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Karadağ D, Ergon MC. Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS. Microbiol Spectr 2024; 12:e0063824. [PMID: 38940589 PMCID: PMC11302275 DOI: 10.1128/spectrum.00638-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods [MBT Sepsityper IVD Kit (Bruker Daltonics GmbH, Germany), sodium dodecyl sulfate (SDS) lysis, and differential centrifugation with protein extraction (Centrifugation +PE)] and compared in standard and Sepsityper modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from 240 positive blood culture bottles of BACTEC FX (Becton Dickinson, USA). By using the standard module, correct identification at species level (score ≥2) was done in 46.7% of the samples with SDS lysis, 44.2% with centrifugation +PE, and 25.4% with the Sepsityper kit. These ratios at the genus level (score range 1.70-1.99) were 34.6%, 31.3%, and 32.5%, respectively. With SDS lysis (195), more bacteria were identified correctly than centrifugation +PE (181) and the Sepsityper kit (139). A statistically significant difference was found between SDS and the Sepsityper kit and Centrifugation +PE and the Sepsityper kit (P < 0.001, both). By using the Sepsityper module, correct identification at species level (score ≥1.8) was determined in 74.2% of the samples with SDS lysis and centrifugation +PE each and 55% with the Sepsityper kit. These ratios at the genus level (score range 1.60-1.79) were 16.3%, 10%, and 19.2%, respectively. SDS lysis (217) had significantly higher identification rates than centrifugation +PE (202) and the Sepsityper kit (178) (P = 0.028 and P < 0.001). A statistically significant difference was also observed between centrifugation +PE and the Sepsityper kit (P < 0.001). Best performance was obtained with SDS lysis among the methods. Although better performance was achieved by using Sepsityper software module, risk of misidentification should not be ignored. IMPORTANCE Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.
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Affiliation(s)
- Dilan Karadağ
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- IMD Labor Oderland, Frankfurt (Oder), Germany
| | - Mahmut Cem Ergon
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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de Brito ACF, Sousa SMD, Morais HLOD, Costa PHMD, Medrado NV, Prado MDC, Barcelos ID, Alvarenga ÉCD, Neves BRA, Barboza APM, Manhabosco TM. Cutting-edge collagen biocomposite reinforced with 2D nano-talc for bone tissue engineering. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 60:102756. [PMID: 38851439 DOI: 10.1016/j.nano.2024.102756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/23/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
The advancement of nanobiocomposites reinforced with 2D nano-materials plays a pivotal role in enhancing bone tissue engineering. In this study, we introduce a nanobiocomposite that reinforces bovine collagen with 2D nano-talc, a recently exfoliated nano-mineral. These nanobiocomposites were prepared by blending collagen with varying concentrations of 2D nano-talc, encompassing mono- and few-layers talc from soapstone nanomaterial. Extensive characterization techniques including AFM, XPS, nano-FTIR, s-SNOM nanoimaging, Force Spectroscopy, and PeakForce QNM® were employed. The incorporation of 2D nano-talc significantly enhanced the mechanical properties of the nanobiocomposites, resulting in increased stiffness compared to pristine collagen. In vitro studies supported the growth and proliferation of osteoblasts onto 2D nano-talc-reinforced nanobiocomposites, as well as showed the highest mineralization potential. These findings highlight the substantial potential of the developed nanobiocomposite as a scaffold material for bone tissue engineering applications.
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Affiliation(s)
- Ana Carolina Ferreira de Brito
- Physics Department, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, 35400-000 Ouro Preto, MG, Brazil; Physics Department, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil.
| | | | | | | | - Nathanael Vieira Medrado
- Departamento de Bioquímica e Imunologia, Laboratório de Sinalização Celular e Nanobiotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Mariana de Castro Prado
- Physics Department, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
| | - Ingrid David Barcelos
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Érika Costa de Alvarenga
- Departamento de Ciências Naturais, Universidade Federal de São João Del Rei, 36301-160 São João Del Rei, MG, Brazil; Departamento de Bioquímica e Imunologia, Laboratório de Sinalização Celular e Nanobiotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Bernardo Ruegger Almeida Neves
- Physics Department, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Ana Paula Moreira Barboza
- Physics Department, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
| | - Taíse Matte Manhabosco
- Physics Department, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
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3
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Babaei Zarch M, Bazargan M, Mirzaei M. Selective Hydrolysis of Ovalbumin by Zr-Based Lacunary Polyoxotungstate in Surfactant Solutions. Inorg Chem 2024; 63:6141-6151. [PMID: 38530420 DOI: 10.1021/acs.inorgchem.3c03411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
This study aims to design an artificial metalloprotease based on a Zr-containing polyoxometalate Na8[Zr(W5O18)2] [Zr(W5)2] for the hydrolysis of ovalbumin (OVA) in the presence of different surfactants, which can be used in many areas of the biological and medical sciences, particularly for targeted proteolytic drug design. For this reason, parameters, including the free energy of binding, the chemical nature of amino acid residues, secondary structures, and electrostatic potentials, of Zr(W5)2-OVA and Zr(W5)2-OVA-surfactant were analyzed by molecular docking simulations. The investigations showed that the presence of surfactants decreases the binding affinity of Zr(W5)2 for OVA amino acids, and hydrogen bonds and van der Waals interactions are formed between Zr(W5)2 and OVA amino acids. Additionally, GROMACS further illustrated the significance of SDS and CTAB surfactants in influencing the conformational changes of the OVA that lead to selective protein hydrolysis. In agreement with molecular dynamics simulation results, the experimental analysis showed more protein hydrolysis for the Zr(W5)2-OVA-surfactant systems. For instance, circular dichroism spectroscopy indicated that Zr(W5)2-OVA-CTAB and Zr(W5)2-OVA-TX-100 were more hydrolytically efficient due to the increased level of β-structures rather than α-chains, which showed that surfactants can facilitate the accessibility of Zr(W5)2 to the cleavage sites by inducing partial unfolding of the OVA structure.
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Affiliation(s)
- Malihe Babaei Zarch
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Maryam Bazargan
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Masoud Mirzaei
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
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4
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Ferreira AM, Sales I, Santos SAO, Santos T, Nogueira F, Mattedi S, Pinho SP, Coutinho JA, Freire MG. Enhanced Antimalarial Activity of Extracts of Artemisia annua L. Achieved with Aqueous Solutions of Salicylate Salts and Ionic Liquids. CHEM & BIO ENGINEERING 2024; 1:44-52. [PMID: 38434799 PMCID: PMC10906083 DOI: 10.1021/cbe.3c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/12/2023] [Accepted: 12/06/2023] [Indexed: 03/05/2024]
Abstract
Artemisinin, a drug used to treat malaria, can be chemically synthesized or extracted from Artemisia annua L. However, the extraction method for artemisinin from biomass needs to be more sustainable while maintaining or enhancing its bioactivity. This work investigates the use of aqueous solutions of salts and ionic liquids with hydrotropic properties as alternative solvents for artemisinin extraction from Artemisia annua L. Among the investigated solvents, aqueous solutions of cholinium salicylate and sodium salicylate were found to be the most promising. To optimize the extraction process, a response surface method was further applied, in which the extraction time, hydrotrope concentration, and temperature were optimized. The optimized conditions resulted in extraction yields of up to 6.50 and 6.44 mg·g-1, obtained with aqueous solutions of sodium salicylate and cholinium salicylate, respectively. The extracts obtained were tested for their antimalarial activity, showing a higher efficacy against the Plasmodium falciparum strain compared with pure (synthetic) artemisinin or extracts obtained with conventional organic solvents. Characterization of the extracts revealed the presence of artemisinin together with other compounds, such as artemitin, chrysosplenol D, arteannuin B, and arteannuin J. These compounds act synergistically with artemisinin and enhance the antimalarial activity of the obtained extracts. Given the growing concern about artemisinin resistance, the results here obtained pave the way for the development of sustainable and biobased antimalarial drugs.
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Affiliation(s)
- Ana M. Ferreira
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Isabela Sales
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Escola
Politécnica, Universidade Federal
da Bahia, Bahia 40210-630, Brazil
| | - Sónia A. O. Santos
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Tiago Santos
- Global
Health and Tropical Medicine, GHTM, Associate Laboratory in Translation
and Innovation towards Global Health, LA-REAL, Instituto de Higiene
e Medicina Tropical, IHMT, Universidade
Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Fátima Nogueira
- Global
Health and Tropical Medicine, GHTM, Associate Laboratory in Translation
and Innovation towards Global Health, LA-REAL, Instituto de Higiene
e Medicina Tropical, IHMT, Universidade
Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
- LAQV-REQUIMTE,
MolSyn, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Silvana Mattedi
- Escola
Politécnica, Universidade Federal
da Bahia, Bahia 40210-630, Brazil
| | - Simão P. Pinho
- Mountain
Research Center − CIMO, Polytechnic
Institute of Bragança, Bragança 5300-253, Portugal
- SusTEC, Instituto Politécnico de Bragança, Bragança 5300-253, Portugal
| | - João A.
P. Coutinho
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mara G. Freire
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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5
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Arya R, Hudson BC, Green TD. Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells. J Forensic Sci 2023; 68:2116-2127. [PMID: 37779342 DOI: 10.1111/1556-4029.15371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023]
Abstract
While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25-200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.
