Search

Photoreactive polymers that generate active species upon irradiation with light are very useful for modifying the surfaces of substrates. However, water solubility decreases as the number of photoreactive functional groups on the polymer increases because most photoreactive functional groups are hydrophobic. In order to improve the hydrophilicity of the photoreactive polymer, we synthesized polyethylene glycol-based photoreactive polymers bearing hydrophobic azidophenyl groups on their side chains. Because of the hydrophilicity of the ethylene glycol main chain, polymers with large numbers of azidophenyl groups were solubilized in protic solvents compared to hydrophobic alkylene chain-based polymers prepared by radical polymerization of methacrylate monomers. Polymers were immobilized on various substrates by irradiation with ultraviolet light and were shown to suppress nonspecific interactions between proteins and cells on the substrate. We conclude that such polymers are useful, highly water soluble antifouling agents.

Successful treatment against infectious agents depends on rapid and accurate detection of the causative organisms. Misdiagnosis can hamper such success while leading to improper advising of antibiotics. In Bangladesh, the majority of the diagnostic centers detect and identify pathogens through culture and biochemical test-based methods and suggest antibiotics based solely on the results of disk-diffusion methods. This pilot study tried to validate the identity of the isolates characterized by diagnostic facilities near Dhaka. One hundred and twenty pre-characterized clinical isolates were analyzed biochemically and genotypically. Random Amplification of Polymorphic DNA-PCR, rcsA, and phoA genes-based PCR, and Loop-Mediated Isothermal Amplification (LAMP)-based identification of Klebsiella pneumoniae and Escherichia coli, respectively, followed by 16S rRNA sequencing confirmed misidentification of some clinical pathogens of other genera as Klebsiella spp. and E. coli. According to the antibiotic susceptibility testing guidelines, antibiotic choice, sensitivity pattern, and breakpoint measurement are different for each group of organisms. The lack of adherence to proper standards results in misdiagnosis and may facilitate the development of antibiotic resistance. The pilot study observers misidentification of clinical pathogens identified by the diagnostic centers. Well-characterized rapid molecular techniques like LAMP are suggested in clinical diagnosis to avoid misdiagnosis and subsequently circumvent antibiotic resistance development.

A fusion protein, designated ELP-D-C, comprised of a hydrophobic elastin-like polypeptide unit, a hydrophilic aspartic acid-rich peptide unit, and an antibody-binding domain as a functional unit, was constructed. Upon heat induction, ELP-D-C forms micellar nanoparticles displaying antibody-binding domains on their surfaces. The protein nanoparticles were able to incorporate hydrophobic fluorescent compounds and subsequently detect target molecules via antibody binding by the resulting fluorescence intensity, which was proportional to the log of the concentration of the target molecule.

Supramolecular protein hydrogels with tunable properties represent promising candidates for advanced designer extracellular matrices (ECMs). To control cellular functions, ECMs should be able to spatiotemporally regulate synergistic signaling between transmembrane receptors and growth factor (GF) receptors. In this study, we developed genetically engineered temperature-responsive multifunctional protein hydrogels. The designed hydrogel was fabricated by combining the following four peptide blocks: thermosensitive elastin-like polypeptides (ELPs), a polyaspartic acid (polyD) chain to control aggregation and delivery of GFs, a de novo-designed helix peptide that forms antiparallel homotetrameric coiled-coils, and a biofunctional peptide. The resultant coiled-coil unit bound ELPs (CUBEs) exhibit a controllable sol-gel transition with tunable mechanical properties. CUBEs were functionalized with bone sialoprotein-derived RGD (bRGD), and human umbilical vein endothelial cells (HUVECs) were three-dimensionally cultured in bRGD-modified CUBE (bRGD-CUBE) hydrogels. Proangiogenic activity of HUVECs was promoted by bRGD. Moreover, heparin-binding angiogenic GFs were immobilized to bRGD-CUBEs via electrostatic interactions. HUVECs cultured in GF-tethered bRGD-CUBE hydrogels formed three-dimensional (3-D) tubulelike structures. The designed CUBE hydrogels may demonstrate utility as advanced smart biomaterials for biomedical applications. Further, the protein hydrogel design strategy may provide a novel platform for constructing designer 3-D microenvironments for specific cell types.

