1
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Zhang Y, Zheng L, Liu G, Shen J, Chen G, Mei X, Chang Y, Xue C. The α-linkage in funoran and agarose could be hydrolyzed by a GH96 family enzyme: Discovery of the α-funoranase. Carbohydr Polym 2024; 338:122201. [PMID: 38763726 DOI: 10.1016/j.carbpol.2024.122201] [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: 11/01/2023] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Agarans represent a group of galactans extracted from red algae. Funoran and agarose are the two major types and commercially applied polysaccharides of agaran. Although the glycoside hydrolases targeting β-glycosidic bonds of agaran have been widely investigated, those capable of degrading α-glycosidic bonds of agarose were limited, and the enzyme degrading α-linkages of funoran has not been reported till now. In this study, a GH96 family enzyme BiAF96A_Aq from a marine bacterium Aquimarina sp. AD1 was heterologously expressed in Escherichia coli. BiAF96A_Aq exhibited dual activities towards the characteristic structure of funoran and agarose, underscoring the multifunctionality of GH96 family members. Glycomics and NMR analysis revealed that BiAF96A_Aq hydrolyzed the α-1,3 glycosidic bonds between 3,6-anhydro-α-l-galactopyranose (LA) and β-d-galactopyranose-6-sulfate (G6S) of funoran, as well as LA and β-d-galactopyranose (G) of agarose, through an endo-acting manner. The end products of BiAF96A_Aq were majorly composed of disaccharides and tetrasaccharides. The identification of the activity of BiAF96A_Aq on funoran indicated the first discovery of the funoran hydrolase for α-1,3 linkage. Considering the novel catalytic reaction, we proposed to name this activity as "α-funoranase" and recommended the assignment of a dedicated EC number for its classification.
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Affiliation(s)
- Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Long Zheng
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China
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2
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Janićijević Ž, Huang T, Bojórquez DIS, Tonmoy TH, Pané S, Makarov D, Baraban L. Design and Development of Transient Sensing Devices for Healthcare Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307232. [PMID: 38484201 PMCID: PMC11132064 DOI: 10.1002/advs.202307232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/12/2023] [Indexed: 05/29/2024]
Abstract
With the ever-growing requirements in the healthcare sector aimed at personalized diagnostics and treatment, continuous and real-time monitoring of relevant parameters is gaining significant traction. In many applications, health status monitoring may be carried out by dedicated wearable or implantable sensing devices only within a defined period and followed by sensor removal without additional risks for the patient. At the same time, disposal of the increasing number of conventional portable electronic devices with short life cycles raises serious environmental concerns due to the dangerous accumulation of electronic and chemical waste. An attractive solution to address these complex and contradictory demands is offered by biodegradable sensing devices. Such devices may be able to perform required tests within a programmed period and then disappear by safe resorption in the body or harmless degradation in the environment. This work critically assesses the design and development concepts related to biodegradable and bioresorbable sensors for healthcare applications. Different aspects are comprehensively addressed, from fundamental material properties and sensing principles to application-tailored designs, fabrication techniques, and device implementations. The emerging approaches spanning the last 5 years are emphasized and a broad insight into the most important challenges and future perspectives of biodegradable sensors in healthcare are provided.
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Affiliation(s)
- Željko Janićijević
- Institute of Radiopharmaceutical Cancer ResearchHelmholtz‐Zentrum Dresden‐Rossendorf e. V.01328DresdenGermany
| | - Tao Huang
- Institute of Radiopharmaceutical Cancer ResearchHelmholtz‐Zentrum Dresden‐Rossendorf e. V.01328DresdenGermany
| | | | - Taufhik Hossain Tonmoy
- Institute of Radiopharmaceutical Cancer ResearchHelmholtz‐Zentrum Dresden‐Rossendorf e. V.01328DresdenGermany
| | - Salvador Pané
- Multi‐Scale Robotics Lab (MSRL)Institute of Robotics & Intelligent Systems (IRIS)ETH ZürichZürich8092Switzerland
| | - Denys Makarov
- Institute of Ion Beam Physics and Materials ResearchHelmholtz‐Zentrum Dresden‐Rossendorf e. V.01328DresdenGermany
| | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer ResearchHelmholtz‐Zentrum Dresden‐Rossendorf e. V.01328DresdenGermany
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Jeon SW, Kim J, Yoon YJ, Yang S, Yang DC, Kim SK, Kim TH. Form Factor-Free Boron Nitride Nanotube-Agarose Composites for Neutron Shielding. NANO LETTERS 2024; 24:1522-1530. [PMID: 38147533 DOI: 10.1021/acs.nanolett.3c03821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Boron nitride nanotubes (BNNTs) have remarkable mechanical and thermal properties and are suitable for neutron shielding due to boron. Because BNNTs exist in bundled and stiff shapes, limiting their practical applications, however, it is essential to improve their formability and processability. In this study, we demonstrate form-factor-free BNNTs and agarose composites for use in neutron shielding for the first time; they are fabricated by mixing hydrophilic agarose with noncovalently functionalized water-soluble BNNTs (p-BNNTs). The mechanical properties of the agarose/p-BNNT composite films surpass those of conventional commodity plastics. When the p-BNNT concentration increased, the neutron linear attenuation coefficient of the composite film increases from 0.574 ± 0.010 to 0.765 ± 0.062 mm-1, which is comparable to that of conventional rigid shielding materials. In particular, the addition of 10 wt % p-BNNTs to agarose results in excellent form-factor flexibility, neutron shielding, and mechanical properties, thus rendering it a promising candidate for the nuclear industry.
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Affiliation(s)
- Sang-Woo Jeon
- Department of Applied Plasma & Quantum Beam Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Research Center for Advanced Nuclear Interdisciplinary Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jiwon Kim
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Young-Jin Yoon
- Department of Applied Plasma & Quantum Beam Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Research Center for Advanced Nuclear Interdisciplinary Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Seonghyeon Yang
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Dong Chul Yang
- Department of Applied Plasma & Quantum Beam Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Research Center for Advanced Nuclear Interdisciplinary Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Sung-Kon Kim
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Tae-Hwan Kim
- Department of Applied Plasma & Quantum Beam Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Research Center for Advanced Nuclear Interdisciplinary Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Quantum System Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- High-Enthalphy Plasma Research Center, Jeonbuk National University, 546 Bongdong-ro, Bongdong-eup, Wanju-gun, Jeollabuk-do 55317, Republic of Korea
- Department of JBNU-KIST Industry-Academia Convergence Research, Jeonbuk National University, Jeonju, Jeollabuk-do 54896, Republic of Korea
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4
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Goicoechea Serrano E, Blázquez-Bondia C, Jaramillo A. T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection. Sci Rep 2024; 14:2377. [PMID: 38287027 PMCID: PMC10824729 DOI: 10.1038/s41598-024-52049-9] [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: 07/19/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
Leveraging riboswitches, non-coding mRNA fragments pivotal to gene regulation, poses a challenge in effectively selecting and enriching these functional genetic sensors, which can toggle between ON and OFF states in response to their cognate inducers. Here, we show our engineered phage T7, enabling the evolution of a theophylline riboswitch. We have replaced T7's DNA polymerase with a transcription factor controlled by a theophylline riboswitch and have created two types of host environments to propagate the engineered phage. Both types host an error-prone T7 DNA polymerase regulated by a T7 promoter along with another critical gene-either cmk or pifA, depending on the host type. The cmk gene is necessary for T7 replication and is used in the first host type for selection in the riboswitch's ON state. Conversely, the second host type incorporates the pifA gene, leading to abortive T7 infections and used for selection in the riboswitch's OFF state. This dual-selection system, termed T7AE, was then applied to a library of 65,536 engineered T7 phages, each carrying randomized riboswitch variants. Through successive passage in both host types with and without theophylline, we observed an enrichment of phages encoding functional riboswitches that conferred a fitness advantage to the phage in both hosts. The T7AE technique thereby opens new pathways for the evolution and advancement of gene switches, including non-coding RNA-based switches, setting the stage for significant strides in synthetic biology.
