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J. Will Thompson

Adjunct Assistant Professor in the Department of Pharmacology & Cancer Biology
Pharmacology & Cancer Biology
Box 91009, 450 Research Drive, Durham, NC 27708
701 W Main St, Ste 320, Durham, NC 27701

Selected Publications


Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring In Vivo Arginine Isotope Incorporation in Alzheimer's Disease Mouse Models.

Journal Article J Am Soc Mass Spectrom · June 2, 2021 Immune-based metabolic reprogramming of arginine utilization in the brain contributes to the neuronal pathology associated with Alzheimer's disease (AD). To enable our long-term goals of differentiation of AD mouse model genotypes, ages, and sexes based on ... Full text Open Access Link to item Cite

A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure.

Journal Article Sci Rep · May 18, 2021 Acute respiratory failure (ARF) requiring mechanical ventilation, a complicating factor in sepsis and other disorders, is associated with high morbidity and mortality. Despite its severity and prevalence, treatment options are limited. In light of accumula ... Full text Link to item Cite

Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.

Journal Article Alzheimers Dement · April 2021 INTRODUCTION: The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age ... Full text Link to item Cite

Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression.

Journal Article Transl Psychiatry · March 2, 2021 Selective serotonin reuptake inhibitors (SSRIs) are the first-line treatment for major depressive disorder (MDD), yet their mechanisms of action are not fully understood and their therapeutic benefit varies among individuals. We used a targeted metabolomic ... Full text Open Access Link to item Cite

APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid.

Journal Article J Alzheimers Dis · 2021 BACKGROUND: APOE4 has been hypothesized to increase Alzheimer's disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear. OBJECTIVE: Characterize cerebrospinal fluid (CSF) proteomic changes related t ... Full text Link to item Cite

Cerebrospinal Fluid Proteome Changes in Older Non-Cardiac Surgical Patients with Postoperative Cognitive Dysfunction.

Journal Article J Alzheimers Dis · 2021 BACKGROUND: Postoperative cognitive dysfunction (POCD), a syndrome of cognitive deficits occurring 1-12 months after surgery primarily in older patients, is associated with poor postoperative outcomes. POCD is hypothesized to result from neuroinflammation; ... Full text Open Access Link to item Cite

Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease.

Journal Article Cell Rep Med · November 17, 2020 Increasing evidence suggests Alzheimer's disease (AD) pathophysiology is influenced by primary and secondary bile acids, the end product of cholesterol metabolism. We analyze 2,114 post-mortem brain transcriptomes and identify genes in the alternative bile ... Full text Link to item Cite

Metabolomic Signature as a Predictor of Liver Disease Events in Patients With HIV/HCV Coinfection.

Journal Article J Infect Dis · November 13, 2020 BACKGROUND: Advanced liver disease due to hepatitis C virus (HCV) is a leading cause of human immunodeficiency virus (HIV)-related morbidity and mortality. There remains a need to develop noninvasive predictors of clinical outcomes in persons with HIV/HCV ... Full text Link to item Cite

Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane.

Journal Article Mol Cell Proteomics · November 2020 Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins o ... Full text Link to item Cite

The effect of pathogen inactivation on cryoprecipitate: a functional and quantitative evaluation.

Journal Article Blood transfusion = Trasfusione del sangue · November 2020 BackgroundAs a pooled donor blood product, cryoprecipitate (cryo) carries risks of pathogen transmission. Pathogen inactivation (PI) improves the safety of cryoprecipitate, but its effects on haemostatic properties remain unclear. This study inves ... Full text Cite

Influence of Sex on Platelet Reactivity in Response to Aspirin.

Journal Article J Am Heart Assoc · July 21, 2020 Background There are sex differences in the efficacy and safety of aspirin for the prevention of myocardial infarction and stroke. Whether this is explained by underlying differences in platelet reactivity and aspirin response remains poorly understood. Me ... Full text Link to item Cite

Alzheimer's Risk Factors Age, APOE Genotype, and Sex Drive Distinct Molecular Pathways.

Journal Article Neuron · June 3, 2020 Evidence suggests interplay among the three major risk factors for Alzheimer's disease (AD): age, APOE genotype, and sex. Here, we present comprehensive datasets and analyses of brain transcriptomes and blood metabolomes from human apoE2-, apoE3-, and apoE ... Full text Link to item Cite

Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.

Journal Article J Proteome Res · April 3, 2020 Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method dev ... Full text Link to item Cite

Sex and APOE ε4 genotype modify the Alzheimer's disease serum metabolome.

Journal Article Nat Commun · March 2, 2020 Late-onset Alzheimer's disease (AD) can, in part, be considered a metabolic disease. Besides age, female sex and APOE ε4 genotype represent strong risk factors for AD that also give rise to large metabolic differences. We systematically investigated group- ... Full text Link to item Cite

Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypes.

Journal Article J Affect Disord · March 1, 2020 BACKGROUND: Acylcarnitines have important functions in mitochondrial energetics and β-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profile ... Full text Link to item Cite

More sensitivity is always better: Measuring sub-clinical levels of serum thyroglobulin on a µLC-MS/MS system.

Journal Article Clinical mass spectrometry (Del Mar, Calif.) · January 2020 Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays for thyroglobulin (Tg) are resistant to autoantibody (TgAb) interference, recent studies have demonstrated approximately 40% of TgAb-positive individuals with recurrent thyroid cance ... Full text Cite

International Ring Trial of a High Resolution Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis.

Journal Article Anal Chem · November 19, 2019 A challenge facing metabolomics in the analysis of large human cohorts is the cross-laboratory comparability of quantitative metabolomics measurements. In this study, 14 laboratories analyzed various blood specimens using a common experimental protocol pro ... Full text Link to item Cite

Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts.

