35 results on '"Pham U"'
Search Results
2. Impulsivity in Parkinson’s disease patients treated with subthalamic nucleus deep brain stimulation—An exploratory study
- Author
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Pham, U., primary, Skogseid, I. M., additional, Pripp, A. H., additional, Bøen, E., additional, and Toft, M., additional
- Published
- 2021
- Full Text
- View/download PDF
3. Identification and quantitation of intact β-endorphin by LC-MS-MS: 94
- Author
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Shaw, P. N., Hewavitharana, A. K., Cabot, P. J., and Pham, U.
- Published
- 2006
4. Outcomes after adrenalectomy for unilateral primary aldosteronism: an international consensus on outcome measures and analysis of remission rates in an international cohort
- Author
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Williams, T.A., Lenders, J.W.M., Mulatero, P., Burrello, J., Rottenkolber, M., Adolf, C., Satoh, F., Amar, L., Quinkler, M., Deinum, J., Beuschlein, F., Kitamoto, K.K., Pham, U., Morimoto, R., Umakoshi, H., Prejbisz, A., Kocjan, T., Naruse, M., Stowasser, M., Nishikawa, T., Young, W.F., Jr., Gomez-Sanchez, C.E., Funder, J.W., Reincke, M., Williams, T.A., Lenders, J.W.M., Mulatero, P., Burrello, J., Rottenkolber, M., Adolf, C., Satoh, F., Amar, L., Quinkler, M., Deinum, J., Beuschlein, F., Kitamoto, K.K., Pham, U., Morimoto, R., Umakoshi, H., Prejbisz, A., Kocjan, T., Naruse, M., Stowasser, M., Nishikawa, T., Young, W.F., Jr., Gomez-Sanchez, C.E., Funder, J.W., and Reincke, M.
- Abstract
Item does not contain fulltext, BACKGROUND: Although unilateral primary aldosteronism is the most common surgically correctable cause of hypertension, no standard criteria exist to classify surgical outcomes. We aimed to create consensus criteria for clinical and biochemical outcomes and follow-up of adrenalectomy for unilateral primary aldosteronism and apply these criteria to an international cohort to analyse the frequency of remission and identify preoperative determinants of successful outcome. METHODS: The Primary Aldosteronism Surgical Outcome (PASO) study was an international project to develop consensus criteria for outcomes and follow-up of adrenalectomy for unilateral primary aldosteronism. An international panel of 31 experts from 28 centres, including six endocrine surgeons, used the Delphi method to reach consensus. We then retrospectively analysed follow-up data from prospective cohorts for outcome assessment of patients diagnosed with unilateral primary aldosteronism by adrenal venous sampling who had undergone a total adrenalectomy, consecutively included from 12 referral centres in nine countries. On the basis of standardised criteria, we determined the proportions of patients achieving complete, partial, or absent clinical and biochemical success in accordance with the consensus. We then used logistic regression analyses to identify preoperative factors associated with clinical and biochemical outcomes. FINDINGS: Consensus was reached for criteria for six outcomes (complete, partial, and absent success of clinical and biochemical outcomes) based on blood pressure, use of antihypertensive drugs, plasma potassium and aldosterone concentrations, and plasma renin concentrations or activities. Consensus was also reached for two recommendations for the timing of follow-up assessment. For the international cohort analysis, we analysed clinical data from 705 patients recruited between 1994 and 2015, of whom 699 also had biochemical data. Complete clinical success was achieved in 259 (37
- Published
- 2017
5. SYNTHESIS OF CALCIUM AND ALUMINUM OXIDES FROM SOLUTION OF PHOSPHATES ON LASER ABLATION OF POROUS SAMPLES
- Author
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Trinh Ngoc Hoang, M.P. Patapovich, Le Thi Kim Anh, Pham Uyen Thi, and A.P. Zajogin
- Subjects
pulsed laser sputtering ,surface laser plasma ,laser spark spectrometry ,metal oxides ,double laser pulses ,Physical and theoretical chemistry ,QD450-801 - Abstract
The spectroscopic investigations of the surface laser plasma formed close to the porous body containing nanoquantities of different calcium and aluminum salts under the effect of two successive laser pulses were performed. The possibility for the development of methods to obtain the nanoclusters of metal oxides was demonstrated. Depending on the concentration of the starting metals in the solutions used, one can vary both the quantity and composition of the metal oxide clusters.
- Published
- 2012
6. Location-biased β-arrestin conformations direct GPCR signaling.
- Author
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Pham U, Chundi A, Stępniewski TM, Darbha S, Eiger DS, Gazula S, Gardner J, Hicks C, Selent J, and Rajagopal S
- Abstract
β-arrestins are multifunctional intracellular proteins that regulate the desensitization, internalization and signaling of over 800 different G protein-coupled receptors (GPCRs) and interact with a diverse array of cellular partners
1,2 . Beyond the plasma membrane, GPCRs can initiate unique signaling cascades from various subcellular locations, a phenomenon known as "location bias"3,4 . Here, we investigate how β-arrestins direct location-biased signaling of the angiotensin II type I receptor (AT1R). Using novel bioluminescence resonance energy transfer (BRET) conformational biosensors and extracellular signal-regulated kinase (ERK) activity reporters, we reveal that in response to the endogenous agonist Angiotensin II and the β-arrestin-biased agonist TRV023, β-arrestin 1 and β-arrestin 2 adopt distinct conformations across different subcellular locations, which are intricately linked to differential ERK activation profiles. We also uncover a population of receptor-free catalytically activated β-arrestins in the plasma membrane that exhibits insensitivity to different agonists and promotes ERK activation on the plasma membrane independent of G proteins. These findings deepen our understanding of GPCR signaling complexity and also highlight the nuanced roles of β-arrestins beyond traditional G protein pathways., Competing Interests: DECLARATION OF INTERESTS The authors declare no competing interests.- Published
- 2024
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7. Phosphorylation patterns in the AT1R C-terminal tail specify distinct downstream signaling pathways.
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Gareri C, Pfeiffer CT, Jiang X, Paulo JA, Gygi SP, Pham U, Chundi A, Wingler LM, Staus DP, Stepniewski TM, Selent J, Lucero EY, Grogan A, Rajagopal S, and Rockman HA
- Subjects
- Phosphorylation, Humans, HEK293 Cells, Molecular Dynamics Simulation, Angiotensin II metabolism, Receptor, Angiotensin, Type 1 metabolism, Receptor, Angiotensin, Type 1 chemistry, Receptor, Angiotensin, Type 1 genetics, Signal Transduction, beta-Arrestins metabolism, beta-Arrestins genetics
- Abstract
Different ligands stabilize specific conformations of the angiotensin II type 1 receptor (AT1R) that direct distinct signaling cascades mediated by heterotrimeric G proteins or β-arrestin. These different active conformations are thought to engage distinct intracellular transducers because of differential phosphorylation patterns in the receptor C-terminal tail (the "barcode" hypothesis). Here, we identified the AT1R barcodes for the endogenous agonist AngII, which stimulates both G protein activation and β-arrestin recruitment, and for a synthetic biased agonist that only stimulates β-arrestin recruitment. The endogenous and β-arrestin-biased agonists induced two different ensembles of phosphorylation sites along the C-terminal tail. The phosphorylation of eight serine and threonine residues in the proximal and middle portions of the tail was required for full β-arrestin functionality, whereas phosphorylation of the serine and threonine residues in the distal portion of the tail had little influence on β-arrestin function. Similarly, molecular dynamics simulations showed that the proximal and middle clusters of phosphorylated residues were critical for stable β-arrestin-receptor interactions. These findings demonstrate that ligands that stabilize different receptor conformations induce different phosphorylation clusters in the C-terminal tail as barcodes to evoke distinct receptor-transducer engagement, receptor trafficking, and signaling.
