Protein separation and identification using magnetic beads encoded with surface-enhanced Raman spectroscopy

This article presents a prototype of a surface-enhanced Raman spectroscopy (SERS)-encoded magnetic bead of 8 μm diameter. The core part of the bead is composed of a magnetic nanoparticle (NP)-embedded sulfonated polystyrene bead. The outer part of the bead is embedded with Ag NPs on which labeling molecules generating specific SERS bands are adsorbed. A silica shell is fabricated for further bioconjugation and protection of SERS signaling. Benzenethiol, 4-mercaptotoluene, 2-naphthalenethiol, and 4-aminothiophenol are used as labeling molecules. The magnetic SERS beads are used as substrates for protein sensing and screening with easy handling. As a model application, streptavidin-bound magnetic SERS beads are used to illustrate selective separation in a flow cytometry system, and the screened beads are spectrally recognized by Raman spectroscopy. The proposed magnetic SERS beads are likely to be used as a versatile solid support for protein sensing and screening in multiple assay technology.     

Separation of magnetic affinity biopolymer adsorbents in a Davis tube magnetic separator

A Davis tube (a matrix-free, flow-through magnetic separator used mainly in mineral processing) has been tested for separation of magnetic affinity biopolymer adsorbents from larger volumes of suspensions. Both magnetic chitosan and magnetic cross-linked erythrocytes could be efficiently separated from litre volumes of suspensions. Up to 90% adsorbent recovery was achieved under optimised separation conditions.     

Multipurpose robot for automated cycle sequencing

Paramagnetic beads have the superior advantages of easy separation and resuspension by controlling the magnetic filed. Previously, we have developed Magtration technology to automate paramagnetic bead handling and have built several automated instruments that handle 1-12 samples simultaneously. To achieve more high-throughput sample processing, two types of a 96-arrayed Integrated Magtration Unit (IMU) were developed, one installed with electromagnets and the other with thin rod-shaped magnets made of neodymium. A multipurpose robot (SX-96GC) equipped with the IMU was also developed for fully automatic processing of 96 samples in parallel. The cleanup of dye-terminator sequencing products was performed using the robot installed with the permanent magnet version of IMU. The results had quality comparable to those by the same protocol in manual handling or to those by the conventional protocols. The robot processed 96 samples in a microplate within 30 min. The protocol that can purify 384 samples within 1 h by processing two microplates concurrently was successfully designed.     

Influence of different magnetites on properties of magnetic Pseudomonas aeruginosa immobilizates used for biosurfactant production

During the last decades, whole‐cell immobilization has been used successfully in many bioprocesses. In particular, it is aimed at implementing continuous production processes, reaching higher production rates, and reusing the biocatalyst. In some cases, effective retention of immobilizates in the bioprocess is not feasible by membranes or sieves due to pore plugging or undesired losses of immobilizates. In the present publication, it is reported about the investigation of magnetic immobilizates of Pseudomonas aeruginosa for application in continuous biosurfactant production of rhamnolipids by foam fractionation and retention of entrained immobilizates by high‐gradient magnetic separation from foam. Different materials and methods were tested with respect to important parameters, such as stability, diffusion properties or magnetic separation. Good magnetic separation of immobilizates was achieved at 5% (w/w) magnetite loading. Best results in terms of homogeneous embedding, good diffusion properties, and stability enhancement vis‐à‐vis pure alginate beads was achieved with alginate beads with embedded Bayoxide® magnetite or MagPrep® silica particles. Although polyurethane immobilizates showed higher stabilities compared with alginate beads, rhamnolipid diffusion in immobilizates was superior in magnetic alginate beads. Regarding bead production, smaller immobilizates were achieved with suspension polymerization compared to droplet extrusion by the JetCutting® technology. In total, magnetic immobilizates are a promising tool for an easier handling of biocatalysts in a continuous biological production process, but they have to be adapted to the current production task.© 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Development of a cell-loaded biosupport separator for continuous immobilized-cell perfusion culture

An efficient cell-loaded biosupport separator of the decantor type was developed and applied for a continuous perfusion culture to produce cyclosporin A (CyA), in which fungal cells were immobilized on Celite beads. In the preliminary experiments employing highly viscous polymer (carboxymethyl cellulose) solutions, the decantor showed good separation performances at high solution viscosites and dilution rates. Two concentric cylindrical tubes installed inside the decantor turned out to play key roles in the efficient separation of the immobilized cells. By installing the decantor on an immobilized-cell perfusion bioprocess system, a stable continuous operation was possible even at a high dilution rate for an extended period, leading to high productivities of free cells and CyA. Almost no immobilized biomass existed in the effluent stream from the bioreactor, demonstrating the effectiveness of the decantor system. It is noteworthy that we could obtain these results despite unfavorable fermentation conditions, i.e., reduced apparent density of cell-loaded beads and increased drag force on the bead particles caused by overgrowth of cells on the bead surface, tubulence caused by large air bubbles, and the existence of a high density of suspended fungal cells (10 g/L) in the fermentation broth.     

