-01-01

There is high demand in environmental health for adoption of a structured process that evaluates and integrates evidence while making decisions and recommendations transparent. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework holds promise to address this demand. For over a decade, GRADE has been applied successfully to areas of clinical medicine, public health, and health policy, but experience with GRADE in environmental and occupational health is just beginning. Environmental and occupational health questions focus on understanding whether an exposure is a potential health hazard or risk, assessing the exposure to understand the extent and magnitude of risk, and exploring interventions to mitigate exposure or risk. Although GRADE offers many advantages, including its flexibility and methodological rigor, there are features of the different sources of evidence used in environmental and occupational health that will require further consideration to assess the need for method refinement. An issue that requires particular attention is the evaluation and integration of evidence from human, animal, in vitro, and in silico (computer modeling) studies when determining whether an environmental factor represents a potential health hazard or risk. Assessment of the hazard of exposures can produce analyses for use in the GRADE evidence-to-decision (EtD) framework to inform risk-management decisions about removing harmful exposures or mitigating risks. The EtD framework allows for grading the strength of the recommendations based on judgments of the certainty in the evidence (also known as quality of the evidence), as well as other factors that inform recommendations such as social values and preferences, resource implications, and benefits. GRADE represents an untapped opportunity for environmental and occupational health to make evidence-based recommendations in a systematic and transparent manner. The objectives of this article are to provide an overview of GRADE, discuss GRADE's applicability to environmental health, and identify priority areas for method assessment and development. Copyright © 2016 Elsevier Ltd. All rights reserved.

GRADE: Assessing the quality of evidence in environmental and occupational health

PubMed Central

Morgan, Rebecca L; Thayer, Kristina A; Bero, Lisa; Bruce, Nigel; Falck-Ytter, Yngve; Ghersi, Davina; Guyatt, Gordon; Hooijmans, Carlijn; Langendam, Miranda; Mandrioli, Daniele; Mustafa, Reem A.; Rehfuess, Eva A; Rooney, Andrew A; Shea, Beverley; Silbergeld, Ellen K; Sutton, Patrice; Wolfe, Mary; Woodruff, Tracey J; Verbeek, Jos H; Holloway, Alison C.; Santesso, Nancy; Schünemann, Holger J

2016-01-01

There is high demand in environmental health for adoption of a structured process that evaluates and integrates evidence while making decisions and recommendations transparent. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework holds promise to address this demand. For over a decade, GRADE has been applied successfully to areas of clinical medicine, public health, and health policy, but experience with GRADE in environmental and occupational health is just beginning. Environmental and occupational health questions focus on understanding whether an exposure is a potential health hazard or risk, assessing the exposure to understand the extent and magnitude of risk, and exploring interventions to mitigate exposure or risk. Although GRADE offers many advantages, including its flexibility and methodological rigor, there are features of the different sources of evidence used in environmental and occupational health that will require further consideration to assess the need for method refinement. An issue that requires particular attention is the evaluation and integration of evidence from human, animal, in vitro, and in silico (computer modelling) studies when determining whether an environmental factor represents a potential health hazard or risk. Assessment of the hazard of exposures can produce analyses for use in the GRADE evidence-to-decision (EtD) framework to inform risk-management decisions about removing harmful exposures or mitigating risks. The EtD framework allows for grading the strength of the recommendations based on judgments of the certainty in the evidence (also known as quality of the evidence), as well as other factors that inform recommendations such as social values and preferences, resource implications, and benefits. GRADE represents an untapped opportunity for environmental and occupational health to make evidence-based recommendations in a systematic and transparent manner. The objectives of this article are to provide an overview of GRADE, discuss GRADE’s applicability to environmental health, and identify priority areas for method assessment and development. PMID:26827182

Multimode electromagnetic target discriminator: preliminary data results

NASA Astrophysics Data System (ADS)

Black, Christopher J.; McMichael, Ian T.; Nelson, Carl V.

2004-09-01

This paper describes the Multi-mode Electromagnetic Target Discriminator (METD) sensor and presents preliminary results from recent field experiments. The METD sensor was developed for the US Army RDECOM NVESD by The Johns Hopkins University Applied Physics Laboratory. The METD, based on the technology of the previously developed Electromagnetic Target Discriminator (ETD), is a spatial scanning electromagnetic induction (EMI) sensor that uses both the time-domain (TD) and the frequency-domain (FD) for target detection and classification. Data is collected with a custom data acquisition system and wirelessly transmitted to a base computer. We show that the METD has a high signal-to-noise ratio (SNR), the ability to detect voids created by plastic anti-tank (AT) mines, and is practical for near real-time data processing.

Biological effects of radiation, metabolic and replication kinetics alterations

NASA Technical Reports Server (NTRS)

Post, J.

1972-01-01

The biological effects of radiation upon normal and cancerous tissues were studied. A macromolecular precursor of DNA, 3ETdR, was incorporated into the cell nucleus during synthesis and provided intranuclear beta radiation. Tritium labeled cells were studied with autoradiographic methods; cell cycle kinetics were determined and cell functions modified by radiation dosage or by drugs were also evaluated. The long term program has included; (1) effects of radiation on cell replication and the correlation with incorporated dose levels, (2) radiation induced changes in cell function, viz., the response of beta irradiated spleen lymphocytes to antigenic stimulation by sheep red blood cells (SRBC), (3) kinetics of tumor and normal cell replication; and (4) megakaryocyte formation and modification by radiomimetic drugs.

Development of Encapsulated Lithium Hydride Thermal Energy Storage for Space Power Systems,

DTIC Science & Technology

1987-12-01

equation can be approximated by dA + I • 27rdr[ dr V0 % % ORNL -DWG 87- 4427 ETD r(min) 0 12 3 4 5 0 2 -. E 4 3 SOLID 4 ~h (r) VAPORLIQUID 5 Fig. 3.11. Bubble...MORRIS ET AL DEC 87 UNCLASSIFIED ORNL /TM-i84t 3 DE-R5-840R214" F/G 14/4 L Iusmommmmi mhnnnnEnhihiI mnEElI/ihliI/E ElllllEll/IlEI ElllhEEEEEElhE EIIEE...E-EhhE IliEEEEEihlEEE 1111 1112.0!’ ’ - 1.8 1.1125 11111 .4 1111.6 MICPOCOP RESOLUTION TEST CHAR *.t 0 0 0 0 0 0 0 *:J* l~.~ omi ORNL /TM-10413 OAK

Safety and efficacy of once-weekly semaglutide vs additional oral antidiabetic drugs in Japanese people with inadequately controlled type 2 diabetes: A randomized trial.

PubMed

Kaku, Kohei; Yamada, Yuichiro; Watada, Hirotaka; Abiko, Atsuko; Nishida, Tomoyuki; Zacho, Jeppe; Kiyosue, Arihiro

2018-05-01

To evaluate the safety and efficacy of once-weekly subcutaneous semaglutide as monotherapy or combined with an oral antidiabetic drug (OAD) vs an additional OAD added to background therapy in Japanese people with type 2 diabetes (T2D) inadequately controlled on diet/exercise or OAD monotherapy. In this phase III, open-label trial, adults with T2D were randomized 2:2:1 to semaglutide 0.5 mg or 1.0 mg, or one additional OAD (a dipeptidyl peptidase-4 inhibitor, biguanide, sulphonylurea, glinide, α-glucosidase inhibitor or thiazolidinedione) with a different mode of action from that of background therapy. The primary endpoint was number of adverse events (AEs) after 56 weeks. Baseline characteristics were balanced between treatment arms (601 randomized). More AEs were reported in the semaglutide 0.5 mg (86.2%) and 1.0 mg (88.0%) groups than in the additional OAD group (71.7%). These were typically mild/moderate. Gastrointestinal AEs were most frequent with semaglutide, which diminished over time. The mean glycated haemoglobin (HbA1c) concentration (baseline 8.1%) was significantly reduced with semaglutide 0.5 mg and 1.0 mg vs additional OAD (1.7% and 2.0% vs 0.7%, respectively; estimated treatment difference [ETD] vs additional OAD -1.08% and -1.37%, both P < .0001). Body weight (baseline 71.5 kg) was reduced by 1.4 kg and 3.2 kg with semaglutide 0.5 mg and 1.0 mg, vs a 0.4-kg increase with additional OAD (ETD -1.84 kg and -3.59 kg; both P < .0001). For semaglutide-treated participants, >80% achieved an HbA1c concentration <7.0% (Japanese Diabetes Society target). Semaglutide was well tolerated, with no new safety issues identified. Semaglutide treatment significantly reduced HbA1c and body weight vs additional OAD treatment in Japanese people with T2D. © 2018 The Authors. Diabetes, Obesity and Metabolism published by John Wiley & Sons Ltd.

National Guidelines for Colorectal Cancer Screening in Saudi Arabia with strength of recommendations and quality of evidence.

PubMed

Alsanea, Nasser; Almadi, Majid A; Abduljabbar, Alaa S; Alhomoud, Samar; Alshaban, Taghreed A; Alsuhaibani, Abdullah; Alzahrani, Ahmad; Batwa, Faisal; Hassan, Abdul-Hameed; Hibbert, Denise; Nooh, Randa; Alothman, Mohammed; Rochwerg, Bram; Alhazzani, Waleed; Morgan, Rebecca L

2015-01-01

Colorectal cancer is the most common cancer among Saudi men and the third commonest among Saudi women. Given the predominance of colorectal cancer compared with other cancers in Saudi Arabia, context-specific guidelines are needed for screening. Experts from the Saudi Society of Colon and Rectal Surgery, Saudi Gastroenterology Association, Saudi Oncology Society, Saudi Chapter of Enterostomal Therapy, Family Medicine and Department of Public Health at the Saudi Arabian Ministry of Health and a patient advocate was assembled by the Saudi Centre for Evidence-Based Healthcare, a subsidiary of the Saudi Arabian Ministry of Health. The panel collaborated with a methodological team from McMaster University, Canada to develop national guidelines for colorectal cancer screening. After identifying key questions, the panel conducted a systematic review of all reports on the utility of screening, the cost of screening for colorectal cancer in Saudi Arabia and on the values and preferences of Saudi patients. Meta- analyses, when appropriate, were performed to generate pooled estimates of effect. Using the GRADE approach, the panel used the evidence-to-decision (EtD) framework to assess all domains important in determining the strength and direction of the recommendations (benefits and harms, values and preferences, resource implications, equity, acceptability, and feasibility). Judgments related to the EtD domains were resolved through consensus or voting, if consensus was not reached. The final recommendations were developed during a two-day meeting held in Riyadh, Saudi Arabia in March 2015. Conflicts of interests among the panel members were handled according to the World Health Organization rules. There is lack of national data on the incidence of adenomatous polyps or the age groups in which the incidence surges. There were no national clinical trials assessing the effectiveness of the different modalities of screening for colorectal cancer and their impact on mortality. The panel recommends screening for colorectal cancer in Saudi Arabia in asymptomatic Saudi patients at average risk of colorectal cancer. An infrastructure should be built to achieve that goal.

Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

DOE PAGES

Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; ...

2015-08-28

The analysis of post-translational modifications (PTMs) by proteomics is regarded as a technically challenging undertaking. While in recent years approaches to examine and quantify protein phosphorylation have greatly improved, the analysis of many protein modifications, such as glycosylation, are still regarded as problematic. Limitations in the standard proteomics workflow, such as use of suboptimal peptide fragmentation methods, can significantly prevent the identification of glycopeptides. The current generation of tandem mass spectrometers has made available a variety of fragmentation options, many of which are becoming standard features on these instruments. Lastly, we have used three common fragmentation techniques, namely CID, HCD,more » and ETD, to analyze a glycopeptide and highlight how an integrated fragmentation approach can be used to identify the modified residue and characterize the N-glycan on a peptide.« less

Assembly of the most topologically regular two-dimensional micro and nanocrystals with spherical, conical, and tubular shapes

NASA Astrophysics Data System (ADS)

Roshal, D. S.; Konevtsova, O. V.; Myasnikova, A. E.; Rochal, S. B.

2016-11-01

We consider how to control the extension of curvature-induced defects in the hexagonal order covering different curved surfaces. In these frames we propose a physical mechanism for improving structures of two-dimensional spherical colloidal crystals (SCCs). For any SCC comprising of about 300 or less particles the mechanism transforms all extended topological defects (ETDs) in the hexagonal order into the point disclinations. Perfecting the structure is carried out by successive cycles of the particle implantation and subsequent relaxation of the crystal. The mechanism is potentially suitable for obtaining colloidosomes with better selective permeability. Our approach enables modeling the most topologically regular tubular and conical two-dimensional nanocrystals including various possible polymorphic forms of the HIV viral capsid. Different HIV-like shells with an arbitrary number of structural units (SUs) and desired geometrical parameters are easily formed. Faceting of the obtained structures is performed by minimizing the suggested elastic energy.

Optimization of parameters for coverage of low molecular weight proteins

PubMed Central

Müller, Stephan A.; Kohajda, Tibor; Findeiß, Sven; Stadler, Peter F.; Washietl, Stefan; Kellis, Manolis; von Bergen, Martin

2010-01-01

Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT-CID and IT-ETD allowed the validation of 75% of the identified proteins using this orthogonal fragmentation technique. Furthermore, a new approach to evaluating and improving the completeness of protein databases that utilizes the program RNAcode was introduced and examined. Electronic supplementary material The online version of this article (doi:10.1007/s00216-010-4093-x) contains supplementary material, which is available to authorized users. PMID:20803007

Effects of Parameter Uncertainty on Long-Term Simulations of Lake Alkalinity

NASA Astrophysics Data System (ADS)

Lee, Sijin; Georgakakos, Konstantine P.; Schnoor, Jerald L.

1990-03-01

A first-order second-moment uncertainty analysis has been applied to two lakes in the Adirondack Park, New York, to assess the long-term response of lakes to acid deposition. Uncertainty due to parameter error and initial condition error was considered. Because the enhanced trickle-down (ETD) model is calibrated with only 3 years of field data and is used to simulate a 50-year period, the uncertainty in the lake alkalinity prediction is relatively large. When a best estimate of parameter uncertainty is used, the annual average alkalinity is predicted to be -11 ±28 μeq/L for Lake Woods and 142 ± 139 μeq/L for Lake Panther after 50 years. Hydrologic parameters and chemical weathering rate constants contributed most to the uncertainty of the simulations. Results indicate that the uncertainty in long-range predictions of lake alkalinity increased significantly over a 5- to 10-year period and then reached a steady state.

The active site of O-GlcNAc transferase imposes constraints on substrate sequence

PubMed Central

Rafie, Karim; Blair, David E.; Borodkin, Vladimir S.; Albarbarawi, Osama; van Aalten, Daan M. F.

2016-01-01

O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoa. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay on a library of peptides. The sites of O-GlcNAc modification were mapped by ETD-mass spectrometry, and found to correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with human OGT suggest that a combination of size and conformational restriction defines sequence specificity in the −3 to +2 subsites. This work reveals that while the N-terminal TPR repeats of hOGT may play a role in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a significant contribution to O-GlcNAc site specificity. PMID:26237509

Transit timing analysis of the exoplanet TrES-5 b. Possible existence of the exoplanet TrES-5 c

NASA Astrophysics Data System (ADS)

Sokov, Eugene N.; Sokova, Iraida A.; Dyachenko, Vladimir V.; Rastegaev, Denis A.; Burdanov, Artem; Rusov, Sergey A.; Benni, Paul; Shadick, Stan; Hentunen, Veli-Pekka; Salisbury, Mark; Esseiva, Nicolas; Garlitz, Joe; Bretton, Marc; Ogmen, Yenal; Karavaev, Yuri; Ayiomamitis, Anthony; Mazurenko, Oleg; Alonso, David Molina; Velichko, Sergey F.

2018-06-01

In this work, we present transit timing variations detected for the exoplanet TrES-5b. To obtain the necessary amount of photometric data for this exoplanet, we have organized an international campaign to search for exoplanets based on the Transit Timing Variation method (TTV) and as a result of this we collected 30 new light curves, 15 light curves from the Exoplanet Transit Database (ETD) and 8 light curves from the literature for the timing analysis of the exoplanet TrES-5b. We have detected timing variations with a semi-amplitude of A ≈ 0.0016 days and a period of P ≈ 99 days. We carried out the N-body modeling based on the three-body problem. The detected perturbation of TrES-5b may be caused by a second exoplanet in the TrES-5 system. We have calculated the possible mass and resonance of the object: M ≈ 0.24MJup at a 1:2 Resonance.

A portable non-contact displacement sensor and its application of lens centration error measurement

NASA Astrophysics Data System (ADS)

Yu, Zong-Ru; Peng, Wei-Jei; Wang, Jung-Hsing; Chen, Po-Jui; Chen, Hua-Lin; Lin, Yi-Hao; Chen, Chun-Cheng; Hsu, Wei-Yao; Chen, Fong-Zhi

2018-02-01

We present a portable non-contact displacement sensor (NCDS) based on astigmatic method for micron displacement measurement. The NCDS are composed of a collimated laser, a polarized beam splitter, a 1/4 wave plate, an aspheric objective lens, an astigmatic lens and a four-quadrant photodiode. A visible laser source is adopted for easier alignment and usage. The dimension of the sensor is limited to 115 mm x 36 mm x 56 mm, and a control box is used for dealing with signal and power control between the sensor and computer. The NCDS performs micron-accuracy with +/-30 μm working range and the working distance is constrained in few millimeters. We also demonstrate the application of the NCDS for lens centration error measurement, which is similar to the total indicator runout (TIR) or edge thickness difference (ETD) of a lens measurement using contact dial indicator. This application has advantage for measuring lens made in soft materials that would be starched by using contact dial indicator.

Analysis of human serum phosphopeptidome by a focused database searching strategy.

PubMed

Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

2013-01-14

As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

International energy: Research organizations, 1986--1990

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

Hendricks, P.; Jordan, S.

The International Energy: Research Organizations publication contains the standardized names of energy research organizations used in energy information databases. Involved in this cooperative task are (1) the technical staff of the USDOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the Energy Technology Data Exchange (ETDE) and (2) the International Nuclear Information System (INIS). This publication identifies current organizations doing research in all energy fields, standardizes the format for recording these organization names in bibliographic citations, assigns a numeric code to facilitate data entry, and identifies report number prefixes assigned by these organizations. Thesemore » research organization names may be used in searching the databases Energy Science Technology'' on DIALOG and Energy'' on STN International. These organization names are also used in USDOE databases on the Integrated Technical Information System. Research organizations active in the past five years, as indicated by database records, were identified to form this publication. This directory includes approximately 34,000 organizations that reported energy-related literature from 1986 to 1990 and updates the DOE Energy Data Base: Corporate Author Entries.« less

2-Aminobenzamide and 2-Aminobenzoic Acid as New MALDI Matrices Inducing Radical Mediated In-Source Decay of Peptides and Proteins

NASA Astrophysics Data System (ADS)

Smargiasso, Nicolas; Quinton, Loic; de Pauw, Edwin

2012-03-01

One of the mechanisms leading to MALDI in-source decay (MALDI ISD) is the transfer of hydrogen radicals to analytes upon laser irradiation. Analytes such as peptides or proteins may undergo ISD and this method can therefore be exploited for top-down sequencing. When performed on peptides, radical-induced ISD results in production of c- and z-ions, as also found in ETD and ECD activation. Here, we describe two new compounds which, when used as MALDI matrices, are able to efficiently induce ISD of peptides and proteins: 2-aminobenzamide and 2-aminobenzoic acid. In-source reduction of the disulfide bridge containing peptide Calcitonin further confirmed the radicalar mechanism of the ISD process. ISD of peptides led, in addition to c- and z-ions, to the generation of a-, x-, and y-ions both in positive and in negative ion modes. Finally, good sequence coverage was obtained for the sequencing of myoglobin (17 kDa protein), confirming the effectiveness of both 2-aminobenzamide and 2-aminobenzoic acid as MALDI ISD matrices.