Visible light-curable alginate was prepared by coupling alginate with furfurylamine. The furan content of the alginate was investigated through Fourier transform infrared spectroscopy and proton nuclear magnetic resonance spectroscopy. The prepared furfuryl alginate (F-Alginate) underwent gelation in the presence of a photosensitizer, such as Rose Bengal or riboflavin, under visible light irradiation. The time course of this gelation was similar to that of conventional Ca2+-induced gelation. When the formed gel was assessed using a rheometer, it was found that F-Alginate has a high storage modulus G′ comparable with that of a Ca2+-cross-linked gel. It was possible to encapsulate substances in the gel through simple mixing. The release rate of encapsulated substances depended on their molecular weight. As the molecular weight of encapsulated dextran increased, slower release was observed. These release behaviors are comparable with those of a Ca2+-cross-linked gel. The release rate of a growth factor protein was the same as that of dextran with the same molecular weight. Cell growth was enhanced in response to a sustained release of insulin-like growth factor-1 from the F-Alginate hydrogel. Visible light-curable alginate was prepared by coupling alginate with furfurylamine. The prepared furfuryl alginate (F-Alginate) underwent gelation in the presence of a photosensitizer under visible light irradiation. The mechanical and release properties of the visible light-induced gel were similar to that of conventional Ca2+-induced cross-linked alginate. The release rate of encapsulated substances depended on their molecular weight. Cell growth was enhanced in response to a sustained release of insulin-like growth factor-1 from the F-Alginate hydrogel.

Artificial materials have no biological functions, but they are important for medical devices such as artificial organs and matrices for regenerative medicine. In this study, mitogenic and differentiation‐inducible materials are devised via the simple coating of polypeptides, which contain the sequence of epidermal growth factor or insulin‐like growth factor with a key amino acid (3,4‐dihydroxyphenylalanine) of underwater adhesive proteins. The adhesive polypeptides prepared via solid‐phase synthesis form layers on various substrates involving organic and inorganic materials to provide biological surfaces. Through the direct activation of cognate receptors on interactive surfaces, the materials enable increased cell growth and differentiation compared to that achieved by soluble growth factors. This superior growth and differentiation are attributed to the long‐lasting signal transduction (triggered by the bound growth factors), which do not cause receptor internalization and subsequent downregulation., 3,4‐dihydroxyphenylalanine‐containing peptides form bioactive layers on organic and inorganic material surfaces. On the adhesive growth factor nanolayers, cells receive long‐term biological signals from immobilized growth factors, leading to improved cell growth and differentiation.

Background: Flow-through dot-blot assay (FT-DBA) for SARS-CoV-2 specific IgG detection will provide a reliable and affordable immunoassay for the rapid serosurveillance against COVID-19. Method: SARS-CoV-2 antigens were immobilized on nitrocellulose membrane to capture IgG immunoglobulins, which were then detected with AuNP anti-human IgG. A total of 181 samples were characterized with in-house and commercial immunoassay. The positive panel consisted of RT-PCR positive samples from patients with both 14 days from the onset of symptoms, while the negative panel contained samples collected either from the pre-pandemic era dengue patients from healthy donors during the pandemic period. Results: In-house ELISA selected a total of 79 true seropositive and 100 seronegative samples. The sensitivity of samples with 14 days. The overall detection sensitivity and specificity were 98.8% and 98%, respectively, whereas the overall PPV and NPV were 97.6% and 99%. Moreover, comparative analysis between ELISA and FT-DBA revealed clinical agreement of Cohen’s Kappa value of 0.944. Conclusion: The assay can confirm past SARS-CoV-2 infection with high accuracy within 2 minutes compared to ELISA. It can help track SARS-CoV-2 disease progression, population screening, and vaccination response.

