scholarly journals Circadian time series proteomics reveals daily dynamics in cartilage physiology

2019 ◽  
Author(s):  
Michal Dudek ◽  
Constanza Angelucci ◽  
Jayalath P.D. Ruckshanthi ◽  
Ping Wang ◽  
Venkatesh Mallikarjun ◽  
...  
Keyword(s):  
Time Series ◽  
Articular Cartilage ◽  
Meta Analysis ◽  
Treatment Strategies ◽  
Time Of Day ◽  
Mass Spectrometry Analysis ◽  
Protein Abundance ◽  
Spectrometry Analysis ◽  
Proteomics Study ◽  
Cartilage Biology

AbstractObjectivesArticular cartilage undergoes cyclical heavy loading and low load recovery during the 24-hour day/night cycle. We investigated the daily changes of protein abundance in mouse femoral head articular cartilage by performing 24-hour time-series proteomics study.MethodsTandem mass spectrometry analysis was used to quantify proteins extracted from mouse cartilage. Bioinformatics analysis was performed to quantify rhythmic changes in protein abundance. Primary chondrocytes were isolated and cultured for independent validation of selected rhythmic proteins.Results145 rhythmic proteins were detected. Among these were key cartilage molecules including CCN2, MATN1, PAI-1 and PLOD1 & 2. Pathway analysis revealed that proteins related to protein synthesis, cytoskeleton and glucose metabolism exhibited time-of-day dependent peaks in their abundance. Meta-analysis of published proteomics datasets from articular cartilage revealed that numerous rhythmic proteins were dysregulated in osteoarthritis and/or ageing.ConclusionsOur circadian proteomics study revealed that articular cartilage is a much more dynamic tissue than previously thought. Chondrocytes exhibit circadian rhythms not only in gene expression but also in protein abundance. Our results clearly call for the consideration of circadian timing in understanding cartilage biology, osteoarthritis pathogenesis, treatment strategies and biomarker detection.

E3 ubiquitin-protein ligases in rat kidney collecting duct: response to vasopressin stimulation and withdrawal

2011 ◽  
Vol 301 (4) ◽  
pp. F883-F896 ◽  
Author(s):  
Yu-Jung Lee ◽  
Jeong-Eun Lee ◽  
Hyo-Jung Choi ◽  
Jung-Suk Lim ◽  
Hyun Jun Jung ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Collecting Duct ◽  
Rat Kidney ◽  
Urine Osmolality ◽  
Urine Concentration ◽  
Mass Spectrometry Analysis ◽  
Protein Abundance ◽  
Sprague Dawley ◽  
Spectrometry Analysis ◽  
Protein Ligases

The E3 ubiquitin (Ub)-protein ligases (E3s) play a role as regulators of protein trafficking and degradation. We aimed to integrate the profile of E3s in rat kidney and examine the changes in protein abundance of the selected E3s in response to 1-deamino-8-d-arginine vasopressin (dDAVP) stimulation/withdrawal. Sprague-Dawley rats were infused with vehicle ( n = 13), dDAVP for 5 days ( n = 13), or dDAVP was withdrawn for periods (15 min, 30 min, 1, 3, 6, 12, or 24 h) after 5-day infusion ( n = 46). Total RNA was isolated from the inner medulla (IM) for transcriptome analysis. Plasma membrane (PM)- or intracellular vesicle (ICV)-enriched fractions of whole kidney were immunoisolated for liquid chromatography-tandem mass spectrometry analysis. dDAVP infusion for 5 days (D5d) significantly increased urine osmolality, which was maintained during 3-h withdrawal of dDAVP after 5-day infusion (D5d-3h). Consistent with this, aquaporin-2 (AQP2) expression in the PM fractions of D5d and D5d-3h increased, whereas AQP2 expression in the ICV fractions of D5d-3h was further increased, indicating internalization of AQP2. Transcriptome analysis revealed 86 genes of E3s and LC-MS/MS analysis demonstrated 16 proteins of E3s. Among these, seven E3s (BRCA1, UBR4, BRE1B, UHRF1, NEDD4, CUL5, and FBX6) were shared. RT-PCR demonstrated mRNA expressions of the seven identified E3s in the kidney, and immunoblotting demonstrated changes in protein abundance of the selected E3s (BRE1B, NEDD4, and CUL5) in response to dDAVP stimulation/withdrawal or lithium-induced nephrogenic diabetes insipidus. The rate of AQP2 degradation was retarded in mpkCCDc14 cells with small interfering RNA-mediated knockdown of NEDD4 or CUL5. Taken together, identified E3s could be involved in the degradation of proteins associated with vasopressin-induced urine concentration.

