Works Published in 2012

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Displaying all 16 works

Sorted by most recent date added to the index first, which may not be the same as publication date order.

2012 journal article

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus.

40(18), 8917–8926.

MeSH headings : Alleles; Animals; DNA Methylation; Genetic Loci; Genomic Imprinting; Mice; Mice, Inbred C57BL; Nerve Tissue Proteins / genetics; Nerve Tissue Proteins / metabolism; Nuclear Proteins; Polyadenylation; Protein Isoforms / genetics; Protein Isoforms / metabolism; RNA, Messenger / metabolism; Transcription, Genetic; Ubiquitin-Protein Ligases / genetics; Ubiquitin-Protein Ligases / metabolism
TL;DR: Changes in DNA methylation on the maternal allele at the Nap1l5 promoter increases the use of an internal Herc3 polyadenylation site and alters exon splicing, which demonstrate the influence of epigenetic mechanisms in regulating HerC3 alternative mRNA processing. (via Semantic Scholar)
Source: ORCID
Added: September 28, 2022

2012 journal article

Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in Nanoflow LC-MS/MS of Complex Proteomic Samples

Journal of The American Society for Mass Spectrometry, 24(1), 148–153.

By: E. Hsieh*, M. Bereman*, S. Durand, G. Valaskovic & M. MacCoss*

author keywords: Shotgun proteomics; Nanoflow liquid chromatography; Peak capacity
MeSH headings : Caenorhabditis elegans Proteins / analysis; Caenorhabditis elegans Proteins / chemistry; Chromatography, Liquid / instrumentation; Chromatography, Liquid / methods; Nanotechnology / instrumentation; Peptide Mapping / instrumentation; Peptide Mapping / methods; Proteome / analysis; Proteome / chemistry; Proteomics / instrumentation; Proteomics / methods; Tandem Mass Spectrometry / methods
TL;DR: It is found that while longer column and gradient lengths generally increase peptide identifications, the degree of improvement is dependent on both parameters and is diminished at longer column, gradient, and gradients. (via Semantic Scholar)
Source: Crossref
Added: January 5, 2021

2012 journal article

Resetting for the Next Generation

Molecular Cell, 48(6), 819–821.

TL;DR: In this issue of Molecular Cell, Seisenberger et al. (2012) refine DNA methylation mapping to interrogate the epigenetic reprogramming of primordial germ cells, defining the timings of methylation loss, linking to pluripotency, and identifying potential routes to transgenerational epigenetic inheritance. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 28, 2020

2012 journal article

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

Molecular Cell, 47(6), 909–920.

MeSH headings : Animals; Blastocyst / metabolism; Cadherins / genetics; DNA Methylation; Embryo, Mammalian / cytology; Embryo, Mammalian / metabolism; Fertilization; Genetic Testing; Genomic Imprinting; Germ Cells / metabolism; Mice; Oocytes / metabolism; Pseudogenes; Sequence Analysis, DNA
TL;DR: Evidence is provided that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 28, 2020

2012 journal article

341 ANDROGENETIC ALOPECIA AT VARIOUS AGES AND PROSTATE CANCER RISK IN AN EQUAL ACCESS MULTIETHNIC CASE CONTROL SERIES OF VETERANS

Journal of Urology, 187(4S).

By: J. Thomas, J. Antonelli, L. Bañez, L. Gerber, C. Hoyo*, D. Grant, W. Demark-Wahnefried*, E. Platz ...

UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: August 28, 2020

2012 journal article

Insulin-Like Growth Factor 2/H19 Methylation at Birth and Risk of Overweight and Obesity in Children

The Journal of Pediatrics, 161(1), 31–39.

By: E. Perkins*, S. Murphy*, A. Murtha*, J. Schildkraut*, R. Jirtle*, W. Demark-Wahnefried*, M. Forman*, J. Kurtzberg* ...