Journal Article Sci Data · October 17, 2019 Alzheimer's disease (AD) is the most common cause of dementia. The mechanism of disease development and progression is not well understood, but increasing evidence suggests multifactorial etiology, with a number of genetic, environmental, and aging-related ... Full text Link to item Cite

Pharmacokinetic Analysis of a Novel Human EGFRvIII:CD3 Bispecific Antibody in Plasma and Whole Blood Using a High-Resolution Targeted Mass Spectrometry Approach.

Journal Article J Proteome Res · August 2, 2019 Bispecific single chain antibody fragments (bi-scFv) represent an emerging class of biotherapeutics. We recently developed a fully human bi-scFv (EGFRvIII:CD3 bi-scFv) with the goal of redirecting CD3-expressing T cells to recognize and destroy malignant, ... Full text Link to item Cite

Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring In Vivo Arginine Isotope Incorporation in Alzheimer's Disease Mouse Models.

Journal Article J Am Soc Mass Spectrom · June 2, 2021 Immune-based metabolic reprogramming of arginine utilization in the brain contributes to the neuronal pathology associated with Alzheimer's disease (AD). To enable our long-term goals of differentiation of AD mouse model genotypes, ages, and sexes based on ... Full text Open Access Link to item Cite

A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure.

Journal Article Sci Rep · May 18, 2021 Acute respiratory failure (ARF) requiring mechanical ventilation, a complicating factor in sepsis and other disorders, is associated with high morbidity and mortality. Despite its severity and prevalence, treatment options are limited. In light of accumula ... Full text Link to item Cite

Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.

Journal Article Alzheimers Dement · April 2021 INTRODUCTION: The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age ... Full text Link to item Cite

Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression.

Journal Article Transl Psychiatry · March 2, 2021 Selective serotonin reuptake inhibitors (SSRIs) are the first-line treatment for major depressive disorder (MDD), yet their mechanisms of action are not fully understood and their therapeutic benefit varies among individuals. We used a targeted metabolomic ... Full text Open Access Link to item Cite

APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid.

Journal Article J Alzheimers Dis · 2021 BACKGROUND: APOE4 has been hypothesized to increase Alzheimer's disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear. OBJECTIVE: Characterize cerebrospinal fluid (CSF) proteomic changes related t ... Full text Link to item Cite

Cerebrospinal Fluid Proteome Changes in Older Non-Cardiac Surgical Patients with Postoperative Cognitive Dysfunction.

Journal Article J Alzheimers Dis · 2021 BACKGROUND: Postoperative cognitive dysfunction (POCD), a syndrome of cognitive deficits occurring 1-12 months after surgery primarily in older patients, is associated with poor postoperative outcomes. POCD is hypothesized to result from neuroinflammation; ... Full text Open Access Link to item Cite

Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease.

Journal Article Cell Rep Med · November 17, 2020 Increasing evidence suggests Alzheimer's disease (AD) pathophysiology is influenced by primary and secondary bile acids, the end product of cholesterol metabolism. We analyze 2,114 post-mortem brain transcriptomes and identify genes in the alternative bile ... Full text Link to item Cite

Metabolomic Signature as a Predictor of Liver Disease Events in Patients With HIV/HCV Coinfection.

Journal Article J Infect Dis · November 13, 2020 BACKGROUND: Advanced liver disease due to hepatitis C virus (HCV) is a leading cause of human immunodeficiency virus (HIV)-related morbidity and mortality. There remains a need to develop noninvasive predictors of clinical outcomes in persons with HIV/HCV ... Full text Link to item Cite

Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane.

Journal Article Mol Cell Proteomics · November 2020 Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins o ... Full text Link to item Cite

The effect of pathogen inactivation on cryoprecipitate: a functional and quantitative evaluation.

Journal Article Blood transfusion = Trasfusione del sangue · November 2020 BackgroundAs a pooled donor blood product, cryoprecipitate (cryo) carries risks of pathogen transmission. Pathogen inactivation (PI) improves the safety of cryoprecipitate, but its effects on haemostatic properties remain unclear. This study inves ... Full text Cite

Influence of Sex on Platelet Reactivity in Response to Aspirin.

Journal Article J Am Heart Assoc · July 21, 2020 Background There are sex differences in the efficacy and safety of aspirin for the prevention of myocardial infarction and stroke. Whether this is explained by underlying differences in platelet reactivity and aspirin response remains poorly understood. Me ... Full text Link to item Cite

Alzheimer's Risk Factors Age, APOE Genotype, and Sex Drive Distinct Molecular Pathways.

Journal Article Neuron · June 3, 2020 Evidence suggests interplay among the three major risk factors for Alzheimer's disease (AD): age, APOE genotype, and sex. Here, we present comprehensive datasets and analyses of brain transcriptomes and blood metabolomes from human apoE2-, apoE3-, and apoE ... Full text Link to item Cite

Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.

Journal Article J Proteome Res · April 3, 2020 Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method dev ... Full text Link to item Cite

Sex and APOE ε4 genotype modify the Alzheimer's disease serum metabolome.

Journal Article Nat Commun · March 2, 2020 Late-onset Alzheimer's disease (AD) can, in part, be considered a metabolic disease. Besides age, female sex and APOE ε4 genotype represent strong risk factors for AD that also give rise to large metabolic differences. We systematically investigated group- ... Full text Link to item Cite

Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypes.

Journal Article J Affect Disord · March 1, 2020 BACKGROUND: Acylcarnitines have important functions in mitochondrial energetics and β-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profile ... Full text Link to item Cite

More sensitivity is always better: Measuring sub-clinical levels of serum thyroglobulin on a µLC-MS/MS system.

Journal Article Clinical mass spectrometry (Del Mar, Calif.) · January 2020 Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays for thyroglobulin (Tg) are resistant to autoantibody (TgAb) interference, recent studies have demonstrated approximately 40% of TgAb-positive individuals with recurrent thyroid cance ... Full text Cite

International Ring Trial of a High Resolution Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis.