- Published
- 2024
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8. GPCR kinases differentially modulate biased signaling downstream of CXCR3 depending on their subcellular localization.
- Author
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Gardner J, Eiger DS, Hicks C, Choi I, Pham U, Chundi A, Namjoshi O, and Rajagopal S
- Subjects
- Ligands, Phosphorylation, Receptors, G-Protein-Coupled metabolism, beta-Arrestins metabolism, Signal Transduction physiology, G-Protein-Coupled Receptor Kinases genetics, G-Protein-Coupled Receptor Kinases metabolism
- Abstract
Some G protein-coupled receptors (GPCRs) demonstrate biased signaling such that ligands of the same receptor exclusively or preferentially activate certain downstream signaling pathways over others. This phenomenon may result from ligand-specific receptor phosphorylation by GPCR kinases (GRKs). GPCR signaling can also exhibit location bias because GPCRs traffic to and signal from subcellular compartments in addition to the plasma membrane. Here, we investigated whether GRKs contributed to location bias in GPCR signaling. GRKs translocated to endosomes after stimulation of the chemokine receptor CXCR3 or other GPCRs in cultured cells. GRK2, GRK3, GRK5, and GRK6 showed distinct patterns of recruitment to the plasma membrane and to endosomes depending on the identity of the biased ligand used to activate CXCR3. Analysis of engineered forms of GRKs that localized to either the plasma membrane or endosomes demonstrated that biased CXCR3 ligands elicited different signaling profiles that depended on the subcellular location of the GRK. Each GRK exerted a distinct effect on the regulation of CXCR3 engagement of β-arrestin, internalization, and activation of the downstream effector kinase ERK. Our work highlights a role for GRKs in location-biased GPCR signaling and demonstrates the complex interactions between ligands, GRKs, and cellular location that contribute to biased signaling.
- Published
- 2024
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9. ACKR3 Proximity Labeling Identifies Novel G protein- and β-arrestin-independent GPCR Interacting Proteins.
- Author
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Hicks C, Gardner J, Eiger DS, Camarda ND, Pham U, Dhar S, Rodriguez H, Chundi A, and Rajagopal S
- Abstract
The canonical paradigm of GPCR signaling recognizes G proteins and β-arrestins as the two primary transducers that promote GPCR signaling. Recent evidence suggests the atypical chemokine receptor 3 (ACKR3) does not couple to G proteins, and β-arrestins are dispensable for some of its functions. Here, we employed proximity labeling to identify proteins that interact with ACKR3 in cells devoid of β-arrestin. We identified proteins involved in the endocytic machinery and evaluated a subset of proteins conserved across several GPCR-based proximity labeling experiments. We discovered that the bone morphogenic protein 2-inducible kinase (BMP2K) interacts with many different GPCRs with varying dependency on β-arrestin. Together, our work highlights the existence of modulators that can act independently of G proteins and β-arrestins to regulate GPCR signaling and provides important evidence for other targets that may regulate GPCR signaling., Competing Interests: DISCLOSURES None.
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- 2024
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10. Location bias: A "Hidden Variable" in GPCR pharmacology.
- Author
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Eiger DS, Hicks C, Gardner J, Pham U, and Rajagopal S
- Abstract
G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors and primarily signal through two main effector proteins: G proteins and β-arrestins. Many agonists of GPCRs promote "biased" responses, in which different cellular signaling pathways are activated with varying efficacies. The mechanisms underlying biased signaling have not been fully elucidated, with many potential "hidden variables" that regulate this behavior. One contributor is "location bias," which refers to the generation of unique signaling cascades from a given GPCR depending upon the cellular location at which the receptor is signaling. Here, we review evidence that GPCRs are expressed at and traffic to various subcellular locations and discuss how location bias can impact the pharmacologic properties and characterization of GPCR agonists. We also evaluate how differences in subcellular environments can modulate GPCR signaling, highlight the physiological significance of subcellular GPCR signaling, and discuss the therapeutic potential of exploiting GPCR location bias., (© 2023 Wiley Periodicals LLC.)
- Published
- 2023
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11. High-Intensity Interval Training is Safe, Feasible and Efficacious in Nonalcoholic Steatohepatitis: A Randomized Controlled Trial.
- Author
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Keating SE, Croci I, Wallen MP, Cox ER, Thuzar M, Pham U, Mielke GI, Coombes JS, Macdonald GA, and Hickman IJ
- Subjects
- Humans, Male, Female, Australia, Exercise physiology, Insulin Resistance, Non-alcoholic Fatty Liver Disease therapy, High-Intensity Interval Training
- Abstract
Background: High-Intensity Interval Training (HIIT) involves bursts of high-intensity exercise interspersed with lower-intensity exercise recovery. HIIT may benefit cardiometabolic health in people with nonalcoholic steatohepatitis (NASH)., Aims: We aimed to examine the safety, feasibility, and efficacy of 12-weeks of supervised HIIT compared with a sham-exercise control (CON) for improving aerobic fitness and peripheral insulin sensitivity in biopsy-proven NASH., Methods: Participants based in the community [(n = 14, 56 ± 10 years, BMI 39.2 ± 6.7 kg/m
2 , 64% male), NAFLD Activity Score 5 (range 3-7)] were randomized to 12-weeks of supervised HIIT (n = 8, 4 × 4 min at 85-95% maximal heart rate, interspersed with 3 min active recovery; 3 days/week) or CON (n = 6, stretching; 3 days/week). Safety (adverse events) and feasibility determined as ≥ 70% program completion and ≥ 70% global adherence (including session attendance, interval intensity adherence, and duration adherence) were assessed. Changes in cardiorespiratory fitness (V̇O2 peak), exercise capacity (time-on-test) and peripheral insulin sensitivity (euglycemic hyperinsulinemic clamp) were assessed. Data were analysed using ANCOVA with baseline value as the covariate., Results: There were no HIIT-related adverse events and HIIT was globally feasible [program completion 75%, global adherence 100% (including adherence to session 95.4 ± 7.3%, interval intensity 95.3 ± 6.0% and duration 96.8 ± 2.4%)]. A large between-group effect was observed for exercise capacity [mean difference 134.2 s (95% CI 19.8, 248.6 s), ƞ2 0.44, p = 0.03], improving in HIIT (106.2 ± 97.5 s) but not CON (- 33.4 ± 43.3 s), and for peripheral insulin sensitivity [mean difference 3.4 mg/KgLegFFM/min (95% CI 0.9,6.8 mg/KgLegFFM/min), ƞ2 0.32, p = 0.046], improving in HIIT (1.0 ± 0.8 mg/KgLegFFM/min) but not CON (- 3.1 ± 1.2 mg/KgLegFFM/min)., Conclusions: HIIT is safe, feasible and efficacious for improving exercise capacity and peripheral insulin sensitivity in people with NASH., Clinical Trial Registration Number: Australian New Zealand Clinical Trial Registry (anzctr.org.au) identifier ACTRN12616000305426 (09/03/2016)., (© 2022. The Author(s).)- Published
- 2023
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12. Location bias contributes to functionally selective responses of biased CXCR3 agonists.
