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Jorge AMS, Silva GMC, Coutinho JAP, Pereira JFB. Unravelling the molecular interactions behind the formation of PEG/PPG aqueous two-phase systems. Phys Chem Chem Phys 2024; 26:7308-7317. [PMID: 38351888 DOI: 10.1039/d3cp05539f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The understanding of molecular interactions that control phase separation in polymer/polymer aqueous two-phase systems (ATPS) has been a subject of debate up to this day. In light of this, we set out to investigate the molecular interactions occurring in ternary mixtures composed of polyethylene glycol (PEG600), polypropylene glycol (PPG400) and water. The ternary phase diagram was plotted at two temperatures (298 K and 323 K), revealing a transition from a type 0 to a type I diagram. Molecular dynamics (MD) simulations were performed to elucidate the polymer-polymer and polymer-water interactions occurring at different temperatures and water concentrations. COnductor-like Screening Model for Realistic Solvents (COSMO-RS) was used to assess the thermodynamic properties of the polymer-water binary mixtures and their correlation with ATPS formation. The MD simulations clearly demonstrate the effect of segregation/separation with increasing water content and temperature, highlighting a significant reduction in PPG-water interactions compared to PEG-water counterparts. Polymer-water interactions were identified as those controlling the phase separation mechanism, and the thermodynamic properties determined with COSMO-RS for the polymer-water binary systems further support this view.
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Affiliation(s)
- Alexandre M S Jorge
- CIEPQPF, FCTUC, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, 3030-790 Coimbra, Portugal.
| | - Gonçalo M C Silva
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal.
| | - João A P Coutinho
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal.
| | - Jorge F B Pereira
- CIEPQPF, FCTUC, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, 3030-790 Coimbra, Portugal.
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Mousseau CB, Pierre CA, Hu DD, Champion MM. Miniprep assisted proteomics (MAP) for rapid proteomics sample preparation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:916-924. [PMID: 36373982 PMCID: PMC9933840 DOI: 10.1039/d2ay01549h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/28/2022] [Indexed: 06/14/2023]
Abstract
Complete enzymatic digestion of proteins for bottom-up proteomics is substantially improved by use of detergents for denaturation and solubilization. Detergents however, are incompatible with many proteases and highly detrimental to LC-MS/MS. Recently; filter-based methods have seen wide use due to their capacity to remove detergents and harmful reagents prior to digestion and mass spectrometric analysis. We hypothesized that non-specific protein binding to negatively charged silica-based filters would be enhanced by addition of lyotropic salts, similar to DNA purification. We sought to exploit these interactions and investigate if low-cost DNA purification spin-filters, 'Minipreps,' efficiently and reproducibly bind proteins for digestion and LC-MS/MS analysis. We propose a new method, Miniprep Assisted Proteomics (MAP), for sample preparation. We demonstrate binding capacity, performance, recovery and identification rates for proteins and whole-cell lysates using MAP. MAP recovered equivalent or greater protein yields from 0.5-50 μg analyses benchmarked against commercial trapping preparations. Nano UHPLC-MS/MS proteome profiling of lysates of Escherichia coli had 99.3% overlap vs. existing approaches and reproducibility of replicate minipreps was 98.8% at the 1% FDR protein level. Label Free Quantitative proteomics was performed and 91.2% of quantified proteins had a %CV <20% (2044/2241). Miniprep Assisted Proteomics can be performed in minutes, shows low variability, high recovery and proteome depth. This suggests a significant role for adventitious binding in developing new proteomics sample preparation techniques. MAP represents an efficient, ultra-low-cost alternative for sample preparation in a commercially obtainable device that costs ∼$0.50 (USD) per miniprep.