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Affiliation(s)
- Eduardo Goicoechea Serrano
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- London BioFoundry, Imperial College Translation & Innovation Hub, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Carlos Blázquez-Bondia
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- De novo Synthetic Biology Lab, i2sysbio, CSIC-University of Valencia, Parc Científic Universitat de València, Calle Catedrático Agustín Escardino, 9, 46980, Paterna, Spain.
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5
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Sowersby DS, Lewis LK. SURE gel electrophoresis: A method for improved detection and purification of dilute nucleic acid samples. Anal Biochem 2024; 684:115373. [PMID: 37926185 DOI: 10.1016/j.ab.2023.115373] [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: 10/06/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Agarose gel electrophoresis is performed routinely by molecular biologists as both an analytical and a preparative method for characterization of nucleic acids. Gel analysis of highly dilute DNA solutions is challenging because of the limited sensitivity of detection available with conventional methods. In this study a new approach is described for concentrating samples directly within gels called SURE (successive reloading) electrophoresis. The approach involves loading of dilute samples multiple times into a single well, with each loading followed by a brief pulse of electrical current before the next sample is loaded. The procedure generates single bands created by molecular stacking that exhibit strongly enhanced signal intensities and minimal band broadening. Using optimized voltages and time intervals as many as 20 successive loadings could be performed and up to 800 μL could be loaded into a single well. Gel extraction and fluorescent quantitation demonstrated that approximately 97 % of the DNA from each loading was incorporated into the resultant band. Highly dilute DNA samples (<0.0007 ng per microliter) could be readily detected after six loadings. The method produced good results with either TAE or TBE as electrophoresis buffers, using loading dyes with or without SDS, and in both minigels and large gels.
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Affiliation(s)
- Drew S Sowersby
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA.
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6
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Kang J, Zhang X, Yang X, Yang X, Wang S, Song W. Mucosa-Inspired Electro-Responsive Lubricating Supramolecular-Covalent Hydrogel. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2307705. [PMID: 37742109 DOI: 10.1002/adma.202307705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/22/2023] [Indexed: 09/25/2023]
Abstract
Enabling the living capability of secreting liquids dynamically triggered by external stimuli while maintaining the bulk frame is a significant challenge for mucosa-inspired hydrogels. A mucosa-inspired electro-responsive hydrogel is developed in this study using the synergy between electro-responsive silk fibroin supramolecular non-covalent networks and covalent polyacrylamide and polyvinyl alcohol polymer networks. The formed supramolecular-covalent hydrogel exhibits a partial gel-sol transition upon the application of an electric field, and the liquid layer on the hydrogel surface near the cathode is used to mimic the mucus-secreting capability to regulate lubrication. The electro-responsive lubricating process can operate under a safe voltage and exhibits good reversibility. It is also a universal strategy to construct an electro-responsive hydrogel by introducing an electro-responsive supramolecular network into the polymer network. This mucosa-inspired electro-responsive supramolecular-covalent hydrogel offers a promising method for designing soft actuators or robots that can regulate lubrication using an electric strategy.
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Affiliation(s)
- Jianye Kang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Xuewei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Xinyu Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Xuhao Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wenlong Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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7
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Chen LM, de Bruin S, Pronk M, Sousa DZ, van Loosdrecht MCM, Lin Y. Sialylation and Sulfation of Anionic Glycoconjugates Are Common in the Extracellular Polymeric Substances of Both Aerobic and Anaerobic Granular Sludges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13217-13225. [PMID: 37604486 PMCID: PMC10483923 DOI: 10.1021/acs.est.2c09586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Anaerobic and aerobic granular sludge processes are widely applied in wastewater treatment. In these systems, microorganisms grow in dense aggregates due to the production of extracellular polymeric substances (EPS). This study investigates the sialylation and sulfation of anionic glyconconjugates in anaerobic and aerobic granular sludges collected from full-scale wastewater treatment processes. Size exclusion chromatography revealed a wide molecular weight distribution (3.5 to >5500 kDa) of the alkaline-extracted EPS. The high-molecular weight fraction (>5500 kDa), comprising 16.9-27.4% of EPS, was dominant with glycoconjugates. Mass spectrometry analysis and quantification assays identified nonulosonic acids (NulOs, e.g., bacterial sialic acids) and sulfated groups contributing to the negative charge in all EPS fractions. NulOs were predominantly present in the high-molecular weight fraction (47.2-84.3% of all detected NulOs), while sulfated glycoconjugates were distributed across the molecular weight fractions. Microorganisms, closely related to genera found in the granular sludge communities, contained genes responsible for NulO and sulfate group synthesis or transfer. The similar distribution patterns of sialylation and sulfation of the anionic glycoconjugates in the EPS samples indicate that these two glycoconjugate modifications commonly occur in the EPS of aerobic and anaerobic granular sludges.
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Affiliation(s)
- Le Min Chen
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Stefan de Bruin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mario Pronk
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Royal
HaskoningDHV, Laan 1914
35, Amersfoort 3800 AL, The Netherlands
| | - Diana Z. Sousa
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Mark C. M. van Loosdrecht
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Yuemei Lin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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8
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Volova LT, Kotelnikov GP, Shishkovsky I, Volov DB, Ossina N, Ryabov NA, Komyagin AV, Kim YH, Alekseev DG. 3D Bioprinting of Hyaline Articular Cartilage: Biopolymers, Hydrogels, and Bioinks. Polymers (Basel) 2023; 15:2695. [PMID: 37376340 DOI: 10.3390/polym15122695] [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: 04/06/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The musculoskeletal system, consisting of bones and cartilage of various types, muscles, ligaments, and tendons, is the basis of the human body. However, many pathological conditions caused by aging, lifestyle, disease, or trauma can damage its elements and lead to severe disfunction and significant worsening in the quality of life. Due to its structure and function, articular (hyaline) cartilage is the most susceptible to damage. Articular cartilage is a non-vascular tissue with constrained self-regeneration capabilities. Additionally, treatment methods, which have proven efficacy in stopping its degradation and promoting regeneration, still do not exist. Conservative treatment and physical therapy only relieve the symptoms associated with cartilage destruction, and traditional surgical interventions to repair defects or endoprosthetics are not without serious drawbacks. Thus, articular cartilage damage remains an urgent and actual problem requiring the development of new treatment approaches. The emergence of biofabrication technologies, including three-dimensional (3D) bioprinting, at the end of the 20th century, allowed reconstructive interventions to get a second wind. Three-dimensional bioprinting creates volume constraints that mimic the structure and function of natural tissue due to the combinations of biomaterials, living cells, and signal molecules to create. In our case-hyaline cartilage. Several approaches to articular cartilage biofabrication have been developed to date, including the promising technology of 3D bioprinting. This review represents the main achievements of such research direction and describes the technological processes and the necessary biomaterials, cell cultures, and signal molecules. Special attention is given to the basic materials for 3D bioprinting-hydrogels and bioinks, as well as the biopolymers underlying the indicated products.