Journal Article Anal Chem · November 19, 2019 A challenge facing metabolomics in the analysis of large human cohorts is the cross-laboratory comparability of quantitative metabolomics measurements. In this study, 14 laboratories analyzed various blood specimens using a common experimental protocol pro ... Full text Link to item Cite

Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts.

Journal Article Sci Data · October 17, 2019 Alzheimer's disease (AD) is the most common cause of dementia. The mechanism of disease development and progression is not well understood, but increasing evidence suggests multifactorial etiology, with a number of genetic, environmental, and aging-related ... Full text Link to item Cite

Pharmacokinetic Analysis of a Novel Human EGFRvIII:CD3 Bispecific Antibody in Plasma and Whole Blood Using a High-Resolution Targeted Mass Spectrometry Approach.

Journal Article J Proteome Res · August 2, 2019 Bispecific single chain antibody fragments (bi-scFv) represent an emerging class of biotherapeutics. We recently developed a fully human bi-scFv (EGFRvIII:CD3 bi-scFv) with the goal of redirecting CD3-expressing T cells to recognize and destroy malignant, ... Full text Link to item Cite

A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins.

Journal Article Evol Dev · July 2019 A dramatic life history switch that has evolved numerous times in marine invertebrates is the transition from planktotrophic (feeding) to lecithotrophic (nonfeeding) larval development-an evolutionary tradeoff with many important developmental and ecologic ... Full text Open Access Link to item Cite

Kinetic and Cross-Sectional Studies on the Genesis of Hypoargininemia in Severe Pediatric Plasmodium falciparum Malaria.

Journal Article Infect Immun · April 2019 The low bioavailability of nitric oxide (NO) and its precursor, arginine, contributes to the microvascular pathophysiology of severe falciparum malaria. To better characterize the mechanisms underlying hypoargininemia in severe malaria, we measured the pla ... Full text Link to item Cite

Respiratory Phenomics across Multiple Models of Protein Hyperacylation in Cardiac Mitochondria Reveals a Marginal Impact on Bioenergetics.

Journal Article Cell Rep · February 5, 2019 Acyl CoA metabolites derived from the catabolism of carbon fuels can react with lysine residues of mitochondrial proteins, giving rise to a large family of post-translational modifications (PTMs). Mass spectrometry-based detection of thousands of acyl-PTMs ... Full text Link to item Cite

Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome.

Journal Article Alzheimers Dement · January 2019 INTRODUCTION: Increasing evidence suggests a role for the gut microbiome in central nervous system disorders and a specific role for the gut-brain axis in neurodegeneration. Bile acids (BAs), products of cholesterol metabolism and clearance, are produced i ... Full text Open Access Link to item Cite

Pathogen Evasion of Chemokine Response Through Suppression of CXCL10.

Journal Article Front Cell Infect Microbiol · 2019 UNLABELLED: Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on an immune response with well-regulated cytokine signaling. Here we describe a pathogen-mediated mechanism of evading CXCL10, a chemokine with diverse antimicrobial ... Full text Link to item Cite

Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae.

Journal Article NPJ Biofilms Microbiomes · 2019 Nontypeable Haemophilus influenzae (NTHI) is a human-restricted pathogen with an essential requirement for heme-iron acquisition. We previously demonstrated that microevolution of NTHI promotes stationary phase survival in response to transient heme-iron r ... Full text Link to item Cite

Epigenetic silencing of tumor suppressor Par-4 promotes chemoresistance in recurrent breast cancer.

Journal Article J Clin Invest · October 1, 2018 Tumor relapse is the leading cause of death in breast cancer, largely due to the fact that recurrent tumors are frequently resistant to chemotherapy. We previously reported that downregulation of the proapoptotic protein Par-4 promotes tumor recurrence in ... Full text Link to item Cite

Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development.

Journal Article mSphere · September 12, 2018 Nutrient limitation restricts bacterial growth in privileged sites such as the middle ear. Transient heme-iron restriction of nontypeable Haemophilus influenzae (NTHI), the major causative agent of chronic and recurrent otitis media (OM), promotes new and ... Full text Link to item Cite

Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death.

Journal Article Cell Res · June 2018 Cellular senescence is a fundamental cell fate playing a significant role throughout the natural aging process. However, the molecular determinants distinguishing senescence from other cell-cycle arrest states such as quiescence and post-mitotic state, and ... Full text Link to item Cite

Bronchoalveolar Lavage Fluid Proteome in Chronic Lung Allograft Dysfunction

Conference The Journal of Heart and Lung Transplantation · April 2018 Full text Cite

CoA synthase regulates mitotic fidelity via CBP-mediated acetylation.

Conference Nat Commun · March 12, 2018 The temporal activation of kinases and timely ubiquitin-mediated degradation is central to faithful mitosis. Here we present evidence that acetylation controlled by Coenzyme A synthase (COASY) and acetyltransferase CBP constitutes a novel mechanism that en ... Full text Open Access Link to item Cite

Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization.

Journal Article J Proteome Res · February 2, 2018 A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative ... Full text Link to item Cite

Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs.

Journal Article J Proteome Res · February 2, 2018 Calcineurin is a critical cell-signaling protein that orchestrates growth, stress response, virulence, and antifungal drug resistance in several fungal pathogens. Blocking calcineurin signaling increases the efficacy of several currently available antifung ... Full text Link to item Cite

Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma.

Journal Article J Lipid Res · December 2017 As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a comm ... Full text Link to item Cite

Acylation of Superoxide Dismutase 1 (SOD1) at K122 Governs SOD1-Mediated Inhibition of Mitochondrial Respiration.

Journal Article Mol Cell Biol · October 15, 2017 In this study, we employed proteomics to identify mechanisms of posttranslational regulation on cell survival signaling proteins. We focused on Cu-Zn superoxide dismutase (SOD1), which protects cells from oxidative stress. We found that acylation of K122 o ... Full text Link to item Cite

The cholesterol metabolite 27 hydroxycholesterol facilitates breast cancer metastasis through its actions on immune cells.