2-Aminobenzamide and 2-aminobenzoic acid as new MALDI matrices inducing radical mediated in-source decay of peptides and proteins.

PubMed

Smargiasso, Nicolas; Quinton, Loic; De Pauw, Edwin

2012-03-01

One of the mechanisms leading to MALDI in-source decay (MALDI ISD) is the transfer of hydrogen radicals to analytes upon laser irradiation. Analytes such as peptides or proteins may undergo ISD and this method can therefore be exploited for top-down sequencing. When performed on peptides, radical-induced ISD results in production of c- and z-ions, as also found in ETD and ECD activation. Here, we describe two new compounds which, when used as MALDI matrices, are able to efficiently induce ISD of peptides and proteins: 2-aminobenzamide and 2-aminobenzoic acid. In-source reduction of the disulfide bridge containing peptide Calcitonin further confirmed the radicalar mechanism of the ISD process. ISD of peptides led, in addition to c- and z-ions, to the generation of a-, x-, and y-ions both in positive and in negative ion modes. Finally, good sequence coverage was obtained for the sequencing of myoglobin (17 kDa protein), confirming the effectiveness of both 2-aminobenzamide and 2-aminobenzoic acid as MALDI ISD matrices.

An EThcD-Based Method for Discrimination of Leucine and Isoleucine Residues in Tryptic Peptides

NASA Astrophysics Data System (ADS)

Zhokhov, Sergey S.; Kovalyov, Sergey V.; Samgina, Tatiana Yu.; Lebedev, Albert T.

2017-08-01

An EThcD-based approach for the reliable discrimination of isomeric leucine and isoleucine residues in peptide de novo sequencing procedure has been proposed. A multistage fragmentation of peptide ions was performed with Orbitrap Elite mass spectrometer in electrospray ionization mode. At the first stage, z-ions were produced by ETD or ETcaD fragmentation of doubly or triply charged peptide precursor ions. These primary ions were further fragmented by HCD with broad-band ion isolation, and the resulting w-ions showed different mass for leucine and isoleucine residues. The procedure did not require manual isolation of specific z-ions prior to HCD stage. Forty-three tryptic peptides (3 to 27 residues) obtained by trypsinolysis of human serum albumin (HSA) and gp188 protein were analyzed. To demonstrate a proper solution for radical site migration problem, three non-tryptic peptides were also analyzed. A total of 93 leucine and isoleucine residues were considered and 83 of them were correctly identified. The developed approach can be a reasonable substitution for additional Edman degradation procedure, which is still used in peptide sequencing for leucine and isoleucine discrimination.

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

Properties of Two Carbon Composite Materials Using LTM25 Epoxy Resin

NASA Technical Reports Server (NTRS)

Cruz, Juan R.; Shah, C. H.; Postyn, A. S.

1996-01-01

In this report, the properties of two carbon-epoxy prepreg materials are presented. The epoxy resin used in these two materials can yield lower manufacturing costs due to its low initial cure temperature, and the capability of being cured using vacuum pressure only. The two materials selected for this study are MR50/LTM25, and CFS003/LTM25 with Amoco T300 fiber; both prepregs are manufactured by The Advanced Composites Group. MR50/LTM25 is a unidirectional prepreg tape using Mitsubishi MR50 carbon fiber impregnated with LTM25 epoxy resin. CRS003/LTM25 is a 2 by 2 twill fabric using Amoco T300 fiber and impregnated with LTM25 epoxy resin. Among the properties presented in this report are strength, stiffness, bolt bearing, and damage tolerance. Many of these properties were obtained at three environmental conditions: cold temperature/dry (CTD), room temperature/dry (RTD), and elevated temperature/wet (ETW). A few properties were obtained at room temperature/wet (RTW), and elevated temperature/dry (ETD). The cold and elevated temperatures used for testing were -125 F and 180 F, respectively. In addition, several properties related to processing are presented.

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

Zhang, Qibin; Schepmoes, Athena A; Brock, Jonathan W

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activationmore » after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.« less

Capacity utilization study for aviation security cargo inspection queuing system

NASA Astrophysics Data System (ADS)

Allgood, Glenn O.; Olama, Mohammed M.; Lake, Joe E.; Brumback, Daryl

2010-04-01

In this paper, we conduct performance evaluation study for an aviation security cargo inspection queuing system for material flow and accountability. The queuing model employed in our study is based on discrete-event simulation and processes various types of cargo simultaneously. Onsite measurements are collected in an airport facility to validate the queuing model. The overall performance of the aviation security cargo inspection system is computed, analyzed, and optimized for the different system dynamics. Various performance measures are considered such as system capacity, residual capacity, throughput, capacity utilization, subscribed capacity utilization, resources capacity utilization, subscribed resources capacity utilization, and number of cargo pieces (or pallets) in the different queues. These metrics are performance indicators of the system's ability to service current needs and response capacity to additional requests. We studied and analyzed different scenarios by changing various model parameters such as number of pieces per pallet, number of TSA inspectors and ATS personnel, number of forklifts, number of explosives trace detection (ETD) and explosives detection system (EDS) inspection machines, inspection modality distribution, alarm rate, and cargo closeout time. The increased physical understanding resulting from execution of the queuing model utilizing these vetted performance measures should reduce the overall cost and shipping delays associated with new inspection requirements.

Yeast proteins Gar1p, Nop1p, Npl3p, Nsr1p, and Rps2p are natively methylated and are substrates of the arginine methyltransferase Hmt1p.

PubMed

Yagoub, Daniel; Hart-Smith, Gene; Moecking, Jonas; Erce, Melissa A; Wilkins, Marc R

2015-09-01

The Hmt1 methyltransferase is the predominant arginine methyltransferase in Saccharomyces cerevisiae. There are 18 substrate proteins described for this methyltransferase, however native sites of methylation have only been identified on two of these proteins. Here we used peptide immunoaffinity enrichment, followed by LC-ETD-MS/MS, to discover 21 native sites of arginine methylation on five putative Hmt1 substrate proteins, namely Gar1p (H/ACA ribonucleoprotein complex subunit 1), Nop1p (rRNA 2'-O-methyltransferase fibrillarin), Npl3p (nucleolar protein 3), Nsr1p (nuclear localization sequence-binding protein), and Rps2p (40S ribosomal protein S2). The sites, many of which were found to be mono- or di-methylated, were predominantly found in RGG (Arg-Gly-Gly) motifs. Heavy methyl-SILAC validated the majority of these peptides. The above proteins, and relevant sites of methylation, were subsequently validated by in vitro methylation with recombinant Hmt1. This brings the total of Hmt1 substrate proteins for which native methylation sites have been identified to five. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring Seasonal Evapotranspiration in Vulnerable Agriculture using Time Series VHSR Satellite Data

NASA Astrophysics Data System (ADS)

Dalezios, Nicolas; Spyropoulos, Nicos V.; Tarquis, Ana M.

2015-04-01

The research work stems from the hypothesis that it is possible to perform an estimation of seasonal water needs of olive tree farms under drought periods by cross correlating high spatial, spectral and temporal resolution (~monthly) of satellite data, acquired at well defined time intervals of the phenological cycle of crops, with ground-truth information simultaneously applied during the image acquisitions. The present research is for the first time, demonstrating the coordinated efforts of space engineers, satellite mission control planners, remote sensing scientists and ground teams to record at specific time intervals of the phenological cycle of trees from ground "zero" and from 770 km above the Earth's surface, the status of plants for subsequent cross correlation and analysis regarding the estimation of the seasonal evapotranspiration in vulnerable agricultural environment. The ETo and ETc derived by Penman-Montieth equation and reference Kc tables, compared with new ETd using the Kc extracted from the time series satellite data. Several vegetation indices were also used especially the RedEdge and the chlorophyll one based on WorldView-2 RedEdge and second NIR bands to relate the tree status with water and nutrition needs. Keywords: Evapotransipration, Very High Spatial Resolution - VHSR, time series, remote sensing, vulnerability, agriculture, vegetation indeces.

Ion Trap Collisional Activation of c and z• Ions Formed via Gas-Phase Ion/Ion Electron Transfer Dissociation

PubMed Central

Han, Hongling; Xia, Yu; McLuckey, Scott A.

2008-01-01

A series of c- and z•-type product ions formed via gas-phase electron transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z• species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-and z-type ions. Most of the fragmentation pathways of z• species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z• species are different from the small losses observed from the charge-reduced peptide molecular species in electron transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues. PMID:17608403

Estimation of Areal Distribution of Evapotranspiration Using Remotely Sensed Data During Vegetation Period in Hungary

NASA Astrophysics Data System (ADS)

Dunkel, Z.; Szenyán, I. G.

The surface temperature measured by satellite can be the basis of evapotranspiration (ET) computation. The possibility of calculation of daily sum of the regional ET using surface temperature was examined under Hungarian weather conditions. A simplified relationship, namely ETd-Rnd = a + b (Tc-Ta), which relates the daily ET to daily net radiation with one measurements of surface and air temperature was used for the calculation. Using NOAA/AVHRR satellite data, no information about the surface inhomogeneity was obtained. The distribution of surface temperature was investigated by infrared thermometer scanning the surface from a board a hang-glider, ultra-light-aeroplane, and light aeroplane. Field observation trials were made during the vegetation period of 1992, 1993, 1994 and 1995. In eastern part of the country a homogeneous field (1 km × 1 km) was scanned before noon and afternoon. In the western part of the country, a much larger area (45 km × 45 km) was investigated. Cultivated area, forest and a large water surface were included in the investigated surface. The problems of calibration of hand-held infrared thermometer and the time shifting are discussed too. Comparison of model output with data from field experiment has played a crucial role in model development and suggested evaluation method

Determination of staphylococcal exotoxins, SCCmec types, and genetic relatedness of Staphylococcus intermedius group isolates from veterinary staff, companion animals, and hospital environments in Korea

PubMed Central

Youn, Jung-Ho; Ahn, Kuk Ju; Lim, Suk-Kyung

2011-01-01

The Staphylococcus (S.) intermedius group (SIG) has been a main research subject in recent years. S. pseudintermedius causes pyoderma and otitis in companion animals as well as foodborne diseases. To prevent SIG-associated infection and disease outbreaks, identification of both staphylococcal exotoxins and staphylococcal cassette chromosome mec (SCCmec) types among SIG isolates may be helpful. In this study, it was found that a single isolate (one out of 178 SIG isolates examined) harbored the canine enterotoxin SEC gene. However, the S. intermedius exfoliative toxin gene was found in 166 SIG isolates although the S. aureus-derived exfoliative toxin genes, such as eta, etb and etd, were not detected. SCCmec typing resulted in classifying one isolate as SCCmec type IV, 41 isolates as type V (including three S. intermedius isolates), and 10 isolates as non-classifiable. Genetic relatedness of all S. pseudintermedius isolates recovered from veterinary staff, companion animals, and hospital environments was determined by pulsed-field gel electrophoresis. Strains having the same band patterns were detected in S. pseudintermedius isolates collected at 13 and 18 months, suggesting possible colonization and/or expansion of a specific S. pseudintermedius strain in a veterinary hospital. PMID:21897094

Determination of staphylococcal exotoxins, SCCmec types, and genetic relatedness of Staphylococcus intermedius group isolates from veterinary staff, companion animals, and hospital environments in Korea.

PubMed

Youn, Jung-Ho; Koo, Hye Cheong; Ahn, Kuk Ju; Lim, Suk-Kyung; Park, Yong Ho

2011-09-01

The Staphylococcus (S.) intermedius group (SIG) has been a main research subject in recent years. S. pseudintermedius causes pyoderma and otitis in companion animals as well as foodborne diseases. To prevent SIG-associated infection and disease outbreaks, identification of both staphylococcal exotoxins and staphylococcal cassette chromosome mec (SCCmec) types among SIG isolates may be helpful. In this study, it was found that a single isolate (one out of 178 SIG isolates examined) harbored the canine enterotoxin SEC gene. However, the S. intermedius exfoliative toxin gene was found in 166 SIG isolates although the S. aureus-derived exfoliative toxin genes, such as eta, etb and etd, were not detected. SCCmec typing resulted in classifying one isolate as SCCmec type IV, 41 isolates as type V (including three S. intermedius isolates), and 10 isolates as non-classifiable. Genetic relatedness of all S. pseudintermedius isolates recovered from veterinary staff, companion animals, and hospital environments was determined by pulsed-field gel electrophoresis. Strains having the same band patterns were detected in S. pseudintermedius isolates collected at 13 and 18 months, suggesting possible colonization and/or expansion of a specific S. pseudintermedius strain in a veterinary hospital.

Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.

PubMed

O'Flaherty, D K; Patra, A; Su, Y; Guengerich, F P; Egli, M; Wilds, C J

2016-08-01

DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O 4 -Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4- O 4 bond on processing by human DNA polymerase η (hPol η ) was studied for oligonucleotides containing O 4 -methylthymidine, O 4 -ethylthymidine, and analogs restricting the O 4 -methylene group in an anti -orientation. Primer extension assays revealed that the O 4 -alkyl orientation influences hPol η bypass. Crystal structures of hPol η •DNA•dNTP ternary complexes with O 4 -methyl- or O 4 -ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn - O 4 -methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O 4 -methylthymidine with hPol η , inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O 4 MedT and O 4 EtdT when acted upon by hPol η .

Capacity Utilization Study for Aviation Security Cargo Inspection Queuing System

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

Allgood, Glenn O; Olama, Mohammed M; Lake, Joe E

In this paper, we conduct performance evaluation study for an aviation security cargo inspection queuing system for material flow and accountability. The queuing model employed in our study is based on discrete-event simulation and processes various types of cargo simultaneously. Onsite measurements are collected in an airport facility to validate the queuing model. The overall performance of the aviation security cargo inspection system is computed, analyzed, and optimized for the different system dynamics. Various performance measures are considered such as system capacity, residual capacity, throughput, capacity utilization, subscribed capacity utilization, resources capacity utilization, subscribed resources capacity utilization, and number ofmore » cargo pieces (or pallets) in the different queues. These metrics are performance indicators of the system s ability to service current needs and response capacity to additional requests. We studied and analyzed different scenarios by changing various model parameters such as number of pieces per pallet, number of TSA inspectors and ATS personnel, number of forklifts, number of explosives trace detection (ETD) and explosives detection system (EDS) inspection machines, inspection modality distribution, alarm rate, and cargo closeout time. The increased physical understanding resulting from execution of the queuing model utilizing these vetted performance measures should reduce the overall cost and shipping delays associated with new inspection requirements.« less

Metastable Atom-Activated Dissociation Mass Spectrometry of Phosphorylated and Sulfonated Peptides in Negative Ion Mode

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-06-01

The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were Cα - C peptide backbone cleavages and neutral losses of CO2, H2O, and [CO2 + H2O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

Spectral imaging based in vivo model system for characterization of tumor microvessel response to vascular targeting agents

NASA Astrophysics Data System (ADS)

Wankhede, Mamta

Functional vasculature is vital for tumor growth, proliferation, and metastasis. Many tumor-specific vascular targeting agents (VTAs) aim to destroy this essential tumor vasculature to induce indirect tumor cell death via oxygen and nutrition deprivation. The tumor angiogenesis-inhibiting anti-angiogenics (AIs) and the established tumor vessel targeting vascular disrupting agents (VDAs) are the two major players in the vascular targeting field. Combination of VTAs with conventional therapies or with each other, have been shown to have additive or supra-additive effects on tumor control and treatment. Pathophysiological changes post-VTA treatment in terms of structural and vessel function changes are important parameters to characterize the treatment efficacy. Despite the abundance of information regarding these parameters acquired using various techniques, there remains a need for a quantitative, real-time, and direct observation of these phenomenon in live animals. Through this research we aspired to develop a spectral imaging based mouse tumor system for real-time in vivo microvessel structure and functional measurements for VTA characterization. A model tumor system for window chamber studies was identified, and then combinatorial effects of VDA and AI were characterized in model tumor system. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Emergence of Nasal Carriage of ST80 and ST152 PVL+ Staphylococcus aureus Isolates from Livestock in Algeria

PubMed Central

Agabou, Amir; Ouchenane, Zouleikha; Ngba Essebe, Christelle; Khemissi, Salim; Chehboub, Mohamed Tedj Eddine; Chehboub, Ilyes Bey; Dunyach-Remy, Catherine

2017-01-01

The spread of toxinogenic Staphylococcus aureus is a public health problem in Africa. The objectives of the study were to investigate the rate of S. aureus nasal carriage and molecular characteristics of these strains in livestock and humans in three Algerian provinces. Nasal samples were collected from camels, horses, cattle, sheep and monkeys, as well as humans in contact with them. S. aureus isolates were genotyped using DNA microarray. The rate of S. aureus nasal carriage varied between species: camels (53%), humans and monkeys (50%), sheep (44.2%), horses (15.2%) and cattle (15%). Nine methicillin-resistant S. aureus (MRSA) isolates (7.6%) were identified, isolated from camels and sheep. The S. aureus isolates belonged to 15 different clonal complexes. Among them, PVL+ (Panton–Valentine Leukocidin) isolates belonging to ST80-MRSA-IV and ST152-MSSA were identified in camels (n = 3, 13%) and sheep (n = 4, 21.1%). A high prevalence of toxinogenic animal strains was noted containing TSST-1- (22.2%), EDINB- (29.6%) and EtD- (11.1%) encoding genes. This study showed the dispersal of the highly human pathogenic clones ST152-MSSA and ST-80-MRSA in animals. It suggests the ability of some clones to cross the species barrier and jump between humans and several animal species. PMID:28946704

DEVELOPMENT OF A METHOD TO QUANTIFY THE IMPACT ...