Pilot-scale process for magnetic bead purification of antibodies directly from non-clarified CHO cell culture

High capacity magnetic protein A agarose beads, LOABeads PrtA, were used in the development of a new process for affinity purification of monoclonal antibodies (mAbs) from non-clarified CHO cell broth using a pilot-scale magnetic separator. The LOABeads had a maximum binding capacity of 65 mg/mL and an adsorption capacity of 25–42 mg IgG/mL bead in suspension for an IgG concentration of 1 to 8 g/L. Pilot-scale separation was initially tested in a mAb capture step from 26 L clarified harvest. Small-scale experiments showed that similar mAb adsorptions were obtained in cell broth containing 40 × 10⁶ cells/mL as in clarified supernatant. Two pilot-scale purification runs were then performed on non-clarified cell broth from fed-batch runs of 16 L, where a rapid mAb adsorption ≥96.6% was observed after 1 h. This process using 1 L of magnetic beads had an overall mAb yield of 86% and 16 times concentration factor. After this single protein A capture step, the mAb purity was similar to the one obtained by column chromatography, while the host cell protein content was very low, <10 ppm. Our results showed that this magnetic bead mAb purification process, using a dedicated pilot-scale separation device, was a highly efficient single step, which directly connected the culture to the downstream process without cell clarification. Purification of mAb directly from non-clarified cell broth without cell separation can provide significant savings in terms of resources, operation time, and equipment, compared to legacy procedure of cell separation followed by column chromatography step. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2775, 2019.     

Facile fabrication of magnetic gold electrode for magnetic beads-based electrochemical immunoassay: application to the diagnosis of Japanese encephalitis virus

A novel magnetic beads-based electrochemical immunoassay strategy has been developed for the detection of Japanese encephalitis virus (JEV). The magnetic gold electrode was fabricated to manipulate magnetic beads for the direct sensing applications. Gold-coated magnetic beads were employed as the platforms for the immobilization and immunoreaction process, and horseradish peroxidase was chosen as an enzymatic tracer. The proteins (e.g., antibodies or immunocomplexes) attached on the surface of magnetic beads were found to induce a significant decline in their electric conductivity. Multiwalled carbon nanotubes were introduced to improve sensitivity of the assay. The envelope (E) protein, a major immunogenic protein of JEV, was utilized to optimize the assay parameters. Under the optimal conditions, the linear response range of E protein was 0.84 to 11,200 ng/mL with a detection limit of 0.56 ng/mL. When applied for detection of JEV, the proposed method generated a linear response range between 2×10(3) and 5×10(5) PFU/mL. The detection limit for JEV was 2.0×10(3) PFU/mL, which was 2 orders of magnitude lower than that of immunochromatographic strip and similar to that obtained from RT-PCR. This method was also successfully applied to detect JEV in clinical specimens.     

在cDNA文库构建中探究癌症病人血浆外泌体miRNA的特异性扩增

血浆外泌体微小核糖核酸(microRNAs,miRNAs)与癌症的发生、诊断和治疗密切相关,但其分子机制尚不明晰。本研究探讨了癌症病人血浆外泌体miRNAs在cDNA文库构建中非特异性扩增的解决方案。在酶切法中,采用核酸外切酶T (exonuclease T, EXOT)和phi29 DNA聚合酶降解引物;在磁珠法中,利用DNA结合磁珠分离模板和引物。随后,采取琼脂糖凝胶电泳和变性聚丙烯酰胺凝胶电泳检测磁珠分离情况,运用RT-qPCR检测癌症病人血浆外泌体miRNA和不同连接物的含量变化。结果显示,非特异性扩增来源于miRNA的连接物USR5SR;核酸外切酶T (EXOT)和phi29 DNA聚合酶虽可降解USR5SR,但模板链也会发生降解;磁珠分离法中以9%PEG沉淀引物片段、15%PEG沉淀模板链效果最佳。综上所述,磁珠分离法能够高效解决cDNA文库构建中的非特异性扩增,从而实现293T细胞和癌症病人血浆外泌体miRNA cDNA文库的成功构建。     

Affinity separations using microfabricated microfluidic devices:<Emphasis Type="Italic">In situ</Emphasis> photopolymerization and use in protein separations

The use of microfabricated microfluidic devices offers significant advantages over current technologies including fast analysis time and small reagent requirements. In the context of proteomic research, the possibility of using affinity-based separations for prefractionation of samples using microfluidic devices has significant potential. We demonstrate the use of microscale devices to achieve affinity separations of proteins using a device fabricated from borosilicate glass wafers. Photolithography and wet etching are used to pattern individual glass wafers and the wafers are fusion bonded at 650°C to obtain enclosed channels. A polymer has been successfully polymerizedin situ and used either as a frit for packing beads or, when derivatized with Cibacron Blue 3GA, as a separation matrix. Both of these technologies are based onin situ UV photopolymerization of glycidyl methacrylate (GMA) and trimethylolpropane trimethacrylate (TRIM) in channels.     