Journal Article Nat Commun · October 11, 2017 Obesity and elevated circulating cholesterol are risk factors for breast cancer recurrence, while the use of statins, cholesterol biosynthesis inhibitors widely used for treating hypercholesterolemia, is associated with improved disease-free survival. Here ... Full text Link to item Cite

Targeted metabolomics and medication classification data from participants in the ADNI1 cohort.

Journal Article Scientific data · October 2017 Alzheimer's disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute t ... Full text Cite

Metabolic network failures in Alzheimer's disease: A biochemical road map.

Journal Article Alzheimers Dement · September 2017 INTRODUCTION: The Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the d ... Full text Link to item Cite

Impact of 27-hydroxylase (CYP27A1) and 27-hydroxycholesterol in breast cancer.

Journal Article Endocr Relat Cancer · July 2017 The impact of systemic 27-hydroxycholesterol (27HC) and intratumoral CYP27A1 expression on pathobiology and clinical response to statins in breast cancer needs clarification. 27HC is an oxysterol produced from cholesterol by the monooxygenase CYP27A1, whic ... Full text Link to item Cite

SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.

Journal Article Cell Metab · April 4, 2017 Sirtuins are NAD+-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control h ... Full text Link to item Cite

A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation.

Journal Article Cell Metab · April 4, 2017 The mechanisms underlying the formation of acyl protein modifications remain poorly understood. By investigating the reactivity of endogenous acyl-CoA metabolites, we found a class of acyl-CoAs that undergo intramolecular catalysis to form reactive interme ... Full text Link to item Cite

CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer.

Journal Article Cancer Res · April 1, 2017 In this study, we used a bioinformatic approach to identify genes whose expression is dysregulated in human prostate cancers. One of the most dramatically downregulated genes identified encodes CYP27A1, an enzyme involved in regulating cellular cholesterol ... Full text Link to item Cite

Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.

Journal Article EBioMedicine · March 2017 Infection of respiratory mucosa with viral pathogens triggers complex immunologic events in the affected host. We sought to characterize this response through proteomic analysis of nasopharyngeal lavage in human subjects experimentally challenged with infl ... Full text Open Access Link to item Cite

Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis.

Journal Article Sci Adv · March 2017 Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mous ... Full text Open Access Link to item Cite

Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl.

Journal Article J Proteome Res · February 3, 2017 Occupational exposures to the diketone flavoring agent, diacetyl, have been associated with bronchiolitis obliterans, a rare condition of airway fibrosis. Model studies in rodents have suggested that the airway epithelium is a major site of diacetyl toxici ... Full text Link to item Cite

Proteomic analysis of SUMOylation in the post-ischemic brain

Chapter · January 1, 2017 Post-translational protein modification by small ubiquitin-like modifier (SUMO) is increasingly recognized as a key modulator in many cellular processes including DNA repair, cell-cycle regulation, gene transcription, RNA processing, and protein quality co ... Full text Cite

Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection.

Journal Article Sci Rep · September 27, 2016 On Earth, biological systems have evolved in response to environmental stressors, interactions dictated by physical forces that include gravity. The absence of gravity is an extreme stressor and the impact of its absence on biological systems is ill-define ... Full text Open Access Link to item Cite

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).

Journal Article Sci Rep · September 9, 2016 The effects of integrative medicine practices such as meditation and Ayurveda on human physiology are not fully understood. The aim of this study was to identify altered metabolomic profiles following an Ayurveda-based intervention. In the experimental gro ... Full text Link to item Cite

Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories.

Journal Article J Appl Lab Med · September 1, 2016 BACKGROUND: The increasing relevance of individual bile acids quantification in biological samples requires analytical standardization to guarantee robustness and reliability of laboratory results. We have organized the first international ring trial, carr ... Full text Link to item Cite

Fasnall, a Selective FASN Inhibitor, Shows Potent Anti-tumor Activity in the MMTV-Neu Model of HER2(+) Breast Cancer.

Journal Article Cell Chem Biol · June 23, 2016 Many tumors are dependent on de novo fatty acid synthesis to maintain cell growth. Fatty acid synthase (FASN) catalyzes the final synthetic step of this pathway, and its upregulation is correlated with tumor aggressiveness. The consequences and adaptive re ... Full text Link to item Cite

Pleiotrophin regulates the ductular reaction by controlling the migration of cells in liver progenitor niches.

Journal Article Gut · April 2016 OBJECTIVE: The ductular reaction (DR) involves mobilisation of reactive-appearing duct-like cells (RDC) along canals of Hering, and myofibroblastic (MF) differentiation of hepatic stellate cells (HSC) in the space of Disse. Perivascular cells in stem cell ... Full text Open Access Link to item Cite

Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment.

Journal Article Mol Cell Proteomics · March 2016 A thorough understanding of the molecular details of the interactions between bacteria and host are critical to ultimately prevent disease. Recent technological advances allow simultaneous analysis of host and bacterial protein and metabolic profiles from ... Full text Link to item Cite

The Acetyl Group Buffering Action of Carnitine Acetyltransferase Offsets Macronutrient-Induced Lysine Acetylation of Mitochondrial Proteins.

Journal Article Cell Rep · January 12, 2016 Lysine acetylation (AcK), a posttranslational modification wherein a two-carbon acetyl group binds covalently to a lysine residue, occurs prominently on mitochondrial proteins and has been linked to metabolic dysfunction. An emergent theory suggests mitoch ... Full text Link to item Cite

Proteomic Analysis Reveals Significant Epithelial Remodeling After In Vitro Exposure To Diacetyl Vapor

Conference AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE · January 1, 2016 Link to item Cite

Plasma Metabolomics Analysis Identifies Candidate Biomarkers Of Flavoring-Induced Bronchiolitis Obliterans

Conference AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE · January 1, 2016 Link to item Cite

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Journal Article Mol Cell Proteomics · December 2015 Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility ... Full text Link to item Cite

S-Nitrosylation of Sarcomeric Proteins Depresses Myofilament Ca2+)Sensitivity in Intact Cardiomyocytes.