EPA Pesticide Factsheets

Advances in human health risk assessment, especially for contaminants encountered by the inhalation route, have evolved so that the uncertainty factors (UF) used in the extrapolation of non-cancer effects across species (UFA) have been split into the respective pharmacodynamic (PD) and pharmacokinetic (PK) components. Present EPA default values for these components are divided into two half-logs (e.g., 10 to the 0.5 power or 3.16), so that their multiplication yields the 10-fold UF customarily seen in Agency risk assessments as UFA. The state of the science at present does not support a detailed evaluation of species-dependent and human interindividual variance of PD, but more data exist by which PK variance can be examined and quantified both across species and within the human species. Because metabolism accounts for much of the PK variance, we sought to examine the impact that differences in hepatic enzyme content exerts upon risk-relevant PK outcomes among humans. Because of the age and ethnic diversity expressed in the human organ donor population and the wide availability of tissues from these human organ donors, a program was developed to include information from those tissues in characterizing human interindividual PK variance. An Interagency Agreement with CDC/NIOSH Taft Laboratory, a Cooperative Agreement with CIIT Centers for Health Research, and a collaborative agreement with NHEERL/ETD were established to successfully complete the project. The di

A Novel Proteomics Approach to Identify SUMOylated Proteins and Their Modification Sites in Human Cells*

PubMed Central

Galisson, Frederic; Mahrouche, Louiza; Courcelles, Mathieu; Bonneil, Eric; Meloche, Sylvain; Chelbi-Alix, Mounira K.; Thibault, Pierre

2011-01-01

The small ubiquitin-related modifier (SUMO) is a small group of proteins that are reversibly attached to protein substrates to modify their functions. The large scale identification of protein SUMOylation and their modification sites in mammalian cells represents a significant challenge because of the relatively small number of in vivo substrates and the dynamic nature of this modification. We report here a novel proteomics approach to selectively enrich and identify SUMO conjugates from human cells. We stably expressed different SUMO paralogs in HEK293 cells, each containing a His6 tag and a strategically located tryptic cleavage site at the C terminus to facilitate the recovery and identification of SUMOylated peptides by affinity enrichment and mass spectrometry. Tryptic peptides with short SUMO remnants offer significant advantages in large scale SUMOylome experiments including the generation of paralog-specific fragment ions following CID and ETD activation, and the identification of modified peptides using conventional database search engines such as Mascot. We identified 205 unique protein substrates together with 17 precise SUMOylation sites present in 12 SUMO protein conjugates including three new sites (Lys-380, Lys-400, and Lys-497) on the protein promyelocytic leukemia. Label-free quantitative proteomics analyses on purified nuclear extracts from untreated and arsenic trioxide-treated cells revealed that all identified SUMOylated sites of promyelocytic leukemia were differentially SUMOylated upon stimulation. PMID:21098080

Deflection Analysis of the Space Shuttle External Tank Door Drive Mechanism

NASA Technical Reports Server (NTRS)

Tosto, Michael A.; Trieu, Bo C.; Evernden, Brent A.; Hope, Drew J.; Wong, Kenneth A.; Lindberg, Robert E.

2008-01-01

Upon observing an abnormal closure of the Space Shuttle s External Tank Doors (ETD), a dynamic model was created in MSC/ADAMS to conduct deflection analyses of the Door Drive Mechanism (DDM). For a similar analysis, the traditional approach would be to construct a full finite element model of the mechanism. The purpose of this paper is to describe an alternative approach that models the flexibility of the DDM using a lumped parameter approximation to capture the compliance of individual parts within the drive linkage. This approach allows for rapid construction of a dynamic model in a time-critical setting, while still retaining the appropriate equivalent stiffness of each linkage component. As a validation of these equivalent stiffnesses, finite element analysis (FEA) was used to iteratively update the model towards convergence. Following this analysis, deflections recovered from the dynamic model can be used to calculate stress and classify each component s deformation as either elastic or plastic. Based on the modeling assumptions used in this analysis and the maximum input forcing condition, two components in the DDM show a factor of safety less than or equal to 0.5. However, to accurately evaluate the induced stresses, additional mechanism rigging information would be necessary to characterize the input forcing conditions. This information would also allow for the classification of stresses as either elastic or plastic.

Improved Methods for the Enrichment and Analysis of Glycated Peptides

PubMed Central

Zhang, Qibin; Schepmoes, Athena A.; Brock, Jonathan W. C.; Wu, Si; Moore, Ronald J.; Purvine, Samuel O.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

2009-01-01

Nonenzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron-transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an online wash of column-bound glycated peptides using 50 mM ammonium acetate, followed by elution with 100 mM acetic acid. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. Acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number of glycated peptides and corresponding glycated proteins identified by LC–MS/MS. PMID:18989935

Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry.

PubMed

Liu, Min; Zhang, Zhongqi; Cheetham, Janet; Ren, Da; Zhou, Zhaohui Sunny

2014-05-20

A novel photo-oxidative cross-linking between two histidines (His-His) has been discovered and characterized in an IgG1 antibody via the workflow of XChem-Finder, (18)O labeling and mass spectrometry (Anal. Chem. 2013, 85, 5900-5908). Its structure was elucidated by peptide mapping with multiple proteases with various specificities (e.g., trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass spectrometry with complementary fragmentation modes (e.g., collision-induced dissociation (CID) and electron-transfer dissociation (ETD)). Our data indicated that cross-linking occurred across two identical conserved histidine residues on two separate heavy chains in the hinge region, which is highly flexible and solvent accessible. On the basis of model studies with short peptides, it has been proposed that singlet oxygen reacts with the histidyl imidazole ring to form an endoperoxide and then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is subject to a nucleophilic attack by the unmodified histidine; and finally, elimination of a water molecule leads to the final adduct with a net mass increase of 14 Da. Our findings are consistent with this mechanism. Successful discovery of cross-linked His-His again demonstrates the broad applicability and utility of our XChem-Finder approach in the discovery and elucidation of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.

Distinctive and Complementary MS2 Fragmentation Characteristics for Identification of Sulfated Sialylated N-Glycopeptides by nanoLC-MS/MS Workflow

NASA Astrophysics Data System (ADS)

Kuo, Chu-Wei; Guu, Shih-Yun; Khoo, Kay-Hooi

2018-04-01

High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS2 fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS2 fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS2 analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics. [Figure not available: see fulltext.

Assessment and management of retraction pockets.

PubMed

Alper, Cuneyt; Olszewska, Ewa

2017-02-28

This manuscript intends to review types, pathogenesis, associated risk factors, and potential methods of prevention and treatment of the retraction pockets in adults and children. The importance of retraction pockets (RP) lies in loss of original histological and anatomical structure which is associated with development of ossicular chain erosion, cho¬lesteatoma formation and potentially life threatening complications of cholesteatoma. The trans-mucosal exchange each gas in the middle ear (ME) is towards equalizing its partial pressures with the partial pressure in the environ¬ment. MEs that have abnormalities in the volume and ventilation pathways in the epitympanic may be more suscep¬tible to retraction pockets. Sustained pressure differences and/or inflammation leads to destruction of collagen fibers in the lamina propria. Inflammatory mediators and cytokines lead to release of collagenases result in viscoelastic properties of the lamina propria. The process of changes in the tympanic membrane structure may evolve to the cho¬lesteatoma formation. There are many different staging systems that clinicians prioritize in their decision making in the management of RP. The authors discuss the management possibilities in different clinical situations: RP without and with ongoing or intermittent evidence of Eustachian Tube Dysfunction (ETD), presence of adenoid hypertrophy or re-growth of adenoids, presence or absence of effusion, invisible depth of RP without effusion. invisible depth of RP with effusion, ongoing RP after VT insertion, and finally suspicion of cholesteatoma in a deep RP with ME effusion. A decision algorithm regarding the management of TM retraction and retraction pockets is provided.

Tailored-waveform Collisional Activation of Peptide Ion Electron Transfer Survivor Ions in Cation Transmission Mode Ion/Ion Reaction Experiments

PubMed Central

Han, Hongling; Londry, Frank A.; Erickson, David E.; McLuckey, Scott A.

2010-01-01

SUMMARY Broad-band resonance excitation via a tailored waveform in a high pressure collision cell (Q2) on a hybrid quadrupole/time-of-flight (QqTOF) tandem mass spectrometer has been implemented for cation transmission mode electron transfer ion/ion reactions of tryptic polypeptides. The frequency components in the broadband waveform were defined to excite the first generation intact electron transfer products for relatively large tryptic peptides. The optimum amplitude of the arbitrary waveform applied has been determined empirically to be 3.0 Vp-p, which is effective for relatively high mass-to-charge (m/z) ratio precursor ions with little elimination of sequence information for low m/z ions. The application of broadband activation during the transmission mode ion/ion reaction obviates frequency and amplitude tuning normally associated with ion trap collision induced dissociation (CID). This approach has been demonstrated with triply and doubly charged tryptic peptides with and without post-translational modifications. Enhanced structural information was achieved by production of a larger number of informative c- and z-type fragments using the tailored waveform on unmodified and modified (phosphorylated and glycosylated) peptides when the first generation intact electron transfer products fell into the defined frequency range. This approach can be applied to a wide range of tryptic peptide ions, making it attractive as a rapid and general approach for ETD LC-MS/MS of tryptic peptides in a QqTOF instrument. PMID:19305916

On determining specifications and selections of alternative technologies for airport checked-baggage security screening.

PubMed

Feng, Qianmei

2007-10-01

Federal law mandates that every checked bag at all commercial airports be screened by explosive detection systems (EDS), explosive trace detection systems (ETD), or alternative technologies. These technologies serve as critical components of airport security systems that strive to reduce security risks at both national and global levels. To improve the operational efficiency and airport security, emerging image-based technologies have been developed, such as dual-energy X-ray (DX), backscatter X-ray (BX), and multiview tomography (MVT). These technologies differ widely in purchasing cost, maintenance cost, operating cost, processing rate, and accuracy. Based on a mathematical framework that takes into account all these factors, this article investigates two critical issues for operating screening devices: setting specifications for continuous security responses by different technologies; and selecting technology or combination of technologies for efficient 100% baggage screening. For continuous security responses, specifications or thresholds are used for classifying threat items from nonthreat items. By investigating the setting of specifications on system security responses, this article assesses the risk and cost effectiveness of various technologies for both single-device and two-device systems. The findings provide the best selection of image-based technologies for both single-device and two-device systems. Our study suggests that two-device systems outperform single-device systems in terms of both cost effectiveness and accuracy. The model can be readily extended to evaluate risk and cost effectiveness of multiple-device systems for airport checked-baggage security screening.

[Characterizing the passive opening of the eustachian tube in a hypo-/hyperbaric pressure chamber].

PubMed

Meyer, M F; Mikolajczak, S; Luers, J C; Lotfipour, S; Beutner, D; Jumah, M D

2013-09-01

Beside arbitrary and not arbitrary active pressure equalization systems there is a passive equalization system via the Eustachian tube (ET) at pressure difference between the epipharyngeal space and the middle ear. Aim of this study was to characterize this passive equalization system in a hypobaric/hyperbaric pressure chamber by continuously measuring the tympanic impedance. In contrast to other studies, which are measured only in a hypobaric pressure chamber it is possible to include participants with Eustachian tube dysfunction (ETD). Following a fixed pressure profile 39 participants were exposed to phases of pressure rising and decompression. By continuously measuring the tympanic impedance in the pressure chamber it was possible to measure data of the Eustachian Tube opening Pressure (ETOP), Eustachian Tube closing pressure (ETCP) and Eustachian Tube opening duration (ETOD). In addition it was possible to characterize the gradient of pressure during decompression, while the ET was open. Beside the measurement of the arithmetic average of the ETOP (30.2 ± 15.1 mbar), ETCP (9.1 ± 7.7 mbar) and ETOD (0.65 ± 0.38 s) it was obvious that there are recurrent samples of pressure progression during the phase of tube opening. Generally it is possible to differentiate between the type of complete opening and partial opening. The fundamental characterization of the action of the passive tube opening, including the measurement of the ETOP, ETCP and ETOD, is a first step in understanding the physiological and pathophysiological function of the ET. © Georg Thieme Verlag KG Stuttgart · New York.

Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures

NASA Astrophysics Data System (ADS)

Pap, Adam; Klement, Eva; Hunyadi-Gulyas, Eva; Darula, Zsuzsanna; Medzihradszky, Katalin F.

2018-05-01

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. [Figure not available: see fulltext.

HPLC enantioseparation of racemic bupropion, baclofen and etodolac: modification of conventional ligand exchange approach by pre-column formation of chiral ligand exchange complexes.

PubMed

Singh, Manisha; Bhushan, Ravi

2016-11-01

Separation of racemic mixture of (RS)-bupropion, (RS)-baclofen and (RS)-etodolac, commonly marketed racemic drugs, has been achieved by modifying the conventional ligand exchange approach. The Cu(II) complexes were first prepared with a few l-amino acids, namely, l-proline, l-histidine, l-phenylalanine and l-tryptophan, and to these was introduced a mixture of the enantiomer pair of (RS)-bupropion, or (RS)-baclofen or (RS)-etodolac. As a result, formation of a pair of diastereomeric complexes occurred by 'chiral ligand exchange' via the competition between the chelating l-amino acid and each of the two enantiomers from a given pair. The diastereomeric mixture formed in the pre-column process was loaded onto HPLC column. Thus, both the phases during chromatographic separation process were achiral (i.e. neither the stationary phase had any chiral structural feature of its own nor did the mobile phase have any chiral additive). Separation of diastereomers was successful using a C 18 column and a binary mixture of MeCN and TEAP buffer of pH 4.0 (60:40, v/v) as mobile phase at a flow rate of 1 mL/min and UV detection at 230 nm for (RS)-Bup, 220 nm for (RS)-Bac and 223 nm for (RS)-Etd. Baseline separation of the two enantiomers was obtained with a resolution of 6.63 in <15 min. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry.

PubMed

Pan, Jingxi; Zhang, Suping; Borchers, Christoph H

2016-12-01

Hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is a powerful technique for higher-order structural characterization of antibodies. Although the peptide-based bottom-up HDX approach and the protein-based top-down HDX approach have complementary advantages, the work done so far on biosimilars has involved only one or the other approach. Herein we have characterized the structures of two bevacizumab (BEV) biosimilars and compared them to the reference BEV using both methods. A sequence coverage of 87% was obtained for the heavy chain and 74% for the light chain in the bottom-up approach. The deuterium incorporation behavior of the peptic peptides from the three BEVs were compared side by side and showed no differences at various HDX time points. Top-down experiments were carried out using subzero temperature LC-MS, and the deuterium incorporation of the intact light chain and heavy chain were obtained. Top-down ETD was also performed to obtain amino acid-level HDX information that covered 100% of the light chain, but only 50% coverage is possible for the heavy chain. Consistent with the intact subunit level data, no differences were observed in the amino acid level HDX data. All these results indicate that there are no differences between the three BEV samples with respect to their high-order structures. The peptide level information from the bottom-up approach, and the residue level and intact subunit level information from the top-down approach were complementary and covered the entire antibody. Copyright © 2016 Elsevier B.V. All rights reserved.

Infrared Ion Spectroscopy at Felix: Applications in Peptide Dissociation and Analytical Chemistry

NASA Astrophysics Data System (ADS)

Oomens, Jos

2016-06-01

Infrared free electron lasers such as those in Paris, Berlin and Nijmegen have been at the forefront of the development of infrared ion spectroscopy. In this contribution, I will give an overview of new developments in IR spectroscopy of stored ions at the FELIX Laboratory. In particular, I will focus on recent developments made possible by the coupling of a new commercial ion trap mass spectrometer to the FELIX beamline. The possibility to record IR spectra of mass-selected molecular ions and their reaction products has in recent years shed new light on our understanding of collision induced dissociation (CID) reactions of protonated peptides in mass spectrometry (MS). We now show that it is possible to record IR spectra for the products of electron transfer dissociation (ETD) reactions [M + nH]n+ + A- → [M + nH](n-1)+ + A → {dissociation of analyte} These reactions are now widely used in novel MS-based protein sequencing strategies, but involve complex radical chemistry. The spectroscopic results allow stringent verification of computationally predicted product structures and hence reaction mechanisms and H-atom migration. The sensitivity and high dynamic range of a commercial mass spectrometer also allows us to apply infrared ion spectroscopy to analytes in complex "real-life" mixtures. The ability to record IR spectra with the sensitivity of mass-spectrometric detection is unrivalled in analytical sciences and is particularly useful in the identification of small (biological) molecules, such as in metabolomics. We report preliminary results of a pilot study on the spectroscopic identification of small metabolites in urine and plasma samples.

Site-Specific N-Glycosylation of Recombinant Pentameric and Hexameric Human IgM

NASA Astrophysics Data System (ADS)

Moh, Edward S. X.; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2016-07-01

Glycosylation is known to play an important role in IgG antibody structure and function. Polymeric IgM, the largest known antibody in humans, displays five potential N-glycosylation sites on each heavy chain monomer. IgM can exist as a pentamer with a connecting singly N-glycosylated J-chain (with a total of 51 glycosylation sites) or as a hexamer (60 glycosylation sites). In this study, the N-glycosylation of recombinant pentameric and hexameric IgM produced by the same human cell type and culture conditions was site-specifically profiled by RP-LC-CID/ETD-MS/MS using HILIC-enriched tryptic and GluC glycopeptides. The occupancy of all putative N-glycosylation sites on the pentameric and hexameric IgM were able to be determined. Distinct glycosylation differences were observed between each of the five N-linked sites on the IgM heavy chains. While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. Asn563, a high mannose-rich glycosylation site that locates in the center of the IgM polymer, was only approximately 60% occupied in both the pentameric and hexameric IgM forms, with a difference in relative abundance of the glycan structures between the pentamer and hexamer. This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling.

N- and O-glycosylation Analysis of Human C1-inhibitor Reveals Extensive Mucin-type O-Glycosylation.

PubMed

Stavenhagen, Kathrin; Kayili, H Mehmet; Holst, Stephanie; Koeleman, Carolien A M; Engel, Ruchira; Wouters, Diana; Zeerleder, Sacha; Salih, Bekir; Wuhrer, Manfred

2018-06-01

Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N - and O -glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD). Various proteases were applied, partly in combination with PNGase F and exoglycosidase treatment, in order to analyze the (glyco)peptides. The analysis revealed an extensively O -glycosylated N-terminal region. Five novel and five known O -glycosylation sites were identified, carrying mainly core1-type O -glycans. In addition, we detected a heavily O -glycosylated portion spanning from Thr 82 -Ser 121 with up to 16 O -glycans attached. Likewise, all known six N -glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. The glycoforms were in accordance with results on released N -glycans by MALDI-TOF/TOF-MS/MS. The comprehensive characterization of C1-Inh glycosylation described in this study will form the basis for further functional studies on the role of these glycan modifications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Top-Down and Bottom-Up Identification of Proteins by Liquid Extraction Surface Analysis Mass Spectrometry of Healthy and Diseased Human Liver Tissue

NASA Astrophysics Data System (ADS)

Sarsby, Joscelyn; Martin, Nicholas J.; Lalor, Patricia F.; Bunch, Josephine; Cooper, Helen J.

