Works Published in 2012
Displaying works 81 - 100 of 223 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2012 journal article
Redesign of Glycopeptide Antibiotics: Back to the Future
ACS Chemical Biology, 7(5), 797–804.
MeSH headings : Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / pharmacology; Drug Design; Enterococcus / drug effects; Glycopeptides / chemistry; Glycopeptides / pharmacology; Gram-Positive Bacterial Infections / drug therapy; Humans; Methicillin Resistance; Models, Molecular; Staphylococcal Infections / drug therapy; Staphylococcus aureus / drug effects; Vancomycin / analogs & derivatives; Vancomycin / pharmacology; Vancomycin Resistance
TL;DR:
Recent efforts to redesign glycopeptide antibiotics for the treatment of resistant microbial infections, including VRE and VRSA, are considered and their future potential for providing an even more powerful class of antibiotics that are even less prone to bacterial resistance is examined.
(via Semantic Scholar)
europepmc.org (repository)
Sources: Crossref, NC State University Libraries
Added: August 28, 2020
2012 journal article
NMR Spectroscopic Assignment and Structure Determination of Membrane Proteins Reconstituted in Magnetically Aligned Bicelles
Biophysical Journal, 102(3), 390a.
TL;DR:
A novel spectroscopic technique is used to obtain spin correlations between the resonances and assigned the spectrum of uniformly 15N labeled Pf1 protein reconstituted in aligned bicelles and developed an algorithm that calculates three-dimensional structures of membrane proteins solely based on the dipolar couplings between the covalently bound spins.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: August 28, 2020
2012 journal article
NaCu(Ta1−yNby)4O11 solid solution: A tunable band gap spanning the visible-light wavelengths
Journal of Solid State Chemistry, 191, 263–270.
author keywords: Semiconducting oxide; Solid solution; Bandgap size
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 28, 2020
2012 journal article
Chaperon and Lipid Composition Requirements for Transmembrane Insertion of CesA Helices 4 and 5
Biophysical Journal, 102(3), 440a.
TL;DR:
It is shown that an alanine-rich and generally non-aggregating membrane-spanning α-helical WALP peptide could also play such a role: when co-inserted with CesA TMHs, WALp promotes formation of transmembrane α-helices and prevents TMHS aggregation.
(via Semantic Scholar)
Sources: Crossref, ORCID, NC State University Libraries
Added: August 28, 2020
2012 journal article
Complex Materials for Molecular Spintronics Applications: Cobalt Bis(dioxolene) Valence Tautomers, from Molecules to Polymers
The Journal of Physical Chemistry B, 116(43), 13141–13148.
TL;DR:
This work predicts a complex multifunctional behavior in cobalt bis(dioxolene) valence tautomeric compounds and proposes these materials as promising candidates for spintronic devices that can couple magnetic bistability with novel electrical and spin conduction properties.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: August 28, 2020
2012 journal article
Synthesis and characterization of new trinuclear copper complexes
Inorganica Chimica Acta, 389, 131–137.
Contributors: R. Ghiladi* , A. Rheingold *, M. Siegler * & K. Karlin *
author keywords: Trinuclear copper; Copper(I) and copper(II); Copper clusters; Trinucleating ligands; Cu clusters in biology
TL;DR:
The approach towards modelling the copper cluster active sites of nitrous oxide reductase and the multicopper oxidases/oxygenases is described and two mesitylene-based trinucleating ligands are synthesized, which employ bis( 2-picolyl)amine (PY1) and bis(2-pyridylethyl)amine(PY2) tridentate copper chelates, respectively.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Sources: Crossref, ORCID, NC State University Libraries
Added: February 24, 2020
2012 journal article
Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry
Journal of Proteome Research, 11(6), 3390–3404.
author keywords: quantification; isotope dilution mass spectrometry; selected reaction monitoring; filter-aided sample preparation; monolignol biosynthesis
MeSH headings : Amino Acid Sequence; Biosynthetic Pathways; Isotope Labeling; Molecular Sequence Data; Plant Proteins / chemistry; Plant Proteins / metabolism; Populus / enzymology; Proteome / chemistry; Proteome / metabolism; Reference Standards; Spectrometry, Mass, Electrospray Ionization / standards; Xylem / enzymology
TL;DR:
This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: February 24, 2020
2012 journal article
Probing Dielectric and Hydrogen Bonding Gradients in Biological Membranes
Biophysical Journal, 102(3), 414a.