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Affiliation(s)
- C Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Camille A Pierre
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
- Berthiaume Institute for Precision Health, University of Notre Dame, Notre Dame, IN 46556, USA
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Kholany M, Coutinho JAP, Ventura SPM. Carotenoid Production from Microalgae: The Portuguese Scenario. Molecules 2022; 27:2540. [PMID: 35458744 PMCID: PMC9030877 DOI: 10.3390/molecules27082540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/23/2022] [Accepted: 04/07/2022] [Indexed: 01/01/2023] Open
Abstract
Microalgae have an outstanding capacity to efficiently produce value-added compounds. They have been inspiring researchers worldwide to develop a blue biorefinery, supporting the development of the bioeconomy, tackling the environmental crisis, and mitigating the depletion of natural resources. In this review, the characteristics of the carotenoids produced by microalgae are presented and the downstream processes developed to recover and purify them are analyzed, considering their main applications. The ongoing activities and initiatives taking place in Portugal regarding not only research, but also industrialization under the blue biorefinery concept are also discussed. The situation reported here shows that new techniques must be developed to make microalgae production more competitive. Downstream pigment purification technologies must be developed as they may have a considerable impact on the economic viability of the process. Government incentives are needed to encourage a constructive interaction between academics and businesses in order to develop a biorefinery that focuses on high-grade chemicals.
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Affiliation(s)
| | | | - Sónia P. M. Ventura
- Chemistry Department, CICECO-Aveiro Institute of Materials, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (M.K.); (J.A.P.C.)
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Factors influencing circulating microRNAs as biomarkers for liver diseases. Mol Biol Rep 2022; 49:4999-5016. [DOI: 10.1007/s11033-022-07170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022]
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Effects of quercetin on the alterations of serum elements in chronic unpredictable mild stress-induced depressed rats. Biometals 2021; 34:589-602. [PMID: 33745087 DOI: 10.1007/s10534-021-00298-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/06/2021] [Indexed: 12/24/2022]
Abstract
Depression is a common and serious psychiatric disorder, but current conventional antidepressants have limited efficacy and significant side effects. Thus, better antidepressants are urgently needed. This study aimed to investigate the antidepressant-like effects and potential mechanism of quercetin by evaluating the changes of serum elements in chronic unpredictable mild stress (CUMS) rats. Based on the results of the sucrose preference test (SPT), 96 rats were randomly assigned to six groups: control, different dosages of quercetin (10 and 50 mg/kg·bw, respectively), depressed, and different dosages quercetin plus depressed groups. After 8 weeks of CUMS modeling, rat serum was collected. Fifteen elements in serum were analyzed by inductively coupled plasma mass spectrometry (ICP-MS), and related enzyme indicators, antioxidant indicators, and inflammatory cytokines were detected to further explore the potential mechanism. Besides, the accuracy and precision of the method were evaluated. The results showed that the levels of iron (Fe), copper (Cu), and calcium (Ca) in serum significantly increased (p ≤ 0.001), while the levels of magnesium (Mg), zinc (Zn), selenium (Se), and cobalt (Co) significantly decreased (p ≤ 0.001) in depressed group compared with the control group. The levels of the remaining eight elements did not change significantly. When high-dose quercetin was administered to depressed rats, the levels of the above seven elements significantly restored (p ≤ 0.001). This study suggests that quercetin (50 mg/kg·bw) has a regulatory effect on serum elements in CUMS rats, which may be mediated by reducing oxidative stress, inhibiting inflammation, and regulating a variety of neurotransmitter systems.
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Pan DS, Yan M, Hassan M, Fang ZB, Chen MT. Plasma 8-iso-Prostaglandin F2α, a possible prognostic marker in aneurysmal subarachnoid hemorrhage. Clin Chim Acta 2017; 469:166-170. [PMID: 28408198 DOI: 10.1016/j.cca.2017.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND 8-iso-Prostaglandin F2α (8-iso-PGF2α) is a potential biomarker of oxidative stress. This study clarified whether plasma 8-iso-PGF2α concentrations were affected and its underlying relevance to prognosis in aneurysmal subarachnoid hemorrhage (aSAH). METHODS In this prospective, observational study, a total of 170 controls and 170 aSAH patients were enrolled. Plasma 8-iso-PGF2α concentrations were detected using an ELISA. Severity was assessed by World Federation of Neurological Surgeons (WFNS) scale and modified Fisher grading scale. Clinical outcomes included 6-month mortality and poor outcome referred to as Glasgow outcome scale score of 1-3. RESULTS As compared to controls, admission plasma 8-iso-PGF2α concentrations were significantly enhanced. Increased concentrations of plasma 8-iso-PGF2α correlated with WFNS scores and modified Fisher scores. 8-iso-PGF2α in plasma was an independent predictor for clinical outcomes. Under ROC curve, the predictive values of 8-iso-PGF2α concentrations resembled those of WFNS scores and modified Fisher scores for clinical outcomes. CONCLUSIONS An elevation in plasma 8-iso-PGF2α concentrations is associated with the severity and poor outcome after aSAH, substantializing 8-iso-PGF2α as a potential prognostic biomarker of aSAH.