2014-09-01

Liquid extraction surface analysis mass spectrometry (LESA MS) has the potential to become a useful tool in the spatially-resolved profiling of proteins in substrates. Here, the approach has been applied to the analysis of thin tissue sections from human liver. The aim was to determine whether LESA MS was a suitable approach for the detection of protein biomarkers of nonalcoholic liver disease (nonalcoholic steatohepatitis, NASH), with a view to the eventual development of LESA MS for imaging NASH pathology. Two approaches were considered. In the first, endogenous proteins were extracted from liver tissue sections by LESA, subjected to automated trypsin digestion, and the resulting peptide mixture was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) (bottom-up approach). In the second (top-down approach), endogenous proteins were extracted by LESA, and analyzed intact. Selected protein ions were subjected to collision-induced dissociation (CID) and/or electron transfer dissociation (ETD) mass spectrometry. The bottom-up approach resulted in the identification of over 500 proteins; however identification of key protein biomarkers, liver fatty acid binding protein (FABP1), and its variant (Thr→Ala, position 94), was unreliable and irreproducible. Top-down LESA MS analysis of healthy and diseased liver tissue revealed peaks corresponding to multiple (~15-25) proteins. MS/MS of four of these proteins identified them as FABP1, its variant, α-hemoglobin, and 10 kDa heat shock protein. The reliable identification of FABP1 and its variant by top-down LESA MS suggests that the approach may be suitable for imaging NASH pathology in sections from liver biopsies.

Profiling post-translational modifications of histones in human monocyte-derived macrophages.

PubMed

Olszowy, Pawel; Donnelly, Maire Rose; Lee, Chanho; Ciborowski, Pawel

2015-01-01

Histones and their post-translational modifications impact cellular function by acting as key regulators in the maintenance and remodeling of chromatin, thus affecting transcription regulation either positively (activation) or negatively (repression). In this study we describe a comprehensive, bottom-up proteomics approach to profiling post-translational modifications (acetylation, mono-, di- and tri-methylation, phosphorylation, biotinylation, ubiquitination, citrullination and ADP-ribosylation) in human macrophages, which are primary cells of the innate immune system. As our knowledge expands, it becomes more evident that macrophages are a heterogeneous population with potentially subtle differences in their responses to various stimuli driven by highly complex epigenetic regulatory mechanisms. To profile post-translational modifications (PTMs) of histones in macrophages we used two platforms of liquid chromatography and mass spectrometry. One platform was based on Sciex5600 TripleTof and the second one was based on VelosPro Orbitrap Elite ETD mass spectrometers. We provide side-by-side comparison of profiling using two mass spectrometric platforms, ion trap and qTOF, coupled with the application of collisional induced and electron transfer dissociation. We show for the first time methylation of a His residue in macrophages and demonstrate differences in histone PTMs between those currently reported for macrophage cell lines and what we identified in primary cells. We have found a relatively low level of histone PTMs in differentiated but resting human primary monocyte derived macrophages. This study is the first comprehensive profiling of histone PTMs in primary human MDM. Our study implies that epigenetic regulatory mechanisms operative in transformed cell lines and primary cells are overlapping to a limited extent. Our mass spectrometric approach provides groundwork for the investigation of how histone PTMs contribute to epigenetic regulation in primary human macrophages.

Top-down and bottom-up identification of proteins by liquid extraction surface analysis mass spectrometry of healthy and diseased human liver tissue.

PubMed

Sarsby, Joscelyn; Martin, Nicholas J; Lalor, Patricia F; Bunch, Josephine; Cooper, Helen J

2014-11-01

Liquid extraction surface analysis mass spectrometry (LESA MS) has the potential to become a useful tool in the spatially-resolved profiling of proteins in substrates. Here, the approach has been applied to the analysis of thin tissue sections from human liver. The aim was to determine whether LESA MS was a suitable approach for the detection of protein biomarkers of nonalcoholic liver disease (nonalcoholic steatohepatitis, NASH), with a view to the eventual development of LESA MS for imaging NASH pathology. Two approaches were considered. In the first, endogenous proteins were extracted from liver tissue sections by LESA, subjected to automated trypsin digestion, and the resulting peptide mixture was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) (bottom-up approach). In the second (top-down approach), endogenous proteins were extracted by LESA, and analyzed intact. Selected protein ions were subjected to collision-induced dissociation (CID) and/or electron transfer dissociation (ETD) mass spectrometry. The bottom-up approach resulted in the identification of over 500 proteins; however identification of key protein biomarkers, liver fatty acid binding protein (FABP1), and its variant (Thr→Ala, position 94), was unreliable and irreproducible. Top-down LESA MS analysis of healthy and diseased liver tissue revealed peaks corresponding to multiple (~15-25) proteins. MS/MS of four of these proteins identified them as FABP1, its variant, α-hemoglobin, and 10 kDa heat shock protein. The reliable identification of FABP1 and its variant by top-down LESA MS suggests that the approach may be suitable for imaging NASH pathology in sections from liver biopsies.

Comprehensive Characterization of Swine Cardiac Troponin T Proteoforms by Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Lin, Ziqing; Guo, Fang; Gregorich, Zachery R.; Sun, Ruixiang; Zhang, Han; Hu, Yang; Shanmuganayagam, Dhanansayan; Ge, Ying

2018-04-01

Cardiac troponin T (cTnT) regulates the Ca2+-mediated interaction between myosin thick filaments and actin thin filaments during cardiac contraction and relaxation. cTnT is released into the blood following injury, and increased serum levels of the protein are used clinically as a biomarker for myocardial infarction. Moreover, mutations in cTnT are causative in a number of familial cardiomyopathies. With the increasing use of large animal (swine) model to recapitulate human diseases, it is essential to characterize species-dependent protein sequence variants, alternative RNA splicing, and post-translational modifications (PTMs), but challenges remain due to the incomplete database and lack of validation of the predicted splicing isoforms. Herein, we integrated top-down mass spectrometry (MS) with online liquid chromatography (LC) and immunoaffinity purification to comprehensively characterize miniature swine cTnT proteoforms, including those arising from alternative RNA splicing and PTMs. A total of seven alternative splicing isoforms of cTnT were identified by LC/MS from swine left ventricular tissue, with each isoform containing un-phosphorylated and mono-phosphorylated proteoforms. The phosphorylation site was localized to Ser1 for the mono-phosphorylated proteoforms of cTnT1, 3, 4, and 6 by online MS/MS combining collisionally activated dissociation (CAD) and electron transfer dissociation (ETD). Offline MS/MS on Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer with CAD and electron capture dissociation (ECD) was then utilized to achieve deep sequencing of mono-phosphorylated cTnT1 (35.2 kDa) with a high sequence coverage of 87%. Taken together, this study demonstrated the unique advantage of top-down MS in the comprehensive characterization of protein alternative splicing isoforms together with PTMs. [Figure not available: see fulltext.

Using patient values and preferences to inform the importance of health outcomes in practice guideline development following the GRADE approach.

PubMed

Zhang, Yuan; Coello, Pablo Alonso; Brożek, Jan; Wiercioch, Wojtek; Etxeandia-Ikobaltzeta, Itziar; Akl, Elie A; Meerpohl, Joerg J; Alhazzani, Waleed; Carrasco-Labra, Alonso; Morgan, Rebecca L; Mustafa, Reem A; Riva, John J; Moore, Ainsley; Yepes-Nuñez, Juan José; Cuello-Garcia, Carlos; AlRayees, Zulfa; Manja, Veena; Falavigna, Maicon; Neumann, Ignacio; Brignardello-Petersen, Romina; Santesso, Nancy; Rochwerg, Bram; Darzi, Andrea; Rojas, Maria Ximena; Adi, Yaser; Bollig, Claudia; Waziry, Reem; Schünemann, Holger J

2017-05-02

There are diverse opinions and confusion about defining and including patient values and preferences (i.e. the importance people place on the health outcomes) in the guideline development processes. This article aims to provide an overview of a process for systematically incorporating values and preferences in guideline development. In 2013 and 2014, we followed the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to adopt, adapt and develop 226 recommendations in 22 guidelines for the Ministry of Health of the Kingdom of Saudi Arabia. To collect context-specific values and preferences for each recommendation, we performed systematic reviews, asked clinical experts to provide feedback according to their clinical experience, and consulted patient representatives. We found several types of studies addressing the importance of outcomes, including those reporting utilities, non-utility measures of health states based on structured questionnaires or scales, and qualitative studies. Guideline panels used the relative importance of outcomes based on values and preferences to weigh the balance of desirable and undesirable consequences of alternative intervention options. However, we found few studies addressing local values and preferences. Currently there are different but no firmly established processes for integrating patient values and preferences in healthcare decision-making of practice guideline development. With GRADE Evidence-to-Decision (EtD) frameworks, we provide an empirical strategy to find and incorporate values and preferences in guidelines by performing systematic reviews and eliciting information from guideline panel members and patient representatives. However, more research and practical guidance are needed on how to search for relevant studies and grey literature, assess the certainty of this evidence, and best summarize and present the findings.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

NASA Astrophysics Data System (ADS)

McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides.

PubMed

McMillen, Chelsea L; Wright, Patience M; Cassady, Carolyn J

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum

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

Nguyen, Tran H.; Brechenmacher, Laurent; Aldrich, Joshua T.

2012-11-11

Root hairs are single hair-forming cells on roots that function to increase root surface area, enhancing water and nutrient uptake. In leguminous plants, root hairs also play a critical role as the site of infection by symbiotic nitrogen fixing rhizobia, leading to the formation of a novel organ, the nodule. The initial steps in the rhizobia-root hair infection process are known to involve specific receptor kinases and subsequent kinase cascades. Here, we characterize the phosphoproteome of the root hairs and the corresponding stripped roots (i.e., roots from which root hairs were removed) during rhizobial colonization and infection to gain insightmore » into the molecular mechanism of root hair cell biology. We chose soybean (Glycine max L.), one of the most important crop plants in the legume family, for this study because of its larger root size, which permits isolation of sufficient root hair material for phosphoproteomic analysis. Phosphopeptides derived from root hairs and stripped roots, mock inoculated or inoculated with the soybean-specific rhizobium Bradyrhizobium japonicum, were labeled with the isobaric tag 8-plex ITRAQ, enriched using Ni-NTA magnetic beads and subjected to nRPLC-MS/MS analysis using HCD and decision tree guided CID/ETD strategy. A total of 1,625 unique phosphopeptides, spanning 1,659 non-redundant phosphorylation sites, were detected from 1,126 soybean phosphoproteins. Among them, 273 phosphopeptides corresponding to 240 phosphoproteins were found to be significantly regulated (>1.5 fold abundance change) in response to inoculation with B. japonicum. The data reveal unique features of the soybean root hair phosphoproteome, including root hair and stripped root-specific phosphorylation suggesting a complex network of kinase-substrate and phosphatase-substrate interactions in response to rhizobial inoculation.« less

Crossing borders: High school science teachers learning to teach the specialized language of science

NASA Astrophysics Data System (ADS)

Patrick, Jennifer Drake

The highly specialized language of science is both challenging and alienating to adolescent readers. This study investigated how secondary science teachers learn to teach the specialized language of science in their classrooms. Three research questions guided this study: (a) what do science teachers know about teaching reading in science? (b) what understanding about the unique language demands of science reading do they construct through professional development? and (c) how do they integrate what they have learned about these specialized features of science language into their teaching practices? This study investigated the experience of seven secondary science teachers as they participated in a professional development program designed to teach them about the specialized language of science. Data sources included participant interviews, audio-taped professional development sessions, field notes from classroom observations, and a prior knowledge survey. Results from this study suggest that science teachers (a) were excited to learn about disciplinary reading practices, (b) developed an emergent awareness of the specialized features of science language and the various genres of science writing, and (c) recognized that the challenges of science reading goes beyond vocabulary. These teachers' efforts to understand and address the language of science in their teaching practices were undermined by their lack of basic knowledge of grammar, availability of time and resources, their prior knowledge and experiences, existing curriculum, and school structure. This study contributes to our understanding of how secondary science teachers learn about disciplinary literacy and apply that knowledge in their classroom instruction. It has important implications for literacy educators and science educators who are interested in using language and literacy practices in the service of science teaching and learning. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

A Comprehensive, Open-source Platform for Mass Spectrometry-based Glycoproteomics Data Analysis.

PubMed

Liu, Gang; Cheng, Kai; Lo, Chi Y; Li, Jun; Qu, Jun; Neelamegham, Sriram

2017-11-01

Glycosylation is among the most abundant and diverse protein post-translational modifications (PTMs) identified to date. The structural analysis of this PTM is challenging because of the diverse monosaccharides which are not conserved among organisms, the branched nature of glycans, their isomeric structures, and heterogeneity in the glycan distribution at a given site. Glycoproteomics experiments have adopted the traditional high-throughput LC-MS n proteomics workflow to analyze site-specific glycosylation. However, comprehensive computational platforms for data analyses are scarce. To address this limitation, we present a comprehensive, open-source, modular software for glycoproteomics data analysis called GlycoPAT (GlycoProteomics Analysis Toolbox; freely available from www.VirtualGlycome.org/glycopat). The program includes three major advances: (1) "SmallGlyPep," a minimal linear representation of glycopeptides for MS n data analysis. This format allows facile serial fragmentation of both the peptide backbone and PTM at one or more locations. (2) A novel scoring scheme based on calculation of the "Ensemble Score (ES)," a measure that scores and rank-orders MS/MS spectrum for N- and O-linked glycopeptides using cross-correlation and probability based analyses. (3) A false discovery rate (FDR) calculation scheme where decoy glycopeptides are created by simultaneously scrambling the amino acid sequence and by introducing artificial monosaccharides by perturbing the original sugar mass. Parallel computing facilities and user-friendly GUIs (Graphical User Interfaces) are also provided. GlycoPAT is used to catalogue site-specific glycosylation on simple glycoproteins, standard protein mixtures and human plasma cryoprecipitate samples in three common MS/MS fragmentation modes: CID, HCD and ETD. It is also used to identify 960 unique glycopeptides in cell lysates from prostate cancer cells. The results show that the simultaneous consideration of peptide and glycan fragmentation is necessary for high quality MS n spectrum annotation in CID and HCD fragmentation modes. Additionally, they confirm the suitability of GlycoPAT to analyze shotgun glycoproteomics data. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

High prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carrying the mecC gene in a semi-extensive red deer (Cervus elaphus hispanicus) farm in Southern Spain.

PubMed

Gómez, Paula; Lozano, Carmen; González-Barrio, David; Zarazaga, Myriam; Ruiz-Fons, Francisco; Torres, Carmen

2015-06-12

The objective was to determine the prevalence of Staphylococcus aureus nasal carriage in red deer of a semi-extensive farm and in humans in contact with the estate animals, and to characterize obtained isolates. Nasal swabs of 65 deer and 15 humans were seeded on mannitol-salt-agar and oxacillin-resistance-screening-agar-base. Isolates were identified by microbiological and molecular methods. Antimicrobial susceptibility profile was determined for 16 antibiotics by disk-diffusion and the presence of eight antibiotic resistance genes, seven virulence genes and genes of immune-evasion-cluster (IEC) was analyzed by PCR. S. aureus was typed by PFGE-SmaI, spa, agr, SCCmec and MLST. Isolates were detected in 16 deer (24.6%). Eleven S. aureus isolates were methicillin-resistant (MRSA), and five were methicillin-susceptible (MSSA). All MRSA harbored mecC gene and were agr-III/SCCmecXI/ST1945 (four spa-t843 and seven spa-t1535). All mecC-MRSA carried blaZ-SCCmecXI and etd2, were IEC-type-E, and belonged to the same PFGE pattern. The five MSSA were typed as spa-t2420/agr-I/ST133. Regarding humans, S. aureus was recovered from six samples (40%). The isolates were MSSA and were typed as spa-t002/agr-II, spa-t012/agr-III or spa-t822/agr-III and showed different IEC types (A, B, D and F). blaZ and erm(A) genes were detected, as well as cna and tst genes. As conclusion, red deer analyzed in this study are frequent carriers of mecC-MRSA CC130 (16.9%), they are characterized by few resistance and virulence determinants, and by the presence of IEC type-E. Deer could be a source of mecC-MRSA which could potentially be transmitted to other animals, or even to humans. Copyright © 2015 Elsevier B.V. All rights reserved.

Toward an Ultralow-Power Onboard Processor for Tongue Drive System

PubMed Central

Viseh, Sina; Ghovanloo, Maysam; Mohsenin, Tinoosh

2015-01-01

The Tongue Drive System (TDS) is a new unobtrusive, wireless, and wearable assistive device that allows for real-time tracking of the voluntary tongue motion in the oral space for communication, control, and navigation applications. The latest TDS prototype appears as a wireless headphone and has been tested in human subject trials. However, the robustness of the external TDS (eTDS) in real-life outdoor conditions may not meet safety regulations because of the limited mechanical stability of the headset. The intraoral TDS (iTDS), which is in the shape of a dental retainer, firmly clasps to the upper teeth and resists sensor misplacement. However, the iTDS has more restrictions on its dimensions, limiting the battery size and consequently requiring a considerable reduction in its power consumption to operate over an extended period of two days on a single charge. In this brief, we propose an ultralow-power local processor for the TDS that performs all signal processing on the transmitter side, following the sensors. Assuming the TDS user on average issuing one command/s, implementing the computational engine reduces the data volume that needs to be wirelessly transmitted to a PC or smartphone by a factor of 1500×, from 12 kb/s to ~8 b/s. The proposed design is implemented on an ultralow-power IGLOO nano field-programmable gate array (FPGA) and is tested on AGLN250 prototype board. According to our post-place-and-route results, implementing the engine on the FPGA significantly drops the required data transmission, while an application-specific integrated circuit (ASIC) implementation in a 65-nm CMOS results in a 15× power saving compared to the FPGA solution and occupies a 0.02-mm2 footprint. As a result, the power consumption and size of the iTDS will be significantly reduced through the use of a much smaller rechargeable battery. Moreover, the system can operate longer following every recharge, improving the iTDS usability. PMID:26185489

Toward an Ultralow-Power Onboard Processor for Tongue Drive System.

PubMed

Viseh, Sina; Ghovanloo, Maysam; Mohsenin, Tinoosh

2015-02-01

The Tongue Drive System (TDS) is a new unobtrusive, wireless, and wearable assistive device that allows for real-time tracking of the voluntary tongue motion in the oral space for communication, control, and navigation applications. The latest TDS prototype appears as a wireless headphone and has been tested in human subject trials. However, the robustness of the external TDS (eTDS) in real-life outdoor conditions may not meet safety regulations because of the limited mechanical stability of the headset. The intraoral TDS (iTDS), which is in the shape of a dental retainer, firmly clasps to the upper teeth and resists sensor misplacement. However, the iTDS has more restrictions on its dimensions, limiting the battery size and consequently requiring a considerable reduction in its power consumption to operate over an extended period of two days on a single charge. In this brief, we propose an ultralow-power local processor for the TDS that performs all signal processing on the transmitter side, following the sensors. Assuming the TDS user on average issuing one command/s, implementing the computational engine reduces the data volume that needs to be wirelessly transmitted to a PC or smartphone by a factor of 1500×, from 12 kb/s to ~8 b/s. The proposed design is implemented on an ultralow-power IGLOO nano field-programmable gate array (FPGA) and is tested on AGLN250 prototype board. According to our post-place-and-route results, implementing the engine on the FPGA significantly drops the required data transmission, while an application-specific integrated circuit (ASIC) implementation in a 65-nm CMOS results in a 15× power saving compared to the FPGA solution and occupies a 0.02-mm 2 footprint. As a result, the power consumption and size of the iTDS will be significantly reduced through the use of a much smaller rechargeable battery. Moreover, the system can operate longer following every recharge, improving the iTDS usability.