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Eiger DS, Boldizsar N, Honeycutt CC, Gardner J, Kirchner S, Hicks C, Choi I, Pham U, Zheng K, Warman A, Smith JS, Zhang JY, and Rajagopal S
- Subjects
- Animals, Chemokines metabolism, Ligands, Mice, Receptors, G-Protein-Coupled metabolism, beta-Arrestins metabolism, GTP-Binding Proteins metabolism, Receptors, CXCR3 genetics, Receptors, CXCR3 metabolism
- Abstract
Some G protein-coupled receptor (GPCR) ligands act as "biased agonists" that preferentially activate specific signaling transducers over others. Although GPCRs are primarily found at the plasma membrane, GPCRs can traffic to and signal from many subcellular compartments. Here, we determine that differential subcellular signaling contributes to the biased signaling generated by three endogenous ligands of the GPCR CXC chemokine receptor 3 (CXCR3). The signaling profile of CXCR3 changes as it traffics from the plasma membrane to endosomes in a ligand-specific manner. Endosomal signaling is critical for biased activation of G proteins, β-arrestins, and extracellular-signal-regulated kinase (ERK). In CD8 + T cells, the chemokines promote unique transcriptional responses predicted to regulate inflammatory pathways. In a mouse model of contact hypersensitivity, β-arrestin-biased CXCR3-mediated inflammation is dependent on receptor internalization. Our work demonstrates that differential subcellular signaling is critical to the overall biased response observed at CXCR3, which has important implications for drugs targeting chemokine receptors and other GPCRs., (© 2022. The Author(s).)
- Published
- 2022
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13. Clinical Characteristics and Implications of Bradycardia in COVID-19 Patients Treated with Remdesivir: A Single-Center Retrospective Cohort Study.
- Author
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Schreiber A, Bauzon JS, Batra K, Mohammed S, Lee K, Houshmand N, Pham U, Cosme C, Inciong K, Al-Taweel O, Nasser K, Rana J, Sossou C, Go A, Hawwass D, Diep J, and Ahsan CH
- Subjects
- Adenosine Monophosphate analogs & derivatives, Adult, Aged, Alanine adverse effects, Alanine analogs & derivatives, Antiviral Agents adverse effects, Bradycardia chemically induced, Bradycardia drug therapy, Bradycardia epidemiology, Humans, Male, Middle Aged, Retrospective Studies, SARS-CoV-2, COVID-19 Drug Treatment
- Abstract
Background and Objectives: Remdesivir is an antiviral drug used to treat coronavirus disease 2019 (COVID-19) with a relatively obscure cardiac effect profile. Previous studies have reported bradycardia associated with remdesivir, but few have examined its clinical characteristics. The objective of this study was to investigate remdesivir associated bradycardia and its associated clinical characteristics and outcomes., Methods: This is a single-institution retrospective study that investigated bradycardia in 600 patients who received remdesivir for treatment of COVID-19. A total of 375 patients were included in the study after screening for other known causes of bradycardia (atrioventricular [AV] nodal blockers). All patients were analyzed for episodes of bradycardia from when remdesivir was initiated up to 5 days after completion, a time frame based on the drug's putative elimination half-life. Univariate and multivariate statistical tests were conducted to analyze the data., Results: The mean age of the sample was 56.63 ± 13.23 years. Of patients who met inclusion criteria, 49% were found to have bradycardia within 5 days of remdesivir administration. Compared to the cohort without a documented bradycardic episode, patients with bradycardia were significantly more likely to experience inpatient mortality (22% vs 12%, p = 0.01). The patients with bradycardia were found to have marginally higher serum D-dimer levels (5.2 vs 3.4 µg/mL, p = 0.05) and were more likely to undergo endotracheal intubation (28% vs 14%, p = 0.008). Male sex, hyperlipidemia, and bradycardia within 5 days of completing remdesivir were significant predictors of inpatient mortality. No significant differences in length of stay were found., Conclusions: Bradycardia that occurs during or shortly after remdesivir treatment in COVID-19 patients may be associated with an increased rate of in-hospital mortality. However, COVID-19 and its cardiac complications cannot be excluded as potential contributors of bradycardia in the present study. Future studies are needed to further delineate the cardiac characteristics of COVID-19 and remdesivir., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)
- Published
- 2022
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14. GPCR systems pharmacology: a different perspective on the development of biased therapeutics.
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Eiger DS, Pham U, Gardner J, Hicks C, and Rajagopal S
- Subjects
- Ligands, Signal Transduction, beta-Arrestins metabolism, Network Pharmacology, Receptors, G-Protein-Coupled metabolism
- Abstract
G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors and are the target of approximately one-third of all Food and Drug Administration (FDA)-approved pharmaceutical drugs. GPCRs interact with many transducers, such as heterotrimeric G proteins, GPCR kinases (GRKs), and β-arrestins. Recent experiments have demonstrated that some ligands can activate distinct effector proteins over others, a phenomenon termed "biased agonism." These discoveries have raised the potential of developing drugs which preferentially activate therapeutic signaling pathways over those that lead to deleterious side effects. However, to date, only one biased GPCR therapeutic has received FDA approval and many others have either failed to meet their specified primary end points and or demonstrate superiority over currently available treatments. In addition, there is a lack of understanding regarding how biased agonism measured at a GPCR leads to specific downstream physiological responses. Here, we briefly summarize the history and current status of biased agonism at GPCRs and suggest adoption of a "systems pharmacology" approach upon which to develop GPCR-targeted drugs that demonstrate heightened therapeutic efficacy with improved side effect profiles.
- Published
- 2022
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15. Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.
- Author
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Shi H, Kimsey IJ, Gu S, Liu HF, Pham U, Schumacher MA, and Al-Hashimi HM
- Subjects
- Base Sequence, Binding Sites genetics, Computational Biology methods, Crystallography, X-Ray, DNA genetics, DNA metabolism, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Databases, Genetic, Hydrogen Bonding, Models, Molecular, Mutation, Protein Binding, Thermodynamics, Base Pairing, DNA chemistry, DNA-Binding Proteins chemistry, Nucleic Acid Conformation, Protein Domains
- Abstract
Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative 'Hoogsteen' bps, expanding the functional complexity of DNA. We developed 'Hoog-finder', which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson-Crick in crystal structures of protein-DNA complexes. We uncovered 17 Hoogsteen bps, 7 of which were in complex with 6 proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2021
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16. Separation of short and medium-chain fatty acids using capillary electrophoresis with indirect photometric detection: Part I: Identification of fatty acids in rat feces.
- Author
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Pham U, Alvarado L, Suess GJ, Shamsi SA, and Frantz K
- Subjects
- Adenosine Monophosphate, Animals, Electrolytes, Feces, Rats, Electrophoresis, Capillary, Fatty Acids
- Abstract
Short and medium-chain fatty acids (SMCFAs) are known as essential metabolites found in gut microbiota that function as modulators in the development and progression of many inflammatory conditions as well as in the regulation of cell metabolism. Currently, there are few simple and low-cost analytical methods available for the determination of SMCFA. This report focuses on SMCFA analysis utilizing CE with indirect photometric detection (CE-IPD). A ribonucleotide electrolyte, 5'-adenosine mono-phosphate (5'-AMP), is investigated as an IPD reagent due to its high molar absorptivity and dynamic reserve compatible with separation and detection of SMCFA. The operating parameters like the composition of organic solvent, millimolar concentrations of the complexing agent (alpha-cyclodextrin), 5'-AMP and non-absorbing electrolyte (boric acid), as well as the applied voltage, are optimized for resolution, efficiency, and signal-to-noise ratio. A baseline resolution of all nine SMCFAs is achieved in less than 15 min. Additionally, the developed CE-IPD method shows promising potential to identifying SMCFA in rat fecal supernatant. The presented analytical assay is simple, economical, and has considerably good repeatability. The intraday and interday RSD of less than 1 and 2% for relative migration time, as well as less than 14 and 15% for peak area, respectively, were obtained for SMCFA in fecal solution., (© 2021 Wiley-VCH GmbH.)