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Affiliation(s)
- Rhea Arya
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Brittany C Hudson
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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Das A, Ahmed Z, Xu L, Jia W. Assessment and verification of chemical inactivation of peste des petits ruminants virus by virus isolation following virus capture using Nanotrap magnetic virus particles. Microbiol Spectr 2023; 11:e0068923. [PMID: 37655907 PMCID: PMC10580900 DOI: 10.1128/spectrum.00689-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 09/02/2023] Open
Abstract
This study reports development and optimization of a new method for the assessment and verification of the inactivation of peste des petits ruminants virus (PPRV) by chemical agents, including Triton X-100 and commercially available viral lysis buffers. Virus inactivation was confirmed by virus isolation (VI) on Vero cells following capture of the potential residual viruses from treated samples using Nanotrap magnetic virus particles (NMVPs). Since chemical agents are cytotoxic, treated PPRV samples could not be used directly for VI on Vero cell monolayers; instead, they were diluted in Eagle's Minimum Essential Medium (EMEM) to neutralize cytotoxicity and then subjected to virus capture using NMVPs. The NMVPs and the captured viruses were then clarified on a magnetic stand, reconstituted in EMEM, and inoculated onto Vero cells that were examined for cytopathic effect (CPE). No CPE was observed on cells inoculated with treated viruses captured by NMVPs; but CPE was observed on cells inoculated with untreated viruses, including those captured by NMVPs. For further verification, the supernatants of the VI cultures (treated or untreated) were subjected to RNA extraction and PPRV-specific real-time RT-PCR (RT-qPCR). The cycle threshold values were undetectable for the supernatants of VI cultures inoculated with NMVPs reconstituted from treated PPRV but detectable for the supernatants of VI cultures inoculated with untreated PPRV or the NMVPs reconstituted from untreated PPRV, indicating complete inactivation of PPRV. This new method of verification of virus inactivation using NMVPs can be applied to other high impact viruses of agricultural or public health importance. IMPORTANCE Research including diagnosis on highly contagious viruses at the molecular level such as PCR and next-generation sequencing requires complete inactivation of the virus to ensure biosafety and biosecurity so that any accidental release of the virus does not compromise the safety of the susceptible population and the environment. In this work, peste des petits ruminants virus (PPRV) was inactivated with chemical agents, and the virus inactivation was confirmed by virus isolation (VI) using Vero cells. Since the chemical agents are cytotoxic, inactivated virus (PPRV) was diluted 1:100 to neutralize cytotoxicity, and the residual viruses (if any) were captured using Nanotrap magnetic virus particles (NMVPs). The NMVPs and the captured viruses were subjected to VI. No CPE was observed, indicating complete inactivation, and the results were further supported by real-time RT-PCR. This new protocol to verify virus inactivation can be applicable to other viruses.
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Affiliation(s)
- Amaresh Das
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Zaheer Ahmed
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Lizhe Xu
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Wei Jia
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
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Al Shboul A, Ketabi M, Skaf D, Nyayachavadi A, Lai Fak Yu T, Rautureau T, Rondeau-Gagné S, Izquierdo R. Graphene Inks Printed by Aerosol Jet for Sensing Applications: The Role of Dispersant on the Inks' Formulation and Performance. SENSORS (BASEL, SWITZERLAND) 2023; 23:7151. [PMID: 37631688 PMCID: PMC10458541 DOI: 10.3390/s23167151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
This study presents graphene inks produced through the liquid-phase exfoliation of graphene flakes in water using optimized concentrations of dispersants (gelatin, triton X-100, and tween-20). The study explores and compares the effectiveness of the three different dispersants in creating stable and conductive inks. These inks can be printed onto polyethylene terephthalate (PET) substrates using an aerosol jet printer. The investigation aims to identify the most suitable dispersant to formulate a high-quality graphene ink for potential applications in printed electronics, particularly in developing chemiresistive sensors for IoT applications. Our findings indicate that triton X-100 is the most effective dispersant for formulating graphene ink (GTr), which demonstrated electrical conductivity (4.5 S·cm-1), a high nanofiller concentration of graphene flakes (12.2%) with a size smaller than 200 nm (<200 nm), a low dispersant-to-graphene ratio (5%), good quality as measured by Raman spectroscopy (ID/IG ≈ 0.27), and good wettability (θ ≈ 42°) over PET. The GTr's ecological benefits, combined with its excellent printability and good conductivity, make it an ideal candidate for manufacturing chemiresistive sensors that can be used for Internet of Things (IoT) healthcare and environmental applications.
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Affiliation(s)
- Ahmad Al Shboul
- Department of Electrical Engineering, École de Technologie Supérieure, Montréal, QC H3C 1K3, Canada (T.R.)
| | - Mohsen Ketabi
- Department of Electrical Engineering, École de Technologie Supérieure, Montréal, QC H3C 1K3, Canada (T.R.)
| | - Daniella Skaf
- Department of Chemistry and Biochemistry, Advanced Materials Centre of Research, University of Windsor, Windsor, ON N9B 3P4, Canada (A.N.); (S.R.-G.)
| | - Audithya Nyayachavadi
- Department of Chemistry and Biochemistry, Advanced Materials Centre of Research, University of Windsor, Windsor, ON N9B 3P4, Canada (A.N.); (S.R.-G.)
| | - Thierry Lai Fak Yu
- Department of Electrical Engineering, École de Technologie Supérieure, Montréal, QC H3C 1K3, Canada (T.R.)
| | - Tom Rautureau
- Department of Electrical Engineering, École de Technologie Supérieure, Montréal, QC H3C 1K3, Canada (T.R.)
| | - Simon Rondeau-Gagné
- Department of Chemistry and Biochemistry, Advanced Materials Centre of Research, University of Windsor, Windsor, ON N9B 3P4, Canada (A.N.); (S.R.-G.)
| | - Ricardo Izquierdo
- Department of Electrical Engineering, École de Technologie Supérieure, Montréal, QC H3C 1K3, Canada (T.R.)
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Drescher DG, Drescher MJ, Selvakumar D, Annam NP. Analysis of Dysferlin Direct Interactions with Putative Repair Proteins Links Apoptotic Signaling to Ca 2+ Elevation via PDCD6 and FKBP8. Int J Mol Sci 2023; 24:4707. [PMID: 36902136 PMCID: PMC10002499 DOI: 10.3390/ijms24054707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Quantitative surface plasmon resonance (SPR) was utilized to determine binding strength and calcium dependence of direct interactions between dysferlin and proteins likely to mediate skeletal muscle repair, interrupted in limb girdle muscular dystrophy type 2B/R2. Dysferlin canonical C2A (cC2A) and C2F/G domains directly interacted with annexin A1, calpain-3, caveolin-3, affixin, AHNAK1, syntaxin-4, and mitsugumin-53, with cC2A the primary target and C2F lesser involved, overall demonstrating positive calcium dependence. Dysferlin C2 pairings alone showed negative calcium dependence in almost all cases. Like otoferlin, dysferlin directly interacted via its carboxy terminus with FKBP8, an anti-apoptotic outer mitochondrial membrane protein, and via its C2DE domain with apoptosis-linked gene (ALG-2/PDCD6), linking anti-apoptosis with apoptosis. Confocal Z-stack immunofluorescence confirmed co-compartmentalization of PDCD6 and FKBP8 at the sarcolemmal membrane. Our evidence supports the hypothesis that prior to injury, dysferlin C2 domains self-interact and give rise to a folded, compact structure as indicated for otoferlin. With elevation of intracellular Ca2+ in injury, dysferlin would unfold and expose the cC2A domain for interaction with annexin A1, calpain-3, mitsugumin 53, affixin, and caveolin-3, and dysferlin would realign from its interactions with PDCD6 at basal calcium levels to interact strongly with FKBP8, an intramolecular rearrangement facilitating membrane repair.
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Affiliation(s)
- Dennis G. Drescher
- Laboratory of Bio-otology, Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Marian J. Drescher
- Laboratory of Bio-otology, Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Dakshnamurthy Selvakumar
- Laboratory of Bio-otology, Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Neeraja P. Annam
- Laboratory of Bio-otology, Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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9
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Guntawang T, Sittisak T, Srivorakul S, Photichai K, Aiumurai P, Thitaram C, Sthitmatee N, Hsu WL, Sookrung N, Pringproa K. Development of an immunochromatographic strip test for antigen detection of elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus). J Virol Methods 2023; 311:114627. [PMID: 36191664 DOI: 10.1016/j.jviromet.2022.114627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/11/2022] [Accepted: 09/27/2022] [Indexed: 02/03/2023]
Abstract
Elephant endotheliotropic herpesvirus (EEHV) is the causative agent of EEHV-hemorrhagic disease (EEHV-HD) in elephants worldwide. This disease is highly virulent and a predominant cause of fatalities in young Asian elephants. Rapid diagnosis and aggressive therapies have been determined to be a key strategy in the successful treatment of this disease. Herein, we have developed the immunochromatographic strip test for EEHV detection. Accordingly, 31.2 kDa of partial EEHV DNA polymerase (DNApol) protein was expressed in Escherichia coli and used to generate rabbit polyclonal anti-EEHV DNApol antibodies. These were then used to develop an ICS test for EEHV antigen detection using the double-antibody sandwich colloidal gold method. Anti-EEHV DNApol antibodies conjugated with 40 nm colloidal gold solution were used as a detector, while rabbit anti-EEHV DNApol and goat anti-rabbit IgG antibodies immobilized on the nitrocellulose membrane were used as the test and control lines, respectively. The test had a detection limit of 1.25 × 105 viral genome copies (vgc)/mL of EEHV obtained from blood samples. Moreover, no specialized equipment or laboratory infrastructure was required in the administration of this test. This developed ICS test for EEHV antigen detection can be used in field application for the rapid detection of EEHV in resource-limited environments.