TL;DR:
An arsenal of advanced spin-labeling EPR methods are employed to profile heterogeneous dielectric and hydrogen bonding environment along the α-helical chain of an alanine-rich WALP peptide that is anchored in a lipid bilayer in a transmembrane orientation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Sources: Crossref, ORCID, NC State University Libraries
Added: February 24, 2020
2012 journal article
Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline
Molecular & Cellular Proteomics, 11(5), 202–214.
MeSH headings : Acetylation; Amino Acid Sequence; Animals; Breast Neoplasms; Calibration / standards; Cell Line, Tumor; Chromatography, High Pressure Liquid; Culture Media, Conditioned / chemistry; Female; Fourier Analysis; Humans; Mice; Mice, Knockout; Mitochondria, Liver / enzymology; Mitochondria, Muscle / metabolism; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Mapping / methods; Phosphorylation; Protein Processing, Post-Translational; Proteome / chemistry; Proteome / isolation & purification; Proteome / metabolism; Proteomics; Pyruvate Dehydrogenase Complex / chemistry; Pyruvate Dehydrogenase Complex / isolation & purification; Pyruvate Dehydrogenase Complex / metabolism; Reference Standards; Software; Tandem Mass Spectrometry / standards
TL;DR:
The capabilities of Skyline were expanded to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments and the utility of the MS1 filtering approach was examined.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2012 journal article
Learning Score Function Parameters for Improved Spectrum Identification in Tandem Mass Spectrometry Experiments
Journal of Proteome Research, 11(9), 4499–4508.
author keywords: machine learning; spectrum identification; shotgun proteomics
MeSH headings : Algorithms; Artificial Intelligence; Caenorhabditis elegans Proteins / chemistry; Peptide Fragments / chemistry; Peptide Mapping / methods; Reproducibility of Results; Saccharomyces cerevisiae Proteins / chemistry; Software; Tandem Mass Spectrometry / methods
TL;DR:
The present work addresses algorithms to rank peptide-spectrum matches with a richer and more flexible feature set representation that is based on the parametrization of the SEQUEST XCorr score and that can be used by all of these algorithms.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2012 journal article
Evaluation of Front-End Higher Energy Collision-Induced Dissociation on a Benchtop Dual-Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics
Analytical Chemistry, 84(3), 1533–1539.
MeSH headings : Animals; Caenorhabditis elegans / metabolism; Glycopeptides / analysis; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Phosphopeptides / analysis; Pressure; Proteomics / instrumentation; Software
TL;DR:
Front-end higher energy collision-induced dissociation (fHCD) on a benchtop dual-pressure linear ion trap offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater than for specta collected using RE-CID.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2012 journal article
Homopteran Vector Biomarkers for Efficient Circulative Plant Virus Transmission are Conserved in Multiple Aphid Species and the Whitefly Bemisia tabaci
Journal of Integrative Agriculture, 11(2), 249–262.
author keywords: aphid; whitefly; Schizaphis graminum; Bemisia tabaci; Acyrthosiphon pisum; Toxoptera citricida; Myzus persicae; proteomics; biomarker; circulative transmission; begomovirus; luteovirus; geminivirus; leafhopper; selected reaction monitoring; SRM; mass spectrometry; targeted proteomics; Skyline
TL;DR:
The conservation of these proteins in multiple insect taxa that transmit plant viruses along the circulative transmission pathway creates the opportunity to use these biomarkers to rapidly identify insect populations that are the most efficient vectors and allow them to be targeted for control prior to the spread of virus within a crop.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2012 journal article
De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics
Journal of The American Society for Mass Spectrometry, 23(12), 2075–2082.
author keywords: Mass spectrometry; Proteomics; Tandem mass spectrometry; Calibration; Mass measurement accuracy; Shotgun proteomics; Resolution
MeSH headings : Algorithms; Calibration; Models, Molecular; Peptide Fragments / chemistry; Peptide Mapping / methods; Proteomics / methods; Saccharomyces cerevisiae Proteins / chemistry; Sensitivity and Specificity; Tandem Mass Spectrometry / methods; Tandem Mass Spectrometry / standards
TL;DR:
The algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves, and the precision in mass measurement was improved due to the correction of non-linear variation inmass measurement accuracy across the m/z range.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2012 journal article
A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome
Analytical and Bioanalytical Chemistry, 403(8), 2397–2402.