Magnetic bead purification of M13 DNA sequencing templates.

A method for the preparation of multiple M13 DNA sequencing templates is described. No phenol extraction is required and the procedure can be carried out in Eppendorf tubes or 96-well microtiter plates. Starting with a phage supernatant, the entire procedure is carried out in the same reaction vessel and all separation steps are based on a novel application of magnetic bead separation. The design of a 96-well magnetic separator is presented and the application of the method for large-scale sequencing is discussed.     

Size changes associated with metal adsorption onto modified bone gelatin beads

Significant quantities of heavy metals will adsorb onto modified bone gelatin beads. As this adsorption occurs, the bead can undergo a substantial volume change. Research has shown that the equilibrium bead diameter was a function of the solution pH and the ion concentration in the solution. Here, we demonstrate that under certain conditions, the volume of the beads that absorbed the metal was only 35% of the bead volume when no metal was adsorbed. By taking advantages of these size changes, a fluidized-bed separator can be operated such that natural segregation of loaded beads occurs. This phenomenon may facilitate the design of continous separators for the recovery and concentration of heavy-metal-contaminated waters. These concepts are demonstrated using Cu(2+) adsorption onto such beads.     

Incorporating fluorescent dyes and quantum dots into magnetic microbeads for immunoassays

Microbeads that are both paramagnetic and fluorescently labeled are commercially available in colors spanning the visible spectrum. Although these commercial beads can be bright, polydispersity in both size and fluorescent intensity limit their use in quantitative assays. Very recently, more monodisperse beads have become available, but their large size and surface properties make them less than ideal for some bioassay applications. Here we describe methods to customize commercial nonfluorescent magnetic microparticles with fluorescent dyes and quantum dots (QDs) without affecting their magnetic or surface chemical properties. Fluorescent dyes and 3.3-nm diameter CdSe/ZnS QDs were sequestered within 0.8-micron diameter magnetic beads by swelling the polystyrene matrix of the bead in organic solvent, letting the chromophores partition, and then collapsing the matrix in polar solvents. Chromophore incorporation has been characterized using both UV-visible absorption spectroscopy and fluorescence microscopy, with an average of 3 x 10(8) rhodamine 6G molecules/bead and 6 x 10(4) QDs/bead. The modified beads are uniform in size and intensity, with optical properties comparable to currently available commercial beads. Immunoassay results obtained with our custom fluorescent magnetic microbeads are consistent with those obtained using conventional magnetic microbeads.     

An integrated microfluidic platform for magnetic microbeads separation and confinement

An innovative microfluidic platform for magnetic beads manipulation is introduced, consisting of novel microfabricated 3D magnetic devices positioned in a microfluidic chamber. Each magnetic device comprises of an embedded actuation micro-coil in various design versions, a ferromagnetic pillar, a magnetic backside plate and a sensing micro-coil. The various designs of the micro-coils enable efficient magnetic beads trapping and concentration in different patterns. The finite element analysis (FEA) results show a significant increase of the developed force on suspended magnetic beads when the magnetic pillar and backside plate were integrated into the device structure. These simulation results were confirmed experimentally by measuring the magnetic beads trapping ratios for the different designs and structures of the devices under continuous flow conditions. The trapping ratios and profiles were studied using beads counting, measuring the change of inductance with the sensing micro-coil and by image processing. The devices have efficiently demonstrated a controlled and localized magnetic beads trapping and concentration at small spatial locations for the first time. The new results shown in this study demonstrate the feasibility of efficiently using these original devices as key elements in complex bio-analysis systems.     

Investigation of alginate gel inhomogeneity in simulated gastro-intestinal conditions using magnetic resonance imaging and transmission electron microscopy

The inhomogeneity of alginate gel beads prepared by an external diffusion method has been characterised using spatially resolved nuclear magnetic resonance or “magnetic resonance imaging” (MRI) and transmission electron microscopy (TEM). The beads exhibited various degrees of inhomogeneity although reducing the length of exposure to the gelling bath and the presence of non-gelling ions decreased gel inhomogeneity. In order to gain information regarding the gastro-intestinal functionality of these beads for in vivo applications, they were exposed to simulated gastro-intestinal conditions. The increased polymer concentration at the edge of the beads was shown to persist throughout our gastro-intestinal model despite the centre of the bead becoming progressively more porous in nature. The porosity of the alginate gels has been quantified by image analysis of transmission electron micrographs and shown to depend on both location within the bead and gastro-intestinal conditions. We suggest that such changes in porosity of these alginate beads during simulated gastro-intestinal conditions may make these an attractive option for controlled delivery applications in vivo.     