Journal Article Antioxid Redox Signal · November 1, 2015 AIMS: The heart responds to physiological and pathophysiological stress factors by increasing its production of nitric oxide (NO), which reacts with intracellular glutathione to form S-nitrosoglutathione (GSNO), a protein S-nitrosylating agent. Although S- ... Full text Link to item Cite

Transcription errors induce proteotoxic stress and shorten cellular lifespan.

Journal Article Nat Commun · August 25, 2015 Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cel ... Full text Link to item Cite

Cerebrospinal fluid proteomics in children during induction for acute lymphoblastic leukemia: A pilot study.

Journal Article Pediatr Blood Cancer · July 2015 BACKGROUND: Thrombosis in patients with acute lymphocytic leukemia (ALL) can develop after treatment with L-asparaginase (asp) and is often localized to the central nervous system (CNS). We hypothesize that changes in the cerebrospinal fluid (CSF) proteome ... Full text Link to item Cite

Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3ζ via deacetylation of lysines within the 14-3-3ζ binding pocket.

Journal Article J Biol Chem · May 15, 2015 The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines within the 14-3-3ζ binding pocket and protein-protein interface can be modified by acetylation. The ... Full text Link to item Cite

Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.

Journal Article PLoS Genet · April 2015 Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger ... Full text Link to item Cite

Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis.

Journal Article J Proteome Res · February 6, 2015 The proteomic analysis of bronchoalveolar lavage fluid (BALF) can give insight into pulmonary disease pathology and response to therapy. Here, we describe the first gel-free quantitative analysis of BALF in idiopathic pulmonary fibrosis (IPF), a chronic an ... Full text Link to item Cite

Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification.

Journal Article Anal Chem · January 20, 2015 Despite recent advances in analytical and computational chemistry, lipid identification remains a significant challenge in lipidomics. Ion-mobility spectrometry provides an accurate measure of the molecules' rotationally averaged collision cross-section (C ... Full text Link to item Cite

An assessment of human gastric fluid composition as a function of PPI usage.

Journal Article Physiol Rep · January 1, 2015 The standard of care for chronic gastro-esophageal reflux disease (GERD), which affects up to 40% of the population, is the use of drugs such as proton pump inhibitors (PPIs) that block the production of stomach acid. Despite widespread use, the effects of ... Full text Link to item Cite

Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells.

Journal Article PLoS One · 2015 The obligate intracellular bacterium Chlamydia trachomatis is a major human pathogen and a main cause of genital and ocular diseases. During its intracellular cycle, C. trachomatis replicates inside a membrane-bound vacuole termed an "inclusion". Acquisiti ... Full text Open Access Link to item Cite

Convergent transcriptional specializations in the brains of humans and song-learning birds.

Journal Article Science · December 12, 2014 Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and huma ... Full text Open Access Link to item Cite

Metabolic-stress-induced rearrangement of the 14-3-3ζ interactome promotes autophagy via a ULK1- and AMPK-regulated 14-3-3ζ interaction with phosphorylated Atg9.

Journal Article Mol Cell Biol · December 2014 14-3-3ζ promotes cell survival via dynamic interactions with a vast network of binding partners, many of which are involved in stress regulation. We show here that hypoxia (low glucose and oxygen) triggers a rearrangement of the 14-3-3ζ interactome to favo ... Full text Link to item Cite

Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum.

Journal Article J Biol Chem · September 12, 2014 Signal sequence-encoding mRNAs undergo translation-dependent localization to the endoplasmic reticulum (ER) and at the ER are anchored via translation on Sec61-bound ribosomes. Recent investigations into the composition and membrane association characteris ... Full text Link to item Cite

Identification and Quantitation of Coding Variants and Isoforms of Pulmonary Surfactant Protein A.

Journal Article J Proteome Res · August 1, 2014 Pulmonary surfactant protein A (SP-A), a heterooligomer of SP-A1 and SP-A2, is an important regulator of innate immunity of the lung. Nonsynonymous single nucleotide variants of SP-A have been linked to respiratory diseases, but the expressed repertoire of ... Full text Link to item Cite

Direct Solvent Extraction and Analysis of Biomarkers in Dried Blood Spots Using a Flow-Through Autosampler

Chapter · June 30, 2014 A new flow-through autosampler designed to extract biologically important small molecules from dried blood spots (DBS) on filter paper for direct analysis by tandem mass spectrometry is described. The device included a microcomputer to control the timing a ... Full text Cite

Ion mobility derived collision cross sections to support metabolomics applications.

Journal Article Anal Chem · April 15, 2014 Metabolomics is a rapidly evolving analytical approach in life and health sciences. The structural elucidation of the metabolites of interest remains a major analytical challenge in the metabolomics workflow. Here, we investigate the use of ion mobility as ... Full text Link to item Cite

Small ubiquitin-like modifier 3-modified proteome regulated by brain ischemia in novel small ubiquitin-like modifier transgenic mice: putative protective proteins/pathways.

Journal Article Stroke · April 2014 BACKGROUND AND PURPOSE: Small ubiquitin-like modifier (SUMO) conjugation is a post-translational modification associated with many human diseases. Characterization of the SUMO-modified proteome is pivotal to define the mechanistic link between SUMO conjuga ... Full text Open Access Link to item Cite

Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia.

Journal Article J Cereb Blood Flow Metab · March 2014 Ubiquitylation is a posttranslational protein modification that modulates various cellular processes of key significance, including protein degradation and DNA damage repair. In animals subjected to transient cerebral ischemia, ubiquitin-conjugated protein ... Full text Open Access Link to item Cite

Proteomic differences between male and female anterior cruciate ligament and patellar tendon.