COVID-19 pandemic situation demands effective serological tests with a view to adopting and developing policy for disease management, determining protective immunity as well as for sero-epidemiological study. Our study aims to develop and evaluate two rapid in-house ELISA assays targeting neutralizing antibodies (IgG) against S1 subunit of spike in SARS-CoV-2 and Receptor Binding Domain (RBD), as well as comparative analysis with nucleocapsid (NCP) ELISA. The assays were conducted with 184 samples in three panels collected from 134 patients. Panel 1 and 2 consist of RT-PCR positive samples collected within two weeks and after two weeks of symptom onset, respectively. Negative samples are included in panel 3 from healthy donors and pre-pandemic dengue patients. The total assay time has been set 30 minutes for both of the ELISA assays. Results show that S1 and RBD ELISA demonstrates 73.68% and 84.21% sensitivities, respectively for samples collected within two weeks, whereas 100% sensitivities were achieved by both for samples that were collected after two weeks of the onset of symptoms. S1-ELISA shows 0% positivity to panel 3 while for RBD-ELISA the figure is 1%. A strong correlation (rs=0.804, ps=0.800, ps=0.740, pHighlightsThe total assay time of these assays are 30 minutes.Sensitivity of S1 specific IgG ELISA for samples tested within 14 days of disease presentation is 73.68% while RBD specific ELISA demonstrates a sensitivity of 84.21%,Both of the assays under investigation can successfully detect all the cases (100% sensitivity) if the samples are tested after 14 days of onset of diseases.Specificity of S1-ELISA assay is 100%, whereas RBD specific IgG ELISA is 99% specific.The assays can be employed in dengue-endemic countriesAmong the three in-house IgG ELISA, assay system specific to S1 is found to be more sensitive and specific for retrospective serosurveillance.For acute to late phase, as well as retrospective serosurveillance of COVID-19, RBD-ELISA can be a method of choice for SARS-CoV-2 prevalent areas.

BackgroundIn the ongoing pandemic situation of COVID-19, serological tests can complement the molecular diagnostic methods, and can be one of the important tools of sero-surveillance and vaccine evaluation.AimTo develop and evaluate a rapid SARS-CoV-2 specific ELISA for detection of anti-SARS-CoV2 IgG from patient’s biological samples.MethodsIn order to develop the ELISA, three panels of samples (n=184) have been used: panel 1 (n=19) and panel 2 (n=60) were collected from RT-PCR positive patients within 14 and after 14 days of onset of clinical symptoms respectively, whereas panel 3 consisted of negative samples (n=105) collected either from healthy donors or pre-pandemic dengue patients. As a capturing agent full-length SARS-CoV2 specific recombinant nucleocapsid was immobilized. Commercial SARS-CoV2 IgG kit based on chemiluminescent assay was used for the selection of samples and optimization of the assay. The threshold cut-off point, inter-assay and intra-assay variations were determined. The total assay time for this in-house ELISA was set for 30 minutes.ResultsThe assay time was set at a total of 30 minutes with the sensitivity of 84% (95% confidence interval, CI, 60.4%, 96.6%) and 98% (95% CI, 91.1%, 100.0%), for panel 1 and 2 respectively, with over all 94.9% sensitivity (95% CI 87.5%, 98.6%). Moreover, the clinical specificity is 97.1% (95% CI, 91.9%, 99.4%) with no cross reaction with dengue sample. The overall positive and negative predictive values are 96.2% (95% CI 89.2%, 99.2%) and 96.2% (95% CI, 90.6% 99.0%) respectively. In-house ELISA demonstrated 100% positive and negative percent agreement with ROCHE (Elecsys; Anti-SARS-CoV-2), with a Cohen’s kappa value of 1.00 (very strong agreement), while comparing 13 positive and 17 negative confirmed cases.ConclusionThe assay is rapid and can be applied as one of the early and retrospective sero-monitoring tools in all over the affected areas.