- Published
- 2021
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17. Systemic regulation of mitochondria by germline proteostasis prevents protein aggregation in the soma of C. elegans .
- Author
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Calculli G, Lee HJ, Shen K, Pham U, Herholz M, Trifunovic A, Dillin A, and Vilchez D
- Abstract
Protein aggregation causes intracellular changes in neurons, which elicit signals to modulate proteostasis in the periphery. Beyond the nervous system, a fundamental question is whether other organs also communicate their proteostasis status to distal tissues. Here, we examine whether proteostasis of the germ line influences somatic tissues. To this end, we induce aggregation of germline-specific PGL-1 protein in germline stem cells of Caenorhabditis elegans Besides altering the intracellular mitochondrial network of germline cells, PGL-1 aggregation also reduces the mitochondrial content of somatic tissues through long-range Wnt signaling pathway. This process induces the unfolded protein response of the mitochondria in the soma, promoting somatic mitochondrial fragmentation and aggregation of proteins linked with neurodegenerative diseases such as Huntington's and amyotrophic lateral sclerosis. Thus, the proteostasis status of germline stem cells coordinates mitochondrial networks and protein aggregation through the organism., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2021
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18. Cell morphology-based machine learning models for human cell state classification.
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Li Y, Nowak CM, Pham U, Nguyen K, and Bleris L
- Subjects
- Cell Size, Flow Cytometry, Humans, Propidium, Machine Learning, Neural Networks, Computer
- Abstract
Herein, we implement and access machine learning architectures to ascertain models that differentiate healthy from apoptotic cells using exclusively forward (FSC) and side (SSC) scatter flow cytometry information. To generate training data, colorectal cancer HCT116 cells were subjected to miR-34a treatment and then classified using a conventional Annexin V/propidium iodide (PI)-staining assay. The apoptotic cells were defined as Annexin V-positive cells, which include early and late apoptotic cells, necrotic cells, as well as other dying or dead cells. In addition to fluorescent signal, we collected cell size and granularity information from the FSC and SSC parameters. Both parameters are subdivided into area, height, and width, thus providing a total of six numerical features that informed and trained our models. A collection of logistical regression, random forest, k-nearest neighbor, multilayer perceptron, and support vector machine was trained and tested for classification performance in predicting cell states using only the six aforementioned numerical features. Out of 1046 candidate models, a multilayer perceptron was chosen with 0.91 live precision, 0.93 live recall, 0.92 live f value and 0.97 live area under the ROC curve when applied on standardized data. We discuss and highlight differences in classifier performance and compare the results to the standard practice of forward and side scatter gating, typically performed to select cells based on size and/or complexity. We demonstrate that our model, a ready-to-use module for any flow cytometry-based analysis, can provide automated, reliable, and stain-free classification of healthy and apoptotic cells using exclusively size and granularity information.
- Published
- 2021
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19. Multi-agent reinforcement learning approach for hedging portfolio problem.
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Pham U, Luu Q, and Tran H
- Abstract
Developing a hedging strategy to reduce risk of losses for a given set of stocks in a portfolio is a difficult task due to cost of the hedge. In Vietnam stock market, cross-hedge is involved hedging a long position of a stock because there is no put option for the stock. In addition, only VN30 stock index futures contracts are traded on Hanoi Stock Exchange. Inspired by recently achievement of deep reinforcement learning, we explore feasibility to construct a hedging strategy automatically by leveraging cooperative multi-agent in reinforcement learning techniques without advanced domain knowledge. In this work, we use 10 popular stocks on Ho Chi Minh Stock Exchange, and VN30F1M (VN30 Index Futures contracts within one month settlement) to develop a stock market simulator (including transaction fee, tax, and settlement date of transactions) for reinforcement learning agent training. We use daily return as input data for training process. Results suggest that the agent can learn trading and hedging policy to make profit and reduce losses. Furthermore, we also find that our agent can protect portfolios and make positive profit in case market collapses systematically. In practice, this work can help Vietnam's stock market investors to improve performance and reduce losses in trading, especially when the volatility cannot be controlled., Competing Interests: Conflict of InterestUyen Pham declares that she has no conflict of interest. Quoc Luu declares that he has no conflict of interest. Hien Tran declares that he has no conflict of interest., (© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021.)
- Published
- 2021
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20. Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.
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Xu Y, Manghrani A, Liu B, Shi H, Pham U, Liu A, and Al-Hashimi HM
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- Base Pairing, DNA chemistry, DNA Methylation, Sulfuric Acid Esters chemistry
- Abstract
As the Watson-Crick faces of nucleobases are protected in dsDNA, it is commonly assumed that deleterious alkylation damage to the Watson-Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. However, damage to the Watson-Crick faces of nucleobases has been reported in dsDNA in vitro through mechanisms that are not understood. In addition, the extent of protection from methylation damage conferred by dsDNA relative to ssDNA has not been quantified. Watson-Crick base pairs in dsDNA exist in dynamic equilibrium with Hoogsteen base pairs that expose the Watson-Crick faces of purine nucleobases to solvent. Whether this can influence the damage susceptibility of dsDNA remains unknown. Using dot-blot and primer extension assays, we measured the susceptibility of adenine-N1 to methylation by dimethyl sulfate (DMS) when in an A-T Watson-Crick versus Hoogsteen conformation. Relative to unpaired adenines in a bulge, Watson-Crick A-T base pairs in dsDNA only conferred ∼130-fold protection against adenine-N1 methylation, and this protection was reduced to ∼40-fold for A( syn )-T Hoogsteen base pairs embedded in a DNA-drug complex. Our results indicate that Watson-Crick faces of nucleobases are accessible to alkylating agents in canonical dsDNA and that Hoogsteen base pairs increase this accessibility. Given the higher abundance of dsDNA relative to ssDNA, these results suggest that dsDNA could be a substantial source of cytotoxic damage. The work establishes DMS probing as a method for characterizing A( syn )-T Hoogsteen base pairs in vitro and also lays the foundation for a sequencing approach to map A( syn )-T Hoogsteen and unpaired adenines genome-wide in vivo., Competing Interests: Conflict of interest—The authors declare that they have no conflict of interest with the contents of this article., (© 2020 Xu et al.)
- Published
- 2020
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21. Characterization of mesoangioblast cell fate and improved promyogenic potential of a satellite cell-like subpopulation upon transplantation in dystrophic murine muscles.
- Author
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Mavoungou LO, Neuenschwander S, Pham U, Iyer PS, and Mermod N
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- Animals, Disease Models, Animal, Mice, Mice, Inbred mdx, Mice, SCID, Cell Differentiation, Multipotent Stem Cells metabolism, Multipotent Stem Cells pathology, Muscular Dystrophy, Duchenne genetics, Muscular Dystrophy, Duchenne metabolism, Muscular Dystrophy, Duchenne pathology, Muscular Dystrophy, Duchenne therapy, Satellite Cells, Skeletal Muscle metabolism, Satellite Cells, Skeletal Muscle pathology, Satellite Cells, Skeletal Muscle transplantation
- Abstract
Duchenne muscular dystrophy (DMD) is a lethal muscle-wasting disease caused by the lack of dystrophin in muscle fibers that is currently without curative treatment. Mesoangioblasts (MABs) are multipotent progenitor cells that can differentiate to a myogenic lineage and that can be used to express Dystrophin upon transplantation into muscles, in autologous gene therapy approaches. However, their fate in the muscle environment remains poorly characterized. Here, we investigated the differentiation fate of MABs following their transplantation in DMD murine muscles using a mass cytometry strategy. This allowed the identification and isolation of a fraction of MAB-derived cells presenting common properties with satellite muscle stem cells. This analysis also indicated that most cells did not undergo a myogenic differentiation path once in the muscle environment, limiting their capacity to restore dystrophin expression in transplanted muscles. We therefore assessed whether MAB treatment with cytokines and growth factors prior to engraftment may improve their myogenic fate. We identified a combination of such signals that ameliorates MABs capacity to undergo myogenic differentiation in vivo and to restore dystrophin expression upon engraftment in myopathic murine muscles., (Copyright © 2019 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2019
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22. Evolutionarily conserved regulation of sleep by epidermal growth factor receptor signaling.
