Search results for: Joshua J. Coon

Items from 1 to 20 out of 94 results

article

Pilot proteomic analysis of cerebrospinal fluid in Alzheimer's disease

Justin McKetney, Daniel J. Panyard, Sterling C. Johnson, Cynthia M. Carlsson, more

PROTEOMICS – Clinical Applications > 15 > 2-3 > n/a - n/a

Proteomic analysis of cerebrospinal fluid (CSF) holds great promise in understanding the progression of neurodegenerative diseases, including Alzheimer's disease (AD). As one of the primary reservoirs of neuronal biomolecules, CSF provides a window into the biochemical and cellular aspects of the neurological environment. CSF can be drawn from living participants allowing the potential alignment of...

article

A deep analysis of the proteomic and phosphoproteomic alterations that occur in skeletal muscle after the onset of immobilization

Kuan‐Hung Lin, Gary M. Wilson, Rocky Blanco, Nathaniel D. Steinert, more

The Journal of Physiology > 599 > 11 > 2887 - 2906

Key points A decrease in protein synthesis plays a major role in the loss of muscle mass that occurs in response to immobilization. In mice, immobilization leads to a rapid (within 6 h) and progressive decrease in the rate of protein synthesis and this effect is mediated by a decrease in translational efficiency. Deep proteomic and phosphoproteomic analyses of mouse skeletal muscles revealed that...

article

Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts

Andrew L. Garfoot, Gary M. Wilson, Joshua J. Coon, Laura J. Knoll

BMC Genomics > 2019 > 20 > 1 > 1-11

Background The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host by transitioning from the fast growing tachyzoite morphology to latent bradyzoite morphology. A hallmark of the bradyzoite is the development of neuronal cysts that are resilient against host immune response and current therapeutics. The bradyzoite parasites within the...

article

Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries

Paul D. Hutchins, Jason D. Russell, Joshua J. Coon

Journal of The American Society for Mass Spectrometry > 2019 > 30 > 4 > 659-668

Libraries of simulated lipid fragmentation spectra enable the identification of hundreds of unique lipids from complex lipid extracts, even when the corresponding lipid reference standards do not exist. Often, these in silico libraries are generated through expert annotation of spectra to extract and model fragmentation rules common to a given lipid class. Although useful for a given sample source...

article

S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells

Elena Strekalova, Dmitry Malin, Erin M. M. Weisenhorn, Jason D. Russell, more

Breast Cancer Research and Treatment > 2019 > 175 > 1 > 39-50

Purpose Many transformed cells and embryonic stem cells are dependent on the biosynthesis of the universal methyl-donor S-adenosylmethionine (SAM) from methionine by the enzyme MAT2A to maintain their epigenome. We hypothesized that cancer stem cells (CSCs) rely on SAM biosynthesis and that the combination of methionine depletion and MAT2A inhibition would eradicate CSCs. Methods Human triple (ER/PR/HER2)-negative...

article

MS-Helios: a Circos wrapper to visualize multi-omic datasets

Harald Marx, Joshua J. Coon

BMC Bioinformatics > 2019 > 20 > 1 > 1-4

Background Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challenge to data analysis and visualization, requiring methods to reduce dimensionality and represent the data in a compact way. To provide a more holistic view, we recently introduced...

article

Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress

Yi-Hsuan Ho, Evgenia Shishkova, James Hose, Joshua J. Coon, more

Current Biology > 2018 > 28 > 16 > 2673-2680.e4

Stress tolerance and rapid growth are often competing interests in cells. Upon severe environmental stress, many organisms activate defense systems concurrent with growth arrest. There has been debate as to whether aspects of the stress-activated transcriptome are regulated by stress or an indirect byproduct of reduced proliferation. For example, stressed Saccharomyces cerevisiae cells mount a common...

article

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Shihui Yang, Jessica M. Vera, Jeff Grass, Giannis Savvakis, more

Biotechnology for Biofuels > 2018 > 11 > 1 > 1-20

Background Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2–8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and...

article

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys

Timothy W. Rhoads, Maggie S. Burhans, Vincent B. Chen, Paul D. Hutchins, more

Cell Metabolism > 2018 > 27 > 3 > 677-688.e5

Caloric restriction (CR) extends lifespan and delays the onset of age-related disorders in diverse species. Metabolic regulatory pathways have been implicated in the mechanisms of CR, but the molecular details have not been elucidated. Here, we show that CR engages RNA processing of genes associated with a highly integrated reprogramming of hepatic metabolism. We conducted molecular profiling of liver...

article

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast

Scott Bottoms, Quinn Dickinson, Mick McGee, Li Hinchman, more

Microbial Cell Factories > 2018 > 17 > 1 > 1-12

Background Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in...

article

Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production

Mike T. Veling, Andrew G. Reidenbach, Elyse C. Freiberger, Nicholas W. Kwiecien, more

Molecular Cell > 2017 > 68 > 5 > 970-977.e11

Mitoproteases are becoming recognized as key regulators of diverse mitochondrial functions, although their direct substrates are often difficult to discern. Through multi-omic profiling of diverse Saccharomyces cerevisiae mitoprotease deletion strains, we predicted numerous associations between mitoproteases and distinct mitochondrial processes. These include a strong association between the mitochondrial...