MeSH headings : DNA Methylation; Female; Humans; Infant; Insulin-Like Growth Factor II / genetics; Male; Obesity / genetics; Overweight / genetics; Prospective Studies; Risk
TL;DR: The findings suggest that IGF2 plasticity may be mechanistically important in early childhood overweight or obese status and suggest aberrant DNA methylation at sequences regulating imprinted genes may be useful identifiers of children at risk for the development of early obesity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: August 28, 2020

2012 journal article

Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke

Gene, 494(1), 36–43.

author keywords: Sex-specific methylation effects; Imprinted gene; Pyrosequencing; Early origins hypothesis
MeSH headings : Adult; Birth Weight; DNA Methylation; Female; Fetal Blood / chemistry; Genomic Imprinting; Humans; Insulin-Like Growth Factor II / genetics; Male; Maternal-Fetal Exchange; Pregnancy; RNA, Long Noncoding; RNA, Untranslated; Sex Characteristics; Smoking / genetics
TL;DR: The findings suggest that IGF2 DMR plasticity is an important mechanism by which in utero adjustments to environmental toxicants are conferred. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: August 28, 2020

2012 journal article

Genetic variants in IGF-I, IGF-II, IGFBP-3, and adiponectin genes and colon cancer risk in African Americans and Whites

Cancer Causes & Control, 23(7), 1127–1138.

By: T. Keku*, A. Vidal*, S. Oliver*, C. Hoyo*, I. Hall*, O. Omofoye*, M. McDoom*, K. Worley* ...

author keywords: Insulin; IGF; Polymorphism; Colon cancer; African Americans
MeSH headings : Adiponectin / genetics; Adiponectin / metabolism; Black or African American / genetics; Aged; C-Peptide / blood; Colonic Neoplasms / blood; Colonic Neoplasms / ethnology; Colonic Neoplasms / genetics; Female; Gene Frequency; Genetic Predisposition to Disease / ethnology; Genetic Predisposition to Disease / genetics; Genotype; Genotyping Techniques / methods; Humans; Insulin-Like Growth Factor Binding Protein 3 / genetics; Insulin-Like Growth Factor Binding Protein 3 / metabolism; Insulin-Like Growth Factor I / genetics; Insulin-Like Growth Factor I / metabolism; Insulin-Like Growth Factor II / genetics; Insulin-Like Growth Factor II / metabolism; Logistic Models; Male; Middle Aged; Polymorphism, Genetic; Risk Factors; White People / genetics
TL;DR: An association between insulin pathway-related genes and elevated colon cancer risk in Whites but not in African Americans is supported, and carrying the IGF BP-3 variant alleles was associated with lower IGFBP-3 protein levels, a difference most pronounced in Whites. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2012 journal article

Association of cord blood methylation fractions at imprinted insulin-like growth factor 2 (IGF2), plasma IGF2, and birth weight

Cancer Causes & Control, 23(4), 635–645.

author keywords: IGF2; H19; ELISA; DNA methylation; Epigenetics; Epidemiology
MeSH headings : Birth Weight / genetics; DNA Methylation / genetics; Enzyme-Linked Immunosorbent Assay; Female; Fetal Blood; Genomic Imprinting; Humans; Infant, Newborn; Insulin-Like Growth Factor II / analysis; Insulin-Like Growth Factor II / genetics; Male
TL;DR: Variation in IGF2 DMR methylation is an important mechanism by which circulating IGF2 concentrations, a putative risk factor for obesity and cancers of the colon, esophagus, and prostate, are modulated; associations that may depend on pre-pregnancy obesity are suggested. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: August 28, 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.

By: B. Schilling*, M. Rardin*, B. MacLean*, A. Zawadzka*, B. Frewen*, M. Cusack*, D. Sorensen*, M. Bereman* ...

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.

By: M. Spivak*, M. Bereman*, M. MacCoss* & W. Noble*

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.

By: M. Bereman*, J. Canterbury*, J. Egertson*, J. Horner*, P. Remes*, J. Schwartz*, V. Zabrouskov*, M. MacCoss*

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

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