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Affiliation(s)
- Larisa T Volova
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Gennadiy P Kotelnikov
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Igor Shishkovsky
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitriy B Volov
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Natalya Ossina
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Nikolay A Ryabov
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Aleksey V Komyagin
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
| | - Yeon Ho Kim
- RokitHealth Care Ltd., 9, Digital-ro 10-gil, Geumcheon-gu, Seoul 08514, Republic of Korea
| | - Denis G Alekseev
- Research and Development Institute of Biotechnologies, Samara State Medical University, Chapayevskaya St. 89, 443099 Samara, Russia
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9
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Wang J, Zhang J, Song Y, Xu X, Cai M, Li P, Yuan W, Xiahou Y. Functionalized agarose hydrogel with in situ Ag nanoparticles as highly recyclable heterogeneous catalyst for aromatic organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43950-43961. [PMID: 36680722 DOI: 10.1007/s11356-023-25420-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
In the present research work, a highly recyclable catalyst of Ag-based agarose (HRC-Ag/Agar) hydrogel was successfully fabricated through a simple and efficient in situ reduction method without the aid of additional surface active agent. The interaction between the rich hydroxyl functional (-OH) groups in agarose and Ag can effectively control the growth and dispersion of Ag nanoparticles (NPs) in the HRC-Ag/Agar hydrogel and keep Ag NPs free from chemical contamination, which also guarantees the reusability of HRC-Ag/Agar hydrogel as catalysts. HRC-Ag/Agar hydrogel without freeze drying and calcination was investigated for their potential applications as highly active/recyclable catalysts in reducing aromatic organic pollutants (p-nitrophenol (4-NP), methylene blue (MB) and rhodamine B (RhB)) by KBH4. The optimal HRC-Ag/Agar-1.9 hydrogel can complete the catalytic reduction of 4-NP within 11 min. Moreover, HRC-Ag/Agar-1.9 hydrogel achieves the high conversion rate (> 99%) through ten catalytic runs. Similarly, HRC-Ag/Agar-1.9 hydrogel was able to achieve a reduction efficiency of RhB at 98% within 17 min and that of MB at 95% within 40 min. The advantages of simple synthetic procedure, no secondary pollution, strong stability and easily separated make the HRC-Ag/Agar hydrogel have great potential prospect for environmental applications.
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Affiliation(s)
- Jin Wang
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China.
| | - Jihui Zhang
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Yahui Song
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Xianmang Xu
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Mengyun Cai
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Peichuang Li
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Wenpeng Yuan
- Heze Branch, Qilu University of Technology (Shandong Academy of Sciences), Biological Engineering Technology Innovation Center of Shandong Province, Heze, 274000, People's Republic of China
| | - Yujiao Xiahou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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10
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Zouganelis GD, Tairis N. Low Throughput Direct Cycle Sequencing of Polymerase Chain Reaction (PCR) Products. Methods Mol Biol 2023; 2633:195-211. [PMID: 36853466 DOI: 10.1007/978-1-0716-3004-4_15] [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: 03/01/2023]
Abstract
Polymerase Chain Reaction (PCR) products have been traditionally characterized by cloning and cycle sequencing. However, when quick sequencing data are required, the cloning step may be omitted and PCR products can be sequenced directly. We describe here a sequencing protocol that involves the gold standard Big Dye chemistry in a low throughput format using one of the latest sequencing platforms the ABI Seqstudio. Our cycle sequencing protocol follows the following steps: (1) purification of the PCR product with a spin column-based kit; (2) quality & quantity assessment of the PCR product with the use of spectrophotometry & gel electrophoresis; (3) setup and amplification of the cycle sequencing reaction; (4) Capillary Electrophoresis; (5) Sequence Data Analysis.
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Affiliation(s)
- George D Zouganelis
- Human Sciences Research Centre, College of Science & Engineering, University of Derby, Derby, UK.
| | - Nikolaos Tairis
- Senior Forensic DNA Analyst & Technical Witness Expert (Greece), Augusta, GA, USA
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11
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Yu X, Wang L, He W. Cytophilic Agarose-Epoxide-Amine Cryogels Engineered with Granulated Microstructures. ACS APPLIED BIO MATERIALS 2023; 6:694-702. [PMID: 36695539 DOI: 10.1021/acsabm.2c00938] [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: 01/26/2023]
Abstract
Inherent cytophobicity of agarose limits its direct use for the growth of anchorage-dependent cells. Here, we report a simple strategy allowing the development of agarose-based hydrogels entailed with both cytophilicity and microstructured morphology. Through the reaction of water-soluble 1,4-butanediol diglycidyl ether (BDDE) with trifunctional polyetheramine Jeffamine T403 in agarose solution followed by cryogelation of the mixtures, a series of macroporous agarose-epoxide-amine cryogels were prepared readily. Results from fluorescent labeling and energy-dispersive X-ray elemental mapping showed the formation of granulated microstructures in the cryogels. Such features closely correlated to the phase separation of BDDE-T403 polymers within the agarose matrix. Cytophilicity of the microstructured cryogels due to the integrated amine moieties was demonstrated through the adhesion of fibroblasts. Functional enrichment of the cryogels was further highlighted by leveraging the granulates as micro-reservoirs for polyphenol proanthocyanidin to enable antioxidation and protection of fibroblasts from H2O2-induced cytotoxic effect in vitro.
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Affiliation(s)
- Xueying Yu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning116024, China.,School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning116024, China
| | - Liwei Wang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning116024, China.,School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning116024, China
| | - Wei He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning116024, China.,School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning116024, China
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12
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Spontaneous and Electrically Induced Anisotropy of Composite Agarose Gels. Gels 2022; 8:gels8110753. [DOI: 10.3390/gels8110753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/22/2022] Open
Abstract
Agarose gels containing and not bacteriorhodopsin purple membranes (incorporated before gelling) manifest spontaneous optical anisotropy. The dependencies of the anisotropy on the agarose concentration and time have been studied. The rise in the anisotropy is explained by the predominant orientation of the agarose fibers during the gelling and subsequent deformation of the gel net. In the electric field, additional optical anisotropy rises, which is caused by the orientation of the membranes. A procedure has been developed to separate electrically induced and spontaneous anisotropy in composite gels. The isoelectric points and surface electric potential of bacteriorhodopsin trimer and purple membranes are calculated by the method of protein electrostatics to explain their electric asymmetry, which leads to perpendicular orientation in the direct electric field and longitudinal in the kilohertz sinusoidal field. The results allow for an increase in the separation capability of composite gels of electrophoresis for macromolecules with different sizes by applying an appropriate electric field to modulate the effective pore size.
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13
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Bochert I, Günther JP, Fischer P, Majer G. Diffusion mechanisms of DNA in agarose gels: NMR studies and Monte Carlo simulations. J Chem Phys 2022; 156:245103. [DOI: 10.1063/5.0092568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on the diffusion mechanism of short, single-stranded DNA molecules with up to 100 nucleobases in agarose gels with concentrations of up to 2.0% with the aim to characterize the DNA–agarose interaction. The diffusion coefficients were measured directly, i.e., without any model assumptions, by pulsed field gradient nuclear magnetic resonance (PFG-NMR). We find that the diffusion coefficient decreases, as expected, with an increase in both DNA strand length and gel concentration. In addition, we performed Monte Carlo simulations of particle diffusion in a model network of polymer chains, considering our experimental conditions. Together, the Monte Carlo simulations and the PFG-NMR results show that the decrease in diffusion coefficients in the presence of the agarose gel is due to a temporary adhesion of the DNA molecules to the surface of gel fibers. The average adhesion time to a given gel fiber increases with the length of the DNA strands but is independent of the number of gel fibers. The corresponding magnitude of the binding enthalpies of DNA strands to gel fibers indicates that a mixture of van der Waals interactions and hydrogen bonding contributes to the decreased diffusion of DNA in agarose gels.