article

A Split-Abl Kinase for Direct Activation in Cells

Juan E. Diaz, Charles W. Morgan, Catherine E. Minogue, Alexander S. Hebert, more

Cell Chemical Biology > 2017 > 24 > 10 > 1250-1258.e4

To dissect the cellular roles of individual kinases, it is useful to design tools for their selective activation. We describe the engineering of a split-cAbl kinase (sKin-Abl) that is rapidly activated in cells with rapamycin and allows temporal, dose, and compartmentalization control. Our design strategy involves an empirical screen in mammalian cells and identification of split site in the N lobe...

article

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

Nicholas M. Riley, Michael S. Westphall, Joshua J. Coon

Journal of The American Society for Mass Spectrometry > 2018 > 29 > 1 > 140-149

The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to ~75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle...

article

The dental calculus metabolome in modern and historic samples

Irina M. Velsko, Katherine A. Overmyer, Camilla Speller, Lauren Klaus, more

Metabolomics > 2017 > 13 > 11 > 1-17

Introduction Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins...

article

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

Evgenia Shishkova, Nicholas W. Kwiecien, Alexander S. Hebert, Michael S. Westphall, more

Journal of The American Society for Mass Spectrometry > 2017 > 28 > 12 > 2523-2531

Speaking engagements, serving as session chairs, and receiving awards at national meetings are essential stepping stones towards professional success for scientific researchers. Studies of gender parity in meetings of national scientific societies repeatedly uncover bias in speaker selection, engendering underrepresentation of women among featured presenters. To continue this dialogue, we analyzed...

article

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia

Kyle J. Hewitt, Koichi R. Katsumura, Daniel R. Matson, Prithvia Devadas, more

Developmental Cell > 2017 > 42 > 3 > 213-225.e4

An enhancer with amalgamated E-box and GATA motifs (+9.5) controls expression of the regulator of hematopoiesis GATA-2. While similar GATA-2-occupied elements are common in the genome, occupancy does not predict function, and GATA-2-dependent genetic networks are incompletely defined. A “+9.5-like” element resides in an intron of Samd14 (Samd14-Enh) encoding a sterile alpha motif (SAM) domain protein...

article

A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

Gregory K. Potts, Rachel M. McNally, Rocky Blanco, Jae‐Sung You, more

The Journal of Physiology > 595 > 15 > 5209 - 5226

Key points Mechanical signals play a critical role in the regulation of muscle mass, but the molecules that sense mechanical signals and convert this stimulus into the biochemical events that regulate muscle mass remain ill‐defined. Here we report a mass spectrometry‐based workflow to study the changes in protein phosphorylation that occur in mouse skeletal muscle 1 h after a bout of electrically...

article

PRELIMINARY FINDINGS FROM AN ONGOING LONGITUDINAL METABOLOME-WIDE ASSOCIATION STUDY OF COGNITIVE DECLINE IN HEALTHY ADULTS WITH INCREASED RISK FOR ALZHEIMER’S DISEASE

Burcu F. Darst, Matthew J.P. Rush, Paul D. Hutchins, Thiruchelvi Rajagobal Reddy, more

Alzheimer's & Dementia > 2017 > 13 > 7(S) > P551-P552

article

Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer

Franklin E. Leach, Nicholas M. Riley, Michael S. Westphall, Joshua J. Coon, more

Journal of The American Society for Mass Spectrometry > 2017 > 28 > 9 > 1844-1854

The structural characterization of sulfated glycosaminoglycan (GAG) carbohydrates remains an important target for analytical chemists attributable to challenges introduced by the natural complexity of these mixtures and the defined need for molecular-level details to elucidate biological structure–function relationships. Tandem mass spectrometry has proven to be the most powerful technique for this...

article

Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity

Dhileepkumar Jayaraman, Alicia L. Richards, Michael S. Westphall, Joshua J. Coon, more

The Plant Journal > 90 > 6 > 1196 - 1207

Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we used a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor‐like kinases. The symbiotic receptor‐like kinases nodulation receptor‐like...