Tegument Glycoproteins and Cathepsins of Newly Excysted Juvenile Fasciola hepatica Carry Mannosidic and Paucimannosidic N-glycans

PubMed Central

Garcia-Campos, Andres; Cwiklinski, Krystyna; Dalton, John P.; Hokke, Cornelis H.; O’Neill, Sandra; Mulcahy, Grace

2016-01-01

Recently, the prevalence of Fasciola hepatica in some areas has increased considerably and the availability of a vaccine to protect livestock from infection would represent a major advance in tools available for controlling this disease. To date, most vaccine-target discovery research on this parasite has concentrated on proteomic and transcriptomic approaches whereas little work has been carried out on glycosylation. As the F. hepatica tegument (Teg) may contain glycans potentially relevant to vaccine development and the Newly Excysted Juvenile (NEJ) is the first lifecycle stage in contact with the definitive host, our work has focused on assessing the glycosylation of the NEJTeg and identifying the NEJTeg glycoprotein repertoire. After in vitro excystation, NEJ were fixed and NEJTeg was extracted. Matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS) analysis of released N-glycans revealed that oligomannose and core-fucosylated truncated N-glycans were the most dominant glycan types. By lectin binding studies these glycans were identified mainly on the NEJ surface, together with the oral and ventral suckers. NEJTeg glycoproteins were affinity purified after targeted biotinylation of the glycans and identified using liquid chromatography and tandem mass spectrometry (LC-MS/MS). From the total set of proteins previously identified in NEJTeg, eighteen were also detected in the glycosylated fraction, including the F. hepatica Cathepsin B3 (FhCB3) and two of the Cathepsin L3 (FhCL3) proteins, among others. To confirm glycosylation of cathepsins, analysis at the glycopeptide level by LC-ESI-ion-trap-MS/MS with collision-induced dissociation (CID) and electron-transfer dissociation (ETD) was carried out. We established that cathepsin B1 (FhCB1) on position N80, and FhCL3 (BN1106_s10139B000014, scaffold10139) on position N153, carry unusual paucimannosidic Man2GlcNAc2 glycans. To our knowledge, this is the first description of F. hepatica NEJ glycosylation and the first report of N-glycosylation of F. hepatica cathepsins. The significance of these findings for immunological studies and vaccine development is discussed. PMID:27139907

Flame blowout and pollutant emissions in vitiated combustion of conventional and bio-derived fuels

NASA Astrophysics Data System (ADS)

Singh, Bhupinder

The widening gap between the demand and supply of fossil fuels has catalyzed the exploration of alternative sources of energy. Interest in the power, water extraction and refrigeration (PoWER) cycle, proposed by the University of Florida, as well as the desirability of using biofuels in distributed generation systems, has motivated the exploration of biofuel vitiated combustion. The PoWER cycle is a novel engine cycle concept that utilizes vitiation of the air stream with externally-cooled recirculated exhaust gases at an intermediate pressure in a semi-closed cycle (SCC) loop, lowering the overall temperature of combustion. It has several advantages including fuel flexibility, reduced air flow, lower flame temperature, compactness, high efficiency at full and part load, and low emissions. Since the core engine air stream is vitiated with the externally cooled exhaust gas recirculation (EGR) stream, there is an inherent reduction in the combustion stability for a PoWER engine. The effect of EGR flow and temperature on combustion blowout stability and emissions during vitiated biofuel combustion has been characterized. The vitiated combustion performance of biofuels methyl butanoate, dimethyl ether, and ethanol have been compared with n-heptane, and varying compositions of syngas with methane fuel. In addition, at high levels of EGR a sharp reduction in the flame luminosity has been observed in our experimental tests, indicating the onset of flameless combustion. This drop in luminosity may be a result of inhibition of processes leading to the formation of radiative soot particles. One of the objectives of this study is finding the effect of EGR on soot formation, with the ultimate objective of being able to predict the boundaries of flameless combustion. Detailed chemical kinetic simulations were performed using a constant-pressure continuously stirred tank reactor (CSTR) network model developed using the Cantera combustion code, implemented in C++. Results have been presented showing comparative trends in pollutant emissions generation, flame blowout stability, and combustion efficiency. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Mass spectrometry methods for the analysis of biodegradable hybrid materials

NASA Astrophysics Data System (ADS)

Alalwiat, Ahlam

This dissertation focuses on the characterization of hybrid materials and surfactant blends by using mass spectrometry (MS), tandem mass spectrometry (MS/MS), liquid chromatography (LC), and ion mobility (IM) spectrometry combined with measurement and simulation of molecular collision cross sections. Chapter II describes the principles and the history of mass spectrometry (MS) and liquid chromatography (LC). Chapter III introduces the materials and instrumentation used to complete this dissertation. In chapter IV, two hybrid materials containing poly(t-butyl acrylate) (PtBA) or poly(acrylic acid) (PAA) blocks attached to a hydrophobic peptide rich in valine and glycine (VG2), as well as the poly(acrylic acid) (PAA) and VG2 peptide precursor materials, are characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ionization mass spectrometry (ESI-MS) and ion mobility mass spectrometry (IM-MS). Collision cross-sections and molecular modeling have been used to determine the final architecture of both hybrid materials. Chapter V investigates a different hybrid material, [BMP-2(HA)2 ], comprised of a dendron with two polyethylene glycol (PEG) branches terminated by a hydroxyapatite binding peptide (HA), and a focal point substituted with a bone morphogenic protein mimicking peptide (BMP-2). MALDI-MS, ESI-MS and IM-MS have been used to characterize the HA and BMP-2 peptides. Collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) have been employed in double stage (i.e. tandem) mass spectrometry (MS/MS) experiments to confirm the sequences of the two peptides HA and BMP-2. The MALDI-MS, ESI-MS and IM-MS methods were also applied to characterize the [BMP-2(HA)2] hybrid material. Collision cross-section measurements and molecular modeling indicated that [BMP-2(HA)2] can attain folded or extended conformation, depending on its degree of protonation (charge state). Chapter VI focuses on the analysis of alkyl polyglycoside (APG) surfactants by MALDI-MS and ESI-MS, MS/MS, and by combining MS and with ion mobility (IM) and/or ultra-performance liquid chromatography (UPLC) separation in LC-IM and LC-IM-MS experiments. Chapter VII summaries this dissertation's findings.

Community-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 80 Type IV (CC80-MRSA-IV) Isolated from the Middle East: A Heterogeneous Expanding Clonal Lineage

PubMed Central

Harastani, Houda H.; Tokajian, Sima T.

2014-01-01

Background The emergence of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) has caused a change in MRSA epidemiology worldwide. In the Middle East, the persistent spread of CA-MRSA isolates that were associated with multilocus sequence type (MLST) clonal complex 80 and with staphylococcal cassette chromosome mec (SCCmec) type IV (CC80-MRSA-IV), calls for novel approaches for infection control that would limit its spread. Methodology/Principal Findings In this study, the epidemiology of CC80-MRSA-IV was investigated in Jordan and Lebanon retrospectively covering the period from 2000 to 2011. Ninety-four S. aureus isolates, 63 (67%) collected from Lebanon and 31 (33%) collected from Jordan were included in this study. More than half of the isolates (56%) were associated with skin and soft tissue infections (SSTIs), and 73 (78%) were Panton-Valentine Leukocidin (PVL) positive. Majority of the isolates (84%) carried the gene for exofoliative toxin d (etd), 19% had the Toxic Shock Syndrome Toxin-1 gene (tst), and seven isolates from Jordan had a rare combination being positive for both tst and PVL genes. spa typing showed the prevalence of type t044 (85%) and pulsed-field gel electrophoresis (PFGE) recognized 21 different patterns. Antimicrobial susceptibility testing showed the prevalence (36%) of a unique resistant profile, which included resistance to streptomycin, kanamycin, and fusidic acid (SKF profile). Conclusions The genetic diversity among the CC80 isolates observed in this study poses an additional challenge to infection control of CA-MRSA epidemics. CA-MRSA related to ST80 in the Middle East was distinguished in this study from the ones described in other countries. Genetic diversity observed, which may be due to mutations and differences in the antibiotic regimens between countries may have led to the development of heterogeneous strains. Hence, it is difficult to maintain “the European CA-MRSA clone” as a uniform clone and it is better to designate as CC80-MRSA-IV isolates. PMID:25078407

Effects of patterned topography on biofilm formation

NASA Astrophysics Data System (ADS)

Vasudevan, Ravikumar

2011-12-01

Bacterial biofilms are a population of bacteria attached to each other and irreversibly to a surface, enclosed in a matrix of self-secreted polymers, among others polysaccharides, proteins, DNA. Biofilms cause persisting infections associated with implanted medical devices and hospital acquired (nosocomial) infections. Catheter-associated urinary tract infections (CAUTIs) are the most common type of nosocomial infections accounting for up to 40% of all hospital acquired infections. Several different strategies, including use of antibacterial agents and genetic cues, quorum sensing, have been adopted for inhibiting biofilm formation relevant to CAUTI surfaces. Each of these methods pertains to certain types of bacteria, processes and has shortcomings. Based on eukaryotic cell topography interaction studies and Ulva linza spore studies, topographical surfaces were suggested as a benign control method for biofilm formation. However, topographies tested so far have not included a systematic variation of size across basic topography shapes. In this study patterned topography was systematically varied in size and shape according to two approaches 1) confinement and 2) wetting. For the confinement approach, using scanning electron microscopy and confocal microscopy, orienting effects of tested topography based on staphylococcus aureus (s. aureus) (SH1000) and enterobacter cloacae (e. cloacae) (ATCC 700258) bacterial models were identified on features of up to 10 times the size of the bacterium. Psuedomonas aeruginosa (p. aeruginosa) (PAO1) did not show any orientational effects, under the test conditions. Another important factor in medical biofilms is the identification and quantification of phenotypic state which has not been discussed in the literature concerning bacteria topography characterizations. This was done based on antibiotic susceptibility evaluation and also based on gene expression analysis. Although orientational effects occur, phenotypically no difference was observed between the patterned topography tested. Another potential strategy for biofilm control through patterned topography is based on the design of robust non-wetting surfaces with undercut feature geometries, characterized by 1) breakthrough pressure and 2) triple phase contact line model. It was found that height and presence of undercut had statistically significant effects, directly proportional to breakthrough pressures, whereas extent of undercut did not. A predictive triple phase contact line model was also developed. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Flow field of flexible flapping wings

NASA Astrophysics Data System (ADS)

Sallstrom, Erik

The agility and maneuverability of natural fliers would be desirable to incorporate into engineered micro air vehicles (MAVs). However, there is still much for engineers to learn about flapping flight in order to understand how such vehicles can be built for efficient flying. The goal of this study is to develop a methodology for capturing high quality flow field data around flexible flapping wings in a hover environment and to interpret it to gain a better understanding of how aerodynamic forces are generated. The flow field data was captured using particle image velocimetry (PIV) and required that measurements be taken around a repeatable flapping motion to obtain phase-averaged data that could be studied throughout the flapping cycle. Therefore, the study includes the development of flapping devices with a simple repeatable single degree of freedom flapping motion. The acquired flow field data has been examined qualitatively and quantitatively to investigate the mechanisms behind force production in hovering flight and to relate it to observations in previous research. Specifically, the flow fields have been investigated around a rigid wing and several carbon fiber reinforced flexible membrane wings. Throughout the whole study the wings were actuated with either a sinusoidal or a semi-linear flapping motion. The semi-linear flapping motion holds the commanded angular velocity nearly constant through half of each half-stroke while the sinusoidal motion is always either accelerating or decelerating. The flow fields were investigated by examining vorticity and vortex structures, using the Q criterion as the definition for the latter, in two and three dimensions. The measurements were combined with wing deflection measurements to demonstrate some of the key links in how the fluid-structure interactions generated aerodynamic forces. The flow fields were also used to calculate the forces generated by the flapping wings using momentum balance methods which yielded details of where along the wing the forces were generated. As expected, these results indicated that the spanwise location of where the forces were generated depended upon the wings membrane material and reinforcement pattern, but in general it was in the outer third of the wing. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Organ dose measurements from multiple-detector computed tomography using a commercial dosimetry system and tomographic, physical phantoms

NASA Astrophysics Data System (ADS)

Lavoie, Lindsey K.

The technology of computed tomography (CT) imaging has soared over the last decade with the use of multi-detector CT (MDCT) scanners that are capable of performing studies in a matter of seconds. While the diagnostic information obtained from MDCT imaging is extremely valuable, it is important to ensure that the radiation doses resulting from these studies are at acceptably safe levels. This research project focused on the measurement of organ doses resulting from modern MDCT scanners. A commercially-available dosimetry system was used to measure organ doses. Small dosimeters made of optically-stimulated luminescent (OSL) material were analyzed with a portable OSL reader. Detailed verification of this system was performed. Characteristics studied include energy, scatter, and angular responses; dose linearity, ability to erase the exposed dose and ability to reuse dosimeters multiple times. The results of this verification process were positive. While small correction factors needed to be applied to the dose reported by the OSL reader, these factors were small and expected. Physical, tomographic pediatric and adult phantoms were used to measure organ doses. These phantoms were developed from CT images and are composed of tissue-equivalent materials. Because the adult phantom is comprised of numerous segments, dosimeters were placed in the phantom at several organ locations, and doses to select organs were measured using three clinical protocols: pediatric craniosynostosis, adult brain perfusion and adult cardiac CT angiography (CTA). A wide-beam, 320-slice, volumetric CT scanner and a 64-slice, MDCT scanner were used for organ dose measurements. Doses ranged from 1 to 26 mGy for the pediatric protocol, 1 to 1241 mGy for the brain perfusion protocol, and 2-100 mGy for the cardiac protocol. In most cases, the doses measured on the 64-slice scanner were higher than those on the 320-slice scanner. A methodology to measure organ doses with OSL dosimeters received from CT imaging has been presented. These measurements are especially important in keeping with the ALARA (as low as reasonably achievable) principle. While diagnostic information from CT imaging is valuable and necessary, the dose to patients is always a consideration. This methodology aids in this important task. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Characterization of staphylococci in urban wastewater treatment plants in Spain, with detection of methicillin resistant Staphylococcus aureus ST398.

PubMed

Gómez, Paula; Lozano, Carmen; Benito, Daniel; Estepa, Vanesa; Tenorio, Carmen; Zarazaga, Myriam; Torres, Carmen

2016-05-01

The objective of this study was to determine the prevalence of Staphylococcus in urban wastewater treatment plants (UWTP) of La Rioja (Spain), and to characterize de obtained isolates. 16 wastewater samples (8 influent, 8 effluent) of six UWTPs were seeded on mannitol-salt-agar and oxacillin-resistance-screening-agar-base for staphylococci and methicillin-resistant Staphylococcus aureus recovery. Antimicrobial susceptibility profile was determined for 16 antibiotics and the presence of 35 antimicrobial resistance genes and 14 virulence genes by PCR. S. aureus was typed by spa, agr, and multilocus-sequence-typing, and the presence of immune-evasion-genes cluster was analyzed. Staphylococcus spp. were detected in 13 of 16 tested wastewater samples (81%), although the number of CFU/mL decreased after treatment. 40 staphylococci were recovered (1-5/sample), and 8 of them were identified as S. aureus being typed as (number of strains): spa-t011/agr-II/ST398 (1), spa-t002/agr-II/ST5 (2), spa-t3262/agr-II/ST5 (1), spa-t605/agr-II/ST126 (3), and spa-t878/agr-III/ST2849 (1). S. aureus ST398 strain was methicillin-resistant and showed a multidrug resistance phenotype. Virulence genes tst, etd, sea, sec, seg, sei, sem, sen, seo, and seu, were detected among S. aureus and only ST5 strains showed genes of immune evasion cluster. Thirty-two coagulase-negative Staphylococcus of 12 different species were recovered (number of strains): Staphylococcus equorum (7), Staphylococcus vitulinus (4), Staphylococcus lentus (4), Staphylococcus sciuri (4), Staphylococcus fleurettii (2), Staphylococcus haemolyticus (2), Staphylococcus hominis (2), Staphylococcus saprophyticus (2), Staphylococcus succinus (2), Staphylococcus capitis (1), Staphylococcus cohnii (1), and Staphylococcus epidermidis (1). Five presented a multidrug resistance phenotype. The following resistance and virulence genes were found: mecA, lnu(A), vga(A), tet(K), erm(C), msr(A)/(B), mph(C), tst, and sem. We found that Staphylococcus spp. are normal contaminants of urban wastewater, including different lineages of S. aureus and a high diversity of coagulase-negative species. The presence of multiple resistance and virulence genes, including mecA, in staphylococci of wastewater can be a concern for the public health. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deformation and fracture behavior of titanium-aluminum-niobium-(chromium,molybdenum) alloys with a gamma+sigma microstructure at ambient temperature

NASA Astrophysics Data System (ADS)

Kesler, Michael Steiner

Titanium aluminides are of interest as a candidate material for aerospace turbine applications due to their high strength to weight ratio. gamma-TiAl + alpha2-Ti3Al alloys have recently been incorporated in the low pressure turbine region but their loss of strength near 750C limits their high temperature use. Additions of Nb have been shown to have several beneficial effects in gamma+alpha2 alloys, including enhancements in strength and ductility of the gamma-phase, along with the stabilization of the cubic BCC beta-phase at forging temperatures allowing for thermomechanical processing. In the ternary Ti-Al-Nb system at high Nb-contents above approximately 10at%, there exists a two-phase gamma-TiAl + sigma-Nb2Al region at and above current service temperature for the target application. Limited research has been conducted on the mechanical properties of alloys with this microstructure, though they have demonstrated excellent high temperature strength, superior to that of gamma+alpha2 alloys. Because the sigma-phase does not deform at room temperature, high volume fractions of this phase result in poor toughness and no tensile elongation. Controlling the microstructural morphology by disconnecting the brittle matrix through heat treatments has improved the toughness at room temperature. In this study, attempts to further improve the mechanical properties of these alloys were undertaken by reducing the volume fraction of the sigma-phase and controlling the scale of the gamma+sigma microstructure through the aging of a meta-stable parent phase, the beta- phase, that was quenched-in to room temperature. Additions of beta-stabilizing elements, Cr and Mo, were needed in order to quench-in the beta-phase. The room temperature mechanical properties were evaluated by compression, Vickers' indentation and single edge notch bend tests at room temperature. The formation of the large gamma-laths at prior beta- phase grain boundaries was found to be detrimental to ductility due to strain localization in this coarsened region of the microstructure. Furthermore, samples aged from beta- phase single crystals proved to have excellent combinations of strength and ductility under compression. In the single crystals, microcracking did not develop until much larger plastic strains were reached. Lowering the volume fraction of the sigma-phase proved to enhance the fracture toughness in these alloys. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