scholarly journals Association of maternal prenatal selenium concentration and preterm birth: a multicountry meta-analysis

2021 ◽  
Vol 6 (9) ◽  
pp. e005856
Author(s):  
Nagendra Monangi ◽  
Huan Xu ◽  
Rasheda Khanam ◽  
Waqasuddin Khan ◽  
Saikat Deb ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Meta Analysis ◽  
Statistical Significance ◽  
Random Effect ◽  
Fixed Effect ◽  
Mass Spectrometry Analysis ◽  
Serum Samples ◽  
Entire Cohort ◽  
Spectrometry Analysis ◽  
Gestational Duration

BackgroundSelenium (Se), an essential trace mineral, has been implicated in preterm birth (PTB). We aimed to determine the association of maternal Se concentrations during pregnancy with PTB risk and gestational duration in a large number of samples collected from diverse populations.MethodsGestational duration data and maternal plasma or serum samples of 9946 singleton live births were obtained from 17 geographically diverse study cohorts. Maternal Se concentrations were determined by inductively coupled plasma mass spectrometry analysis. The associations between maternal Se with PTB and gestational duration were analysed using logistic and linear regressions. The results were then combined using fixed-effect and random-effect meta-analysis.FindingsIn all study samples, the Se concentrations followed a normal distribution with a mean of 93.8 ng/mL (SD: 28.5 ng/mL) but varied substantially across different sites. The fixed-effect meta-analysis across the 17 cohorts showed that Se was significantly associated with PTB and gestational duration with effect size estimates of an OR=0.95 (95% CI: 0.9 to 1.00) for PTB and 0.66 days (95% CI: 0.38 to 0.94) longer gestation per 15 ng/mL increase in Se concentration. However, there was a substantial heterogeneity among study cohorts and the random-effect meta-analysis did not achieve statistical significance. The largest effect sizes were observed in UK (Liverpool) cohort, and most significant associations were observed in samples from Malawi.InterpretationWhile our study observed statistically significant associations between maternal Se concentration and PTB at some sites, this did not generalise across the entire cohort. Whether population-specific factors explain the heterogeneity of our findings warrants further investigation. Further evidence is needed to understand the biologic pathways, clinical efficacy and safety, before changes to antenatal nutritional recommendations for Se supplementation are considered.

scholarly journals Unique Protein Interaction Networks Define The Chromatin Remodeling Module of The NuRD Complex

2021 ◽  
Author(s):  
Mehdi Sharifi Tabar ◽  
Caroline Giardina ◽  
Yue Julie Feng ◽  
Habib Francis ◽  
Hakimeh Moghaddas Sani ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Protein Interaction ◽  
Treatment Strategies ◽  
Interaction Network ◽  
Terminal Segment ◽  
Mass Spectrometry Analysis ◽  
Nurd Complex ◽  
Nucleosome Remodeling ◽  
Spectrometry Analysis ◽  
Underlying Mechanisms

AbstractThe combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1, and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodeling module of the Nucleosome Remodeling and Deacetylase (NuRD) complex, a gene repressor complex. Specific paralogues of the MGCC subunits such as MBD2 and CHD4 are amongst the key repressors of adult-stage fetal globin and provide important targets for molecular therapies in beta (β)-thalassemia. However, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed to date. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential in defining underlying mechanisms and developing treatment strategies. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS) we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodeling activity into both the ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the Nuclear Receptor Co-Repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.