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Affiliation(s)
- Thunyamas Guntawang
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Tidaratt Sittisak
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Saralee Srivorakul
- Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Kornravee Photichai
- Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Pisinee Aiumurai
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Chiang Mai University, Chiang Mai 50100, Thailand; Department of Companion Animals and Wildlife Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Nattawooti Sthitmatee
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Nitat Sookrung
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kidsadagon Pringproa
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; Center of Elephant and Wildlife Health, Chiang Mai University, Chiang Mai 50100, Thailand.
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10
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Danko K, Lukasheva E, Zhukov VA, Zgoda V, Frolov A. Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. Int J Mol Sci 2022; 23:13903. [PMID: 36430380 PMCID: PMC9695859 DOI: 10.3390/ijms232213903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
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Affiliation(s)
- Katerina Danko
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin, 196608 St. Petersburg, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrej Frolov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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11
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Hasan T, Mahbub S, Kumar D, Gatasheh MK, R. Joy MT, Goni MA, Rana S, Hoque MA. Phase separation and thermodynamics of the mixture of metformin hydrochloride + triton X-100 in ammonium salts media: impacts of composition of media. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2121776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Tajmul Hasan
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
| | - Shamim Mahbub
- Nuclear Safety, Security & Safeguards Division, Bangladesh Atomic Energy Regulatory Authority, Dhaka, Bangladesh
| | - Dileep Kumar
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Md. Tuhinur R. Joy
- Department of Chemistry, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Abdul Goni
- Department of Biological and Physical Sciences, South Carolina State University, Orangeburg, SC, USA
| | - Shahed Rana
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Anamul Hoque
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
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12
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Chetoni P, Burgalassi S, Zucchetti E, Granchi C, Minutolo F, Tampucci S, Monti D. MAGL inhibitor NanoMicellar formulation (MAGL-NanoMicellar) for the development of an antiglaucoma eye drop. Int J Pharm 2022; 625:122078. [PMID: 35932931 DOI: 10.1016/j.ijpharm.2022.122078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/04/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022]
Abstract
The ocular endocannabinoid system (ECS) including enzymes and CB1/CB2 receptors determines various substantial effects, such as anti-inflammatory activity and reduction of the intraocular pressure (IOP). The modulation of 2-arachidonoylglycerol (2-AG) levels obtained via MAGL inhibition is considered as a promising pharmacological strategy to activate the ECS. Within the scope of this study, the effect of a selective monoacylglycerol lipase (MAGL) inhibitor (MAGL17b) was investigated by measuring the IOP reduction in normotensive rabbits after performing a solubilisation process of the molecule with non-ionic surfactants, to produce suitable eye drops containing the highest possible concentration of the drug. Furthermore, the study involved the evaluation of cytotoxicity and of in vitro/ex vivo corneal permeation of MAG17b of selected formulations based on polyoxyl(35)castor oil (C-EL) and polyethylene glycol (80) sorbitan monolaurate (TW80). The solubilisation of 0.5 mM MAGL17b with 3% w/w TW80 (TW80/3-17b), through the formation of NanoMicellar structures (diameter of 12.3 nm), determined a significant permeation of MAGL17b, both through excised rabbits corneas and reconstituted corneal epithelium, with a limited corneal epithelial cells death. The blockade of MAGL activity induced a IOP reduction up to 4 mmHg in albino and pigmented rabbits after topical instillation, thus confirming the potential efficacy of the MAGL inhibition approach in the treatment of ocular pathologies.
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Affiliation(s)
- Patrizia Chetoni
- Department of Pharmacy, University of Pisa, Pisa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
| | - Susi Burgalassi
- Department of Pharmacy, University of Pisa, Pisa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
| | | | | | | | - Silvia Tampucci
- Department of Pharmacy, University of Pisa, Pisa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
| | - Daniela Monti
- Department of Pharmacy, University of Pisa, Pisa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
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13
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Büyük Nİ, Tüfekçi K, Cumbul A, Ayşan E, Torun Köse G. A novel method for providing scaffold: Decellularization of parathyroid capsule. J Biomater Appl 2021; 36:1201-1212. [PMID: 34918999 DOI: 10.1177/08853282211054321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study aimed to generate a novel biomatrix from the decellularized human parathyroid capsule using different methods and to compare the efficiency of decellularization in the means of cell removal, structural integrity and extracellular matrix preservation. The parathyroid capsules, which were carefully dissected from the parathyroid tissue, were randomly divided into four groups and then decellularized using three different protocols: freeze-thaw only, sodium dodecyl sulphate and Triton X-100 treatments after freeze-thawing. Quantitative DNA analysis, agarose gel electrophoresis, sulphated glycosaminoglycan assay, histological analysis, immunohistochemistry and scanning electron microscopy were used to observe the efficiency of parathyroid capsule decellularization and preservation of extracellular matrix components. Considering all the results, it can be said that only freeze-thawing is not an effective method in parathyroid capsule decellularization. When the tissue was treated with a detergent agent in addition to freeze-thawing, the amount of DNA decreased by 90% while sulphated glycosaminoglycan amount maintained 50% compared to untreated tissue. Comparing the effects of the two detergents on the preservation of extracellular matrix such as collagen and sulphated glycosaminoglycan, it was seen that the integrity of tissues treated with Triton X-100 was preserved more than tissues treated with sodium dodecyl sulphate. It is concluded that Triton X-100 treatment with freeze-thawing is the most suitable and effective method for decellularizing the human parathyroid capsule. The biomatrix obtained with this method can be applied in the transplantation of parathyroid tissue and other endocrine tissue types in the body.
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Affiliation(s)
- Nisa İrem Büyük
- Genetics & Bioengineering, 52998Yeditepe University, Istanbul, Turkey
| | - Kardelen Tüfekçi
- Genetics & Bioengineering, 52998Yeditepe University, Istanbul, Turkey
| | - Alev Cumbul
- Histology and Embryology, 52998Yeditepe University, Istanbul, Turkey
| | - Erhan Ayşan
- General Surgery, 64173Yeditepe Üniversity Hospital, Istanbul, Turkey
| | - Gamze Torun Köse
- Genetics & Bioengineering, 52998Yeditepe University, Istanbul, Turkey
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14
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Holl J, Pawlukianiec C, Corton Ruiz J, Groth D, Grubczak K, Hady HR, Dadan J, Reszec J, Czaban S, Kowalewski C, Moniuszko M, Eljaszewicz A. Skin Substitute Preparation Method Induces Immunomodulatory Changes in Co-Incubated Cells through Collagen Modification. Pharmaceutics 2021; 13:2164. [PMID: 34959443 PMCID: PMC8705760 DOI: 10.3390/pharmaceutics13122164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
Chronic ulcerative and hard-healing wounds are a growing global concern. Skin substitutes, including acellular dermal matrices (ADMs), have shown beneficial effects in healing processes. Presently, the vast majority of currently available ADMs are processed from xenobiotic or cadaveric skin. Here we propose a novel strategy for ADM preparation from human abdominoplasty-derived skin. Skin was processed using three different methods of decellularization involving the use of ionic detergent (sodium dodecyl sulfate; SDS, in hADM 1), non-ionic detergent (Triton X-100 in hADM 2), and a combination of recombinant trypsin and Triton X-100 (in hADM 3). We next evaluated the immunogenicity and immunomodulatory properties of this novel hADM by using an in vitro model of peripheral blood mononuclear cell culture, flow cytometry, and cytokine assays. We found that similarly sourced but differentially processed hADMs possess distinct immunogenicity. hADM 1 showed no immunogenic effects as evidenced by low T cell proliferation and no significant change in cytokine profile. In contrast, hADMs 2 and 3 showed relatively higher immunogenicity. Moreover, our novel hADMs exerted no effect on T cell composition after three-day of coincubation. However, we observed significant changes in the composition of monocytes, indicating their maturation toward a phenotype possessing anti-inflammatory and pro-angiogenic properties. Taken together, we showed here that abdominoplasty skin is suitable for hADM manufacturing. More importantly, the use of SDS-based protocols for the purposes of dermal matrix decellularization allows for the preparation of non-immunogenic scaffolds with high therapeutic potential. Despite these encouraging results, further studies are needed to evaluate the beneficial effects of our hADM 1 on deep and hard-healing wounds.