Electrochemical detection of thrombin based on aptamer and ferrocenylhexanethiol loaded silica nanocapsules

A sensitive and specific electrochemical assay for detection of thrombin based on aptamer and ferrocenylhexanethiol loaded silica nanocapsules (FcSH/SiNCs) amplification is described. In the protocol, a double aptamer sandwich structure was formed in the presence of thrombin, in which an aptamer-labeled FcSH/SiNCs for electrochemical detection, and a streptavidin-coated magnetic bead immobilized aptamer for rapid and specific separation of target protein. After separated from the sample mixture under a magnetic field, the sandwich complex was treated with NaOH to release the loaded ferrocenylhexanethiol (FcSH) from the silica nanocapsules (SiNCs). Differential pulse voltammetry (DPV) was employed to detect the released FcSH, which was related to the concentration of the thrombin. The method took advantage of sandwich binding of two affinity aptamers for increased specificity, high payload of FcSH in SiNCs for signal amplification, magnetic beads for fast magnetic separation. The peak current of released FcSH had a good linear relationship with the thrombin concentration in the range of 0.1-5 nmol/L, and the detection limit of thrombin in the method was 0.06 nmol/L. The detection was also specific for thrombin without being affected by other proteins, such as immunoglobulin G, bovine serum albumin, lysozyme and human serum albumin. The method has been used to detect thrombin in human serum albumin with minimum background interference.     

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.     

Rheological properties of chromosomal and plasmid DNA during alkaline lysis reaction

The experimental apparatus for the simultaneous L-lactic acid fermentation by Rhizopus oryzae immobilized in calcium alginate beads and product separation process was set up in which a three-phase fluidized-bed bioreactor was used as a fermentor and an external electrodialyzer as a separator, and a pump was applied to recycle the fermentation broth between the bioreactor and the separator. The L-lactic acid produced in the fermentor was separated in the separator, product inhibition was alleviated without any addition of alkali or alkali salts and the product purification process could be simplified. The specific productivity and the yield in electrodialysis fermentation (ED-F) process operated in continuous feeding mode were almost the same as that in CaCO₃-buffered fermentation process. A mathematical model of L-lactic acid production in ED-F process was also suggested, in which the model equations for the bioreactor and the electrodialyzer were combined to describe the simultaneous fermentation and product separation. The model predictions were in good agreement with the experimental data.     

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control

Background

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to acquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorporate many capabilities that have been only demonstrated separately.

Methods

Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads.

Results

Here we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies.

Conclusion

This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

     

Regulation of helper cell activity by specifically adsorbable T lymphocytes.

Mice immunized with soluble proteins such as human serum albumin (HSA) or ovalbumin (OA) develop in their spleens antigen-specific T and B lymphocytes. These populations of lymphocytes can be separated from each other by different means; e.g. treatment with anti-theta-antiserum and complement removes selectively T lymphocytes, whereas passage through glass bead columns coated with mouse immunoglobulin (Ig): anti-Ig complexes creates a relatively pure population of T lymphocytes. During the course of such separation studies it was observed that the helper capacity of HSA (or OA) immune mouse spleen cells after Ig:anti-Ig column passage frequently was higher than expected from the enrichment in theta-positive cells. In addition, after adsorption onto antigen coated Bio-Gel beads this effect was even more pronounced, i.e., and increase in the relative helper capacity of about 3 or 4 times compared with an increase in the content of theta-positive cells from about 30% to 40 to 50% after adsorption. The present results will demonstrate that the increased helper capacity was a specific phenomenon which was regulated by theta-positive cells. The regulatory cells specifically adsorbed onto antigen-coated Bio-Gel beads have not been successfully eluted by EDTA or excess-free antigen so far, and they were still adsorbed after pre-incubation with anti-Ig antibodies under conditions where specific B lymphocyte adsorption was almost prevented.     

Immunomagnetic separation as a final purification step of liver endothelial cells

Summary We describe a fast and reproducible method that can be used as a final step in obtaining pure populations of liver endothelial cells. This method employs endothelial cell specific lectin covalently bound to magnetic polystyrene beads (Dynabeads). Evonymus europaeus agglutinin (EEA)-coated Dynabeads were used to purify monkey liver endothelium from Percoll gradient separated nonparenchymal cells. EEA-coated beads were also successfully used to purify monkey aortic endothelial cells. The endothelial cells grew to confluence as a cobblestonelike monolayer, expressed Factor VIII related antigen, and incorporated acetylated-low density lipoprotein. The magnetic beads seemed not to modify the normal properties of the isolated endothelium, thus facilitating their use in experimental studies. This immunomagnetic separation technique may be applicable for purification of endothelial cells from a wide variety of tissue sources.