scholarly journals Phototropin Interactions with SUMO Proteins

2021 ◽  
Author(s):  
Justyna Łabuz ◽  
Olga Sztatelman ◽  
Dominika Jagiełło-Flasińska ◽  
Paweł Hermanowicz ◽  
Aneta Bażant ◽  
...  
Keyword(s):  
Blue Light ◽  
Covalent Modification ◽  
Mass Spectrometry Analysis ◽  
Protein Abundance ◽  
Growth Responses ◽  
Yeast Two Hybrid ◽  
Spectrometry Analysis ◽  
Mature Leaves ◽  
The Stability ◽  
Two Hybrid

Abstract The disruption of the sumoylation pathway affects processes controlled by the two phototropins (phots) of Arabidopsis thaliana, phot1 and phot2. Phots, plant UVA/blue light photoreceptors, regulate growth responses and fast movements aimed at optimizing photosynthesis, such as phototropism, chloroplast relocations and stomatal opening. Sumoylation is a posttranslational modification, consisting of the addition of a SUMO (SMALL UBIQUITIN-RELATED MODIFIER) protein to a lysine residue in the target protein. In addition to affecting the stability of proteins, it regulates their activity, interactions and subcellular localization. We examined physiological responses controlled by phots, phototropism and chloroplast movements, in sumoylation pathway mutants. Chloroplast accumulation in response to both continuous and pulse light was enhanced in the E3 ligase siz1 mutant, in a manner dependent on phot2. A significant decrease in phot2 protein abundance was observed in this mutant after blue light treatment both in seedlings and mature leaves. Using plant transient expression and yeast two-hybrid assays, we found that phots interacted with SUMO proteins mainly through their N-terminal parts, which contain the photosensory LOV domains. The covalent modification in phots by SUMO was verified using an Arabidopsis sumoylation system reconstituted in bacteria followed by the mass spectrometry analysis. Lys 297 was identified as the main target of SUMO3 in the phot2 molecule. Finally, sumoylation of phot2 was detected in Arabidopsis mature leaves upon light or heat stress treatment.

Spectrophotometry Measurement of Polynuclear Aromatic Hydrocarbons in Hamilton Harbour Sediments

1991 ◽  
Vol 26 (1) ◽  
pp. 1-16 ◽  
Author(s):  
T.P. Murphy ◽  
H. Brouwer ◽  
M.E. Fox ◽  
E. Nagy
Keyword(s):  
Aromatic Hydrocarbons ◽  
Total Concentration ◽  
Coal Tar ◽  
Sediment Cores ◽  
Polynuclear Aromatic Hydrocarbons ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Near Surface ◽  
Spectrometry Analysis ◽  
Hamilton Harbour

Abstract Eighty-one sediment cores were collected to determine the extent of coal tar contamination in a toxic area of Hamilton Harbour. Over 800 samples were analyzed by a UV spectrophotometric technique that was standardized with gas chromatography/mass spectrometry analysis. The coal tar distribution was variable. The highest concentrations were near the Stelco outfalls and the Hamilton-Wentworth combined sewer outfalls. The total concentration of the 16 polynuclear aromatic hydrocarbons (PAHs) in 48,300 m3 of near-surface sediments exceeded 200 µg/g.

Meta-Analysis and Time Series Modeling Allow a Systematic Review of Primary HIV-1 Drug-Resistant Prevalence in Latin America and Caribbean

2015 ◽  
Vol 13 (2) ◽  
pp. 125-142 ◽  
Author(s):  
Antonio Coelho ◽  
Ronald Moura ◽  
Ronaldo Silva ◽  
Anselmo Kamada ◽  
Rafael Guimaraes ◽  
...  
Keyword(s):  
Systematic Review ◽  
Time Series ◽  
Latin America ◽  
Meta Analysis ◽  
Drug Resistant ◽  
Time Series Modeling ◽  
Latin America And Caribbean ◽  
Hiv 1
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