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ELECTRON TRANSFER DISSOCIATION (11)
MASS SPECTROMETRY (7)
PROTEOMICS (7)
PHOSPHOPROTEOMICS (4)
BIOFUEL (3)
ETD (3)
MITOCHONDRIA (3)
ORBITRAP (3)
PHOSPHORYLATION (3)
SACCHAROMYCES CEREVISIAE (3)
AB INITIO CALCULATIONS (2)
BIOCATALYSTS (2)
BIOINFORMATICS (2)
CASCADE DISSOCIATIONS (2)
CHEMICAL GENOMICS (2)
ELECTRON CAPTURE DISSOCIATION (2)
FTMS (2)
IMAC (2)
INSTRUMENTATION (2)
INTACT PROTEINS (2)
ION ATTACHMENT (2)
ION TRAP (2)
ION-ION REACTIONS (2)
ION/ION REACTIONS (2)
ION–ION REACTIONS (2)
LIGNOCELLULOSIC (2)
MEDICAGO TRUNCATULA (2)
NEGATIVE ELECTRON TRANSFER DISSOCIATION (2)
NEUCODE (2)
PEPTIDE Z IONS (2)
PROTEIN SYNTHESIS (2)
RNA-SEQ (2)
SKELETAL MUSCLE (2)
TANDEM MASS SPECTROMETRY (2)
ABL KINASE (1)
ACCURATE MASS (1)
ADAPTATION (1)
AFEX™ (1)
AGING (1)
AI-ETD (1)
ALZHEIMER'S DISEASE (1)
AMINO ACID SEQUENCE (1)
ANALYSEMETHODEN (1)
ANALYTICAL METHODS (1)
ANEMIA (1)
ANNOTATION (1)
ARCHAEOLOGY (1)
ATROPHY (1)
BIOENERGETICS (1)
BRADYZOITES (1)
BREAST CANCER (1)
C15ORF48 (1)
C2ORF47 (1)
CALIBRATION (1)
CALORIC RESTRICTION (1)
CANCER STEM CELL (1)
CARBOXYL GROUP DERIVATIZATION (1)
CB4856 (1)
CELL RECYCLING (1)
CELLULOSIC ETHANOL (1)
CEREBROSPINAL FLUID (1)
CHARGE STATE (1)
CHARGE TRANSFER (1)
CHEMICAL LABEL (1)
CITRATE SYNTHASE (1)
COENZYME Q (1)
COLLISION-INDUCED DISSOCIATION (1)
CONFERENCE PARTICIPATION (1)
COPY NUMBER (1)
COQ5P (1)
CORN STOVER (1)
CYSTS (1)
CZE‐MS/MS (1)
CZE–MS/MS (1)
DATA CLEANING (1)
DENTAL PLAQUE (1)
DERIVATIZED PROTEIN (1)
DHRS4 (1)
DISULFIDE BOND (1)
DROUGHT (1)
ELECTRON TRANSFER DISSOCIATION (ETD) MASS SPECTROMETRY (1)
ELECTROPHORESIS (1)
ELEKTROPHORESE (1)
ENERGY-RESOLVED CID (1)
ENERGY-RESOLVED COLLISION-INDUCED DISSOCIATION (1)
ENHANCER (1)
ERYTHROID (1)
EXERCISE (1)
FAIMS (1)
FERMENTATION (1)
FERMENTATION INHIBITION (1)
FIXED CHARGE MODIFICATION (1)
FRAGMENTATION (1)
FT MS/MS (1)
GAMMA-VALEROLACTONE (1)
GATA-2 (1)
GC–MS (1)
GENDER DIVERSITY IN STEM (1)
GENDER EQUALITY (1)
GENOME (1)
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Elsevier (36)
Springer (27)
ACS (22)
Wiley (9)

Journal

Journal of The American Society for Mass Spectrometry (19)
Analytical Chemistry (15)
International Journal of Mass Spectrometry (5)
Journal of Proteome Research (5)
Molecular Cell (5)
Cell Metabolism (4)
Journal of the American Society for Mass Spectrometry (3)
Biotechnology for Biofuels (2)
Cell Reports (2)
Cell Systems (2)
Current Opinion in Chemical Biology (2)
Microbial Cell Factories (2)
PROTEOMICS (2)
Stem Cell Reports (2)
The Journal of Physiology (2)
ACS Chemical Biology (1)
Alzheimer's & Dementia (1)
Analytica Chimica Acta (1)
Angewandte Chemie (1)
Angewandte Chemie International Edition (1)
BBA - Proteins and Proteomics (1)
BMC Bioinformatics (1)
BMC Genomics (1)
Bioresource Technology (1)
Breast Cancer Research and Treatment (1)
Cell (1)
Cell Chemical Biology (1)
Current Biology (1)
Developmental Cell (1)
FEBS Letters (1)
Journal of Molecular Biology (1)
Journal of the American Chemical Society (1)
Metabolomics (1)
PROTEOMICS – Clinical Applications (1)
Protein Expression and Purification (1)
Rapid Communications in Mass Spectrometry (1)
The Plant Journal (1)
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INFONA - science communication portal

Search results for: Joshua J. Coon

Pilot proteomic analysis of cerebrospinal fluid in Alzheimer's disease

A deep analysis of the proteomic and phosphoproteomic alterations that occur in skeletal muscle after the onset of immobilization

Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts

Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries

S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells

MS-Helios: a Circos wrapper to visualize multi-omic datasets

Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast

Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production

A Split-Abl Kinase for Direct Activation in Cells

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

The dental calculus metabolome in modern and historic samples

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia

A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

PRELIMINARY FINDINGS FROM AN ONGOING LONGITUDINAL METABOLOME-WIDE ASSOCIATION STUDY OF COGNITIVE DECLINE IN HEALTHY ADULTS WITH INCREASED RISK FOR ALZHEIMER’S DISEASE

Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer

Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity

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