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Affiliation(s)
- Ida Bochert
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- Institute of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Jan-Philipp Günther
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- Institute of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Peer Fischer
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- Institute of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Günter Majer
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
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14
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Borri C, Centi S, Chioccioli S, Bogani P, Micheletti F, Gai M, Grandi P, Laschi S, Tona F, Barucci A, Zoppetti N, Pini R, Ratto F. Paper-based genetic assays with bioconjugated gold nanorods and an automated readout pipeline. Sci Rep 2022; 12:6223. [PMID: 35418671 PMCID: PMC9007582 DOI: 10.1038/s41598-022-10227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/21/2022] [Indexed: 01/10/2023] Open
Abstract
Paper-based biosensors featuring immunoconjugated gold nanoparticles have gained extraordinary momentum in recent times as the platform of choice in key cases of field applications, including the so-called rapid antigen tests for SARS-CoV-2. Here, we propose a revision of this format, one that may leverage on the most recent advances in materials science and data processing. In particular, we target an amplifiable DNA rather than a protein analyte, and we replace gold nanospheres with anisotropic nanorods, which are intrinsically brighter by a factor of ~ 10, and multiplexable. By comparison with a gold-standard method for dot-blot readout with digoxigenin, we show that gold nanorods entail much faster and easier processing, at the cost of a higher limit of detection (from below 1 to 10 ppm in the case of plasmid DNA containing a target transgene, in our current setup). In addition, we test a complete workflow to acquire and process photographs of dot-blot membranes with custom-made hardware and regression tools, as a strategy to gain more analytical sensitivity and potential for quantification. A leave-one-out approach for training and validation with as few as 36 sample instances already improves the limit of detection reached by the naked eye by a factor around 2. Taken together, we conjecture that the synergistic combination of new materials and innovative tools for data processing may bring the analytical sensitivity of paper-based biosensors to approach the level of lab-grade molecular tests.
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Affiliation(s)
- Claudia Borri
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Sonia Centi
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy.
| | - Sofia Chioccioli
- Dipartimento di Biologia, Università degli Studi di Firenze, 50019, Sesto Fiorentino, FI, Italy
| | - Patrizia Bogani
- Dipartimento di Biologia, Università degli Studi di Firenze, 50019, Sesto Fiorentino, FI, Italy
| | - Filippo Micheletti
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Gai
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Paolo Grandi
- Laboratori Victoria S.R.L, 51100, Pistoia, Italy
| | - Serena Laschi
- Ecobioservices & Researches S.R.L, 50019, Sesto Fiorentino, FI, Italy
| | - Francesco Tona
- Ecobioservices & Researches S.R.L, 50019, Sesto Fiorentino, FI, Italy
| | - Andrea Barucci
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Nicola Zoppetti
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Roberto Pini
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Fulvio Ratto
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
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15
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Braccini S, Tacchini C, Chiellini F, Puppi D. Polymeric Hydrogels for In Vitro 3D Ovarian Cancer Modeling. Int J Mol Sci 2022; 23:3265. [PMID: 35328686 PMCID: PMC8954571 DOI: 10.3390/ijms23063265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer (OC) grows and interacts constantly with a complex microenvironment, in which immune cells, fibroblasts, blood vessels, signal molecules and the extracellular matrix (ECM) coexist. This heterogeneous environment provides structural and biochemical support to the surrounding cells and undergoes constant and dynamic remodeling that actively promotes tumor initiation, progression, and metastasis. Despite the fact that traditional 2D cell culture systems have led to relevant medical advances in cancer research, 3D cell culture models could open new possibilities for the development of an in vitro tumor microenvironment more closely reproducing that observed in vivo. The implementation of materials science and technology into cancer research has enabled significant progress in the study of cancer progression and drug screening, through the development of polymeric scaffold-based 3D models closely recapitulating the physiopathological features of native tumor tissue. This article provides an overview of state-of-the-art in vitro tumor models with a particular focus on 3D OC cell culture in pre-clinical studies. The most representative OC models described in the literature are presented with a focus on hydrogel-based scaffolds, which guarantee soft tissue-like physical properties as well as a suitable 3D microenvironment for cell growth. Hydrogel-forming polymers of either natural or synthetic origin investigated in this context are described by highlighting their source of extraction, physical-chemical properties, and application for 3D ovarian cancer cell culture.
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Affiliation(s)
| | | | | | - Dario Puppi
- BioLab Research Group, Department of Chemistry and Industrial Chemistry, University of Pisa, UdR INSTM-Pisa, Via Moruzzi 13, 56124 Pisa, Italy; (S.B.); (C.T.)
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16
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Sarkozy D, Guttman A. Capillary Sodium Dodecyl Sulfate Agarose Gel Electrophoresis of Proteins. Gels 2022; 8:gels8020067. [PMID: 35200449 PMCID: PMC8871118 DOI: 10.3390/gels8020067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Capillary sodium dodecyl sulfate gel electrophoresis has long been used for the analysis of proteins, mostly either with entangled polymer networks or translationally cross-linked gels. In this paper capillary agarose gel electrophoresis is introduced for the separation of low molecular weight immunoglobulin subunits. The light (LC~24 kDa) and heavy (HC~50 kDa) chain fragments of a monoclonal antibody therapeutic drug were used to optimize the sieving matrix composition of the agarose/Tris-borate-EDTA (TBE) systems. The agarose and boric acid contents were systematically varied between 0.2–1.0% and 320–640 mM, respectively. The influence of several physical parameters such as viscosity and electroosmotic flow were also investigated, the latter to shed light on its effect on the electrokinetic injection bias. Three dimensional Ferguson plots were utilized to better understand the sieving performance of the various agarose/TBE ratio gels, especially relying on their slope (retardation coefficient, KR) value differences. The best resolution between the LC and non-glycosylated HC IgG subunits was obtained by utilizing the molecular sieving effect of the 1% agarose/320 mM boric acid composition (ΔKR = 0.035). On the other hand, the 0.8% agarose/640 mM boric acid gel showed the highest separation power between the similar molecular weight, but different surface charge density non-glycosylated HC and HC fragments (ΔKR = 0.005). It is important to note that the agarose-based gel-buffer systems did not require any capillary regeneration steps between runs other than simple replenishment of the sieving matrix, significantly speeding up analysis cycle time.
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Affiliation(s)
- Daniel Sarkozy
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032 Debrecen, Hungary;
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032 Debrecen, Hungary;
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200 Veszprem, Hungary
- Correspondence:
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17
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Yin X, Yao D, Lam MHW, Liang H. A facile biosynthesis strategy of plasmid DNA-derived nanowires for readable microRNA logic operations. J Mater Chem B 2022; 10:3055-3063. [DOI: 10.1039/d1tb02699b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple microRNAs (miRNAs) logical assays have attracted wide attention recently, which can be applied to mimic and reveal cellular events at the molecular level. However, it remains challenging to develop...
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18
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Mujtaba MG, Baliban T, Bhagu J, Herrera M. A Laboratory Exercise Simulating Antibody and Antigen Reactions of the Ouchterlony Double Immunodiffusion Assay Using Inorganic Salts. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:e00103-21. [PMID: 34594450 PMCID: PMC8442017 DOI: 10.1128/jmbe.00103-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/12/2021] [Indexed: 06/13/2023]
Abstract
The Ouchterlony double immunodiffusion assay is a serological technique used in the detection of antibodies and antigens for diagnostic purposes and also used in immunology laboratory courses as a common teaching assay where students observe the geometrical precipitation line patterns that form in the agarose, elucidating degrees of homology between antigens. In this classical technique, students must wait several hours to days to obtain results when protein antigens and antibodies are used. Furthermore, these proteins degrade over time if not frozen or stored in the refrigerator and are the most expensive consumables of the laboratory exercise. In this study, inexpensive and commonly used inorganic ionic salt solutions that are stable and can be stored at room temperature for several years were used to mimic antigens and antibodies. The precipitation lines started to form in the agarose plates after 15 min and fully developed within an hour, showing different geometrical precipitation patterns and spur formations that could be identified by students as full identity, partial identity, and nonidentity between the simulated (inorganic) antigens. Students conducting this exercise in a combined lecture and laboratory immunology course were able to finish the exercise as well as record and discuss results within class time, and tvhey showed increased interest in the laboratory exercise and had a better understanding of antibody-antigen reactions. Thus, this simulated laboratory experiment is an inexpensive, safe, and fast exercise that allows students to observe precipitations reactions of the Ouchterlony assay within the class session time.