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Affiliation(s)
- Jordan Holl
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
| | - Cezary Pawlukianiec
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
| | - Javier Corton Ruiz
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
| | - Dawid Groth
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
| | - Kamil Grubczak
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
| | - Hady Razak Hady
- 1st Clinical Department of General and Endocrine Surgery, Faculty of Medicine, Medical University of Białystok, 15-276 Białystok, Poland; (H.R.H.); (J.D.)
| | - Jacek Dadan
- 1st Clinical Department of General and Endocrine Surgery, Faculty of Medicine, Medical University of Białystok, 15-276 Białystok, Poland; (H.R.H.); (J.D.)
| | - Joanna Reszec
- Department of Medical Pathomorphology, Faculty of Medicine, Medical University of Białystok, 15-269 Białystok, Poland;
| | - Slawomir Czaban
- Department of Anesthesiology & Intensive Therapy, Faculty of Medicine, Medical University of Białystok, 15-276 Białystok, Poland;
| | - Cezary Kowalewski
- Department of Dermatology and Immunodermatology, Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
- Department of Allergology and Internal Medicine, Faculty of Health Sciences, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Andrzej Eljaszewicz
- Department of Regenerative Medicine and Immune Regulation, Faculty of Medicine, Medical University of Bialystok, 15-269 Białystok, Poland; (J.H.); (C.P.); (J.C.R.); (D.G.); (K.G.)
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15
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Conductivity and cloud point studies of the interaction of lomefloxacin hydrochloride with anionic and nonionic surfactants in electrolytes solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Gupta A, Costa AP, Xu X, Burgess DJ. Continuous processing of paclitaxel polymeric micelles. Int J Pharm 2021; 607:120946. [PMID: 34333023 DOI: 10.1016/j.ijpharm.2021.120946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/15/2022]
Abstract
A continuous polymeric micelle processing platform was successfully developed, which eliminated batch-to-batch variation in critical quality attributes (for example, size and polydispersity that are typically associated with batch processing). A continuous precipitation process was achieved via coaxial turbulent jet in co-flow technology allowing precise control of particle size with average particle size in the range 15 to 70 nm and low polydispersity. Critical relationships between material attributes (e.g., block copolymer design), process parameters (e.g., polymer concentration, organic to aqueous flow rate ratios, and temperature), and critical quality attributes (e.g., size and polydispersity) of the polymeric micelles were realized via multiple designs of experiments studies. Both polymer molecular weight and concentration were shown to influence the micelle polydispersity index. Notably, higher molecular weight polymer required higher processing temperatures to produce monodispersed particles and were generally of larger size. Using optimized conditions, paclitaxel polymeric micelles that are qualitatively and quantitatively equivalent to commercial Genexol PM were produced, exhibiting comparable quality attributes including particle size, size distribution, morphology, drug loading, release characteristics, and stability. Lastly, a dynamic light scattering method was adapted to determine the critical micelle concentration and aggregation number of the block copolymers, providing useful information about the raw material.
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Affiliation(s)
- Anand Gupta
- Department of Pharmaceutical Sciences, UConn, Storrs, CT 06269, United States
| | - Antonio P Costa
- Department of Pharmaceutical Sciences, UConn, Storrs, CT 06269, United States
| | - Xiaoming Xu
- Division of Product Quality Research, OTR/OPQ/CDER/FDA, Silver Spring, MD 20993, United States
| | - Diane J Burgess
- Department of Pharmaceutical Sciences, UConn, Storrs, CT 06269, United States.
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17
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Zhu Y, Zhang Q, Wang S, Zhang J, Fan S, Lin X. Current Advances in the Development of Decellularized Plant Extracellular Matrix. Front Bioeng Biotechnol 2021; 9:712262. [PMID: 34368105 DOI: 10.3389/fbioe.2021.712262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
An imbalance exists between the supply of organs for transplantation and the number of patients in the donor transplant waiting lists. Current use of autologous, synthetic, and animal-derived grafts for tissue replacement is limited by the low availability, poor biocompatibility, and high cost. Decellularized plant scaffolds with remarkable physical similarities to human organs have recently emerged and have been found to present favorable characteristics that make them suitable as an alternative biomaterial, such as a superficial surface area, excellent water transport and retention, pre-existing vascular networks, interconnected porosity, and a wide range of mechanical properties. In addition to their unique and superior biocompatibility, plant-derived scaffolds present the advantages of low production cost, no ethical or supply constraints, simple operation and suitability for large-scale production and research. However, there are still some problems and deficiencies in this field, such as immature decellularization standards and methods, insufficient research on the biocompatibility of plant extracellular matrix. At present, research on decellularized plant extracellular matrix is still in its infancy, and its applicability to tissue engineering needs to be further improved. In this review, the current research progress on decellularized plant scaffolds is reviewed, the problems to be solved and future research directions are discussed.
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Affiliation(s)
- Yiwei Zhu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China.,Department of Orthopaedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qi Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shengyu Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China.,Department of Orthopaedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianfeng Zhang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China
| | - Shunwu Fan
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China
| | - Xianfeng Lin
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China.,Department of Orthopaedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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18
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Trestrail C, Walpitagama M, Miranda A, Nugegoda D, Shimeta J. Microplastics alter digestive enzyme activities in the marine bivalve, Mytilus galloprovincialis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146418. [PMID: 33744572 DOI: 10.1016/j.scitotenv.2021.146418] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Microplastics are eaten by many invertebrates, particularly filter-feeding organisms like mussels. Since microplastics can be retained in the digestive system for extended periods, there is ample opportunity for them to interact with the functions of digestive enzymes. This study determined how the polymer type, size and concentration of ingested spherical microplastics affects the activities of seven key digestive enzymes in the digestive gland of Mytilus galloprovincialis, a common marine mussel. Polymer type significantly affected the activities of carbohydrase enzymes: polystyrene reduced amylase and xylanase activities, and increased cellulase activity. High concentrations of microplastics (5 × 104 microplastics L-1) caused a 2.5-fold increase in total protease activity. The activities of laminarinase, lipases and lipolytic esterases were unaffected by the polymer type, size or concentration of microplastics. Microplastics-induced changes to digestive enzyme activities can affect mussels' ability to acquire energy from food and reduce their energy reserves.
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Affiliation(s)
- Charlene Trestrail
- Ecotoxicology Research Group, RMIT University, Bundoora West Campus, VIC, Australia; School of Science, RMIT University, Bundoora West Campus, VIC, Australia.
| | - Milanga Walpitagama
- School of Science, RMIT University, Bundoora West Campus, VIC, Australia; Aquatic Environmental Stress research group (AQUEST), RMIT University, Bundoora West Campus, VIC, Australia
| | - Ana Miranda
- Aquatic Environmental Stress research group (AQUEST), RMIT University, Bundoora West Campus, VIC, Australia
| | - Dayanthi Nugegoda
- Ecotoxicology Research Group, RMIT University, Bundoora West Campus, VIC, Australia; Aquatic Environmental Stress research group (AQUEST), RMIT University, Bundoora West Campus, VIC, Australia
| | - Jeff Shimeta
- School of Science, RMIT University, Bundoora West Campus, VIC, Australia
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19
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Brian BF, Guerrero CR, Freedman TS. Immunopharmacology and Quantitative Analysis of Tyrosine Kinase Signaling. ACTA ACUST UNITED AC 2021; 130:e104. [PMID: 32931655 PMCID: PMC7583487 DOI: 10.1002/cpim.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this article we describe the use of pharmacological and genetic tools coupled with immunoblotting (Western blotting) and targeted mass spectrometry to quantify immune signaling and cell activation mediated by tyrosine kinases. Transfer of the ATP γ phosphate to a protein tyrosine residue activates signaling cascades regulating the differentiation, survival, and effector functions of all cells, with unique roles in immune antigen receptor, polarization, and other signaling pathways. Defining the substrates and scaffolding interactions of tyrosine kinases is critical for revealing and therapeutically manipulating mechanisms of immune regulation. Quantitative analysis of the amplitude and kinetics of these effects is becoming ever more accessible experimentally and increasingly important for predicting complex downstream effects of therapeutics and for building computational models. Secondarily, quantitative analysis is increasingly expected by reviewers and journal editors, and statistical analysis of biological replicates can bolster claims of experimental rigor and reproducibility. Here we outline methods for perturbing tyrosine kinase activity in cells and quantifying protein phosphorylation in lysates and immunoprecipitates. The immunoblotting techniques are a guide to probing the dynamics of protein abundance, protein–protein interactions, and changes in post‐translational modification. Immunoprecipitated protein complexes can also be subjected to targeted mass spectrometry to probe novel sites of modification and multiply modified or understudied proteins that cannot be resolved by immunoblotting. Together, these protocols form a framework for identifying the unique contributions of tyrosine kinases to cell activation and elucidating the mechanisms governing immune cell regulation in health and disease. © 2020 The Authors. Basic Protocol 1: Quantifying protein phosphorylation via immunoblotting and near‐infrared imaging Alternate Protocol: Visualizing immunoblots using chemiluminescence Basic Protocol 2: Enriching target proteins and isolation of protein complexes by immunoprecipitation Support Protocol: Covalent conjugation of antibodies to functionalized beads Basic Protocol 3: Quantifying proteins and post‐translational modifications by targeted mass spectrometry
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Affiliation(s)
- Ben F Brian
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Candace R Guerrero
- College of Biological Sciences Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, Minnesota
| | - Tanya S Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota.,Center for Immunology, Masonic Cancer Center, Center for Autoimmune Diseases Research, University of Minnesota, Minneapolis, Minnesota
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20
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Tailor-made novel electrospun polystyrene/poly(d,l-lactide-co-glycolide) for oxidoreductases immobilization: Improvement of catalytic properties under extreme reaction conditions. Bioorg Chem 2021; 114:105036. [PMID: 34120021 DOI: 10.1016/j.bioorg.2021.105036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/15/2021] [Accepted: 05/28/2021] [Indexed: 11/24/2022]
Abstract
Immobilized enzymes find applications in many areas such as pharmacy, medicine, food production and environmental protection. However, protecting these biocatalysts against harsh reaction conditions and retaining their enzymatic activity even after several biocatalytic cycles are major challenges. Properly selected supports and type of surface modifier therefore seem to be crucial for achieving high retention of catalytic activity of immobilized biomolecules. Here we propose production of novel composite electrospun fibers from polystyrene/poly(d,l-lactide-co-glycolide) (PS/PDLG) and its application as a support for immobilization of oxidoreductases such as alcohol dehydrogenase (ADH) and laccase (LAC). Two strategies of covalent binding, (i) (3-aminopropyl)triethoxysilane (APTES) with glutaraldehyde (GA) and (ii) polydopamine (PDA), were applied to attach oxidoreductases to PS/PDLG. The average fiber diameter was shown to increase from 1.252 µm to even 3.367 µm after enzyme immobilization. Effective production of PS/PDLG fibers and biomolecule attachment were confirmed by Fourier transform infrared spectroscopy analysis. The highest substrate conversion efficiency was observed at pH 6.5 and 5 for ADH and LAC, respectively, and at 25 °C for enzymes attached using the APTES + GA approach. Improvement of enzyme stabilization at high temperatures was confirmed in that relative activities of enzymes immobilized onto PS/PDLG fibers were over 20% higher than those of the free biomolecules, and enzyme leaching from the support using acetate and MES buffers was below 10 mg/g.