author keywords: Protein turnover; Respiratory distress syndrome; Selected reaction monitoring; SRM; Protein kinetics; Protein metabolism
MeSH headings : Amino Acid Sequence; Complement Factor B / analysis; Complement Factor B / metabolism; Humans; Infant, Newborn; Kinetics; Mass Spectrometry / methods; Molecular Sequence Data; Protein Precursors / analysis; Protein Precursors / metabolism; Proteins / analysis; Proteins / metabolism; Proteolipids / analysis; Proteolipids / metabolism; Proteomics / methods; Pulmonary Surfactant-Associated Protein B / analysis; Pulmonary Surfactant-Associated Protein B / metabolism; Respiratory Distress Syndrome, Newborn / metabolism; Trachea / metabolism
TL;DR:
In vivo turnover of four proteins from sequential tracheal aspirates obtained from human newborn infants with respiratory distress syndrome using targeted proteomics is measured and complement factor B, a component of the alternative pathway of complement activation, had an approximately twofold-longer half-life than the other three proteins.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2012 journal article
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
PROTEOMICS, 12(8), 1134–1141.
author keywords: Selected reaction monitoring; Skyline; SRM assays; Targeted proteomics; Technology
MeSH headings : Amino Acid Sequence; Calibration; Humans; Infant, Newborn; Lung / physiopathology; Mass Spectrometry / methods; Mass Spectrometry / standards; Molecular Sequence Data; Peptides / analysis; Peptides / chemical synthesis; Proteomics / methods; Proteomics / standards; Pulmonary Surfactant-Associated Protein B / analysis; Reference Standards; Reproducibility of Results; Respiratory Distress Syndrome, Newborn / diagnosis; Respiratory Distress Syndrome, Newborn / physiopathology; Sensitivity and Specificity; Software
TL;DR:
A method, which uses the in‐house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2012 journal article
Stimuli-Responsive Polymer Brushes for Flow Control through Nanopores
Journal of Functional Biomaterials, 3(2), 239–256.
author keywords: smart membranes; signal responsive polymers; polymer brushes; computational modeling; flow control; nanofluidic valve; simulation
TL;DR:
In this work, an overview of nanoporous materials functionalized with responsive polymers is given and a theoretical treatment that accounts for polymer conformational change in response to a stimulus and the associated flow-control effect is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
Source: Crossref
Added: December 15, 2019
2012 journal article
The Vibrational Properties of Ultrananocrystalline Diamond Based on Molecular dynamics Simulations
MRS Proceedings, 1404.
Source: Crossref
Added: December 15, 2019
2012 journal article
Mass spectrometry-based proteomics: existing capabilities and future directions
Chemical Society Reviews, 41(10), 3912–3928.
Contributors: T. Angel *, U. Aryal *, S. Hengel *, E. Baker* , R. Kelly *, E. Robinson *, R. Smith *
MeSH headings : Animals; Chromatography, Liquid / methods; Humans; Mass Spectrometry / methods; Protein Processing, Post-Translational; Proteome / analysis; Proteome / metabolism; Proteomics / methods
TL;DR:
MS-based proteomics increasingly contribute to the authors' understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing the understanding of biology on a systems wide level for a wide range of applications including investigations of microbial communities, bioremediation, and human health.
(via Semantic Scholar)
Source: ORCID
Added: December 5, 2019
2012 journal article
Uterine Deletion of Trp53 Compromises Antioxidant Responses in the Mouse Decidua
Endocrinology, 153(9), 4568–4579.
Contributors: K. Burnum*, Y. Hirota *, E. Baker* , M. Yoshie *, Y. Ibrahim *, M. Monroe *, G. Anderson*, R. Smith *, T. Daikoku *, S. Dey *
MeSH headings : Animals; Antioxidants / metabolism; Decidua / metabolism; Female; Mice; Oxidative Stress / genetics; Premature Birth / genetics; Premature Birth / metabolism; Tumor Suppressor Protein p53 / deficiency; Tumor Suppressor Protein p53 / genetics; Uterus / metabolism
TL;DR:
Functional categorization of 183 candidate proteins unveiled new pathways that are influenced by p53, and down-regulation of a cluster of antioxidant enzymes in p53-deficient deciduae suggests that increased oxidative stress could be one cause of preterm birth in mice harboring uterine deletion of Trp53.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: December 5, 2019
2012 journal article
Mass spectrometry for translational proteomics: progress and clinical implications
Genome Medicine, 4(8).
Contributors: E. Baker* , T. Liu *, V. Petyuk *, K. Burnum-Johnson *, Y. Ibrahim *, G. Anderson*, R. Smith *
author keywords: biomarker; clinical proteomics; ion mobility separations; mass spectrometry; multiple reaction monitoring; selected reaction monitoring; shotgun proteomics; targeted proteomics; translational proteomics
TL;DR:
The current state of MS-based proteomics is reviewed with regard to its advantages and current limitations, and its translational applications in studies of protein biomarkers are highlighted.
(via Semantic Scholar)
Source: ORCID
Added: December 5, 2019
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