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Affiliation(s)
- Mustafa G. Mujtaba
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Tara Baliban
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Jamini Bhagu
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Michael Herrera
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
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19
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Convenient Agarose Preparation with Hydrogen Peroxide and Desulfation Process Analysis. Mar Drugs 2021; 19:md19060297. [PMID: 34070967 PMCID: PMC8224637 DOI: 10.3390/md19060297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
Agarose is a natural seaweed polysaccharide and widely used in the medicine, food, and biological fields because of its high gel strength, non-toxicity, and electrical neutrality. The sulfate group is one of the main charged groups that affect the performance of agarose. In the present study, a simple, eco-friendly, and efficient method was explored for agarose preparation. After desulfation with hydrogen peroxide (H2O2), the sulfate content of agar reached 0.21%. Together with gel strength, electroendosmosis, gelling and melting temperature, the indicators of desulfated agar met the standards of commercially available agarose. Notably, the desulfated agar can be used as an agarose gel electrophoresis medium to separate DNA molecules, and the separation effect is as good as that of commercially available agarose. Further, the H2O2 desulfation process was analyzed. The addition of a hydroxyl radical (HO•) scavenger remarkably decreased the H2O2 desulfation rate, indicating that HO• has a certain role in agar desulfation. Sulfate content detection indicated that sulfur was removed from agar molecules in the form of sulfate ions (SO42−) and metal sulfate. The band absence at 850 cm−1 indicated that the sulfate groups at C-4 of D-galactose in sulfated galactan were eliminated.
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20
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Change of network structure in agarose gels by aging during storage studied by NMR and electrophoresis. Carbohydr Polym 2020; 245:116497. [DOI: 10.1016/j.carbpol.2020.116497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/20/2022]
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21
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Serwer P, Wright ET. In-Gel Isolation and Characterization of Large (and Other) Phages. Viruses 2020; 12:v12040410. [PMID: 32272774 PMCID: PMC7232213 DOI: 10.3390/v12040410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.
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22
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Jönsson M, Allahgholi L, Sardari RR, Hreggviðsson GO, Nordberg Karlsson E. Extraction and Modification of Macroalgal Polysaccharides for Current and Next-Generation Applications. Molecules 2020; 25:E930. [PMID: 32093097 PMCID: PMC7070867 DOI: 10.3390/molecules25040930] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 11/16/2022] Open
Abstract
Marine macroalgal (seaweed) polysaccharides are highly promising for next-generation applications in several industries. However, despite the reported comprehensive potential of these polysaccharides, commercial products are scarce on the market. Seaweed cultivations are increasing in number and production quantity, owing to an elevated global trend of utilization interest in seaweed. The extraction of polysaccharides from seaweed generally generates low yields, but novel methods are being developed to facilitate and improve the extraction processes. Current areas of applications for seaweed polysaccharides mainly take advantage of the physicochemical properties of certain polysaccharides, such as gelling, thickening and emulsifying. However, many of the numerous bioactivities reported are still only at research level and lack clinical evidence for commercialization. It has been suggested the construction of smaller units may generate better defined molecules that are more suitable for biomedical applications. Enzymatic modification is a promising tool for the generation of more defined, targeted biomolecules. This review covers; structural differences between the most predominant marine algal polysaccharides, extraction processes, modification alternatives, as well as a summary of current and potential next-generation application areas.
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Affiliation(s)
- Madeleine Jönsson
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Leila Allahgholi
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Roya R.R. Sardari
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Guðmundur O. Hreggviðsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, IS-101 Reykjavík, Iceland;
- Matis Ohf, Vinlandsleid 12, IS-113 Reykjavik, Iceland
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
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23
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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24
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Kim C, Jeong D, Kim S, Kim Y, Jung S. Cyclodextrin functionalized agarose gel with low gelling temperature for controlled drug delivery systems. Carbohydr Polym 2019; 222:115011. [PMID: 31320040 DOI: 10.1016/j.carbpol.2019.115011] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022]
Abstract
Conventional agaroses with high gelling temperature are limited to apply to the field of drug delivery. In this study, β-cyclodextrin (βCD) functionalized agarose (CFA) with low gelling temperature was successfully prepared from ethylenediamine-functionalized agarose using mono-succinyl βCD. The gelling temperature of CFA dramatically decreased to 26.7 °C from 65 °C and the melting temperature declined from 95 °C to 66.1 °C. Upon drug loading, CFA can be used at 30 °C because of its low gelling temperature compared to agarose. CFA gel could be used both for bovine serum albumin as a full release, and for the doxorubicin (DOX) for sustained release, via inclusion complexation of βCD. Furthermore, cytotoxicity tests revealed that CFA was noncytotoxic. DOX in the CFA gel could retain the anti-cancer activity. Newly synthesized CFA with low gelling temperature offer a new means for the development of hydrogel-based delivery systems for a variety of therapeutic drugs.
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Affiliation(s)
- Chulgu Kim
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Daham Jeong
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea; Institute for Ubiquitous Information Technology and Applications (UBITA), Center for Biotechnology Research in UBITA (CBRU), Konkuk University, Seoul, 05029, South Korea
| | - Seonmok Kim
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Yohan Kim
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Seunho Jung
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea; Institute for Ubiquitous Information Technology and Applications (UBITA), Center for Biotechnology Research in UBITA (CBRU), Konkuk University, Seoul, 05029, South Korea.
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25
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Abstract
The feasibility of using hydrogels as a water bolus during hyperthermia treatment was assessed. Three types of gels, high methoxyl (HM) pectin/alginate, xanthan/locust bean gum (LBG) and xanthan/LBG/agarose were evaluated based on their dielectric, rheological and mechanical properties. The most suitable, xanthan/LBG/agarose gel was further used as a water bolus in a hyperthermia array applicator. The gels composed of polysaccharides carrying low charge displayed dielectric properties close to those of water, while the dielectric properties of HM pectin/alginate gel was deemed unsuitable for the current application. The mechanical examination shows that the xanthan/LBG gel has a non-brittle behaviour at room temperature, in contrast to the agarose gel. The moduli of the xanthan/LBG gel weaken however considerably between the temperature range of 40 °C and 50 °C, reducing its potential to be used as water bolus. The ternary system of xanthan/LBG/agarose had advantageous behaviour as it was dominated by the thermal hysteresis typical of agarose upon temperature increase, but governed by the typical non-brittle behaviour of the xanthan/LBG at low temperatures. The final evaluation within the hyperthermia applicator showed excellent signal transmission from the antennas. The agarose/xanthan/LBG gel reduced the scattering of electromagnetic waves, enabled a tight closure between the body and the antennas, and offered a less bulky solution than the currently used water-filled plastic bags. The results presented here open up a new application area for hydrogels in improving heat delivery during hyperthermia treatment and other near-field microwave applications.
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Affiliation(s)
- Hana Dobšíček Trefná
- Department of Electrical Engineering, Chalmers University of Technology, Göteborg, Sweden
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26
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Liu J, Sun L, Xu W, Wang Q, Yu S, Sun J. Current advances and future perspectives of 3D printing natural-derived biopolymers. Carbohydr Polym 2019; 207:297-316. [DOI: 10.1016/j.carbpol.2018.11.077] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/20/2022]
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Abstract
In this work, monodisperse agarose gel nanoparticles were prepared using a W/O microemulsion as a template to control the size of the obtained particles. The combination of this template method with a temperature-induced gelling and a solvent exchange methodology has allowed preparing stable aqueous dispersions of monodisperse agarose gel nanoparticles in water. The average size, measured as an apparent hydrodynamic diameter, of the obtained particles was around 150 nm. The ability of the obtained hydrogel particles for the encapsulation and release of a synthetic insecticide (azamethiphos) was tested. The results evidence that the insecticide molecules encapsulated in the fabricated nanoparticles are released following a diffusion-controlled mechanism. These results combined with the biodegradability of the agarose provide the bases for the design of a new vector with application in the control of parasites in water reservoirs.