A Straightforward and Highly Efficient Precipitation/On-pellet Digestion Procedure Coupled to a Long Gradient Nano-LC Separation and Orbitrap Mass Spectrometry for Label-free Expression Profiling of the Swine Heart Mitochondrial Proteome

PubMed Central

Duan, Xiaotao; Young, Rebecca; Straubinger, Robert M.; Page, Brian J.; Cao, Jin; Wang, Hao; Yu, Haoying; Canty, John M.; Qu, Jun

2009-01-01

For label-free expression profiling of tissue proteomes, efficient protein extraction, thorough and quantitative sample cleanup and digestion procedures, as well as sufficient and reproducible chromatographic separation, are highly desirable but remain challenging. However, optimal methodology has remained elusive, especially for proteomes that are rich in membrane proteins, such as the mitochondria. Here we describe a straightforward and reproducible sample preparation procedure, coupled with a highly selective and sensitive nano-LC/Orbitrap analysis, which enables reliable and comprehensive expression profiling of tissue mitochondria. The mitochondrial proteome of swine heart was selected as a test system. Efficient protein extraction was accomplished using a strong buffer containing both ionic and non-ionic detergents. Overnight precipitation was used for cleanup of the extract, and the sample was subjected to an optimized 2-step, on-pellet digestion approach. In the first step, the protein pellet was dissolved via a 4 h tryptic digestion under vigorous agitation, which nano-LC/LTQ/ETD showed to produce large and incompletely cleaved tryptic peptides. The mixture was then reduced, alkylated, and digested into its full complement of tryptic peptides with additional trypsin. This solvent precipitation/on-pellet digestion procedure achieved significantly higher and more reproducible peptide recovery of the mitochondrial preparation, than observed using a prevalent alternative procedure for label-free expression profiling, SDS-PAGE/in-gel digestion (87% vs. 54%). Furthermore, uneven peptide losses were lower than observed with SDS-PAGE/in-gel digestion. The resulting peptides were sufficiently resolved by a 5 h gradient using a nano-LC configuration that features a low-void-volume, high chromatographic reproducibility, and an LTQ/Orbitrap analyzer for protein identification and quantification. The developed method was employed for label-free comparison of the mitochondrial proteomes of myocardium from healthy animals vs. those with hibernating myocardium. Each experimental group consisted of a relatively large number of animals (n=10), and samples were analyzed in random order to minimize quantitative false-positives. Using this approach, 904 proteins were identified and quantified with high confidence, and those mitochondrial proteins that were altered significantly between groups were compared with the results of a parallel 2D-DIGE analysis. The sample preparation and analytical strategy developed here represents an advancement that can be adapted to analyze other tissue proteomes. PMID:19290621

Using remote sensing to create indicators of ecosystem variability for a semi-arid savanna watershed in the Kavango-Zambezi region of Southern Africa

NASA Astrophysics Data System (ADS)

Pricope, Narcisa Gabriela

This dissertation addresses changes in land and resource availability occurring as a result of climate, water variability and changes in fire regimes in a semi-arid savanna region in Southern Africa. The research combines geospatial analyses of climatological and hydrologic data and various remotely-sensed datasets to create measures of ecosystem variability and adaptability to natural and anthropogenic changes in sensitive ecosystems. The study area is the Chobe River Basin (CRB), a watershed shared between Botswana and Namibia situated at the heart of one of the world.s largest transfrontier conservation areas, where different land-use management strategies and economic policies affect both the ecosystem and the livelihoods support system differentially. The southern African savanna is a highly variable environment and people have adapted to its harshness through the generations. However, in light of past and ongoing environmental changes, their ability to adapt may become threatened. By mapping and then analyzing the spatial and temporal variability of two important factors, namely flooding and fires, in conjunction with indices of vegetation health and productivity, the findings of this research can ultimately contribute to enhancing our understanding of local adaptation mechanisms to future environmental change. This is the first reconstruction of the spatial and temporal patterns of inundation for the last 25 years in the CRB, a transboundary basin with an unusual hydrologic regime and an important water resource for both human and wildlife populations. In the context of increasing temperatures, decreasing precipitation trends and increasing frequencies and intensities of El Nino episodes in southern Africa (Boko et al., 2007), I also investigated changes in fire incidences and marked shifts in fire seasonality both within and outside of protected areas of central Kavango Zambezi Transfrontier Conservation Area (KAZA TFCA). These changes are likely to have a series of strong impacts on other components of fire regimes in semi-arid ecosystems that will, in turn, affect their ecology, structure, and function. This dissertation contributes to the field of land use and land change science by proposing a novel spatial coincidence analysis framework for analyzing how the interand intra-annual extents of inundation and fire are correlated with both annual patterns of vegetation productivity and multi-date changes in vegetation productivity. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Application of liquid-liquid interactions with single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Wang, Randy Kai-Wei

This study covers three important research topics related to the application of liquid-liquid interaction with single-walled carbon nanotubes (SWNTs). The first topic describes the removal of SWNT bundles from liquid suspensions of nanotubes. The key to this work includes the use of liquid-liquid interfaces to trap the SWNT bundles due to the free energy change of the system during the process. SWNTs pack into crystalline ropes that form bundles due to strong van der Waals attraction. Bundling diminishes mechanical and electronic properties because it could interrupt the electronic structure of the nanotubes. Also, the electronic devices based on as-grown nanotubes, which contains a mixture of individual nanotubes and nanotube bundles, make the electrical response unpredictable. We developed a new simple process to remove bundles by liquid-liquid interaction. SWNTs bundles are trapped at the interface because bundles stabilize the emulsions. Eliminating the use of ultracentrifugation to remove SWNT bundles enables large-scale production with reduced production costs and time savings. The second topic presented the swelling effect of the surfactant layer surrounding SWNTs with nonpolar solvents. Solvatochromic shifts in the absorbance and fluorescence spectra are observed when surfactant-stabilized aqueous SWNT suspensions are mixed with immiscible organic solvents. When aqueous surfactant-suspended SWNTs are mixed with certain solvents, the spectra closely match the peaks for SWNTs dispersed in only that solvent. These spectral changes suggest the hydrophobic region of the micelle surrounding SWNTs swells with the organic solvent when mixed. The solvatochromic shifts of the aqueous SWNT suspensions are reversible once the solvent evaporates. However, some surfactant-solvent systems show permanent changes to the fluorescence emission intensity after exposure to the organic solvent. The intensity of some large diameter SWNT (n, m) types increase by more than 175%. These differences are attributed to surfactant reorganization, which can improve nanotube coverage, resulting in decreased exposure to quenching mechanisms from the aqueous phase. The third topic describes the further study of the solvatochromism of the SWNTs. Since SWNTs are encapsulated with microenvironments of nonpolar solvents, it provides a new method to measure the photophysical properties of nanotubes in environments with known properties. Fluorescence and absorbance spectra of SWNTs show solvatochromic shifts in 16 nonpolar solvents, which are proportional to the solvent induction polarization. The photophysical properties of SWNTs were used to determine the relationship between the longitudinal polarizability and other nanotube properties, alpha11,|| ∝ 1/(R2E11 3). (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Characterization and reliability of aluminum gallium nitride/gallium nitride high electron mobility transistors

NASA Astrophysics Data System (ADS)

Douglas, Erica Ann

Compound semiconductor devices, particularly those based on GaN, have found significant use in military and civilian systems for both microwave and optoelectronic applications. Future uses in ultra-high power radar systems will require the use of GaN transistors operated at very high voltages, currents and temperatures. GaN-based high electron mobility transistors (HEMTs) have proven power handling capability that overshadows all other wide band gap semiconductor devices for high frequency and high-power applications. Little conclusive research has been reported in order to determine the dominating degradation mechanisms of the devices that result in failure under standard operating conditions in the field. Therefore, it is imperative that further reliability testing be carried out to determine the failure mechanisms present in GaN HEMTs in order to improve device performance, and thus further the ability for future technologies to be developed. In order to obtain a better understanding of the true reliability of AlGaN/GaN HEMTs and determine the MTTF under standard operating conditions, it is crucial to investigate the interaction effects between thermal and electrical degradation. This research spans device characterization, device reliability, and device simulation in order to obtain an all-encompassing picture of the device physics. Initially, finite element thermal simulations were performed to investigate the effect of device design on self-heating under high power operation. This was then followed by a study of reliability of HEMTs and other tests structures during high power dc operation. Test structures without Schottky contacts showed high stability as compared to HEMTs, indicating that degradation of the gate is the reason for permanent device degradation. High reverse bias of the gate has been shown to induce the inverse piezoelectric effect, resulting in a sharp increase in gate leakage current due to crack formation. The introduction of elevated temperatures during high reverse gate bias indicated that device failure is due to the breakdown of an unintentional gate oxide. RF stress of AlGaN/GaN HEMTs showed comparable critical voltage breakdown regime as that of similar devices stressed under dc conditions. Though RF device characteristics showed stability up to a drain bias of 20 V, Schottky diode characteristics degraded substantially at all voltages investigated. Results from both dc and RF stress conditions, under several bias regimes, confirm that the primary root for stress induced degradation was due to the Schottky contact. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

ETDEWEB versus the World-Wide-Web: a specific database/web comparison

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

Cutler, Debbie

2010-06-28

A study was performed comparing user search results from the specialized scientific database on energy-related information, ETDEWEB, with search results from the internet search engines Google and Google Scholar. The primary objective of the study was to determine if ETDEWEB (the Energy Technology Data Exchange – World Energy Base) continues to bring the user search results that are not being found by Google and Google Scholar. As a multilateral information exchange initiative, ETDE’s member countries and partners contribute cost- and task-sharing resources to build the largest database of energy-related information in the world. As of early 2010, the ETDEWEB databasemore » has 4.3 million citations to world-wide energy literature. One of ETDEWEB’s strengths is its focused scientific content and direct access to full text for its grey literature (over 300,000 documents in PDF available for viewing from the ETDE site and over a million additional links to where the documents can be found at research organizations and major publishers globally). Google and Google Scholar are well-known for the wide breadth of the information they search, with Google bringing in news, factual and opinion-related information, and Google Scholar also emphasizing scientific content across many disciplines. The analysis compared the results of 15 energy-related queries performed on all three systems using identical words/phrases. A variety of subjects was chosen, although the topics were mostly in renewable energy areas due to broad international interest. Over 40,000 search result records from the three sources were evaluated. The study concluded that ETDEWEB is a significant resource to energy experts for discovering relevant energy information. For the 15 topics in this study, ETDEWEB was shown to bring the user unique results not shown by Google or Google Scholar 86.7% of the time. Much was learned from the study beyond just metric comparisons. Observations about the strengths of each system and factors impacting the search results are also shared along with background information and summary tables of the results. If a user knows a very specific title of a document, all three systems are helpful in finding the user a source for the document. But if the user is looking to discover relevant documents on a specific topic, each of the three systems will bring back a considerable volume of data, but quite different in focus. Google is certainly a highly-used and valuable tool to find significant ‘non-specialist’ information, and Google Scholar does help the user focus on scientific disciplines. But if a user’s interest is scientific and energy-specific, ETDEWEB continues to hold a strong position in the energy research, technology and development (RTD) information field and adds considerable value in knowledge discovery. (auth)« less

Dipole and Coulomb forces in electron capture dissociation and electron transfer dissociation mass spectroscopy.

PubMed

Świerszcz, Iwona; Skurski, Piotr; Simons, Jack

2012-02-23

Ab initio electronic structure calculations were performed on a doubly charged polypeptide model H(+)-Lys(Ala)(19)-CO-CH(NH(2))-CH(2)-SS-CH(2)-(NH(2))CH-CO-(Ala)(19)-Lys-H(+) consisting of a C-terminal protonated Lys followed by a 19-Ala α-helix with a 20th Ala-like unit whose side chain is linked by a disulfide bond to a corresponding Ala-like unit connected to a second 19-Ala α-helix terminated by a second C-terminal-protonated Lys. The Coulomb potentials arising from the two charged Lys residues and dipole potentials arising from the two oppositely directed 72 D dipoles of the α-helices act to stabilize the SS bond's σ* orbital. The Coulomb potentials provide stabilization of 1 eV, while the two large dipoles generate an additional 4 eV. Such stabilization allows the SS σ* orbital to attach an electron and thereby generate disulfide bond cleavage products. Although calculations are performed only on SS bond cleavage, discussion of N-C(α) bond cleavage caused by electron attachment to amide π* orbitals is also presented. The magnitudes of the stabilization energies as well as the fact that they arise from Coulomb and dipole potentials are supported by results on a small model system consisting of a H(3)C-SS-CH(3) molecule with positive and negative fractional point charges to its left and right designed to represent (i) two positive charges ca. 32 Å distant (i.e., the two charged Lys sites of the peptide model) and (ii) two 72 D dipoles (i.e., the two α-helices). Earlier workers suggested that internal dipole forces in polypeptides could act to guide incoming free electrons (i.e., in electron capture dissociation (ECD)) toward the positive end of the dipole and thus affect the branching ratios for cleaving various bonds. Those workers argued that, because of the huge mass difference between an anion donor and a free electron, internal dipole forces would have a far smaller influence over the trajectory of a donor (i.e., in electron transfer dissociation (ETD)). The present findings suggest that, in addition to their effects on guiding electron or donor trajectories, dipole potentials (in combination with Coulomb potentials) also alter the energies of SS σ* and amide π* orbitals, which then affects the ability of these orbitals to bind an electron. Thus, both by trajectory-guiding and by orbital energy stabilization, Coulomb and dipole potentials can have significant influences on the branching ratios of ECD and ETC in which disulfide or N-C(α) bonds are cleaved. © 2012 American Chemical Society

Architecture in motion: A model for music composition

NASA Astrophysics Data System (ADS)

Variego, Jorge Elias

2011-12-01

Speculations regarding the relationship between music and architecture go back to the very origins of these disciplines. Throughout history, these links have always reaffirmed that music and architecture are analogous art forms that only diverge in their object of study. In the 1 st c. BCE Vitruvius conceived Architecture as "one of the most inclusive and universal human activities" where the architect should be educated in all the arts, having a vast knowledge in history, music and philosophy. In the 18th c., the German thinker Johann Wolfgang von Goethe, described Architecture as "frozen music". More recently, in the 20th c., Iannis Xenakis studied the similar structuring principles between Music and Architecture creating his own "models" of musical composition based on mathematical principles and geometric constructions. The goal of this document is to propose a compositional method that will function as a translator between the acoustical properties of a room and music, to facilitate the creation of musical works that will not only happen within an enclosed space but will also intentionally interact with the space. Acoustical measurements of rooms such as reverberation time, frequency response and volume will be measured and systematically organized in correspondence with orchestrational parameters. The musical compositions created after the proposed model are evocative of the spaces on which they are based. They are meant to be performed in any space, not exclusively in the one where the acoustical measurements were obtained. The visual component of architectural design is disregarded; the room is considered a musical instrument, with its particular sound qualities and resonances. Compositions using the proposed model will not result as sonified shapes, they will be musical works literally "tuned" to a specific space. This Architecture in motion is an attempt to adopt scientific research to the service of a creative activity and to let the aural properties of enclosed spaces travel through music. 'We have two ways of positing the outside world. Numbers. Through their effect there is a plurality of individuals: sympathy, order harmony, beauty, etc. [...] in short, everything that is of mind. Space. This gives us objects "having extension" In the spatial world the images of the numerical world are projected, first by nature itself, then by men and above all by artists. It can be said that our duty on earth and during the whole of our life consists precisely in this projection of forms issued forth from numbers, and that you, the artists, fulfill that moral law to the highest degree. Not only is it possible to appeal simultaneously to geometry and to numbers, but to do so is the true purpose of our life.' Andreas Speiser (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Dissolved organic carbon (DOC) in soil extracts investigated by FT-ICR-MS

NASA Astrophysics Data System (ADS)

Hofmann, D.; Steffen, D.; Jablonowski, N. D.; Burauel, P.

2012-04-01

Soil drying and rewetting usually increases the release of xenobiotics like pesticides present in agricultural soils. Besides the effect on the release of two aged 14C-labeled pesticide residues we focus on the characterisation of simultaneously remobilized dissolved organic carbon (DOC) to gain new insights into structure and stability aspects of soil organic carbon fractions. The test soil (gleyic cambisol; Corg 1.2%, pH 7.2) was obtained from the upper soil layer of two individual outdoor lysimeter studies containing either environmentally long-term aged 14C residues of the herbicide ethidimuron (0-10 cm depth; time of aging: 9 years) or methabenzthiazuron (0-30 cm depth; time of aging: 17 years). Soil samples (10 g dry soil equivalents) were (A=dry/wet) previously dried (45°C) or (B=wet/wet) directly mixed with pure water (1+2, w:w), shaken (150 rpm, 1 h), and centrifuged (2000 g). This extraction procedure was repeated several individual times, for both setups. The first three individual extractions, respectively were used for further investigations. Salt was removed from samples prior analysis because of a possible quench effect in the electrospray (ESI) source by solid phase extraction (SPE) with Chromabond C18 Hydra-cartridges (Macherey-Nagel) and methanol as backextraction solvent. The so preconcentrated and desalted samples were introduced by flow injection analysis (FIA) in a fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS), equipped with an ESI source and a 7 T supra-conducting magnet (LTQ-FT Ultra, ThermoFisher Scientific). This technique is the key technique for complex natural systems attributed by their outstanding mass resolution (used 400.000 at m/z 400 Da) and mass accuracy (≤ 1ppm) by simultaneously providing molecular level details of thousands of compounds and was successful applied for the investigations of natural organic matter (NOM) different sources like marine and surface water, soil, sediment, bog and crude oil. The characteristics of measured DOM mass spectra were demonstrated. Furthermore, an algorithm to compute all chemically relevant C,H,O-, C,H,(O,S),N- as well as C,H,(O),S molecular compositions, designed and exercised by ourself using Scilab routines, was used for entire structure elucidation. Various methods for data evaluation of such an amount of peaks are applied to describe the characteristics of DOC. The van Krevelen diagram is widely used to classify the DOC compounds regarding polarity and aromaticity, whereas the Kendrick diagram allow to identify ions with elemental formulas that differ only in CH2, and molecular formulas with similar Kendrick Mass Defect (KMD) can be sorted by nominal mass series. Both kind of diagrams were developed and results are discussed together with the findings of ETD, MBT, and metabolites after soil drying and rewetting. Overall, the results suggest that intermittent soil drying and rewetting alters the disaggregation of soil aggregates, resulting in a release of entrapped organic carbon as well as pesticide molecules.