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Lee DA, Liu J, Hong Y, Lane JM, Hill AJ, Hou SL, Wang H, Oikonomou G, Pham U, Engle J, Saxena R, and Prober DA
- Subjects
- Animals, Animals, Genetically Modified, Evolution, Molecular, Extracellular Signal-Regulated MAP Kinases genetics, Humans, Mitogen-Activated Protein Kinases genetics, ErbB Receptors genetics, Gene Expression Regulation, Neuropeptides genetics, Signal Transduction genetics, Sleep genetics, Zebrafish genetics
- Abstract
The genetic bases for most human sleep disorders and for variation in human sleep quantity and quality are largely unknown. Using the zebrafish, a diurnal vertebrate, to investigate the genetic regulation of sleep, we found that epidermal growth factor receptor (EGFR) signaling is necessary and sufficient for normal sleep levels and is required for the normal homeostatic response to sleep deprivation. We observed that EGFR signaling promotes sleep via mitogen-activated protein kinase/extracellular signal-regulated kinase and RFamide neuropeptide signaling and that it regulates RFamide neuropeptide expression and neuronal activity. Consistent with these findings, analysis of a large cohort of human genetic data from participants of European ancestry revealed that common variants in genes within the EGFR signaling pathway are associated with variation in human sleep quantity and quality. These results indicate that EGFR signaling and its downstream pathways play a central and ancient role in regulating sleep and provide new therapeutic targets for sleep disorders., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2019
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23. Cyclophilins and cyclophilin inhibitors in nidovirus replication.
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de Wilde AH, Pham U, Posthuma CC, and Snijder EJ
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- Animals, Humans, Peptidylprolyl Isomerase antagonists & inhibitors, Peptidylprolyl Isomerase metabolism, Cyclophilins antagonists & inhibitors, Cyclophilins metabolism, Host-Pathogen Interactions, Nidovirales physiology, Virus Replication
- Abstract
Cyclophilins (Cyps) belong to the family of peptidyl-prolyl isomerases (PPIases). The PPIase activity of most Cyps is inhibited by the immunosuppressive drug cyclosporin A and several of its non-immunosuppressive analogs, which can also block the replication of nidoviruses (arteriviruses and coronaviruses). Cyclophilins have been reported to play an essential role in the replication of several other RNA viruses, including human immunodeficiency virus-1, hepatitis C virus, and influenza A virus. Likewise, the replication of various nidoviruses was reported to depend on Cyps or other PPIases. This review summarizes our current understanding of this class of nidovirus-host interactions, including the potential function of in particular CypA and the inhibitory effect of Cyp inhibitors. Also the involvement of the FK-506-binding proteins and parvulins is discussed. The nidovirus data are placed in a broader perspective by summarizing the most relevant data on Cyp interactions and Cyp inhibitors for other RNA viruses., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
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24. Multiple Microelectrode Recordings in STN-DBS Surgery for Parkinson's Disease: A Randomized Study.
- Author
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Bjerknes S, Toft M, Konglund AE, Pham U, Waage TR, Pedersen L, Skjelland M, Haraldsen I, Andersson S, Dietrichs E, and Skogseid IM
- Abstract
Background: Subthalamic nucleus deep brain stimulation improves motor symptoms and fluctuations in advanced Parkinson's disease, but the degree of clinical improvement depends on accurate anatomical electrode placement. Methods used to localize the sensory-motor part of the nucleus vary substantially. Using microelectrode recordings, at least three inserted microelectrodes are needed to obtain a three-dimensional map. Therefore, multiple simultaneously inserted microelectrodes should provide better guidance than single sequential microelectrodes. We aimed to compare the use of multiple simultaneous versus single sequential microelectrode recordings on efficacy and safety of subthalamic nucleus stimulation., Methods: Sixty patients were included in this double-blind, randomized study, 30 in each group. Primary outcome measures were the difference from baseline to 12 months in the MDS-UPDRS motor score (part III) in the off-medication state and quality of life using the Parkinson's Disease Questionnaire-39 (PDQ-39) scores., Results: The mean reduction of the MDS-UPDRS III off score was 35 (SD 12) in the group investigated with multiple simultaneous microelectrodes compared to 26 (SD 10) in the single sequential microelectrode group ( p = 0.004). The PDQ-39 Summary Index did not differ between the groups, but the domain scores activities of daily living and bodily discomfort improved significantly more in the multiple microelectrodes group. The frequency of serious adverse events did not differ significantly., Conclusions: After 12 months of subthalamic nucleus stimulation, the multiple microelectrodes group had a significantly greater improvement both in MDS-UPDRS III off score and in two PDQ-39 domains. Our results may support the use of multiple simultaneous microelectrode recordings., Trial Registration: http://ClinicalTrials.gov Identifier: NCT00855621 (first received March 3, 2009).
- Published
- 2018
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25. Genetic and neuronal regulation of sleep by neuropeptide VF.
- Author
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Lee DA, Andreev A, Truong TV, Chen A, Hill AJ, Oikonomou G, Pham U, Hong YK, Tran S, Glass L, Sapin V, Engle J, Fraser SE, and Prober DA
- Subjects
- Animals, Neurons physiology, Signal Transduction, Zebrafish, Gene Expression Regulation, Neuropeptides metabolism, Sleep
- Abstract
Sleep is an essential and phylogenetically conserved behavioral state, but it remains unclear to what extent genes identified in invertebrates also regulate vertebrate sleep. RFamide-related neuropeptides have been shown to promote invertebrate sleep, and here we report that the vertebrate hypothalamic RFamide neuropeptide VF (NPVF) regulates sleep in the zebrafish, a diurnal vertebrate. We found that NPVF signaling and npvf -expressing neurons are both necessary and sufficient to promote sleep, that mature peptides derived from the NPVF preproprotein promote sleep in a synergistic manner, and that stimulation of npvf -expressing neurons induces neuronal activity levels consistent with normal sleep. These results identify NPVF signaling and npvf -expressing neurons as a novel vertebrate sleep-promoting system and suggest that RFamide neuropeptides participate in an ancient and central aspect of sleep control.
- Published
- 2017
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26. Outcomes after adrenalectomy for unilateral primary aldosteronism: an international consensus on outcome measures and analysis of remission rates in an international cohort.