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21
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Emadi E, Khoradmehr A, Shams A, Kalantar SM. Appropriate fixative for MEM-G/9 staining of cultured human HLA-G-positive JEG-3 trophoblast tumor cells. Biotech Histochem 2021; 97:136-142. [PMID: 33910426 DOI: 10.1080/10520295.2021.1916837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Human leukocyte antigen (HLA-G) participates in immunosuppression and is useful for prenatal diagnostics. Isolation of fetal cells positive for HLA-G by HLA-G antibody conjugated nanoparticles from the cervix of pregnant women is the basis for non-invasive prenatal testing. Endocervical specimens are fixed in transport medium before isolation using antibody conjugated nanoparticles. Staining of HLA-G using MEM-G/9 antibody, however, is restricted to unfixed cells. We investigated the effect of several fixatives on the interaction of HLA-G with MEM-G/9 in the HLA-G-positive cell line, JEG-3. We investigated absolute methanol, 1:1 acetate buffer:methanol, Pap solution and paraformaldehyde. The effects of these fixatives were evaluated using immunofluorescence. We found no MEM-G/9 surface staining of methanol fixed cells. Approximately 40% of JEG-3 cells fixed with paraformaldehyde failed to stain. Nearly all cells were stained with MEM-G/9 following fixation with acetate buffer:methanol or Pap solution. Our findings indicate the importance of using an appropriate fixative for preserving HLA-G cell surface antigen for studies using the MEM-G/9 antibody.
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Affiliation(s)
- Elaheh Emadi
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Research Sciences Center Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ali Shams
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Mehdi Kalantar
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Research & Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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22
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Effects of Detergent on α-Synuclein Structure. A Native MS-Ion Mobility Study. Int J Mol Sci 2020; 21:ijms21217884. [PMID: 33114222 PMCID: PMC7660655 DOI: 10.3390/ijms21217884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The intrinsically disordered protein α-synuclein plays a major role in Parkinson’s disease. The protein can oligomerize resulting in the formation of various aggregated species in neuronal cells, leading to neurodegeneration. The interaction of α-synuclein with biological cell membranes plays an important role for specific functions of α-synuclein monomers, e.g., in neurotransmitter release. Using different types of detergents to mimic lipid molecules present in biological membranes, including the presence of Ca2+ ions as an important structural factor, we aimed to gain an understanding of how α-synuclein interacts with membrane models and how this affects the protein conformation and potential oligomerization. We investigated detergent binding stoichiometry, affinity and conformational changes of α-synuclein taking detergent concentration, different detergent structures and charges into account. With native nano-electrospray ionization ion mobility-mass spectrometry, we were able to detect unique conformational patterns resulting from binding of specific detergents to α-synuclein. Our data demonstrate that α-synuclein monomers can interact with detergent molecules irrespective of their charge, that protein-micelle interactions occur and that micelle properties are an important factor.
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Chakraborty J, Roy S, Ghosh S. Regulation of decellularized matrix mediated immune response. Biomater Sci 2020; 8:1194-1215. [PMID: 31930231 DOI: 10.1039/c9bm01780a] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The substantially growing gap between suitable donors and patients waiting for new organ transplantation has compelled tissue engineers to look for suitable patient-specific alternatives. Lately, a decellularized extracellular matrix (dECM), obtained primarily from either discarded human tissues/organs or other species, has shown great promise in the constrained availability of high-quality donor tissues. In this review, we have addressed critical gaps and often-ignored aspects of understanding the innate and adaptive immune response to the dECM. Firstly, although most of the studies claim preservation of the ECM ultrastructure, almost all methods employed for decellularization would inevitably cause a certain degree of disruption to the ECM ultrastructure and modulation in secondary conformations, which may elicit a distinct immunogenic response. Secondly, it is still a major challenge to find ways to conserve the native biochemical, structural and biomechanical cues by making a judicious decision regarding the choice of decellularization agents/techniques. We have critically analyzed various decellularization protocols and tried to find answers on various aspects such as whether the secondary structural conformation of dECM proteins would be preserved after decellularization. Thirdly, to keep the dECM ultrastructure as close to the native ECM we have raised the question "How good is good enough?" Even residual cellular antigens or nucleic acid fragments may elicit antigenicity leading to a low-grade immune response. A combinative knowledge of macrophage plasticity in the decellularized tissue and limits of decellularization will help achieve the native ultrastructure. Lastly, we have shifted our focus on the scientific basis of the presently accepted criteria for decellularization, and the effect on immune response concerning the interaction between the decellularized extracellular matrix and macrophages with the subsequent influence of T-cell activation. Amalgamating suitable decellularization approaches, sufficient knowledge of macrophage plasticity and elucidation of molecular pathways together will help fabricate functional immune informed decellularized tissues in vitro that will have substantial implications for efficient clinical translation and prediction for in vivo reprogramming and tissue regeneration.
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Affiliation(s)
- Juhi Chakraborty
- Regenerative Engineering Laboratory, Department of Textile & Fibre Engineering, Indian Institute of Technology Delhi, 110016 India.
| | - Subhadeep Roy
- Regenerative Engineering Laboratory, Department of Textile & Fibre Engineering, Indian Institute of Technology Delhi, 110016 India.
| | - Sourabh Ghosh
- Regenerative Engineering Laboratory, Department of Textile & Fibre Engineering, Indian Institute of Technology Delhi, 110016 India.
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24
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Bender AT, Sullivan BP, Lillis L, Posner JD. Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics. J Mol Diagn 2020; 22:1030-1040. [PMID: 32450280 DOI: 10.1016/j.jmoldx.2020.04.211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington; Department of Chemical Engineering, University of Washington, Seattle, Washington; Department of Family Medicine, University of Washington, Seattle, Washington.
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25
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Mayer M, Hahn M, Gerstl F, Köwer T, Rink S, Kunz W, Duerkop A, Baeumner AJ. Shedding Light on the Diversity of Surfactant Interactions with Luminol Electrochemiluminescence for Bioanalysis. Anal Chem 2019; 91:13080-13087. [PMID: 31524378 DOI: 10.1021/acs.analchem.9b03275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Luminol is a major probe for chemiluminescence (CL) and electrochemiluminescence (ECL) detection technologies in (bio)analysis. Surfactants are added to ECL assay cocktails to enhance signals or are present, owing to given bioassay protocols, yet little is known regarding their effects on luminol ECL. In-depth understanding is provided here through a broad study with bioanalytically relevant surfactants (cationic, anionic, and nonionic), four common electrode materials, and two luminol derivatives. Naturally, in ECL, surface effects are dominant; however, bulk solution, diffusion, and luminescence-stabilization processes also contribute significantly to the overall reaction. It was found that in contrast to CL the effect surfactants have on luminol ECL cannot be linked to general surfactant characteristics such as ionic nature, hydrophilic lipophilic balance (HLB) value, and critical micellar concentration (CMC). Instead, surfactants act in an all-encompassing mechanism, including surface electrochemistry, their solution and interfacial phases, and the chemical luminescence pathway. This leads to dramatic differences in signals obtained, ranging from 5-fold increases to total quenching. Within this complexity, we defined six guiding principles that are extrapolated from the underlying mechanisms and selection guides for surfactant, electrode, and environmental condition combinations. Those will now assist in developing highly sensitive luminol-ECL-based bioassays, because the surfactant selection can be based not only on properties needed for the assay protocol but also on identifying the optimal electrode-surfactant pair to maximize detection efficiency.