41. DISCOVERY, SEARCH, AND COMMUNICATION OF TEXTUAL KNOWLEDGE RESOURCES IN DISTRIBUTED SYSTEMS a. Discovering and Utilizing Knowledge Sources for Metasearch Knowledge Systems

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

Zamora, Antonio

Advanced Natural Language Processing Tools for Web Information Retrieval, Content Analysis, and Synthesis. The goal of this SBIR was to implement and evaluate several advanced Natural Language Processing (NLP) tools and techniques to enhance the precision and relevance of search results by analyzing and augmenting search queries and by helping to organize the search output obtained from heterogeneous databases and web pages containing textual information of interest to DOE and the scientific-technical user communities in general. The SBIR investigated 1) the incorporation of spelling checkers in search applications, 2) identification of significant phrases and concepts using a combination of linguisticmore » and statistical techniques, and 3) enhancement of the query interface and search retrieval results through the use of semantic resources, such as thesauri. A search program with a flexible query interface was developed to search reference databases with the objective of enhancing search results from web queries or queries of specialized search systems such as DOE's Information Bridge. The DOE ETDE/INIS Joint Thesaurus was processed to create a searchable database. Term frequencies and term co-occurrences were used to enhance the web information retrieval by providing algorithmically-derived objective criteria to organize relevant documents into clusters containing significant terms. A thesaurus provides an authoritative overview and classification of a field of knowledge. By organizing the results of a search using the thesaurus terminology, the output is more meaningful than when the results are just organized based on the terms that co-occur in the retrieved documents, some of which may not be significant. An attempt was made to take advantage of the hierarchy provided by broader and narrower terms, as well as other field-specific information in the thesauri. The search program uses linguistic morphological routines to find relevant entries regardless of whether terms are stored in singular or plural form. Implementation of additional inflectional morphology processes for verbs can enhance retrieval further, but this has to be balanced by the possibility of broadening the results too much. In addition to the DOE energy thesaurus, other sources of specialized organized knowledge such as the Medical Subject Headings (MeSH), the Unified Medical Language System (UMLS), and Wikipedia were investigated. The supporting role of the NLP thesaurus search program was enhanced by incorporating spelling aid and a part-of-speech tagger to cope with misspellings in the queries and to determine the grammatical roles of the query words and identify nouns for special processing. To improve precision, multiple modes of searching were implemented including Boolean operators, and field-specific searches. Programs to convert a thesaurus or reference file into searchable support files can be deployed easily, and the resulting files are immediately searchable to produce relevance-ranked results with builtin spelling aid, morphological processing, and advanced search logic. Demonstration systems were built for several databases, including the DOE energy thesaurus.« less

Critical flaw size in silicon nitride ball bearings

NASA Astrophysics Data System (ADS)

Levesque, George Arthur

Aircraft engine and bearing manufacturers have been aggressively pursuing advanced materials technology systems solutions to meet main shaft-bearing needs of advanced military aircraft engines. Ceramic silicon nitride hybrid bearings are being developed for such high performance applications. Though silicon nitride exhibits many favorable properties such as high compressive strength, high hardness, a third of the density of steel, low coefficient of thermal expansion, and high corrosion and temperature resistance, they also have low fracture toughness and are susceptible to failure from fatigue spalls emanating from pre-existing surface flaws that can grow under rolling contact fatigue (RCF). Rolling elements and raceways are among the most demanding components in aircraft engines due to a combination of high cyclic contact stresses, long expected component lifetimes, corrosive environment, and the high consequence of fatigue failure. The cost of these rolling elements increases exponentially with the decrease in allowable flaw size for service applications. Hence the range of 3D non-planar surface flaw geometries subject to RCF is simulated to determine the critical flaw size (CFS) or the largest allowable flaw that does not grow under service conditions. This dissertation is a numerical and experimental investigation of surface flaws in ceramic balls subjected to RCF and has resulted in the following analyses: Crack Shape Determination: the nucleation of surface flaws from ball impact that occurs during the manufacturing process is simulated. By examining the subsurface Hertzian stresses between contacting spheres, their applicability to predicting and characterizing crack size and shape is established. It is demonstrated that a wide range of cone and partial cone cracks, observed in practice, can be generated using the proposed approaches. RCF Simulation: the procedure and concerns in modeling nonplanar 3D cracks subject to RCF using FEA for stress intensity factor (SIF) trends observed from parametrically varying different physical effects are plotted and discussed. Included are developments in contact algorithms for 3D nonplanar cracks, meshing of nonplanar cracks for SIFs, parametric studies via MATLAB and other subroutines in python and FORTRAN. Establishing Fracture Parameters: the fracture toughness, K c, is determined by using numerical techniques on experimental tests namely the Brazilian disc test and a novel compression test on an indented ball. The fatigue threshold for mixed-mode loading, Keff, is determined by using a combination of numerical modeling and results from the V-ring single ball RCF test. CFS Determination: the range of 3D non-planar surface flaw geometries subject to RCF are simulated to calculate mixed mode SIFs to determine the critical flaw size, or the largest allowable flaw that does not grow under service conditions. The CFS results are presented as a function of Hertzian contact stress, traction magnitude, and crack size. Empirical Equations: accurate empirical equations (response functions) for the KI, KII, and K III SIFs for semi-elliptical surface cracks subjected to RCF as a function of the contact patch diameter, angle of crack to the surface, max pressure, position along the crack front, and aspect ratio of the crack are developed via parametric 3D FEA. Statistical Probability of Failure: since the variability in mechanical properties for brittle materials is high a probabilistic investigation of variations in flaw size, flaw orientation, fracture toughness, and Hertzian load on failure probability is conducted to statistically determine the probability of ball failure for an existing flaw subjected to the service conditions. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar

Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS measurements and gas-phase HDX studies at the amino acid residue level, for the first time a drift tube is connected to a linear ion trap (LIT) with electron transfer dissociation (ETD) capability[19, 20]. In this manner CCS and per-residue deuterium uptake measurements for a model peptide carried out successfully[19]. In this study, the gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined. Using ion structures obtained from molecular dynamics (MD) simulation and considering charge-site/exchange-site density the level of the maximum total deuterium uptake for the gas-phase ions is explained. Also a new hydrogen accessibility scoring (HAS) model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) is applied to the in-silico structures to describe the expected HDX behavior for these structures. Further investigation to improve the accuracy of the model is accomplished by a "per-residue" HDX kinetics study of the model peptide [21]. In this study, the ion residence time and the deuterium uptake of each residue is measured at different partial pressures of D2O. Subsequently the contribution each residue to the overall HDX rate of the intact peptide ion is calculated. These rate contributions of the residues exhibit a better fit to HAS than their maximum deuterium uptake. Proteins and peptides with very frequent acidic residue in their sequence provide very poor signal levels when employing positive polarity ESI. Also, the comparison of protonated and deprotonated ions of these biomolecules offers the potential to provide a better structural characterization [22]. Per-residue deuterium uptake values resulting from collision-induced dissociation (CID) of the model peptide KKDDDDIIKIIK were used to investigated the degree of hydrogen deuterium scrambling for deprotonated ions [23]. Remarkably, limited isotopic scrambling was observed in this study of this small model peptide. This data and the per-residue deuterium uptake of the triply-protonated model peptide Acetyl-PAAAAKAAAAKAAAAKAAAAK are exploited to propose a lemma to allocate protonation and deprotonation sites for peptide ions in the gas-phase. Insulin ions, as a small protein model system, are examined to investigate the relation of the maximum deuterium uptake value for each insulin chain to the exposed surface area of each insulin subunit [22]. The results show that the methodology can be applied on the protein complexes to provide information about the exposed surface area of each subunit.