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Pan Q, Yamauchi KA, Herr AE. Controlling Dispersion during Single-Cell Polyacrylamide-Gel Electrophoresis in Open Microfluidic Devices. Anal Chem 2018; 90:13419-13426. [PMID: 30346747 PMCID: PMC6777840 DOI: 10.1021/acs.analchem.8b03233] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
New tools for measuring protein expression in individual cells complement single-cell genomics and transcriptomics. To characterize a population of individual mammalian cells, hundreds to thousands of microwells are arrayed on a polyacrylamide-gel-coated glass microscope slide. In this "open" fluidic device format, we explore the feasibility of mitigating diffusional losses during lysis and polyacrylamide-gel electrophoresis (PAGE) through spatial control of the pore-size of the gel layer. To reduce in-plane diffusion-driven dilution of each single-cell lysate during in-microwell chemical lysis, we photopattern and characterize microwells with small-pore-size sidewalls ringing the microwell except at the injection region. To reduce out-of-plane-diffusion-driven-dilution-caused signal loss during both lysis and single-cell PAGE, we scrutinize a selectively permeable agarose lid layer. To reduce injection dispersion, we photopattern and study a stacking-gel feature at the head of each <1 mm separation axis. Lastly, we explore a semienclosed device design that reduces the cross-sectional area of the chip, thus reducing Joule-heating-induced dispersion during single-cell PAGE. As a result, we observed a 3-fold increase in separation resolution during a 30 s separation and a >2-fold enhancement of the signal-to-noise ratio. We present well-integrated strategies for enhancing overall single-cell-PAGE performance.
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Affiliation(s)
- Qiong Pan
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Kevin A. Yamauchi
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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29
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Chew KW, Juan JC, Phang SM, Ling TC, Show PL. An overview on the development of conventional and alternative extractive methods for the purification of agarose from seaweed. SEP SCI TECHNOL 2017. [DOI: 10.1080/01496395.2017.1394881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kit Wayne Chew
- Nanotechnology & Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Joon Ching Juan
- Nanotechnology & Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Advanced Catalysis and Environmental Technology, Monash University Sunway Campus, Bandar Sunway, Malaysia
| | - Siew Moi Phang
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Tau Chuan Ling
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor Darul Ehsan, Malaysia
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30
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Vieira VMP, Hay LL, Smith DK. Multi-component hybrid hydrogels - understanding the extent of orthogonal assembly and its impact on controlled release. Chem Sci 2017; 8:6981-6990. [PMID: 29147525 PMCID: PMC5642149 DOI: 10.1039/c7sc03301j] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022] Open
Abstract
This paper reports self-assembled multi-component hybrid hydrogels including a range of nanoscale systems and characterizes the extent to which each component maintains its own unique functionality, demonstrating that multi-functionality can be achieved by simply mixing carefully-chosen constituents. Specifically, the individual components are: (i) pH-activated low-molecular-weight gelator (LMWG) 1,3;2,4-dibenzylidenesorbitol-4',4''-dicarboxylic acid (DBS-COOH), (ii) thermally-activated polymer gelator (PG) agarose, (iii) anionic biopolymer heparin, and (iv) cationic self-assembled multivalent (SAMul) micelles capable of binding heparin. The LMWG still self-assembles in the presence of PG agarose, is slightly modified on the nanoscale by heparin, but is totally disrupted by the micelles. However, if the SAMul micelles are bound to heparin, DBS-COOH self-assembly is largely unaffected. The LMWG endows hybrid materials with pH-responsive behavior, while the PG provides mechanical robustness. The rate of heparin release can be controlled through network density and composition, with the LMWG and PG behaving differently in this regard, while the presence of the heparin binder completely inhibits heparin release through complexation. This study demonstrates that a multi-component approach can yield exquisite control over self-assembled materials. We reason that controlling orthogonality in such systems will underpin further development of controlled release systems with biomedical applications.
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Affiliation(s)
- Vânia M P Vieira
- Department of Chemistry , University of York , Heslington , York , YO10 5DD , UK . ; http://www.york.ac.uk/chemistry/staff/academic/o-s/dsmith/
| | - Laura L Hay
- Department of Chemistry , University of York , Heslington , York , YO10 5DD , UK . ; http://www.york.ac.uk/chemistry/staff/academic/o-s/dsmith/
| | - David K Smith
- Department of Chemistry , University of York , Heslington , York , YO10 5DD , UK . ; http://www.york.ac.uk/chemistry/staff/academic/o-s/dsmith/
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31
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Abstract
We characterize the porosity of hydrogels by imaging the displacement trajectories of embedded tracer particles. This offers the possibility of characterizing the size and projected shape of individual pores as well as direct, real-space maps of heterogeneous porosity and its distribution. The scheme shows that when fluorescent spherical particles treated to avoid specific adsorption are loaded into the gel, their displacement trajectories from Brownian motion report on the size and projected shape in which the pore resides, convoluted by the particle size. Of special interest is how pores and their distribution respond to stimuli. These ideas are validated in agarose gels loaded with latex particles stabilized by adsorbed bovine serum albumin. Gels heated from room temperature produced an increasingly more monodisperse pore size distribution because increasing temperature preferentially enlarges smaller pores, but this was irreversible upon cooling, and shearing agarose gels beyond the yield point destroyed larger pores preferably. The method is considered to be generalizable beyond the agarose system presented here as proof of concept.
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Affiliation(s)
- Lingxiang Jiang
- Department of Materials Science and Engineering, Jinan University , Guangzhou 510632, China
| | - Steve Granick
- IBS Center for Soft and Living Matter and UNIST, Ulsan 689-798, South Korea
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32
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Wu J, Black JJ, Aldous L. Thermoelectrochemistry using conventional and novel gelled electrolytes in heat-to-current thermocells. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2016.12.152] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Khairulina K, Chung UI, Sakai T. New design of hydrogels with tuned electro-osmosis: a potential model system to understand electro-kinetic transport in biological tissues. J Mater Chem B 2017; 5:4526-4534. [DOI: 10.1039/c7tb00064b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of charged polymer gels with precisely controlled magnitude and direction of electro-osmotic flow was prepared and opens up the possibility for understanding the contribution of electro-osmosis to transport phenomenon in native biological tissues.
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Affiliation(s)
- Kateryna Khairulina
- Department of Bioengineering
- School of Engineering
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Ung-il Chung
- Department of Bioengineering
- School of Engineering
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Takamasa Sakai
- Department of Bioengineering
- School of Engineering
- The University of Tokyo
- Bunkyo-ku
- Japan
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34
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Thompson BR, Horozov TS, Stoyanov SD, Paunov VN. An ultra melt-resistant hydrogel from food grade carbohydrates. RSC Adv 2017. [DOI: 10.1039/c7ra08590g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have formulated an ultra melt-resistant composite hydrogel with tailorable rheology over a range of temperatures.