Journal Article PLoS One · 2014 The risk of anterior cruciate ligament (ACL) injury and re-injury is greater for women than men. Among other factors, compositional differences may play a role in this differential risk. Patellar tendon (PT) autografts are commonly used during reconstructi ... Full text Link to item Cite

Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.

Journal Article PLoS One · 2014 The molecular differences between ischemic (IF) and non-ischemic (NIF) heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart fail ... Full text Open Access Link to item Cite

A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

Journal Article BMC Bioinformatics · December 16, 2013 BACKGROUND: The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, a ... Full text Open Access Link to item Cite

Proteomic analysis of the NOS2 interactome in human airway epithelial cells.

Journal Article Nitric Oxide · November 1, 2013 The cytokine-inducible isoform of nitric oxide synthase (NOS2) is constitutively expressed in human respiratory epithelia and is upregulated in inflammatory lung disease. Here, we sought to better define the protein interactions that may be important for N ... Full text Link to item Cite

Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase.

Journal Article J Proteome Res · October 4, 2013 Alzheimer's disease (AD) is a complex neurodegenerative process that involves altered brain immune, neuronal and metabolic functions. Understanding the underlying mechanisms has relied on mouse models that mimic components of AD pathology. We used gel-free ... Full text Link to item Cite

Solid-phase capture for the detection and relative quantification of S-nitrosoproteins by mass spectrometry.

Journal Article Methods · August 1, 2013 The proteomic analysis of S-nitrosylated protein (SNO-proteins) has long depended on the biotin switch technique (BST), which requires blocking of free thiols, ascorbate-based denitrosylation of SNO-Cys, biotinylation of nascent thiol and avidin-based affi ... Full text Link to item Cite

An integrated clinico-metabolomic model improves prediction of death in sepsis.

Journal Article Sci Transl Med · July 24, 2013 Sepsis is a common cause of death, but outcomes in individual patients are difficult to predict. Elucidating the molecular processes that differ between sepsis patients who survive and those who die may permit more appropriate treatments to be deployed. We ... Full text Link to item Cite

Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration.

Journal Article J Proteome Res · June 7, 2013 Visual signal transduction takes place on the surface of flat membrane vesicles called photoreceptor discs, which reside inside the light-sensitive outer segment organelle of vertebrate photoreceptor cells. Although biochemical studies have indicated that ... Full text Link to item Cite

Latent protein trees

Journal Article Annals of Applied Statistics · June 1, 2013 Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated intensities for each sa ... Full text Open Access Cite

Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure.

Journal Article J Proteome Res · May 3, 2013 The analysis of airway fluid, as sampled by bronchoalveolar lavage (BAL), provides a minimally invasive route to interrogate lung biology in health and disease. Here, we used immunodepletion, coupled with gel- and label-free LC-MS/MS, for quantitation of t ... Full text Link to item Cite

Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics.

Journal Article Journal of biomolecular techniques : JBT · April 2013 An automated phosphopeptide enrichment strategy is described using titanium dioxide (TiO2)-packed, fused silica capillaries for use with liquid chromatography (LC)-mass spectrometry (MS)/MS-based, label-free proteomics workflows. To correlate an optimum pe ... Full text Cite

NADPH:quinone oxidoreductase 1 regulates host susceptibility to ozone via isoprostane generation.

Journal Article J Biol Chem · February 15, 2013 NADPH:quinone oxidoreductase 1 (NQO1) is recognized as a major susceptibility gene for ozone-induced pulmonary toxicity. In the absence of NQO1 as can occur by genetic mutation, the human airway is protected from harmful effects of ozone. We recently repor ... Full text Link to item Cite

Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes.

Journal Article J Proteome Res · February 1, 2013 Many insect groups have coevolved with bacterial endosymbionts that live within specialized host cells. As a salient example, ants in the tribe Camponotini rely on Blochmannia, an intracellular bacterial mutualist that synthesizes amino acids and recycles ... Full text Link to item Cite

Proteomic analysis of ERK1/2-mediated human sickle red blood cell membrane protein phosphorylation.

Journal Article Clin Proteomics · January 3, 2013 BACKGROUND: In sickle cell disease (SCD), the mitogen-activated protein kinase (MAPK) ERK1/2 is constitutively active and can be inducible by agonist-stimulation only in sickle but not in normal human red blood cells (RBCs). ERK1/2 is involved in activatio ... Full text Open Access Link to item Cite

Proteomic Analysis Of Human Bronchoalveolar Lavage Fluid After Subsegmental Challenge

Journal Article AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE · 2013 Cite

Identification of deacetylase substrates with the biotin switch approach.

Journal Article Methods Mol Biol · 2013 The identification of lysine-acetylated proteins and deacetylase substrates has primarily relied on protein immune-affinity techniques with antibodies that recognize acetylated lysine residues (Kac antibodies). While these antibody-based techniques are con ... Full text Link to item Cite

Plasma proteomics of patients with non-valvular atrial fibrillation on chronic anti-coagulation with warfarin or a direct factor Xa inhibitor.

Journal Article Thromb Haemost · December 2012 Plasma proteins mediate thrombogenesis, inflammation, endocardial injury and structural remodelling in atrial fibrillation (AF). We hypothesised that anti-coagulation with rivaroxaban, a direct factor Xa inhibitor, would differentially modulate biologicall ... Full text Link to item Cite

Extraction and analysis of carnitine and acylcarnitines by electrospray ionization tandem mass spectrometry directly from dried blood and plasma spots using a novel autosampler.

Journal Article Rapid Commun Mass Spectrom · November 15, 2012 RATIONALE: Acylcarnitines are routinely analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS) both in clinical diagnostic and public health newborn screening laboratories from plasma and dried whole blood spots (DBS) on filter paper. The ... Full text Link to item Cite

Design and application of a data-independent precursor and product ion repository.