Poster Session B

PubMed Central

2014-01-01

B.1 Development of a Proximity Labeling Method to Identify the Protein Targets of Bioactive Small Molecules Zachary Hill, Min Zhuang, James Wells University of California, San Francisco, CA, USA Identifying the direct protein targets of a bioactive small molecule gives insight into the compound's mechanism of action, its efficacy, and possible toxicity. Target identification is becoming an increasingly important part of the drug- development process. However, given the transient and heterogeneous nature of interactions between small molecules and proteins, this step is often difficult, greatly slowing the development of new therapeutics. For this reason, new methods to rapidly identify the direct protein targets of bioactive small molecules are of great importance. Enrichment strategies coupled with quantitative mass spectrometry have shown great promise in target identification. Here we will present our progress toward developing an engineered enzymatic tagging method that enables specific labeling and enrichment of protein targets from complex lysates. This method couples the binding of a small molecule to a proximity-based labeling event. Labeled target proteins are enriched and subsequently identified using quantitative LC-MS/MS. We will discuss several variations of this method, and highlight our progress towards applying proximity labeling to small-molecule target identification and validation. B.2 Modelling Atherosclerosis: Molecular Changes in the Ascending Aorta of Cholesterol-fed Rabbits Jingshu Xu1,2, Mia Jüllig1,2, Martin J. Middleditch1,2, Garth J.S. Cooper1,2,3,4 1School of Biological Sciences, University of Auckland, New Zealand; 2Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, New Zealand; 3Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK; 4Centre for Advanced Discovery and Experimental Therapeutics, NIHR Manchester Biomedical Research Centre, the University of Manchester, Manchester, UK The cholesterol-fed rabbit is commonly used to study the effect of hypercholesterolaemia and the associated atherosclerotic lesions. Here we maintained New Zealand White rabbits on a diet containing 2% (w/w) cholesterol (HC diet) for 12 weeks, after which their ascending aortas were excised and subjected to proteomic analysis. Extracts from ten individually obtained ascending aorta samples were labelled with isobaric (iTRAQ) tags and analyzed by LC-MS/MS to profile the proteomic changes in response to the HC diet (n=5) in comparison with non-HC, standard diet (n=5). ProteinPilot was used to search the LC-MS/MS output against the NCBI rabbit protein sequence database, leading to identification of 453 unique proteins. Of these, 74 showed significant differences in relative abundance (p<0.05), with 69 proteins higher and five lower in ascending aorta from HC diet-fed rabbits compared to controls. Many of the observed protein changes are consistent with molecular perturbations within the ascending aorta in response to the HC diet in rabbits, e.g. elevation of apolipoproteins, extracellular matrix adhesion proteins, collagens, glycolytic enzymes, heat shock proteins, proteins involved in immune defence, and proteins regulating the polymeric state of actin. We also made a number of novel observations, including an extreme (16-fold) elevation of a protein previously linked to angiogenesis but not atherosclerosis. Numerous other proteins not previously associated with atherosclerosis were also increased in ascending aorta from HC-fed rabbits. These novel observations merit further investigation as these perturbations may play important and yet undiscovered roles in the pathogenesis of atherosclerosis. B.3 Post-translational Modification Networks Vera van Noort Katholieke Universiteit Leuven, Leuven, Belgium Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications (1). We have systematically investigated the interplay of protein phosphorylation with other post-transcriptional regulatory mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae (2). Systematic perturbations by deletion of its only two protein kinases and its unique protein phosphatase identified not only the protein-specific effect on the phosphorylation network, but also a modulation of proteome abundance and lysine acetylation patterns, mostly in the absence of transcriptional changes. Reciprocally, deletion of the two putative N-acetyltransferases affects protein phosphorylation, confirming cross-talk between the two PTMs. The measured M. pneumoniae phosphoproteome and lysine acetylome revealed that both PTMs are very common, that (as in Eukaryotes) they often co-occur within the same protein and that they are frequently observed at interaction interfaces and in proteins that can be part of multiple protein complexes (3). The results imply previously unreported hidden layers of post-transcriptional regulation intertwining phosphorylation with lysine acetylation and other mechanisms that define the functional state of a cell. Aiming at a more global view of the interplay between PTM types, we collected modifications for 13 frequent PTM types in 8 eukaryotes, compared their speed of evolution and developed a method for measuring PTM co-evolution within proteins based on the co-occurrence of sites across eukaryotes (4). We found that PTM types are vastly interconnected, forming a global network that comprise in human alone >50,000 residues in about 6000 proteins. 1. Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol 9, 714. (2013) 2. van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol 8, 571. (2012) 3. Kühner S*, van Noort V*, etal. Proteome organization in a genome-reduced bacterium Science 326, 1235–1240. (2009) 4. Minguez P, Parca L, etal. Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol 8, 599. (2012) B.4 Extracellular Phosphorylation in the Murine Synaptosome Jonathan C Trinidad1, Ralf Schoepfer2, Alma L Burlingame3, Katalin F Medzihradszky3* 1Department of Chemistry, Indiana University, Bloomington, IN, USA; 2Department of Pharmacology, University College London, England, UK; 3Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, CA, USA Post-translational modifications (PTMs) play key regulatory roles in cellular localization and/or biological function of proteins. The site of modification within a protein; their fixed or transient nature; the stoichiometry and potential crosstalk between modifications have been the focus of numerous large-scale studies. Most of this research is focused on PTMs involved in intracellular processes, such as phosphorylation, methylation, GlcNAcylation, acetylation, and ubiquitination. Of these, phosphorylation is the most studied due to the biological importance of this modification as well as the availability of tools for such studies. While the majority of protein phosphorylation occurs on intracellular proteins, phosphorylation of secreted proteins is well established. Well-characterized examples include the secreted milk protein, beta-casein, and the serum protein fetuin. Our current understanding of the biological role of extracellular phosphorylation, as well as knowledge regarding the process by which they are modified, is incomplete. A kinase known as FAM20 has been identified and is localized to the Golgi as well as secreted. It has been shown to phosphorylate extracellular proteins with a SXE motif. We recently conducted extensive studies on the interplay between intracellular phosphorylation and GlcNAcylation on proteins isolated from murine synaptosomes. This data also allowed us to identify specific glycan structures on more than 500 secreted or transmembrane proteins. We have subsequently examined the extent to which phosphorylation was present in our sample on secreted proteins or extracellular regions of transmembrane proteins. Our goal was to determine the extent to which such phosphorylation can be explained by the known motif of Golgi-resident kinases. We analyzed the sequences around the extracellular phosphorylation sites, and the spatial relationship on the linear amino acid sequence between glycosylated and phosphorylated residues. This work was supported by NIH grant NIGMS 8P41GM103481, and by the Howard Hughes Medical Institute. B.5 Using Selective Reaction Monitoring (SRM) Mass Spectrometry To Unmask Regulatory Feedback Loops Controlling Adipogenesis Robert Ahrends1,2, Asuka Ota2, Kyle M. Kovary2, Takamasa Kudo2, Byung Ouk Park2, Mary N. Teruel2 1ISAS, Dortmund, Germany; 2Clinical and Systems Biology, Stanford University, Stanford, CA, USA Background: Due to modern lifestyle changes, obesity has a worldwide impact on human health. The obesity epidemic is now recognized as one of the most important public health problems facing the world today. Understanding adipogenesis is crucial to understanding obesity; failure of adipogenesis was shown to be a key factor in the development of diabetes. In earlier work using single-cell imaging, we demonstrated that there is a distinct decision made during the time course of adipogenesis. Thereby positive feedback loops between PPARg and other transcription factors (TFs) in the differentiation network are regulating this decision. We identified a positive feedback loop between PPARg and C/EBPb that plays a critical role in regulating adipogenesis. Since multiple feedback loops with different timing and strengths can sharpen the decision process and control the number of cells which are differentiating, we wanted to gain a better understanding of how many other proteins could be involved in the decision process. Objective: The objective of this work is to search for feedback loops that could play a key role in the commitment decision. Methods: Using Selected Reaction Monitoring (SRM) mass spectrometry combined with perturbations, we analyzed OP9 cells to detect peptides of TFs which can serve as probes. We validated these probes with isotopically coded internal peptide standards and established a SRM library of transcriptional key regulators. These probes were subsequently used to quantitatively profile different stages of adipogenesis to obtain time courses of different TFs. To achieve our major goal to elucidate the TF control network in more detail, we furthermore searched for hidden feedback loops in this differentiation system. To do so we chemically manipulated the activity level of PPARg and its potential feedback partners individually. If a protein was a component of one or several feedback loops and was experimentally manipulated, all the other components of feedback loops associated with this protein should display a relative change in abundance and vice versa. Results: We developed a SRM methodology to monitor the concentration changes of TFs during adipogenesis. Using this SRM methodology together the perturbation of PPARg, and single cell analysis we were able to validate known feedback loops (C/EBPa, C/EBPb) and to identify several new feedback Loops. Conclusions: PPARg is the master regulator of adipogenesis. To successfully differentiate preadipocytes into adipocytes, its activity needs to be tightly regulated by a network of feedback loops. Overall, the study provides a new SRM MS-based method to uncover novel feedback loops regulating TFs. Based on this method; we have identified 7 new proteins which are fundamental regulators of PPARg and the fat cell commitment decision. B.6 Application of Quantitative and Functional Phosphoproteomics In Study of Ethylene Signaling Ning Li 1 1The Hong Kong University of Science and Technology, Hong Kong, China Ethylene is a major plant hormone that regulates a diverse aspect of plant growth and development. The regulatory roles of ethylene in plants include promotion of leaf and flower petal senescence, yellowing and abscission, as well as promotion of fruit abscission and ripening. This key hormone is also involved in regulation of a number of plant biotic and abiotic stress responses. A dramatic effect of ethylene on tropic response is the dual-and-opposing effect of ethylene on stem negative gravitropic response, in which short-term ethylene treatment (0.5 hour) appears to inhibit stem bending up following re-orientation of inflorescence of Arabidopsis. In contrast, a long-term treatment (12 hours) stimulates gravitropic response and promote stem curve up faster. This time-dependent and dose- independent dual-and-opposing effect of ethylene on stem gravitropism may involve multiple signaling pathways. Stable isotope metabolic labeling-based quantitative phosphoproteomics performed on ein2–5, ctr1–1 and rcn1–1 ethylene signaling mutants indeed confirmed the time-dependent protein phosphorylation changes and some of phosphorylation events are independent to ein2 loss-of- function gene in response to ethylene treatment. Functional studies on the phosphorylated transcription factor ERF110 isoform suggest that it is required for the control of flowering time via multiple ethylene signaling pathways. B.7 Intact N- and O-linked Glycopeptide Identification from HCD Data Using Byonic Katalin F. Medzihradszky1, Jason Maynard1, Krista Kaasik1, Marshall Bern2 1University of California, San Francisco, CA, USA; 2Protein Metrics, San Carlos, CA, USA The importance of high quality analysis of glycosylated proteins is steadily increasing. Both the regulatory and signaling functions of the intracellular GlcNAc modification are widely documented, and different enrichment strategies for GlcNAcylated peptides have been developed. Extracellular glycosylation has been linked to a wide variety of diseases and both N- and O-glycosylation play important roles in providing the structural integrity of certain proteins, controlling protein clearance, protein-protein interaction, and enzymatic processing. Furthermore, most protein pharmaceuticals are glycosylated, and thus, batch to batch characterization of these drugs also involves glycosylation analysis. Towards the end of the last century mass spectrometry has become the method of choice for the analysis of post-translational modifications, and high throughput workflows have been developed for a number of different PTMs. Though mass spectrometry has been used for the characterization of N- and O-glycosylation of single proteins, its high-throughput application was prevented by a number of issues. These issues include the non-pattern based complex oligosaccharide structures, the isomeric building blocks, as well as the extensive carbohydrate fragmentation upon collisional activation. In-depth carbohydrate analysis still requires different tools: the released glycan pools are studied derivatized or unmodified using a wide variety of analytical methods, such as capillary electrophoresis, chromatography, exoglycosidase cocktails, and NMR. While such techniques will provide information on the identity of the sugar units and their linkages, the information on the localization of glycans within the protein sequence and of their site-specific heterogeneity is lost. Electron-transfer dissociation, which preserves peptide side-chain modifications, has enabled the MS/MS analysis of intact glycopeptides, and led to the successful assignment of thousands of GlcNAcylated sequences and Golgi-derived glycopeptides. This gave a boost to intact glycopeptide analysis, and search engines such as Protein Prospector and Byonic can handle even complex glycan mixtures. The most recommended acquisition workflow uses the diagnostic HexNAc oxonium ion produced by HCD analysis to trigger ETD analysis. Unfortunately, because extracellular glycosylation increases the peptide mass significantly without additional charge added, glycopeptides frequently produce low charge-density precursor ions that will yield only charge-reduced molecules upon ETD activation. However, properly acquired HCD data may contain sufficient information for glycopeptide identification. Byonic has been adjusted for the interpretation of such spectra. We will present the results from a complex N- and O-linked glycopeptide-containing mixture isolated from mouse brain synaptosome using WGA lectin weak affinity chromatography, highlighting the advantages and limitations of this approach. This work was supported by NIH grant NIGMS 8P41GM103481, and by the Howard Hughes Medical Institute (to the Bio-Organic Biomedical Mass Spectrometry Resource at UCSF, Director: A.L. Burlingame). B.8 Factors that Contribute to the Complexity of Glycopeptide Analysis – Besides Site-specific Heterogeneity Katalin F. Medzihradszky1, Zsuzsa Darula 1University of California, San Francisco, CA, USA; 2Laboratory of Proteomics Research, Biological Research Centre, Szeged, Hungary Data about the biological significance of extracellular glycosylation are compiling. Aberrant glycosylation has been implicated in diseases. Extracellular glycan remodeling has been linked to intracellular signaling. At the same time high-throughput intact glycopeptide analysis still is in its infancy. Glycosylation is a ‘special’ PTM. It includes a wide variety of structures formed by different biological pathways, performing very different biological functions. It is also unique in that aspect that the different MS/MS activation techniques provide different clues to solve the glycopeptide ‘puzzle’, but none delivers all the necessary information. Ion trap CID provides information about the glycan structure and usually reveals the mass of the peptide modified. Beam-type CID (HCD) frequently provides sufficient fragmentation information to assign the sequence modified. However, site assignment for O-glycopeptides is rarely possible. ETD identifies the sequence and site(s) modified, but one has to know the glycans present. Thus, using all these data together would offer the best solution. However, even the search engines aimed at glycopeptide identification cannot utilize all information available. We analyzed large and complex intact glycopeptide datasets, generated by LC/MS analysis of lectin-affinity-enriched mouse synaptosome and bovine or human serum samples. We will show that ETD data alone with faulty monoisotopic precursor peak-assignment, non-specific proteolytic digestion or covalent peptide modification will ‘assign’ an incorrect glycan structure. We will also present that a common buffer ingredient, Tris – widely used, even recommended for lectin-affinity chromatography- modifies sialic acid, altering not only its mass but also the chromatographic behavior of the glycopeptides. HCD analysis was instrumental in deciphering this unexpected side reaction. Acknowledgments – KFM was supported by NIH grant NIGMS 8P41GM103481, and by the Howard Hughes Medical Institute (to the Bio-Organic Biomedical Mass Spectrometry Resource at UCSF, Director: A.L. Burlingame) and by the following grants: OTKA 105611 (to Z. Darula), and BAROSS-DA07-DA-ESZK-07–2008-0036 (to the Biological Research Centre, HAS, director: P. Ormos). Z. Darula was supported by the Janos Bolyai Fellowship of the HAS. B.9 Characterizing Qualitative and Quantitative Global Changes in the Aging Heart Using pSMART, a Novel Acquisition Method Maryann S. Vogelsang, Amol Prakas, David Sarracino, Gouri Vadali, Scott Peterman Thermo Fisher Scientific, BRIMS Center, Cambridge, MA, USA The cardiovascular system has been shown to undergo significant changes as it ages. These changes range from genomic to structural. We have completed a label-free quantitative global profiling and targeted analysis of the cardiac proteome in aging mice using a novel data acquisition method, pSMART. Heart tissue was isolated and homogenized from both young (2 months old) and old (2 years old) mice. Solubilized and digested protein samples were spiked with the PRTC peptide retention time trainer kit and analyzed using unbiased data-dependent acquisition (DDA) method. Initial characterization experiments using unbiased DDA facilitated the building of detailed murine cardiac tissue spectral library. The spectral library records contain the relative retention time information based on the standard peptides as well as highly confident endogenous peptides, precursor and product ion information such as measured mass values and relative abundance used to create a consensus product ion spectrum. The spectral library information was used to create reference information to perform qual/quan determination in real-time. The pSMART method was used to acquire qualitative/ quantitative data analysis using one HR/AM MS and a series of narrow DIA mass windows. Our pSMART strategy resulted in 30% more peptide identifications per run than a standard DDA run. Additionally, using pSMART, we were able to confirm MS1 quantitation at low abundance levels with MS/MS for each peptide. This novel acquisition enabled quantitation of previously identified peptides as well as novel putative targets of aging. By identifying and quantifying more targets, we were able to better characterize the dynamic proteomic changes of cardio-dysfunction in aging mice. B.10 Quantitative Site-Specific Profiling S-glutathionylation in Macrophages in Response to Engineered Nanomaterial-induced Oxidative Stress Jicheng Duan, Vamsi K. Kodali, Matthew J. Gaffrey, Jia Guo, Rosalie K. Chu, David G. Camp, Richard D. Smith, Brian Thrall, Wei-Jun Qian Pacific Northwest National Laboratory, Richland, WA, USA Engineered nanoparticles are emerging functional materials with unique physicochemical properties, which make them desirable for commercial and medical applications. It is important to assess the toxicity of nanomaterials and recognize the underlying mechanisms of their toxicity. Oxidative stress is known to play important roles in nanomaterial-induced cellular toxicity, which leads to the generation of reactive oxygen species and alteration of protein activities and functions in cells. However, the knowledge about proteins and signaling pathways associated with nanomaterial-induced oxidative stress and nanotoxicity is still limited. Reversible cysteine-based protein modifications, such as S-glutathionylation (SSG) and S-nitrosylation (SNO), represent an important mechanism that modulates diverse cellular pathways in response to the disturbance of redox balance in cells. These redox modifications would be a potential regulatory mechanism in response to nanomaterials-induced oxidative stress and nanotoxicity. Recently, we have developed an effective proteomic approach for site-specific identification and quantification of different cysteine-based redox modifications by integrating selective reduction of oxidized cysteines, resin-assisted enrichment of thiol-containing proteins, and isobaric labeling to enable LC-MS/MS-based quantification. Herein, we present the preliminary results about the alteration of protein SSG modifications in mouse macrophages after exposure to different nanoparticles (CoO, Fe3O4 and SiO2 nanoparticles) by quantitative site-specific profiling. We observed that among these nanoparticles, CoO nanoparticles led to the most significant dose-dependent cytotoxicity and increase of protein SSG modifications in macrophages. Our site-specific SSG data highlighted redox sensitive proteins and their specific Cys residues potentially implicated in oxidative stress response. Functional analysis revealed that the most significantly enriched molecular function categories for SSG-modified proteins were free radical scavenging and cell death/survival. This preliminary result provides some insights on protein SSG modification as a potential regulatory mechanism of nanomaterial-induced oxidative stress. B.11 O-GlcNAc Regulates SOX2 Activity in Embryonic Stem Cells by Altering Protein-SOX2 Interactions Samuel Myers1, Sailaja Pedadda, Tara Freidrich, Sean Thomas, Gregor Krings, Michael Lopez, Marena Trinidad, Barbara Panning, Al Burlingame University of California, San Francisco, CA, USA SOX2 is a versatile transcription factor that maintains embryonic stem cell (ESC) pluripotency and self-renewal, and is important for proper lineage specification and adult stem cell maintenance. This versatility is likely due to post-translational modifications (PTMs) as SOX2 has been reported to be modified by numerous chemical moieties in a variety of cell types. One such PTM is O-GlcNAc, the dynamic and regulatory glycosylation of intracellular proteins. Global O-GlcNAc is essential for ESC self-renewal though the function of SOX2 O-GlcNAcylation in ESC is not understood. Here, we show that SOX2 is O-GlcNAc modified in the transactivation domain and alterations of self-renewing signals induce changes in SOX2 O-GlcNAc stoichiometry. Replacement of wild-type SOX2 with an O-GlcNAc-deficient mutant SOX2 in ESCs increases the pluripotency transcriptional network while down-regulating genes involved in differentiation. Analysis of SOX2-interacting proteins from ESCs revealed that the WT and mutant SOX2 interact with distinct subsets of transcriptional regulatory complexes. Thus, SOX2 O-GlcNAcylation modulates the transcriptional landscape of ESCs by modulating SOX2 activity and interactions with epigenetic regulatory complexes. B.12 Development of Multiplexed Assays for Oral Cancer Biomarker Verification by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry Yung-Chin Hsiao1, Lang-Ming Chi2, Kun-Yi Chien1, Yi-Ting Chen1, Yu-Sun Chang1, Jau-Song Yu1 1Chang Gung University, Tao-Yuan, Taiwan; 2Chang Gung Memorial Hospital, Tao-Yuan, Taiwan Oral cancer, one of the common cancers in Taiwan and other areas of Southern Asia, has become an increasing burden on the health care system in this region. Although numerous potential oral cancer biomarkers have been discovered in the past decades, very few of them have been verified and validated in parallel to compare their clinical utility. Recently, a multiplexed, targeted proteomics assay platform, termed SISCAPA-MRM-MS (stable isotope standards and capture by anti-peptide antibodies combined with multiple reaction monitoring mass spectrometry) has been shown to be a feasible approach for verifying multiple protein biomarker candidates in body fluid samples. Therefore, we sought to prioritize biomarker candidates from published literature and our in-house database and develop a high-throughput/multiplexed SISCAPA-MRM-MS assay for quantifying potential oral cancer biomarker candidates. We produced ∼400 clones of anti-peptide mAbs against 50 selected targets and effectively sieved out the high quality anti-peptide mAbs against 24 targets according to their binding affinity to peptide antigens (using peptide-immobilized SPR system) and immuno-capture capability (using SISCAPA-MS assay). These mAbs were then assembled into a 24-plex SISCAPA-MRM MS assay and applied to preliminarily evaluation of these 24 candidates in pooled saliva samples obtained from oral cancer patients and healthy controls. Eight of the 24 candidates were found to be drastically increased in pooled saliva samples from oral cancer patients as compared with healthy controls. The promise of this 24-plex SISCAPA LC-MRM MS assay allows us to systematically evaluate the abundance of targets in clinical samples for oral cancer biomarker discovery in the near future. B.13 Characterisation of Glycosylation of Paramyxovirus Surface Glycoproteins by Mass Spectrometry Cassandra L. Pegg1, C. Hoogland1, S.M. Johnson2, C.C. Gonzalez2, M.E. Peeples2, J.J. Gorman1 1QIMR Berghofer Medical Research Institute, Herston, Australia; 2Center for Vaccines & Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA The family Paramyxoviridae (paramyxovirus) contains a number of significant human and animal pathogens. Represented within this family are human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV) and Newcastle disease virus (NDV). The former two cause severe respiratory tract disease in infants, children and immunocompromised individuals. At present, safe and effective vaccines are not available for hRSV and hMPV. NDV is the causative agent of Newcastle disease (ND) afflicting a wide range of avian species. The desire to study NDV is due not only to the significant economic impact it has on the poultry industry worldwide but also its potential use as an oncolytic agent and vaccine vector for human and animal use. Additionally, findings on NDV may be translated to closely related viruses that cause disease in humans, such as parainfluenza viruses. Of great importance to paramyxoviruses are the variable attachment glycoproteins, hemagglutinin (H), hemagglutinin-neuraminidase (HN) and major surface glycoprotein (G) along with the fusion (F) glycoprotein. Glycoproteins H, HN and G are involved in viral attachment to the host cell, while F is responsible for viral entry by means of fusion with host cell membranes. Research has shown that the glycosylation sites present on these proteins can modulate the ability of the virus to infect host cells and stimulate the host immune system. Characterisation of site-specific glycan heterogeneity remains one of the few unexplored areas related to hRSV, hMPV and NDV surface glycoproteins. Previous research has been conducted to determine glycan heterogeneity, but not glycan site specificity, of NDV F. As yet, glycan site occupancy and glycan heterogeneity for glycoproteins G and F of hRSV and hMPV and HN of NDV, have not been defined at a chemical level. Revealing the glycosylation profile of these proteins may help elucidate mechanisms of viral attachment, replication and immune evasion within paramyxoviruses. Additionally, accurate identification and characterisation of protein glycosylation is required for producing glycoprotein therapeutics and for the development of targeted treatments. Liquid chromatography-MS/MS strategies utilising ETD, HCD and CID fragmentation were implemented to structurally characterise the digested glycoproteins. Initial research has revealed complex N-linked and mucin-like O-linked glycosylation of recombinant RSV G. Analysis of NDV revealed high-mannose N-linked glycans of F glycoprotein as well as high mannose and sialylated and sulphated complex N-linked glycans and a novel sialylated O-linked glycan of NDV HN. B.14 Developing A New In Vivo Cross-linking Mass Spectrometry Platform to Define Protein-Protein Interactions in Living Cells Robyn M. Kaake1, Xiaorong Wang1, Anthony Burke1, Clinton Yu1, Wynne Kandur1, Yingying Yang1, Eric J. Novtisky1, Tonya Second2, Jicheng Duan1, Athit Kao1, Shenheng Guan3, Danielle Vellucci1, Scott D. Rychnovsky1, Lan Huang1 1University of California, Irvine, CA, USA; 2Thermo Fisher Scientific, Waltham, MA, USA; 3University of California, San Francisco, CA, USA Protein-protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, we have developed a new in vivo cross-linking mass spectrometry platform that couples a novel membrane permeable, enrichable and MS-cleavable cross-linker with multistage tandem mass spectrometry. This strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells, and thus enables the determination of protein interaction interfaces. The utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and at the targeted protein complex level. Our work represents a general approach in studying in vivo PPIs, and provides a solid foundation for future studies towards the complete mapping of PPI networks in living systems. B.15 High-resolution Orbitrap Characterization of Preferential Chain Pairing in Co-expressed Bispecific Antibody Production by MS Under Native and Acidic Conditions Luis Schachner, Jianhui Zhou, Luke McCarty, Diego Ellerman, Michael Dillon, Christoph Spiess, Jennie Lill, Paul Carter, Wendy Sandoval Departments of Protein Chemistry and Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA Bispecific antibodies possess the characteristics and binding specificity of two distinct monoclonal antibodies, and as such can bind to two targets or epitopes simultaneously. Bispecific antibodies have recently received great attention for their promising results in clinical trials or potential new modes to deliver therapeutics. Generation of a bispecific antibody by co-expression of two light and heavy chains, would result in several mispaired species. While the “knobs-into-holes” technology enables efficient hetero-dimerization of the two heavy chains, the presumed random mispairing of the light chains has not been studied in detail as technologies to readily characterize and quantify the heterodimer species were missing. Using an anti-IL-4/IL-13, a bispecific antibody, which targets the IL-4 and IL-13 cytokines involved in type 2 cytokine-induced inflammation, we describe a mass spectrometry characterization assay under native and acidic conditions for co-expressed bispecific antibodies using an Exactive Plus Extended Mass Range (EMR) Orbitrap instrument. The high mass resolving power of the EMR Orbitrap allows unambiguous identification of all light and heavy chain pairing variants in a mixture of bispecific antibodies randomly assembled in vivo upon co-expression. Using the EMR Orbitrap technology, we identify and characterize the preferential pairing of the anti-IL-13 light chain to its cognate heavy chain. This unexpected, non-random pairing may be leveraged to guide the design of a single-cell solution for the production of bispecific antibodies. B.16 Controlling Low Rates of Cell Differentiation through Noise and Ultra-high Feedback Robert Ahrends, Asuka Ota, Kyle M. Kovary, Takamasa Kudo, Byung Ouk Park, Mary N. Teruel Dept. of Chemical and Systems Biology, Stanford University, Stanford, CA, USA The tissue size of adult mammals is maintained by replacement of aging or damaged cells by slow, ongoing cell differentiation. Disruption of this rate of ongoing differentiation results in serious disease. For example, acute myeloid leukaemia (AML) is caused by a block in differentiation which results in precursor cells proliferating uncontrollably rather than differentiating into a more terminal state. Adipocytes, the key regulators of glucose and lipid metabolism, make up 10–40% of human body mass and are renewed at a rate of approximately 10% per year [1]. The adipocyte system that will be used has the unique advantage that the terminal differentiation transition is relatively short and experimentally accessible using single cell microscopy. Understanding how cells regulate such very slow differentiation rates may enable better treatments of metabolic diseases and obesity. Here we combine quantitative mass spectrometry [2–4], computational modeling, and single-cell microscopy [5] to identify the network architecture that enables pre-adipocytes to differentiate at a rate of only 0.5% every 4 days. We show that that cell-to-cell variability, or noise, in protein abundance acts within a network of more than six positive feedbacks to permit pre-adipocytes to differentiate at very low rates. This system architecture resolves two fundamental opposing requirements: to irreversibly lock cells in the differentiated state and to create large cell-to-cell signal variability to enable differentiation at very low rates. The resolution of this optimization problem by noise and ultra-high feedback connectivity provides a generalizable mechanism for mammalian tissue size control. References: 1. [1] Spalding KL et al. (2008). Dynamics of fat cell turnover in humans. Nature. Jun 5; 453(7196):783–7. 2. [2] Abell E, Ahrends R, Bandara S, Park BO, Teruel MN. (2011). Parallel adaptive feedback enhances reliability of the Ca2+ signaling system. Proc Natl Acad Sci U S A. Aug 30; 108(35):14485–90. 3. [3] Ahrends R, Ota A, Kovary KM, Kudo T, Park BO, Teruel MN. (2014). Controlling low rates of cell differentiation through noise and ultra-high feedback. Science 345, June 20. 4. [4] Ota A, Kovary KM, Shen W, Ahrends R, Kraemer FB, Teruel MN. Using selective reaction monitoring (SRM) mass spectrometry to profile nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice. (submitted) 5. [5] Park BO, Ahrends R, Teruel MN. (2012). Consecutive positive feedback loops create a bistable switch that controls preadipocyte to adipocyte conversion. Cell Reports Oct 25.