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Affiliation(s)
| | - Tommy S. Horozov
- School of Mathematics and Physical Sciences (Chemistry)
- University of Hull
- Hull
- UK
| | - Simeon D. Stoyanov
- Unilever R&D Vlaardingen
- 3133 AT Vlaardingen
- The Netherlands
- Laboratory of Physical Chemistry and Soft Matter
- Wageningen University
| | - Vesselin N. Paunov
- School of Mathematics and Physical Sciences (Chemistry)
- University of Hull
- Hull
- UK
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35
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Mitrev Y, Simova S, Jeannerat D. NMR analysis of weak molecular interactions using slice-selective experiments via study of concentration gradients in agar gels. Chem Commun (Camb) 2016; 52:5418-20. [DOI: 10.1039/c6cc01853j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Weak molecular interactions can be localized and quantified using a single NMR experiment analysing concentration gradients generated in agar gels.
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Affiliation(s)
- Y. Mitrev
- Department of Organic Chemistry
- University of Geneva
- Geneva 4
- Switzerland
- Institute of Organic Chemistry with Centre of Phytochemistry
| | - S. Simova
- Institute of Organic Chemistry with Centre of Phytochemistry
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
| | - D. Jeannerat
- Department of Organic Chemistry
- University of Geneva
- Geneva 4
- Switzerland
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36
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Tang Z, Liang Z, Lu B, Li J, Hu R, Zhao Q, Yu D. Gel mesh as "brake" to slow down DNA translocation through solid-state nanopores. NANOSCALE 2015; 7:13207-13214. [PMID: 26181489 DOI: 10.1039/c5nr03084f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Agarose gel is introduced onto the cis side of silicon nitride nanopores by a simple and low-cost method to slow down the speed of DNA translocation. DNA translocation speed is slowed by roughly an order of magnitude without losing signal to noise ratio for different DNA lengths and applied voltages in gel-meshed nanopores. The existence of the gel moves the center-of-mass position of the DNA conformation further from the nanopore center, contributing to the observed slowing of translocation speed. A reduced velocity fluctuation is also noted, which is beneficial for further applications of gel-meshed nanopores. The reptation model is considered in simulation and agrees well with the experimental results.
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Affiliation(s)
- Zhipeng Tang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, P. R. China.
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37
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Homogeneous tosylation of agarose as an approach toward novel functional polysaccharide materials. Carbohydr Polym 2015; 127:236-45. [DOI: 10.1016/j.carbpol.2015.03.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 11/19/2022]
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38
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You B, Yin P, Zhang J, He D, Chen G, Kang F, Wang H, Deng Z, Li Y. Hydrogel-derived non-precious electrocatalysts for efficient oxygen reduction. Sci Rep 2015; 5:11739. [PMID: 26130371 PMCID: PMC4486930 DOI: 10.1038/srep11739] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 05/11/2015] [Indexed: 11/12/2022] Open
Abstract
The development of highly active, cheap and robust oxygen reduction reaction (ORR) electrocatalysts to replace precious metal platinum is extremely urgent and challenging for renewable energy devices. Herein we report a novel, green and especially facile hydrogel strategy to construct N and B co-doped nanocarbon embedded with Co-based nanoparticles as an efficient non-precious ORR catalyst. The agarose hydrogel provides a general host matrix to achieve a homogeneous distribution of key precursory components including cobalt (II) acetate and buffer salts, which, upon freeze-drying and carbonization, produces the highly active ORR catalyst. The gel buffer containing Tris base, boric acid and ethylenediaminetetraacetic acid, commonly adopted for pH and ionic strength control, plays distinctively different roles here. These include a green precursor for N- and B-doping, a salt porogen and a Co2+ chelating agent, all contributing to the excellent ORR activity. This hydrogel-based process is potentially generalizable for many other catalytic materials.
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Affiliation(s)
- Bo You
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Peiqun Yin
- Center of Advanced Nanocatalysis (CAN-USTC), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junli Zhang
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Daping He
- Center of Advanced Nanocatalysis (CAN-USTC), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Gaoli Chen
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fei Kang
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huiqiao Wang
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry &Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.,Center of Advanced Nanocatalysis (CAN-USTC), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yadong Li
- Center of Advanced Nanocatalysis (CAN-USTC), University of Science and Technology of China, Hefei, Anhui 230026, China.,Department of Chemistry, Tsinghua University, Beijing, 100084, China
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39
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Development and applicability of an agarose-based tart cherry phantom for computer tomography imaging. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2015. [DOI: 10.1007/s11694-015-9234-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Chau M, Sriskandha SE, Thérien-Aubin H, Kumacheva E. Supramolecular Nanofibrillar Polymer Hydrogels. SUPRAMOLECULAR POLYMER NETWORKS AND GELS 2015. [DOI: 10.1007/978-3-319-15404-6_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Sanderson BA, Araki N, Lilley JL, Guerrero G, Lewis LK. Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis. Anal Biochem 2014; 454:44-52. [PMID: 24637158 PMCID: PMC4021863 DOI: 10.1016/j.ab.2014.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022]
Abstract
Agarose gel electrophoresis of DNA and RNA is routinely performed using buffers containing either Tris, acetate, and EDTA (TAE) or Tris, borate, and EDTA (TBE). Gels are run at a low, constant voltage (∼10 V/cm) to minimize current and asymmetric heating effects, which can induce band artifacts and poor resolution. In this study, alterations of gel structure and conductive media composition were analyzed to identify factors causing higher electrical currents during horizontal slab gel electrophoresis. Current was reduced when thinner gels and smaller chamber buffer volumes were used, but was not influenced by agarose concentration or the presence of ethidium bromide. Current was strongly dependent on the amount and type of EDTA used and on the concentrations of the major acid-base components of each buffer. Interestingly, resolution and the mobilities of circular versus linear plasmid DNAs were also affected by the chemical form and amount of EDTA. With appropriate modifications to gel structure and buffer constituents, electrophoresis could be performed at high voltages (20-25 V/cm), reducing run times by up to 3-fold. The most striking improvements were observed with small DNAs and RNAs (10-100 bp): high voltages and short run times produced sharper bands and higher resolution.
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Affiliation(s)
- Brian A Sanderson
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Naoko Araki
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Jennifer L Lilley
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Gilberto Guerrero
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
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42
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Koo HJ, Kim SK, Braun PV. Facile fabrication of graphene composite microwires via drying-induced size reduction of hydrogel filaments. RSC Adv 2014. [DOI: 10.1039/c4ra01154f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Graphene composite microwires with good electrical conductivities are formed by extrusion of a graphene oxide–agarose suspension followed by drying and reduction of graphene oxide to graphene.
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Affiliation(s)
- Hyung-Jun Koo
- Materials Science and Engineering Department
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | - Sung-Kon Kim
- Materials Science and Engineering Department
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | - Paul V. Braun
- Materials Science and Engineering Department
- University of Illinois at Urbana-Champaign
- Urbana, USA
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43
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Kim M, Kim T. Integration of nanoporous membranes into microfluidic devices: electrokinetic bio-sample pre-concentration. Analyst 2013; 138:6007-15. [PMID: 23951567 DOI: 10.1039/c3an00965c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The integration of nanoporous membranes into microfluidic devices allows a wide range of analytical and biochemical applications such as stable concentration gradient generation, sample pre-concentration, and ion and biomolecule filtration in a controllable manner. However, further applications of nanoporous membranes in microfluidic devices require rapid and controllable fabrication methods of various nanoporous precursor materials; currently, few such methods exist. Here, we describe simple and robust methods that can be used for microfabricating four different precursor materials as leakage-tight membranes in a microfluidic channel network. The methods consist of a common integration process and individual solidification processes such as solvent evaporation, UV-curing, and temperature treatment. We demonstrate that the fabricated membranes can be used for electrokinetic, nanofluidic pre-concentration of bio-samples such as proteins, cells, and microspheres on either the anodic or cathodic side of the membranes. In addition, we not only characterize the physicochemical properties of the membranes such as conductance of membrane-integrated microchannels, relative permselectivity, and pre-concentration ability, but also compare fabrication availability, membrane robustness, surface charge density tunability and biocompatibility with buffer solutions. The methods are versatile for many nanoporous precursor materials and easy to control the location and dimension of the membranes. Hence, the methods developed and the characterized properties of the membranes tested in this work could be widely employed for further applications of nanoporous membranes in microfluidic systems.