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Affiliation(s)
- Michael Mayer
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Maximilian Hahn
- Institute of Physical and Theoretical Chemistry , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Florian Gerstl
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Thomas Köwer
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Simone Rink
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Werner Kunz
- Institute of Physical and Theoretical Chemistry , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Axel Duerkop
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
| | - Antje J Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors , University of Regensburg , Universitätsstraße 31 , 93053 Regensburg , Germany
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26
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Verma D, Antil M, Gupta V. Recombinant production of active Streptococcus pneumoniae CysE in E. coli facilitated by codon optimized BL21(DE3)-RIL and detergent. Prep Biochem Biotechnol 2019; 49:368-374. [PMID: 30734630 DOI: 10.1080/10826068.2019.1573194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The emergence of drug resistance in Streptococcus pneumoniae (Spn) is a global health threat and necessitates discovery of novel therapeutics. The serine acetyltransferase (also known as CysE) is an enzyme of cysteine biosynthesis pathway and is reported to be essential for the survival of several pathogenic bacteria. Therefore, it appears to be a very attractive target for structure-function understanding and inhibitor design. This study describes the molecular cloning of cysE from Spn in the pET21c vector and efforts carried out for expression and purification of active recombinant CysE. Significant expression of recombinant Spn cysE could be achieved in codon optimized BL21(DE3)-RIL strain as opposed to conventional BL21(DE3) strain. Analysis of codon adaptation index (CAI) with levels of eukaryotic genes and prokaryotic cysEs expressed in heterologous E. coli host suggests that codon optimized E. coli BL21(DE3)-RIL may be a better host for expressing genes with low CAI. Here, an efficient protocol has been developed for recovery of recombinant Spn CysE in soluble and biologically active form by the usage of nonionic detergent Triton X-100 at a concentration as low as 1%. Altogether, this study reports a simple strategy for producing functionally active Spn CysE in E. coli.
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Affiliation(s)
- Deepali Verma
- a Department of Biotechnology , Jaypee Institute of Information Technology , Noida , India
| | - Monika Antil
- a Department of Biotechnology , Jaypee Institute of Information Technology , Noida , India
| | - Vibha Gupta
- a Department of Biotechnology , Jaypee Institute of Information Technology , Noida , India
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27
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Gengenbach BB, Müschen CR, Buyel JF. Expression and purification of human phosphatase and actin regulator 1 (PHACTR1) in plant-based systems. Protein Expr Purif 2018; 151:46-55. [PMID: 29894805 DOI: 10.1016/j.pep.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022]
Abstract
Cardiovascular diseases are a prevalent cause of morbidity and mortality especially in industrialized countries. The human phosphatase and actin regulator 1 (PHACTR1) may be involved in such diseases, but its precise regulatory function remains unclear due to the large number of potential interaction partners. The same phenomenon makes this protein difficult to express in mammalian cells, but it is also an intrinsically disordered protein that likely aggregates when expressed in bacteria due to the absence of chaperones. We therefore used a design of experiments approach to test the suitability of three plant-based systems for the expression of satisfactory quantities of recombinant PHACTR1, namely transient expression in tobacco (Nicotiana tabacum) BY-2 plant cell packs (PCPs), whole N. benthamiana leaves and BY-2 cell lysate (BYL). The highest yield was achieved using the BYL: up to 120 mg product kg-1 biomass equivalent within 48 h of translation. This was 1.3-fold higher than transient expression in N. benthamiana together with the silencing inhibitor p19, and 6-fold higher than the PCP system. The presence of Triton X-100 in the extraction buffer increased the recovery of PHACTR1 by 2-200-fold depending on the conditions. PHACTR1 was incompatible with biomass blanching and was stable for less than 16 h in raw plant extracts. Purification using a DDK-tag proved inefficient whereas 15% purity was achieved by immobilized metal affinity chromatography.
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Affiliation(s)
- B B Gengenbach
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - C R Müschen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany.
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28
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Chang CC, Wang K, Zhang Y, Chen D, Fan B, Hsieh CH, Wang J, Wu MH, Chen J. Mechanical property characterization of hundreds of single nuclei based on microfluidic constriction channel. Cytometry A 2018; 93:822-828. [PMID: 30063818 DOI: 10.1002/cyto.a.23386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/18/2018] [Accepted: 04/02/2018] [Indexed: 12/31/2022]
Abstract
As label-free biomarkers, the mechanical properties of nuclei are widely treated as promising biomechanical markers for cell type classification and cellular status evaluation. However, previously reported mechanical parameters were derived from only around 10 nuclei, lacking statistical significances due to low sample numbers. To address this issue, nuclei were first isolated from SW620 and A549 cells, respectively, using a chemical treatment method. This was followed by aspirating them through two types of microfluidic constriction channels for mechanical property characterization. In this study, hundreds of nuclei were characterized, producing passage times of 0.5 ± 1.2 s for SW620 nuclei in type I constriction channel (n = 153), 0.045 ± 0.047 s for SW620 nuclei in type II constriction channel (n = 215) and 0.50 ± 0.86 s for A549 nuclei in type II constriction channel. In addition, neural network based pattern recognition was used to classify the nuclei isolated from SW620 and A549 cells, producing successful classification rates of 87.2% for diameters of nuclei, 85.5% for passage times of nuclei and 89.3% for both passage times and diameters of nuclei. These results indicate that the characterization of the mechanical properties of nuclei may contribute to the classification of different tumor cells.
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Affiliation(s)
- Chun-Chieh Chang
- Graduate Institute of Biochemical and Biomedical Engineering, Chang Gung University, Taoyuan City, Taiwan
| | - Ke Wang
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yi Zhang
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Beiyuan Fan
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chia-Hsun Hsieh
- Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Min-Hsien Wu
- Graduate Institute of Biochemical and Biomedical Engineering, Chang Gung University, Taoyuan City, Taiwan.,Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, People's Republic of China.,School of Electronic, Electrical and Communication Engineering/School of Future Technology, University of Chinese Academy of Sciences, Beijing, People's Republic of China
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29
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Nitenberg M, Bénarouche A, Maniti O, Marion E, Marsollier L, Géan J, Dufourc EJ, Cavalier JF, Canaan S, Girard-Egrot AP. The potent effect of mycolactone on lipid membranes. PLoS Pathog 2018; 14:e1006814. [PMID: 29320578 PMCID: PMC5779694 DOI: 10.1371/journal.ppat.1006814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/23/2018] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
Mycolactone is a lipid-like endotoxin synthesized by an environmental human pathogen, Mycobacterium ulcerans, the causal agent of Buruli ulcer disease. Mycolactone has pleiotropic effects on fundamental cellular processes (cell adhesion, cell death and inflammation). Various cellular targets of mycolactone have been identified and a literature survey revealed that most of these targets are membrane receptors residing in ordered plasma membrane nanodomains, within which their functionalities can be modulated. We investigated the capacity of mycolactone to interact with membranes, to evaluate its effects on membrane lipid organization following its diffusion across the cell membrane. We used Langmuir monolayers as a cell membrane model. Experiments were carried out with a lipid composition chosen to be as similar as possible to that of the plasma membrane. Mycolactone, which has surfactant properties, with an apparent saturation concentration of 1 μM, interacted with the membrane at very low concentrations (60 nM). The interaction of mycolactone with the membrane was mediated by the presence of cholesterol and, like detergents, mycolactone reshaped the membrane. In its monomeric form, this toxin modifies lipid segregation in the monolayer, strongly affecting the formation of ordered microdomains. These findings suggest that mycolactone disturbs lipid organization in the biological membranes it crosses, with potential effects on cell functions and signaling pathways. Microdomain remodeling may therefore underlie molecular events, accounting for the ability of mycolactone to attack multiple targets and providing new insight into a single unifying mechanism underlying the pleiotropic effects of this molecule. This membrane remodeling may act in synergy with the other known effects of mycolactone on its intracellular targets, potentiating these effects.
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Affiliation(s)
- Milène Nitenberg
- Univ. Lyon, Université Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS—UMR 5246, GEMBAS team, Lyon, France
| | | | - Ofelia Maniti
- Univ. Lyon, Université Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS—UMR 5246, GEMBAS team, Lyon, France
| | - Estelle Marion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Laurent Marsollier
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Julie Géan
- Univ. Bordeaux, CNRS, Bordeaux INP, Chemistry and Biology of Membranes and Nano-objects, CBMN UMR 5248, Pessac, France
| | - Erick J. Dufourc
- Univ. Bordeaux, CNRS, Bordeaux INP, Chemistry and Biology of Membranes and Nano-objects, CBMN UMR 5248, Pessac, France
| | - Jean-François Cavalier
- Aix-Marseille Univ, CNRS, EIPL, Marseille, France
- Aix-Marseille Univ, CNRS, LISM, Marseille, France
| | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, EIPL, Marseille, France
- Aix-Marseille Univ, CNRS, LISM, Marseille, France
| | - Agnès P. Girard-Egrot
- Univ. Lyon, Université Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS—UMR 5246, GEMBAS team, Lyon, France
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30
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Ezenarro JJ, Uria N, Castillo-Fernández Ó, Párraga N, Sabrià M, Muñoz Pascual FX. Development of an integrated method of concentration and immunodetection of bacteria. Anal Bioanal Chem 2017; 410:105-113. [PMID: 29063163 DOI: 10.1007/s00216-017-0695-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/07/2017] [Accepted: 10/06/2017] [Indexed: 11/27/2022]
Abstract
The microbial quality of water is a key aspect to avoid environmental and public health problems. The low pathogen concentration needed to produce a disease outbreak makes it essential to process large water volumes and use sensitive and specific methods such as immunoassays for its detection. In the present work, we describe the development of a device based on microfiltration membranes to integrate the concentration and the immunodetection of waterborne bacteria. A microfiltration membrane treatment protocol was designed to reduce the non-specific binding of antibodies, for which different blocking agents were tested. Thus, the proof of concept of the microbial detection system was also carried out using Escherichia coli as the bacterial pathogen model. E. coli suspensions were filtered through the membranes at 0.5 mL s-1, and the E. coli concentration measurements were made by absorbance, at 620 nm, of the resultant product of the enzymatic reaction among the horseradish peroxidase (HRP) bonded to the antibody, and the substrate 3,3',5,5'-tetramethylbenzidine (TMB). The results showed that the homemade concentration system together with the developed membrane treatment protocol is able to detect E. coli cells with a limit of detection (LoD) of about 100 CFU in 100 mL. Graphical abstract Scheme of the integrated method of concentration and immunodetection of bacteria.