Monoclonal antibodies have been developed as anticancer agents to block immune checkpoint pathways associated with programmed cell death 1 (PD-1) and its ligand PD-L1. However, the high cost of antibodies has encouraged researchers to develop other inhibitor types. Here, biphenyl compounds were conjugated with poly(ethylene glycol) (PEG) to enhance the activity of small molecular inhibitors. Immunoassay results revealed the decrease in the inhibition activity following conjugation with linear PEG, suggesting that the PEG moiety reduced the interaction between the biphenyl structure and PD-L1. However, the inhibitory effect on PD-1/PD-L1 interaction was further enhanced by using branched PEG conjugates. The increase in the number of conjugated biphenyl compounds resulted in increased inhibitory activity. The highest IC50 value was 0.33 μM, which was about 5 times higher than that observed for a non-conjugated monovalent compound. The inhibitory activity was more than 20 times the activity reported for the starting compound. Considering the increase in the inhibition activity, this multivalent strategy can be useful in the design of new immune checkpoint inhibitors.

E-cadherin is a key Ca-dependent cell adhesion molecule, which is expressed on many cell surfaces and involved in cell morphogenesis, embryonic development, EMT, etc. The fusion protein E-cad-Fc consists of the extracellular domain of E-cadherin and the IgG Fc domain. On plates coated with this chimeric protein, ES/iPS cells are cultivated particularly well and induced to differentiate. The cells adhere to the plate via E-cad-Fc in the presence of Ca2+ and detach by a chelating agent. For the purpose of clarifying the structures of E-cad-Fc in the presence and absence of Ca2+, we analyzed the molecular structure of E-cad-Fc by AFM in liquid. Our AFM observations revealed a rod-like structure of the entire extracellular domain of E-cad-Fc in the presence of Ca2+ as well as trans-binding of E-cad-Fc with adjacent molecules, which may be the first, direct confirmation of trans-dimerization of E-cadherin. The observed structures were in good agreement with an X-ray crystallographic model. Furthermore, we succeeded in visualizing the changes in the rod-like structure of the EC domains with and without calcium. The biomatrix surface plays an important role in cell culture, so the analysis of its structure and function may help promote cell engineering based on cell recognition.

Control of the cross-linking reaction is imperative when developing a sophisticated in situ forming hydrogel in the body. In this study, a heteroarmed thermoresponsive (TR) nanoparticle was designed to investigate the mechanism of controlling reactivity of the functional groups introduced into the nanoparticles. The coupling reaction was suppressed/proceeded by utilizing temperature-induced morphological changes of the TR polymer. The heteroarmed TR nanoparticle was prepared by the coassembly of amphiphilic block copolymers possessing both a TR segment and hydrophilic segment with reactive functional groups of succinimide. The longer TR chain on the nanoparticle covered the succinimide group and suppressed the reaction with the primary amine on the external nanoparticle. In contrast, the coupling reaction was promoted at a high temperature to create the chemical cross-linking structure between the nanoparticles because of the exposure of the succinimide group on the surface of the particle as a consequence of the morphological change of the TR polymer. In addition, the thermally controlled chemical reaction modulated initiation of the gelation using a highly concentrated nanoparticle solution. The heteroarmed TR nanoparticle offers great practical advantages for clinical uses, such as embolization agents, through precise control of the reaction.

Cancer immunotherapy has been revolutionized by the development of monoclonal antibodies (mAbs) that inhibit interactions between immune checkpoint molecules, such as programmed cell-death 1 (PD-1), and its ligand PD-L1. However, mAb-based drugs have some drawbacks, including poor tumor penetration and high production costs, which could potentially be overcome by small molecule drugs. BMS-8, one of the potent small molecule drugs, induces homodimerization of PD-L1, thereby inhibiting its binding to PD-1. Our assay system revealed that BMS-8 inhibited the PD-1/PD-L1 interaction with IC50 of 7.2 &mu, M. To improve the IC50 value, we designed and synthesized a small molecule based on the molecular structure of BMS-8 by in silico simulation. As a result, we successfully prepared a biphenyl-conjugated bromotyrosine (X) with IC50 of 1.5 &mu, M, which was about five times improved from BMS-8. We further prepared amino acid conjugates of X (amino-X), to elucidate a correlation between the docking modes of the amino-Xs and IC50 values. The results suggested that the displacement of amino-Xs from the BMS-8 in the pocket of PD-L1 homodimer correlated with IC50 values. This observation provides us a further insight how to derivatize X for better inhibitory effect.