- Author
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Williams TA, Lenders JWM, Mulatero P, Burrello J, Rottenkolber M, Adolf C, Satoh F, Amar L, Quinkler M, Deinum J, Beuschlein F, Kitamoto KK, Pham U, Morimoto R, Umakoshi H, Prejbisz A, Kocjan T, Naruse M, Stowasser M, Nishikawa T, Young WF Jr, Gomez-Sanchez CE, Funder JW, and Reincke M
- Subjects
- Adult, Consensus, Delphi Technique, Female, Humans, Male, Middle Aged, Prospective Studies, Retrospective Studies, Adrenalectomy standards, Hyperaldosteronism surgery, Outcome Assessment, Health Care
- Abstract
Background: Although unilateral primary aldosteronism is the most common surgically correctable cause of hypertension, no standard criteria exist to classify surgical outcomes. We aimed to create consensus criteria for clinical and biochemical outcomes and follow-up of adrenalectomy for unilateral primary aldosteronism and apply these criteria to an international cohort to analyse the frequency of remission and identify preoperative determinants of successful outcome., Methods: The Primary Aldosteronism Surgical Outcome (PASO) study was an international project to develop consensus criteria for outcomes and follow-up of adrenalectomy for unilateral primary aldosteronism. An international panel of 31 experts from 28 centres, including six endocrine surgeons, used the Delphi method to reach consensus. We then retrospectively analysed follow-up data from prospective cohorts for outcome assessment of patients diagnosed with unilateral primary aldosteronism by adrenal venous sampling who had undergone a total adrenalectomy, consecutively included from 12 referral centres in nine countries. On the basis of standardised criteria, we determined the proportions of patients achieving complete, partial, or absent clinical and biochemical success in accordance with the consensus. We then used logistic regression analyses to identify preoperative factors associated with clinical and biochemical outcomes., Findings: Consensus was reached for criteria for six outcomes (complete, partial, and absent success of clinical and biochemical outcomes) based on blood pressure, use of antihypertensive drugs, plasma potassium and aldosterone concentrations, and plasma renin concentrations or activities. Consensus was also reached for two recommendations for the timing of follow-up assessment. For the international cohort analysis, we analysed clinical data from 705 patients recruited between 1994 and 2015, of whom 699 also had biochemical data. Complete clinical success was achieved in 259 (37%) of 705 patients, with a wide variance (range 17-62), and partial clinical success in an additional 334 (47%, range 35-66); complete biochemical success was seen in 656 (94%, 83-100) of 699 patients. Female patients had a higher likelihood of complete clinical success (odds ratio [OR] 2·25, 95% CI 1·40-3·62; p=0·001) and clinical benefit (complete plus partial clinical success; OR 2·89, 1·49-5·59; p=0·002) than male patients. Younger patients had a higher likelihood of complete clinical success (OR 0·95 per extra year, 0·93-0·98; p<0·001) and clinical benefit (OR 0·95 per extra year, 0·92-0·98; p=0·004). Higher levels of preoperative medication were associated with lower levels of complete clinical success (OR 0·80 per unit increase, 0·70-0·90; p<0·001)., Interpretation: These standardised outcome criteria are relevant for the assessment of the success of surgical treatment in individual patients and will allow the comparison of outcome data in future studies. The variable baseline clinical characteristics of our international cohort contributed to wide variation in clinical outcomes. Most patients derive clinical benefit from adrenalectomy, with younger patients and female patients more likely to have a favourable surgical outcome. Screening for primary aldosteronism should nonetheless be done in every individual fulfilling US Endocrine Society guideline criteria because biochemical success without clinical success is by itself clinically important and older women and men can also derive post-operative clinical benefit., Funding: European Research Council; European Union's Horizon 2020; Else Kröner-Fresenius Stiftung; Netherlands Organisation for Health Research and Development-Medical Sciences; Japanese Ministry of Health, Labour and Welfare; Ministry of Health, Slovenia; US National Institutes of Health; and CONICYT-FONDECYT (Chile)., (Copyright © 2017 Elsevier Ltd. All rights reserved.)
- Published
- 2017
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27. Caveolin-3 plays a critical role in autophagy after ischemia-reperfusion.
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Kassan A, Pham U, Nguyen Q, Reichelt ME, Cho E, Patel PM, Roth DM, Head BP, and Patel HH
- Subjects
- Animals, Apoptosis Regulatory Proteins metabolism, Caspase 3 metabolism, Caveolae metabolism, Cytochromes c metabolism, Heart physiology, Mice, Myocytes, Cardiac metabolism, Myocytes, Cardiac pathology, Reperfusion methods, Autophagy physiology, Caveolin 3 metabolism, Ischemia metabolism, Ischemia pathology, Myocardial Reperfusion Injury metabolism, Myocardial Reperfusion Injury pathology
- Abstract
Autophagy is a dynamic recycling process responsible for the breakdown of misfolded proteins and damaged organelles, providing nutrients and energy for cellular renovation and homeostasis. Loss of autophagy is associated with cardiovascular diseases. Caveolin-3 (Cav-3), a muscle-specific isoform, is a structural protein within caveolae and is critical to stress adaptation in the heart. Whether Cav-3 plays a role in regulating autophagy to modulate cardiac stress responses remains unknown. In the present study, we used HL-1 cells, a cardiac muscle cell line, with stable Cav-3 knockdown (Cav-3 KD) and Cav-3 overexpression (Cav-3 OE) to study the impact of Cav-3 in regulation of autophagy. We show that traditional stimulators of autophagy (i.e., rapamycin and starvation) result in upregulation of the process in Cav-3 OE cells while Cav-3 KD cells have a blunted response. Cav-3 coimmunoprecipitated with beclin-1 and Atg12, showing an interaction of caveolin with autophagy-related proteins. In the heart, autophagy may be a major regulator of protection from ischemic stress. We found that Cav-3 KD cells have a decreased expression of autophagy markers [beclin-1, light chain (LC3-II)] after simulated ischemia and ischemia-reperfusion (I/R) compared with WT, whereas OE cells showed increased expression. Moreover, Cav-3 KD cells showed increased cell death and higher level of apoptotic proteins (cleaved caspase-3 and cytochrome c) with suppressed mitochondrial function in response to simulated ischemia and I/R, whereas Cav-3 OE cells were protected and had preserved mitochondrial function. Taken together, these results indicate that autophagy regulates adaptation to cardiac stress in a Cav-3-dependent manner.
- Published
- 2016
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28. A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States.
- Author
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Chiu CN, Rihel J, Lee DA, Singh C, Mosser EA, Chen S, Sapin V, Pham U, Engle J, Niles BJ, Montz CJ, Chakravarthy S, Zimmerman S, Salehi-Ashtiani K, Vidal M, Schier AF, and Prober DA
- Subjects
- Age Factors, Aniline Compounds pharmacology, Animals, Brain Stem cytology, Brain Stem growth & development, Brain Stem metabolism, Gene Expression Regulation drug effects, Humans, Hypothalamo-Hypophyseal System metabolism, Larva, Mice, Transgenic, Motor Activity genetics, Neurons drug effects, Neurons metabolism, Pituitary-Adrenal System metabolism, Pyrimidines pharmacology, Receptors, Complement 3b metabolism, Receptors, Neurotransmitter metabolism, Signal Transduction drug effects, Signal Transduction genetics, Zebrafish, Zebrafish Proteins genetics, Gene Expression Regulation genetics, Neuropeptides genetics, Neuropeptides metabolism, Sleep genetics, Wakefulness genetics
- Abstract
Neuromodulation of arousal states ensures that an animal appropriately responds to its environment and engages in behaviors necessary for survival. However, the molecular and circuit properties underlying neuromodulation of arousal states such as sleep and wakefulness remain unclear. To tackle this challenge in a systematic and unbiased manner, we performed a genetic overexpression screen to identify genes that affect larval zebrafish arousal. We found that the neuropeptide neuromedin U (Nmu) promotes hyperactivity and inhibits sleep in zebrafish larvae, whereas nmu mutant animals are hypoactive. We show that Nmu-induced arousal requires Nmu receptor 2 and signaling via corticotropin releasing hormone (Crh) receptor 1. In contrast to previously proposed models, we find that Nmu does not promote arousal via the hypothalamic-pituitary-adrenal axis, but rather probably acts via brainstem crh-expressing neurons. These results reveal an unexpected functional and anatomical interface between the Nmu system and brainstem arousal systems that represents a novel wake-promoting pathway., (Copyright © 2016 Elsevier Inc. All rights reserved.)