Journal Article J Am Soc Mass Spectrom · October 2012 The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results ... Full text Link to item Cite

Hierarchical factor modeling of proteomics data

Journal Article 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 · May 8, 2012 This paper presents a hierarchical bayesian factor model specifically designed to model the known correlation structure of both peptides and proteins in unbiased, label free proteomics. The model utilizes partial identification information from peptide seq ... Full text Cite

Metaprotein expression modeling for label-free quantitative proteomics.

Journal Article BMC Bioinformatics · May 4, 2012 BACKGROUND: Label-free quantitative proteomics holds a great deal of promise for the future study of both medicine and biology. However, the data generated is extremely intricate in its correlation structure, and its proper analysis is complex. There are i ... Full text Link to item Cite

The protein expression landscape of the Arabidopsis root.

Journal Article Proc Natl Acad Sci U S A · May 1, 2012 Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root pro ... Full text Link to item Cite

Proteomic characterization of the cellular response to nitrosative stress mediated by s-nitrosoglutathione reductase inhibition.

Journal Article J Proteome Res · April 6, 2012 The S-nitrosoglutathione-metabolizing enzyme, GSNO reductase (GSNOR), has emerged as an important regulator of protein S-nitrosylation. GSNOR ablation is protective in models of asthma and heart failure, raising the idea that GSNOR inhibitors might hold th ... Full text Link to item Cite

Proteomics of Preeclamptic Placenta

Journal Article REPRODUCTIVE SCIENCES · March 1, 2012 Link to item Cite

Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics.

Journal Article J Proteome Res · February 3, 2012 Transient cerebral ischemia dramatically activates small ubiquitin-like modifier (SUMO2/3) conjugation. In cells exposed to 6 h of transient oxygen/glucose deprivation (OGD), a model of ischemia, SUMOylation increases profoundly between 0 and 30 min follow ... Full text Open Access Link to item Cite

Erythrocyte plasma membrane-bound ERK1/2 activation promotes ICAM-4-mediated sickle red cell adhesion to endothelium.

Journal Article Blood · February 2, 2012 The core pathology of sickle cell disease (SCD) starts with the erythrocyte (RBC). Aberration in MAPK/ERK1/2 signaling, which can regulate cell adhesion, occurs in diverse pathologies. Because RBCs contain abundant ERK1/2, we predicted that ERK1/2 is funct ... Full text Link to item Cite

Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms.

Journal Article Mol Microbiol · December 2011 Chlamydia trachomatis is an obligate intracellular pathogen responsible for ocular and genital infections of significant public health importance. C. trachomatis undergoes a biphasic developmental cycle alternating between two distinct forms: the infectiou ... Full text Link to item Cite

Staphylococcus aureus sortase A contributes to the Trojan horse mechanism of immune defense evasion with its intrinsic resistance to Cys184 oxidation.

Journal Article Biochemistry · September 6, 2011 Staphylococcus aureus is a Gram-positive bacterial pathogen that causes serious infections which have become increasingly difficult to treat due to antimicrobial resistance and natural virulence strategies. Bacterial sortase enzymes are important virulence ... Full text Link to item Cite

A biotin switch-based proteomics approach identifies 14-3-3ζ as a target of Sirt1 in the metabolic regulation of caspase-2.

Journal Article Mol Cell · September 2, 2011 While lysine acetylation in the nucleus is well characterized, comparatively little is known about its significance in cytoplasmic signaling. Here we show that inhibition of the Sirt1 deacetylase, which is primarily cytoplasmic in cancer cell lines, sensit ... Full text Link to item Cite

High predictive accuracy of an unbiased proteomic profile for sustained virologic response in chronic hepatitis C patients.

Journal Article Hepatology · June 2011 UNLABELLED: Chronic hepatitis C (CHC) infection is a leading cause of endstage liver disease. Current standard-of-care (SOC) interferon-based therapy results in sustained virological response (SVR) in only one-half of patients, and is associated with signi ... Full text Link to item Cite

Quantitative label-free phosphoproteomics strategy for multifaceted experimental designs.

Journal Article Anal Chem · May 15, 2011 Protein phosphorylation is a critical regulator of signaling in nearly all eukaryotic cellular pathways and dysregulated phosphorylation has been implicated in an array of diseases. The majority of MS-based quantitative phosphorylation studies are currentl ... Full text Link to item Cite

Abstract 4697: Metabolic regulation of caspase-2

Journal Article Cancer Research · April 15, 2011 AbstractCaspase-2 has been shown to act as an apical caspase, upstream of cytochrome c release, in a variety of cell death settings including chemotherapy-induced apoptosis. However, the mechanism governing ... Full text Cite

Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells.

Journal Article Mol Cell Proteomics · March 2011 The retina is a highly ordered tissue whose outermost layers are formed by subcellular compartments of photoreceptors generating light-evoked electrical responses. We studied protein distributions among individual photoreceptor compartments by separating t ... Full text Link to item Cite

Site-specific analysis of protein S-acylation by resin-assisted capture.

Journal Article J Lipid Res · February 2011 Protein S-acylation is a major posttranslational modification whereby a cysteine thiol is converted to a thioester. A prototype is S-palmitoylation (fatty acylation), in which a protein undergoes acylation with a hydrophobic 16 carbon lipid chain. Although ... Full text Link to item Cite

Association of calcineurin with the COPI protein Sec28 and the COPII protein Sec13 revealed by quantitative proteomics.

Journal Article PLoS One · 2011 Calcineurin is a calcium-calmodulin-dependent serine/threonine specific protein phosphatase operating in key cellular processes governing responses to extracellular cues. Calcineurin is essential for growth at high temperature and virulence of the human fu ... Full text Link to item Cite

Characterization of serum proteins associated with IL28B genotype among patients with chronic hepatitis C.