We developed a DNA-NanoLuc luciferase (NnaoLuc) conjugates for DNA aptamer-based sandwich assay using the catalytic domain of the replication initiator protein derived from porcine circovirus type 2 (pRep). For construction of DNA aptamer and NanoLuc conjugate using the catalytic domain of Rep from PCV2. pRep fused to NanoLuc was genetically constructed and expressed in E. coli. After purification, the activities of fused pRep and NanoLuc were evaluated, and DNA-NanoLuc conjugates were constructed via the fused pRep. Finally, constructed DNA-NanoLuc conjugates were applied for use in a DNA aptamer-based sandwich assay. Here, pRep was used not only for conjugation of the NanoLuc to the detection aptamer, but also for immobilization of the capture aptamer on the plate surface. We have demonstrated that DNA-NanoLuc conjugates via the catalytic domain of PCV2 Rep could be applied for DNA aptamer-based sandwich assay system.

Tissue-specific transcription factors are key regulators of cellular differentiation. Previously, we succeeded in introducing basic helix–loop–helix tissue-specific transcription factor proteins into cells to induce cellular differentiation. Based on these results, we decided to focus on the use of tissue-specific transcription factor proteins in the construction of biomaterials. In this proof-of-concept study, we demonstrate the construction of a tissue-specific transcription factor-tethered extracellular matrix protein. Here, the tissue-specific transcription factor Olig2 was tethered to a designed artificial extracellular matrix protein via coiled-coil helix formation. Tethered Olig2 was introduced into mouse embryonic carcinoma P19 cells attached to our designed extracellular matrix protein, and was shown to exhibit the ability to induce neural differentiation.

Modification of protein-based drug carriers with tumor-targeting properties is an important area of research in the field of anticancer drug delivery. To this end, we developed nanoparticles comprised of elastin-like polypeptides (ELPs) with fused poly-aspartic acid chains (ELP-D) displaying DNA aptamers. DNA aptamers were enzymatically conjugated to the surface of the nanoparticles via genetic incorporation of Gene A* protein into the sequence of the ELP-D fusion protein. Gene A* protein, derived from bacteriophage ϕX174, can form covalent complexes with single-stranded DNA via the latter's recognition sequence. Gene A* protein-displaying nanoparticles exhibited the ability to deliver the anticancer drug paclitaxel (PTX), whilst retaining activity of the conjugated Gene A* protein. PTX-loaded protein nanoparticles displaying DNA aptamers known to bind to the MUC1 tumor marker resulted in increased cytotoxicity with MCF-7 breast cancer cells compared to PTX-loaded protein nanoparticles without the DNA aptamer modification.

We explored the co-localization of multiple enzymes on a DNA backbone via a DNA-binding protein, Gene-A* (A*-tag) to increase the efficiency of cascade enzymatic reactions. Firefly luciferase (FLuc) and pyruvate orthophosphate dikinase (PPDK) were genetically fused with A*-tag and modified with single-stranded (ss) DNA via A*-tag. The components were assembled on ssDNA by hybridization, thereby enhancing the efficiency of the cascading bioluminescent reaction producing light emission from pyrophosphate. The activity of A*-tag in each enzyme was investigated with dye-labeled DNA. Co-localization of the enzymes via hybridization was examined using a gel shift assay. The multi-enzyme complex showed significant improvement in the overall efficiency of the cascading reaction in comparison to a mixture of free enzymes. A*-tag is highly convenient for ssDNA modification of versatile enzymes, and it can be used for construction of functional DNA–enzyme complexes.