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Affiliation(s)
- Josune J Ezenarro
- Institut de Microelectrònica de Barcelona, CNM-CSIC, Esfera UAB-CEI, Campus UAB, 08193, Bellaterra, Spain.
| | - Naroa Uria
- Institut de Microelectrònica de Barcelona, CNM-CSIC, Esfera UAB-CEI, Campus UAB, 08193, Bellaterra, Spain
| | - Óscar Castillo-Fernández
- Institut de Microelectrònica de Barcelona, CNM-CSIC, Esfera UAB-CEI, Campus UAB, 08193, Bellaterra, Spain
| | - Noemí Párraga
- Unitat de Malalties Infeccioses, Fundació Institut d'Investigació Germans Trias I Pujol, 08916, Badalona, Spain
- CIBER de Enfermedades Respiratorias, 28029, Madrid, Spain
| | - Miquel Sabrià
- CIBER de Enfermedades Respiratorias, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
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31
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Yim YY, McDonald WH, Hyde K, Cruz-Rodríguez O, Tesmer JJG, Hamm HE. Quantitative Multiple-Reaction Monitoring Proteomic Analysis of Gβ and Gγ Subunits in C57Bl6/J Brain Synaptosomes. Biochemistry 2017; 56:5405-5416. [PMID: 28880079 DOI: 10.1021/acs.biochem.7b00433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gβγ dimers are one of the essential signaling units of activated G protein-coupled receptors (GPCRs). There are five Gβ and 12 Gγ subunits in humans; numerous studies have demonstrated that different Gβ and Gγ subunits selectively interact to form unique Gβγ dimers, which in turn may target specific receptors and effectors. Perturbation of Gβγ signaling can lead to impaired physiological responses. Moreover, previous targeted multiple-reaction monitoring (MRM) studies of Gβ and Gγ subunits have shown distinct regional and subcellular localization patterns in four brain regions. Nevertheless, no studies have quantified or compared their individual protein levels. In this study, we have developed a quantitative MRM method not only to quantify but also to compare the protein abundance of neuronal Gβ and Gγ subunits. In whole and fractionated crude synaptosomes, we were able to identify the most abundant neuronal Gβ and Gγ subunits and their subcellular localizations. For example, Gβ1 was mostly localized at the membrane while Gβ2 was evenly distributed throughout synaptosomal fractions. The protein expression levels and subcellular localizations of Gβ and Gγ subunits may affect the Gβγ dimerization and Gβγ-effector interactions. This study offers not only a new tool for quantifying and comparing Gβ and Gγ subunits but also new insights into the in vivo distribution of Gβ and Gγ subunits, and Gβγ dimer assembly in normal brain function.
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Affiliation(s)
- Yun Young Yim
- Department of Pharmacology, Vanderbilt University , Nashville, Tennessee 37232-6600, United States
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232-6600, United States
| | - Karren Hyde
- Department of Pharmacology, Vanderbilt University , Nashville, Tennessee 37232-6600, United States
| | | | | | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University , Nashville, Tennessee 37232-6600, United States
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32
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McClellan P, Jacquet R, Yu Q, Landis WJ. A Method for the Immunohistochemical Identification and Localization of Osterix in Periosteum-Wrapped Constructs for Tissue Engineering of Bone. J Histochem Cytochem 2017; 65:407-420. [PMID: 28415912 PMCID: PMC5490846 DOI: 10.1369/0022155417705300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
A novel immunohistochemistry (IHC) approach has been developed to label and localize osterix, a bone-specific transcription factor, within formalin-fixed, paraffin-embedded, tissue-engineered constructs uniquely containing synthetic polymers and human periosteal tissue. Generally, such specimens consisting in part of polymeric materials and mineral are particularly difficult for IHC identification of proteins. Samples here were fabricated from human periosteum, electrospun poly-l-lactic acid (PLLA) nanofibers, and polycaprolactone/poly-l-lactic acid (PCL/PLLA, 75/25) scaffolds and harvested following 10 weeks of implantation in athymic mice. Heat-induced and protease-induced epitope retrieval methods from selected existing protocols were examined to identify osterix. All such protease-induced techniques were unsuccessful. Heat-induced retrieval gave positive results for osterix immunohistochemical staining in sodium citrate/EDTA/Tween 20 with high heat (120C) and pressure (~30 psi) for 10 min, but the heat and pressure levels resulted in tissue damage and section delamination from slides that limited protocol effectiveness. Heat-induced epitope retrieval led to other osterix-positive staining results achieved with minimal impact on structural integrity of the tissue and polymers in sodium citrate/EDTA/Tween 20 buffer at 60C and normal pressure (14.5 psi) for 72 hr. The latter approach identified osterix-positive cells by IHC within periosteal tissue, layers of electrospun PLLA nanofibers, and underlying PCL/PLLA scaffolds of the tissue-engineered constructs.
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Affiliation(s)
- Phillip McClellan
- Department of Polymer Science, The University of Akron, Akron, Ohio (PM, RJ, QY, WJL)
| | - Robin Jacquet
- Department of Polymer Science, The University of Akron, Akron, Ohio (PM, RJ, QY, WJL)
| | - Qing Yu
- Department of Polymer Science, The University of Akron, Akron, Ohio (PM, RJ, QY, WJL)
| | - William J. Landis
- Department of Polymer Science, The University of Akron, Akron, Ohio (PM, RJ, QY, WJL)
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33
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Sap A, Vandebroek L, Goovaerts V, Martens E, Proost P, Parac-Vogt TN. Highly Selective and Tunable Protein Hydrolysis by a Polyoxometalate Complex in Surfactant Solutions: A Step toward the Development of Artificial Metalloproteases for Membrane Proteins. ACS OMEGA 2017; 2:2026-2033. [PMID: 30023653 PMCID: PMC6044816 DOI: 10.1021/acsomega.7b00168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/28/2017] [Indexed: 05/17/2023]
Abstract
This study represents the first example of protein hydrolysis at pH = 7.4 and 60 °C by a metal-substituted polyoxometalate (POM) in the presence of a zwitterionic surfactant. Edman degradation results show that in the presence of 0.5% w/v 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) detergent, a Zr(IV)-substituted Wells-Dawson-type POM, K15H[Zr(α2-P2W17O61)2]·25H2O (Zr1-WD2), selectively hydrolyzes human serum albumin exclusively at peptide bonds involving Asp or Glu residues, which contain carboxyl groups in their side chains. The selectivity and extent of protein cleavage are tuned by the CHAPS surfactant by an unfolding mechanism that provides POM access to the hydrolyzed peptide bonds.
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Affiliation(s)
- Annelies Sap
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001 Leuven, Belgium
| | - Laurens Vandebroek
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001 Leuven, Belgium
| | - Vincent Goovaerts
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001 Leuven, Belgium
| | - Erik Martens
- Department
of Microbiology and Immunology, KU Leuven, Herestraat 49,
Box 1042, 3000 Leuven, Belgium
| | - Paul Proost
- Department
of Microbiology and Immunology, KU Leuven, Herestraat 49,
Box 1042, 3000 Leuven, Belgium
| | - Tatjana N. Parac-Vogt
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001 Leuven, Belgium
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Zhang T, Wei W, Dirsch O, Krüger T, Kan C, Xie C, Kniemeyer O, Fang H, Settmacher U, Dahmen U. Identification of Proteins Interacting with Cytoplasmic High-Mobility Group Box 1 during the Hepatocellular Response to Ischemia Reperfusion Injury. Int J Mol Sci 2017; 18:ijms18010167. [PMID: 28275217 PMCID: PMC5297800 DOI: 10.3390/ijms18010167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/03/2017] [Accepted: 01/09/2017] [Indexed: 01/22/2023] Open
Abstract
Ischemia/reperfusion injury (IRI) occurs inevitably in liver transplantations and frequently during major resections, and can lead to liver dysfunction as well as systemic disorders. High-mobility group box 1 (HMGB1) plays a pathogenic role in hepatic IRI. In the normal liver, HMGB1 is located in the nucleus of hepatocytes; after ischemia reperfusion, it translocates to the cytoplasm and it is further released to the extracellular space. Unlike the well-explored functions of nuclear and extracellular HMGB1, the role of cytoplasmic HMGB1 in hepatic IRI remains elusive. We hypothesized that cytoplasmic HMGB1 interacts with binding proteins involved in the hepatocellular response to IRI. In this study, binding proteins of cytoplasmic HMGB1 during hepatic IRI were identified. Liver tissues from rats with warm ischemia reperfusion (WI/R) injury and from normal rats were subjected to cytoplasmic protein extraction. Co-immunoprecipitation using these protein extracts was performed to enrich HMGB1-protein complexes. To separate and identify the immunoprecipitated proteins in eluates, 2-dimensional electrophoresis and subsequent mass spectrometry detection were performed. Two of the identified proteins were verified using Western blotting: betaine–homocysteine S-methyltransferase 1 (BHMT) and cystathionine γ-lyase (CTH). Therefore, our results revealed the binding of HMGB1 to BHMT and CTH in cytoplasm during hepatic WI/R. This finding may help to better understand the cellular response to IRI in the liver and to identify novel molecular targets for reducing ischemic injury.