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Affiliation(s)
- De-Sheng Pan
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China.
| | - Min Yan
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
| | - Muhammad Hassan
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
| | - Ze-Bin Fang
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
| | - Man-Tao Chen
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
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Kurutas EB, Ozturk P. The evaluation of local oxidative/nitrosative stress in patients with pityriasis versicolor: a preliminary study. Mycoses 2016; 59:720-725. [DOI: 10.1111/myc.12522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/22/2016] [Accepted: 05/16/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Ergul Belge Kurutas
- Department of Medical Biochemistry; Faculty of Medicine; Sutcu Imam University; Kahramanmaras Turkey
| | - Perihan Ozturk
- Department of Dermatology; Faculty of Medicine; Sutcu Imam University; Kahramanmaras Turkey
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Abstract
Fungal infections, which are named according to the body site involved, can affect any skin area, the fingernails, or the toenails. Numerous fungal agents are responsible for both superficial and deep fungal diseases. Dermatophytes and Candida spp are the most common causative organisms on the surface of the hands, feet, and nails of patients with superficial fungal diseases; however, although deep fungal infections of the skin are less common compared with superficial fungal diseases, their incidence is increasing worldwide due to cross-border travel. Most superficial fungal diseases are diagnosed clinically, but sometimes direct microscopic examination with potassium hydroxide and fungal culture may be necessary for diagnosis, especially in patients suspected of having tinea incognito. In cases of superficial fungal infections except for onychomycosis and tinea incognito, topical treatments are usually sufficient and effective, but systemic treatments may be required in recalcitrant cases. Deep fungal diseases may resemble each other clinically; therefore, the organism must be identified with laboratory methods and should be treated for a long period. We review the most important clinical, diagnostic, and therapeutic aspects of fungal diseases. This paper covers fungal problems encountered both in hospitals and in general practice.
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Kurutas EB. The importance of antioxidants which play the role in cellular response against oxidative/nitrosative stress: current state. Nutr J 2016; 15:71. [PMID: 27456681 PMCID: PMC4960740 DOI: 10.1186/s12937-016-0186-5] [Citation(s) in RCA: 997] [Impact Index Per Article: 124.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/29/2016] [Indexed: 02/06/2023] Open
Abstract
Remarkable interest has risen in the idea that oxidative/nitrosative stress is mediated in the etiology of numerous human diseases. Oxidative/Nitrosative stress is the result of an disequilibrium in oxidant/antioxidant which reveals from continuous increase of Reactive Oxygen and Reactive Nitrogen Species production. The aim of this review is to emphasize with current information the importance of antioxidants which play the role in cellular responce against oxidative/nitrosative stress, which would be helpful in enhancing the knowledge of any biochemist, pathophysiologist, or medical personnel regarding this important issue. Products of lipid peroxidation have commonly been used as biomarkers of oxidative/nitrosative stress damage. Lipid peroxidation generates a variety of relatively stable decomposition end products, mainly α, β-unsaturated reactive aldehydes, such as malondialdehyde, 4-hydroxy-2-nonenal, 2-propenal (acrolein) and isoprostanes, which can be measured in plasma and urine as an indirect index of oxidative/nitrosative stress. Antioxidants are exogenous or endogenous molecules that mitigate any form of oxidative/nitrosative stress or its consequences. They may act from directly scavenging free radicals to increasing antioxidative defences. Antioxidant deficiencies can develop as a result of decreased antioxidant intake, synthesis of endogenous enzymes or increased antioxidant utilization. Antioxidant supplementation has become an increasingly popular practice to maintain optimal body function. However, antoxidants exhibit pro-oxidant activity depending on the specific set of conditions. Of particular importance are their dosage and redox conditions in the cell.
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Affiliation(s)
- Ergul Belge Kurutas
- Department of Medical Biochemistry, Faculty of Medicine, Sutcu Imam University, Avsar Campus, Kahramanmaras, 46050, Turkey.
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