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Affiliation(s)
- Minseok Kim
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan 689-798, Republic of Korea.
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44
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Kopesky PW, Byun S, Vanderploeg EJ, Kisiday JD, Frisbie DD, Grodzinsky AJ. Sustained delivery of bioactive TGF-β1 from self-assembling peptide hydrogels induces chondrogenesis of encapsulated bone marrow stromal cells. J Biomed Mater Res A 2013; 102:1275-85. [PMID: 23650117 DOI: 10.1002/jbm.a.34789] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 01/25/2023]
Abstract
Tissue engineering strategies for cartilage defect repair require technology for local targeted delivery of chondrogenic and anti-inflammatory factors. The objective of this study was to determine the release kinetics of transforming growth factor β1 (TGF-β1) from self-assembling peptide hydrogels, a candidate scaffold for cell transplant therapies, and stimulate chondrogenesis of encapsulated young equine bone marrow stromal cells (BMSCs). Although both peptide and agarose hydrogels retained TGF-β1, fivefold higher retention was found in peptide. Excess unlabeled TGF-β1 minimally displaced retained radiolabeled TGF-β1, demonstrating biologically relevant loading capacity for peptide hydrogels. The initial release from acellular peptide hydrogels was nearly threefold lower than agarose hydrogels, at 18% of loaded TGF-β1 through 3 days as compared to 48% for agarose. At day 21, cumulative release of TGF-β1 was 32-44% from acellular peptide hydrogels, but was 62% from peptide hydrogels with encapsulated BMSCs, likely due to cell-mediated TGF-β1 degradation and release of small labeled species. TGF-β1 loaded peptide hydrogels stimulated chondrogenesis of young equine BMSCs, a relevant preclinical model for treating injuries in young human cohorts. Self-assembling peptide hydrogels can be used to deliver chondrogenic factors to encapsulated cells making them a promising technology for in vivo, cell-based regenerative medicine.
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Affiliation(s)
- Paul W Kopesky
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139
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45
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Ding Y, Huang E, Lam KS, Pan T. Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning. LAB ON A CHIP 2013; 13:1902-10. [PMID: 23525299 PMCID: PMC4565160 DOI: 10.1039/c3lc41372a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets challenges on biocompatibility, thermal and chemical sensitivity, as well as limited availability of reagents. In this paper, we aim at combining the desired features from non-contact inkjet printing and dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, sub-microliter ink loading with a minimal dead volume, high-throughput printing, biocompatible non-contact processing, sequential patterning with self-alignment, wide adaptability for complex media (e.g., cell suspension or colloidal solutions), interchangeable/disposable cartridge design, and simple assembly and configuration, all highly desirable towards laboratory-based research and development. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analysed. Optimal printing resolution of 80 μm has been repeatedly obtained. Furthermore, two useful functions of the MI-printer, multiplexed printing and combinatorial printing, have been experimentally demonstrated with less than 10 μm misalignment. Moreover, molecular and biological patterning, utilizing the multiplexed and combinatorial printing, has been implemented to illustrate the utility of this versatile printing technique for emerging biomedical applications.
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Affiliation(s)
- Yuzhe Ding
- Micro-Nano Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, CA, USA
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46
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Successful preparation and characterization of biotechnological grade agarose from indigenous Gelidium amansii of Taiwan. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.12.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Adsorption of peptides and small proteins with control access polymer permeation to affinity binding sites. Part II: Polymer permeation-ion exchange separation adsorbents with polyethylene glycol and strong anion exchange groups. J Chromatogr A 2012; 1227:126-37. [DOI: 10.1016/j.chroma.2011.12.092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 12/09/2011] [Accepted: 12/27/2011] [Indexed: 11/21/2022]
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48
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González-Ortega O, Porath J, Guzmán R. Adsorption of peptides and small proteins with control access polymer permeation to affinity binding sites. Part I: Polymer permeation-immobilized metal ion affinity chromatography separation adsorbents with polyethylene glycol and immobilized metal ions. J Chromatogr A 2012; 1227:115-25. [PMID: 22281505 DOI: 10.1016/j.chroma.2011.12.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/09/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
Abstract
Despite the many efforts to develop efficient protein purification techniques, the isolation of peptides and small proteins on a larger than analytical scale remains a significant challenge. Recovery of small biomolecules from diluted complex biological mixtures, such as human serum, employing porous adsorbents is a difficult task mainly due to the presence of concentrated large biomolecules that can add undesired effects in the system such as blocking of adsorbent pores, impairing diffusion of small molecules, or competition for adsorption sites. Adsorption and size exclusion chromatography (AdSEC) controlled access media, using polyethylene glycol (PEG) as a semi-permeable barrier on a polysaccharide matrix, have been developed and explored in this work to overcome such effects and to preferentially adsorb small molecules while rejecting large ones. In the first part of this work, adsorption studies were performed with small peptides and proteins from synthetic mixtures using controlled access polymer permeation adsorption (CAPPA) media created by effectively grafting PEG on an immobilized metal affinity chromatography (IMAC) agarose resin, where chelating agents and immobilized metal ions were used as the primary affinity binding sites. Synthetic mixtures consisted of bovine serum albumin (BSA) with small proteins, peptides, amino acids (such as histidine or Val⁴-Angiotensin III), and small molecules-spiked human serum. The synthesized hybrid adsorbent consisted of agarose beads modified with iminodiacetic (IDA) groups, loaded with immobilized Cu(II) ions, and PEG. These CAPPA media with grafted PEG on the interior and exterior surfaces of the agarose matrix were effective in rejecting high molecular weight proteins. Different PEG grafting densities and PEG of different molecular weight were tested to determine their effect in rejecting and controlling adsorbent permeation properties. Low grafting density of high molecular weight PEG was found to be as effective as high grafting density of low molecular weight PEG in the rejecting properties of the semi-permeable synthesized media.
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Affiliation(s)
- Omar González-Ortega
- Department of Chemical and Environmental Engineering, The University of Arizona, Tucson, AZ 85721,USA
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49
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Ko HC, Yuan CT, Tang J. Probing and controlling fluorescence blinking of single semiconductor nanoparticles. NANO REVIEWS 2011; 2:NANO-2-5895. [PMID: 22110871 PMCID: PMC3215194 DOI: 10.3402/nano.v2i0.5895] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 11/14/2022]
Abstract
In this review we present an overview of the experimental and theoretical development on fluorescence intermittency (blinking) and the roles of electron transfer in semiconductor crystalline nanoparticles. Blinking is a very interesting phenomenon commonly observed in single molecule/particle experiments. Under continuous laser illumination, the fluorescence time trace of these single nanoparticles exhibit random light and dark periods. Since its first observation in the mid-1990s, this intriguing phenomenon has attracted wide attention among researchers from many disciplines. We will first present the historical background of the discovery and the observation of unusual inverse power-law dependence for the waiting time distributions of light and dark periods. Then, we will describe our theoretical modeling efforts to elucidate the causes for the power-law behavior, to probe the roles of electron transfer in blinking, and eventually to control blinking and to achieve complete suppression of the blinking, which is an annoying feature in many applications of quantum dots as light sources and fluorescence labels for biomedical imaging.
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Affiliation(s)
- Hsien-Chen Ko
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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50
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Koo HJ, Chang ST, Velev OD. Ion-current diode with aqueous gel/SiO(2) nanofilm interfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:1393-1397. [PMID: 20564481 DOI: 10.1002/smll.200902069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Hyung-Jun Koo
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh, NC 27695-7905, USA
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