- Published
- 2016
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29. Personality changes after deep brain stimulation in Parkinson's disease.
- Author
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Pham U, Solbakk AK, Skogseid IM, Toft M, Pripp AH, Konglund AE, Andersson S, Haraldsen IR, Aarsland D, Dietrichs E, and Malt UF
- Abstract
Objectives. Deep brain stimulation of the subthalamic nucleus (STN-DBS) is a recognized therapy that improves motor symptoms in advanced Parkinson's disease (PD). However, little is known about its impact on personality. To address this topic, we have assessed personality traits before and after STN-DBS in PD patients. Methods. Forty patients with advanced PD were assessed with the Temperament and Character Inventory (TCI): the Urgency, Premeditation, Perseverance, Sensation Seeking impulsive behaviour scale (UPPS), and the Neuroticism and Lie subscales of the Eysenck Personality Questionnaire (EPQ-N, EPQ-L) before surgery and after three months of STN-DBS. Collateral information obtained from the UPPS was also reported. Results. Despite improvement in motor function and reduction in dopaminergic dosage patients reported lower score on the TCI Persistence and Self-Transcendence scales, after three months of STN-DBS, compared to baseline (P = 0.006; P = 0.024). Relatives reported significantly increased scores on the UPPS Lack of Premeditation scale at follow-up (P = 0.027). Conclusion. STN-DBS in PD patients is associated with personality changes in the direction of increased impulsivity.
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- 2015
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30. Methods for measuring CoA and CoA derivatives in biological samples.
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Tsuchiya Y, Pham U, and Gout I
- Subjects
- Acetyl Coenzyme A analysis, Animals, Chromatography, High Pressure Liquid, Humans, Coenzyme A analysis, Enzyme Assays methods
- Abstract
CoA (coenzyme A) is a ubiquitous and essential cofactor that acts as an acyl group carrier in biochemical reactions. Apart from participating in numerous metabolic pathways as substrates and intermediates, CoA and a number of its thioester derivatives, such as acetyl-CoA, can also directly regulate the activity of proteins by allosteric mechanisms and by affecting protein acetylation reactions. Cellular levels of CoA and CoA thioesters change under various physiological and pathological conditions. Defective CoA biosynthesis is implicated in NBIA (neurodegeneration with brain iron accumulation). However, the exact role of CoA in the pathogenesis of NBIA is not well understood. Accurate and reliable assays for measuring CoA species in biological samples are essential for studying the roles of CoA and CoA derivatives in health and disease. The present mini-review discusses methods that are commonly used to measure CoA species in biological samples.
- Published
- 2014
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31. Changes in acetyl CoA levels during the early embryonic development of Xenopus laevis.
- Author
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Tsuchiya Y, Pham U, Hu W, Ohnuma S, and Gout I
- Subjects
- Acetylation, Animals, Embryo, Nonmammalian embryology, Embryo, Nonmammalian metabolism, Embryonic Development, Histones metabolism, Protein Processing, Post-Translational, Xenopus Proteins metabolism, Xenopus laevis embryology, Acetyl Coenzyme A metabolism, Xenopus laevis metabolism
- Abstract
Coenzyme A (CoA) is a ubiquitous and fundamental intracellular cofactor. CoA acts as a carrier of metabolically important carboxylic acids in the form of CoA thioesters and is an obligatory component of a multitude of catabolic and anabolic reactions. Acetyl CoA is a CoA thioester derived from catabolism of all major carbon fuels. This metabolite is at a metabolic crossroads, either being further metabolised as an energy source or used as a building block for biosynthesis of lipids and cholesterol. In addition, acetyl CoA serves as the acetyl donor in protein acetylation reactions, linking metabolism to protein post-translational modifications. Recent studies in yeast and cultured mammalian cells have suggested that the intracellular level of acetyl CoA may play a role in the regulation of cell growth, proliferation and apoptosis, by affecting protein acetylation reactions. Yet, how the levels of this metabolite change in vivo during the development of a vertebrate is not known. We measured levels of acetyl CoA, free CoA and total short chain CoA esters during the early embryonic development of Xenopus laevis using HPLC. Acetyl CoA and total short chain CoA esters start to increase around midblastula transition (MBT) and continue to increase through stages of gastrulation, neurulation and early organogenesis. Pre-MBT embryos contain more free CoA relative to acetyl CoA but there is a shift in the ratio of acetyl CoA to CoA after MBT, suggesting a metabolic transition that results in net accumulation of acetyl CoA. At the whole-embryo level, there is an apparent correlation between the levels of acetyl CoA and levels of acetylation of a number of proteins including histones H3 and H2B. This suggests the level of acetyl CoA may be a factor, which determines the degree of acetylation of these proteins, hence may play a role in the regulation of embryogenesis.
- Published
- 2014
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32. Differential constitutive and cytokine-modulated expression of human Toll-like receptors in primary neutrophils, monocytes, and macrophages.
- Author
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O'Mahony DS, Pham U, Iyer R, Hawn TR, and Liles WC
- Subjects
- Cell Culture Techniques, Cells, Cultured, Cytokines genetics, Gene Expression Regulation immunology, Granulocyte Colony-Stimulating Factor genetics, Granulocyte Colony-Stimulating Factor physiology, Granulocyte-Macrophage Colony-Stimulating Factor genetics, Granulocyte-Macrophage Colony-Stimulating Factor physiology, Humans, Interferon-gamma genetics, Interferon-gamma metabolism, Interferon-gamma physiology, Macrophage Activation, Macrophage Colony-Stimulating Factor genetics, Macrophage Colony-Stimulating Factor physiology, Macrophages immunology, Monocytes immunology, Neutrophil Activation, Neutrophils immunology, RNA, Messenger metabolism, Recombinant Proteins metabolism, Toll-Like Receptor 2 metabolism, Toll-Like Receptor 2 physiology, Toll-Like Receptor 4 metabolism, Toll-Like Receptor 4 physiology, Toll-Like Receptor 5 metabolism, Toll-Like Receptor 5 physiology, Toll-Like Receptor 9 metabolism, Toll-Like Receptor 9 physiology, Toll-Like Receptors physiology, Cytokines physiology, Macrophages physiology, Monocytes physiology, Neutrophils physiology, Toll-Like Receptors metabolism
- Abstract
Human Toll-like receptors (TLRs) comprise a family of proteins that recognizes pathogen-associated molecular patterns (PAMPs) and initiates host innate immune responses. Neutrophils, monocytes, and macrophages are critical cellular components of the human innate immune system. Proinflammatory cytokines, such as granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage colony-stimulating factor (GM-CSF), macrophage colony-stimulating factor (M-CSF), and interferon-gamma (IFN-gamma), have been shown to up-regulate microbicidal activity in these effector cells of innate immunity. Currently, the cellular and molecular mechanisms responsible for these effects are not completely understood. We hypothesized that these cytokines may up-regulate TLR expression as a mechanism to facilitate microbial recognition and augment the innate immune response. Using quantitative realtime rt-PCR technology, we examined constitutive expression of TLR2, TLR4, TLR5, and TLR9 mRNA and the effects of G-CSF, GM-CSF, M-CSF, and IFN-gamma on TLR mRNA expression in purified populations of normal human neutrophils, monocytes, and monocyte-derived macrophages. Relative constitutive expression of TLR2, TLR4, and TLR9 was similar in neutrophils and monocytes. Constitutive expression of TLR5 was less in neutrophils compared to monocytes. Constitutive expression of TLR4 was greater and that of TLR9 lower in monocyte-derived macrophages compared to monocytes. Of the cytokines examined, IFN-gamma and GM-CSF caused the greatest effects on TLR expression. IFN- gamma up-regulated TLR2 and TLR4 in neutrophils and monocytes. GM-CSF up-regulated expression of TLR2 and TLR4 in neutrophils and TLR2 in monocytes. TLR5 was down-regulated by inflammatory cytokines in monocytes. These results suggest a potential role for IFN- gamma and/or GM-CSF as therapeutic immunomodulators of the host defense to infection.