Journal Article PLoS One · 2011 INTRODUCTION: Polymorphisms near the IL28B gene (e.g. rs12979860) encoding interferon λ3 have recently been associated with both spontaneous clearance and treatment response to pegIFN/RBV in chronic hepatitis C (CHC) patients. The molecular consequences of ... Full text Link to item Cite

A Proteomic Investigation Of GSNOR-Regulated Pathways In Cytokine-Stimulated Mouse Alveolar Macrophages

Conference AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE · January 1, 2011 Link to item Cite

Survival defects of Cryptococcus neoformans mutants exposed to human cerebrospinal fluid result in attenuated virulence in an experimental model of meningitis.

Journal Article Infect Immun · October 2010 Cryptococcus neoformans is a fungal pathogen that encounters various microenvironments during growth in the mammalian host, including intracellular vacuoles, blood, and cerebrospinal fluid (CSF). Because the CSF is isolated by the blood-brain barrier, we h ... Full text Link to item Cite

Identification of S-nitrosylated targets of thioredoxin using a quantitative proteomic approach.

Journal Article Biochemistry · August 17, 2010 Reversible protein cysteine nitrosylation (S-nitrosylation) is a common mechanism utilized in signal transduction and other diverse cellular processes. Protein denitrosylation is largely mediated by cysteine denitrosylases, but the functional scope and sig ... Full text Open Access Link to item Cite

Kinetic characterization of Salmonella FliK-FlhB interactions demonstrates complexity of the Type III secretion substrate-specificity switch.

Journal Article Biochemistry · August 3, 2010 The bacterial flagellum is a complex macromolecular machine consisting of more than 20 000 proteins, most of which must be exported from the cell via a dedicated Type III secretion apparatus. At a defined point in flagellar morphogenesis, hook completion i ... Full text Open Access Link to item Cite

Mass spectrometry-based thermal shift assay for protein-ligand binding analysis.

Journal Article Anal Chem · July 1, 2010 Described here is a mass spectrometry-based screening assay for the detection of protein-ligand binding interactions in multicomponent protein mixtures. The assay utilizes an oxidation labeling protocol that involves using hydrogen peroxide to selectively ... Full text Open Access Link to item Cite

Resistance to ErbB2 tyrosine kinase inhibitors in breast cancer is mediated by calcium-dependent activation of RelA.

Journal Article Mol Cancer Ther · February 2010 The widespread clinical use of therapies targeting the ErbB2 receptor tyrosine kinase oncogene represents a significant advance in breast cancer treatment. However, the development of therapeutic resistance represents a dilemma limiting their clinical effi ... Full text Link to item Cite

Hydrodynamic chromatography for the size classification of micron and sub-micron sized packing materials.

Journal Article J Chromatogr A · November 6, 2009 Hydrodynamic chromatography (HDC) was used as a size classification and purification method for porous bridged ethyl hybrid (BEH) packing materials (particles) in the micron to sub-micron range. Using packed column HDC, a batch of particles with size 0.76+ ... Full text Link to item Cite

Restraint of apoptosis during mitosis through interdomain phosphorylation of caspase-2.

Journal Article EMBO J · October 21, 2009 The apoptotic initiator caspase-2 has been implicated in oocyte death, in DNA damage- and heat shock-induced death, and in mitotic catastrophe. We show here that the mitosis-promoting kinase, cdk1-cyclin B1, suppresses apoptosis upstream of mitochondrial c ... Full text Link to item Cite

Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture.

Journal Article Nat Biotechnol · June 2009 We have modified the biotin switch assay for protein S-nitrosothiols (SNOs), using resin-assisted capture (SNO-RAC). Compared with existing methodologies, SNO-RAC requires fewer steps, detects high-mass S-nitrosylated proteins more efficiently, and facilit ... Full text Link to item Cite

Capillary-based instrument for the simultaneous measurement of solution viscosity and solute diffusion coefficient at pressures up to 2000 bar and implications for ultrahigh pressure liquid chromatography

Journal Article Analytical Chemistry · April 15, 2009 An instrument based on the Poiseuille flow principle capable of measuring solution viscosities at high pressures has been modified to observe UV-absorbent analytes in order to allow for the simultaneous measurement of analyte diffusivity. A capillary time- ... Full text Cite

Viscosity measurements of methanol-water and acetonitrile-water mixtures at pressures up to 3500 bar using a novel capillary time-of-flight viscometer.

Journal Article J Chromatogr A · November 17, 2006 A new type of viscometer based on the Poiseuille flow principle has been developed that is capable of measuring solution viscosities at ultrahigh pressures. The capillary time-of-flight (CTOF) viscometer has been used to measure the viscosity of methanol-w ... Full text Link to item Cite

Recent advances in ultrahigh-pressure liquid chromatography

Journal Article LCGC North America · January 1, 2006 Ultrahigh-pressure liquid chromatography (UHPLC) is a technique that is experiencing continued growth due to the benefits in separation power and speed of analysis over traditional HPLC. We attempt here to give an overview of some of the advances that have ... Cite

Linear velocity surge caused by mobile-phase compression as a source of band broadening in isocratic ultrahigh-pressure liquid chromatography

Journal Article Analytical Chemistry · October 1, 2005 A linear velocity surge caused by mobile-phase compression was investigated as a source of band broadening for ultrahigh-pressure liquid chromatography (UHPLC). To measure the effect of compression on mobile-phase velocity, ionic sample fronts were monitor ... Full text Cite

Investigation of electrospray ionization and electrostatic focusing devices using a three-dimensional electrospray current density profiler

Journal Article Journal of the American Society for Mass Spectrometry · March 1, 2005 A novel instrument for profiling the current density of nanoelectrospray ionization plumes in three dimensions has been developed. A hemispherically- shaped electrostatic lens at atmospheric pressure is found to be able to compress the space-charge in nano ... Full text Cite