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Affiliation(s)
- Tianjiao Zhang
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
| | - Weiwei Wei
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
| | - Olaf Dirsch
- Institute of Pathology, Klinikum Chemnitz gGmbH, 09116 Chemnitz, Germany.
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany.
| | - Chunyi Kan
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
- Department of Obstetrics and Gynecology, Wuhan Central Hospital, Wuhan 430014, China.
| | - Chichi Xie
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany.
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei 230032, China.
| | - Utz Settmacher
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747 Jena, Germany.
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35
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Cao F, Bourven I, Lens PNL, van Hullebusch ED, Pechaud Y, Guibaud G. Hydrophobic features of EPS extracted from anaerobic granular sludge: an investigation based on DAX-8 resin fractionation and size exclusion chromatography. Appl Microbiol Biotechnol 2016; 101:3427-3438. [PMID: 28012045 DOI: 10.1007/s00253-016-8053-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/14/2016] [Accepted: 12/05/2016] [Indexed: 12/23/2022]
Abstract
The hydrophobic fractionation of extracellular polymeric substances (EPS) extracted from anaerobic granular sludge was performed on the DAX-8 resin (two elution pH conditions, i.e., pH 2 and pH 5 were tested). The impact of seven different EPS extraction methods on EPS hydrophobicity features was assessed. The results showed that the extraction methods and bulk solution pH influenced dramatically the biochemical composition of the EPS, and in turn, the hydrophobicity determined. Besides, EPS extracting reagents i.e., formaldehyde, ethanol, sodium dodecyl sulfate (SDS), and Tween 20 not only introduced extra carbon content in the total organic carbon (TOC) measurement but also interacted with the DAX-8 resin. By comparing the apparent molecular weight (aMW) distribution of untreated and pH-adjusted EPS samples, more complete EPS aMW information was preserved at pH 5. Thus, elution at pH 5 was preferred in this study for the qualitative analysis of EPS hydrophobic features. The hydrophobic fraction of EPS retained by the resin at pH 5 was ascribed to a wide aMW range, ranging from >440 to 0.3 kDa. Within this range, EPS molecules ranging from 175 to 31 kDa were mostly retained by the DAX-8 resin, which indicates that these EPS molecules are highly hydrophobic.
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Affiliation(s)
- Feishu Cao
- Laboratoire Géomatériaux et Environnement (EA 4508), Université Paris-Est, UPEM, 77454, Marne-la-Vallée, France.,Groupement de Recherche Eau Sol Environnement (EA 4330), Faculté des Sciences et Techniques, Université de Limoges, 123 Avenue A. Thomas, 87060, Limoges Cedex, France.,UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
| | - Isabelle Bourven
- Groupement de Recherche Eau Sol Environnement (EA 4330), Faculté des Sciences et Techniques, Université de Limoges, 123 Avenue A. Thomas, 87060, Limoges Cedex, France
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
| | - Eric D van Hullebusch
- Laboratoire Géomatériaux et Environnement (EA 4508), Université Paris-Est, UPEM, 77454, Marne-la-Vallée, France.,UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
| | - Yoan Pechaud
- Laboratoire Géomatériaux et Environnement (EA 4508), Université Paris-Est, UPEM, 77454, Marne-la-Vallée, France
| | - Gilles Guibaud
- Groupement de Recherche Eau Sol Environnement (EA 4330), Faculté des Sciences et Techniques, Université de Limoges, 123 Avenue A. Thomas, 87060, Limoges Cedex, France.
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36
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Neira JL, Martínez-Rodríguez S, Hernández-Cifre JG, Cámara-Artigas A, Clemente P, Peralta S, Fernández-Moreno MÁ, Garesse R, García de la Torre J, Rizzuti B. Human COA3 Is an Oligomeric Highly Flexible Protein in Solution. Biochemistry 2016; 55:6209-6220. [PMID: 27791355 DOI: 10.1021/acs.biochem.6b00644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The assembly of the protein complex of cytochrome c oxidase (COX), which participates in the mitochondrial respiratory chain, requires a large number of accessory proteins (the so-called assembly factors). Human COX assembly factor 3 (hCOA3), also known as MITRAC12 or coiled-coil domain-containing protein 56 (CCDC56), interacts with the first subunit protein of COX to form its catalytic core and promotes its assemblage with the other units. Therefore, hCOA3 is involved in COX biogenesis in humans and can be exploited as a drug target in patients with mitochondrial dysfunctions. However, to be considered a molecular target, its structure and conformational stability must first be elucidated. We have embarked on the description of such features by using spectroscopic and hydrodynamic techniques, in aqueous solution and in the presence of detergents, together with computational methods. Our results show that hCOA3 is an oligomeric protein, forming aggregates of different molecular masses in aqueous solution. Moreover, on the basis of fluorescence and circular dichroism results, the protein has (i) its unique tryptophan partially shielded from solvent and (ii) a relatively high percentage of secondary structure. However, this structure is highly flexible and does not involve hydrogen bonding. Experiments in the presence of detergents suggest a slightly higher content of nonrigid helical structure. Theoretical results, based on studies of the primary structure of the protein, further support the idea that hCOA3 is a disordered protein. We suggest that the flexibility of hCOA3 is crucial for its interaction with other proteins to favor mitochondrial protein translocation and assembly of proteins involved in the respiratory chain.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , Elche, Alicante, Spain.,Biocomputation and Complex Systems Physics Institute , Zaragoza, Spain
| | | | | | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Paula Clemente
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Susana Peralta
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Rafael Garesse
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | | | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria , 87036 Rende, Italy
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37
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Gugliuzza A, Perrotta ML, Drioli E. Controlled Bulk Properties of Composite Polymeric Solutions for Extensive Structural Order of Honeycomb Polysulfone Membranes. MEMBRANES 2016; 6:membranes6020027. [PMID: 27196938 PMCID: PMC4931522 DOI: 10.3390/membranes6020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/28/2016] [Accepted: 05/05/2016] [Indexed: 01/01/2023]
Abstract
This work provides additional insights into the identification of operating conditions necessary to overcome a current limitation to the scale-up of the breath figure method, which is regarded as an outstanding manufacturing approach for structurally ordered porous films. The major restriction concerns, indeed, uncontrolled touching droplets at the boundary. Herein, the bulk of polymeric solutions are properly managed to generate honeycomb membranes with a long-range structurally ordered texture. Water uptake and dynamics are explored as chemical environments are changed with the intent to modify the hydrophilic/hydrophobic balance and local water floatation. In this context, a model surfactant such as the polyoxyethylene sorbitan monolaurate is used in combination with alcohols at different chain length extents and a traditional polymer such as the polyethersufone. Changes in the interfacial tension and kinematic viscosity taking place in the bulk of composite solutions are explored and examined in relation to competitive droplet nucleation and growth rate. As a result, extensive structurally ordered honeycomb textures are obtained with the rising content of the surfactant while a broad range of well-sized pores is targeted as a function of the hydrophilic-hydrophobic balance and viscosity of the composite polymeric mixture. The experimental findings confirm the consistency of the approach and are expected to give propulsion to the commercially production of breath figures films shortly.
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Affiliation(s)
- Annarosa Gugliuzza
- Research Institute on Membrane Technology-National Research Council (CNR-ITM), Via Pietro Bucci 17C, Rende (CS) 87036, Italy.
| | - Maria Luisa Perrotta
- Research Institute on Membrane Technology-National Research Council (CNR-ITM), Via Pietro Bucci 17C, Rende (CS) 87036, Italy.
| | - Enrico Drioli
- Research Institute on Membrane Technology-National Research Council (CNR-ITM), Via Pietro Bucci 17C, Rende (CS) 87036, Italy.
- Department of Chemical Engineering and Materials, University of Calabria, Via Pietro Bucci, 33C, Rende (CS) 87036, Italy.
- WCU Energy Engineering Department, College of Engineering, Hanyang University, Seoul OK763, Korea.
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38
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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39
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Sai-Ut S, Benjakul S, Sumpavapol P, Kishimura H. Purification and Characterization of Extracellular Gelatinolytic Protease from B
acillus Amyloliquefaciens
H11. J Food Biochem 2015. [DOI: 10.1111/jfbc.12114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samart Sai-Ut
- Department of Food Technology; Faculty of Agro-Industry; Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
| | - Soottawat Benjakul
- Department of Food Technology; Faculty of Agro-Industry; Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
| | - Punnanee Sumpavapol
- Department of Food Technology; Faculty of Agro-Industry; Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
| | - Hideki Kishimura
- Department of Marine Bioresources Chemistry; Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
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