- Published
- 2008
- Full Text
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33. Hyper-IgE syndrome is not associated with defects in several candidate toll-like receptor pathway genes.
- Author
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Hawn TR, Ozinsky A, Williams LM, Rodrigues S, Clark A, Pham U, Hill HR, Ochs H, Aderem A, and Liles WC
- Subjects
- Adaptor Proteins, Signal Transducing genetics, Adult, Antigens, Differentiation genetics, Bacteria immunology, Female, Humans, Interferon-gamma blood, Interleukins metabolism, Job Syndrome blood, Lipopolysaccharides pharmacology, Male, Middle Aged, Myeloid Differentiation Factor 88, Peptidoglycan pharmacology, Polymorphism, Genetic genetics, Receptors, Immunologic genetics, Signal Transduction drug effects, TNF Receptor-Associated Factor 6 genetics, Teichoic Acids pharmacology, Toll-Like Receptor 1 genetics, Toll-Like Receptor 2 genetics, Toll-Like Receptor 6 genetics, Toll-Like Receptors immunology, Tumor Necrosis Factor-alpha metabolism, Zymosan pharmacology, Job Syndrome genetics, Signal Transduction genetics, Toll-Like Receptors genetics
- Abstract
The genetic basis of hyper-IgE syndrome (HIES), also known as Job syndrome, a primary immunodeficiency associated with recurrent skin and pulmonary infections, is unknown. We hypothesized that HIES is due to a defect in the Toll-like receptor signaling pathway. We used a whole blood cytokine assay to compare inflammatory responses to stimulation with specific Toll-like receptor (TLR) pathway agonists in four individuals with HIES and nine healthy controls. Production of tumor necrosis factor-alpha, interleukin (IL)-1beta, IL-6, and IL-12 was not impaired in response to stimulation with lipopolysaccharide, peptidoglycan, zymosan, lipoteichoic acid, Staphylococcus aureus, Escherichia coli, or Streptococcus pneumoniae. Interferon (IFN)-gamma was reduced in HIES subjects in response to each of these stimuli. We sequenced several candidate genes from the TLR pathway in HIES individuals to determine whether any mutations were associated with this syndrome. No novel mutations or polymorphisms were found in the coding regions of TLR1, TLR2, TLR6, MyD88, or TRAF6. In summary, although HIES individuals had an IFN-gamma secretion defect, they also produced normal levels of several TLR-regulated proinflammatory cytokines. No unique mutations or polymorphisms were observed in several candidate genes from the TLR pathway. Our studies do not support a role for a defective TLR response in HIES individuals.
- Published
- 2005
- Full Text
- View/download PDF
34. Differential role of MyD88 in macrophage-mediated responses to opportunistic fungal pathogens.
- Author
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Marr KA, Balajee SA, Hawn TR, Ozinsky A, Pham U, Akira S, Aderem A, and Liles WC
- Subjects
- Adaptor Proteins, Signal Transducing, Animals, Antigens, Differentiation genetics, Aspergillosis immunology, Aspergillus fumigatus immunology, Aspergillus fumigatus pathogenicity, Candida albicans immunology, Candida albicans pathogenicity, Candidiasis immunology, Cytokines biosynthesis, Immunity, Innate, In Vitro Techniques, Mice, Mice, Inbred C57BL, Mice, Knockout, Myeloid Differentiation Factor 88, Phagocytosis, Receptors, Immunologic deficiency, Receptors, Immunologic genetics, Signal Transduction, Antigens, Differentiation physiology, Macrophages immunology, Mycoses immunology, Opportunistic Infections immunology, Receptors, Immunologic physiology
- Abstract
Toll-like receptors mediate macrophage recognition of microbial ligands, inducing expression of microbicidal molecules and cytokines via the adapter protein MyD88. We investigated the role of MyD88 in regulating murine macrophage responses to a pathogenic yeast (Candida albicans) and mold (Aspergillus fumigatus). Macrophages derived from bone marrow of MyD88-deficient mice (MyD88(-/-)) demonstrated impaired phagocytosis and intracellular killing of C. albicans compared to wild-type (MyD88(+/+)) macrophages. In contrast, ingestion and killing of A. fumigatus conidia was MyD88 independent. Cytokine production by MyD88(-/-) macrophages in response to C. albicans yeasts and hyphae was substantially decreased, but responses to A. fumigatus hyphae were preserved. These results provide evidence that MyD88 signaling is involved in phagocytosis and killing of live C. albicans, but not A. fumigatus. The differential role of MyD88 may represent one mechanism by which macrophages regulate innate responses specific to different pathogenic fungi.
- Published
- 2003
- Full Text
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35. Fas (CD95) induces proinflammatory cytokine responses by human monocytes and monocyte-derived macrophages.
- Author
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Park DR, Thomsen AR, Frevert CW, Pham U, Skerrett SJ, Kiener PA, and Liles WC
- Subjects
- Apoptosis genetics, Apoptosis immunology, Caspase Inhibitors, Caspases physiology, Cells, Cultured, Chemotaxis, Leukocyte immunology, Cytokines antagonists & inhibitors, Cytokines genetics, Enzyme Inhibitors pharmacology, Fas Ligand Protein, Humans, Interleukin-1 antagonists & inhibitors, Interleukin-1 biosynthesis, Interleukin-8 biosynthesis, Ligands, Macrophages cytology, Macrophages enzymology, Membrane Glycoproteins immunology, Membrane Glycoproteins metabolism, Monocytes cytology, Monocytes enzymology, NF-kappa B metabolism, Neutrophils immunology, Signal Transduction genetics, Signal Transduction immunology, fas Receptor metabolism, Cytokines biosynthesis, Inflammation Mediators metabolism, Macrophages immunology, Macrophages metabolism, Monocytes immunology, Monocytes metabolism, fas Receptor pharmacology
- Abstract
Fas (CD95, APO-1) is regarded as the prototypical cell death receptor of the TNFR superfamily. Fas-induced apoptosis is generally considered to be a noninflammatory process, contributing to the silent resolution of immune and inflammatory responses. However, accumulating evidence indicates that Fas may also induce cellular activation signals. We hypothesized that Fas could activate proinflammatory cytokine responses by normal human monocytes and macrophages. Monocytes were isolated by negative immunoselection from the PBMC fraction of venous blood from healthy volunteers, and monocyte-derived macrophages were cultivated in vitro. Both monocytes and monocyte-derived macrophages released TNF-alpha and IL-8 following Fas ligation, and conditioned medium from Fas-activated monocytes and macrophages induced the directed migration of neutrophils in a chemotaxis assay. Fas-induced monocyte cytokine responses were associated with monocyte apoptosis, nuclear translocation of NF-kappaB, and cytokine gene expression and were blocked by caspase inhibition but not by inhibition of IL-1beta signaling. In contrast, Fas-induced macrophage cytokine responses occurred in the absence of apoptosis and were caspase independent, indicating maturation-dependent differences in the Fas signaling pathways that lead to proinflammatory cytokine induction. Rather than contributing to the resolution of inflammation, Fas ligation on circulating monocytes and tissue macrophages may induce proinflammatory cytokine responses that can initiate acute inflammatory responses and tissue injury.
- Published
- 2003
- Full Text
- View/download PDF
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