The amyloid beta (Aβ) peptide is regarded as a causative agent of Alzheimer's disease. In this study, fluorescent and luminescent fusion proteins were constructed to analyze Aβ aggregation. A system was developed to monitor changes in luminescence that provides information about Aβ aggregation. In the presence of monomeric Aβ, the fusion protein exhibits higher luminescence intensity, and the luminescence intensity is diminished after aggregation of the fusion protein and Aβ. In contrast, the fluorescence is sustained in the presence of Aβ. In the absence of Aβ, the fusion protein self-aggregates, and its luminescence and fluorescence are quenched, thus decreasing the background fluorescence and enhancing the detection of Aβ inside and outside the cells. The ratio of the luminescence intensity to the fluorescence intensity would allow the aggregation degrees of Aβ to be distinguished. This study would be a promising method for analyzing the aggregation state of a particular amyloid protein/peptide (monomer, oligomer, or fibril), as well as the distribution of the amyloid protein/peptide within and at the cell surface, by using a single fusion protein. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

There is growing interest in the functional roles of the extracellular matrix (ECM) in regulating the fate of pluripotent stem cells (PSCs). An artificially bioengineered ECM provides an excellent model for studying the molecular mechanisms underlying self-renewal and differentiation of PSCs, without multiple unknown and variable factors associated with natural substrates. Here, we have engineered multifunctional fusion proteins that are based on peptides from laminin, including p20, RGD, and elastin-like polypeptide (ELP), where laminin peptides work as cell adhesion molecules (CAMs) and ELP to promote anchorage. The functionality of these chimeric proteins, referred to as ERE-p20 and E-p20, was assessed by determining their ability to immobilize cells on a hydrophobic polystyrene surface, improve mouse induced pluripotent stem cells (miPSCs) attachment, and promote miPSC differentiation to neural progenitors. ERE-p20 and E-p20 proteins showed hydrophobic binding saturation to the polystyrene plates around 500 nM (2.39 μg/cm2 ) and 750 nM (2.27 μg/cm2 ) protein concentrations, respectively. The apparent maximum cell binding to ERE-p20 and E-p20 was approximately 81% and 73%, respectively, relative to gelatin. For neural precursors, neurite outgrowth was enhanced by the presence of RGD and p20 peptides. The expression levels of neuronal marker protein MAP2 were upregulated approximately 2.5-fold and threefold by ERE-p20 and E-p20, respectively, relative to laminin. Overall, we have shown that elastin-mimetic fusion proteins consisting of p20 with and without RGD peptides are able to induce neuronal differentiation. In conclusion, our newly designed bioengineered fusion proteins allow preparation of specific bioactive matrices or coating/scaffold for miPSCs differentiation.

In this study, we developed a protein nanoparticle-based immunoassay to detect cancer biomarkers using a bioluminescent fusion protein. This method relies on the use of protein nanoparticles comprised of genetically-engineered elastin-like polypeptides (ELPs) fused with poly-aspartic acid tails (ELP-D), previously developed in our lab. The sizes of the self-assembled ELP-D nanoparticles can be regulated at the nanoscale by charged repulsion of the poly-aspartic acid chains. To improve the sensitivity of enzyme-linked immunosorbent assays (ELISAs), we herein demonstrate the multivalent display of NanoLuc® (Nluc) luciferase and a biotin acceptor peptide (BAP) on the surfaces of ELP-D nanoparticles, and demonstrate the sensitivity of these multivalent nanoparticles as detection probes. The fusion protein comprised of ELP-D and Nluc-BAP (ELP-D-Nluc-BAP) was found to form nanoparticles with Nluc and BAP displayed multivalently on their surfaces. Moreover, the use of the nanoparticles in ELISA resulted in a detection sensitivity for α-fetoprotein (AFP) about 10 times higher than that of an assay relying on the use of the monomeric version of the fusion protein. Taken together, ELP-D-based nanoparticles displaying multivalent luciferases on their surfaces enable the construction of an ELISA with enhanced sensitivity.

The split SNAP-tag protein-fragment complementation assay (PCA) is a useful tool for imaging protein-protein interactions (PPIs) in living cells. In contrast to conventional methods employed for imaging PPIs, the split SNAP-tag PCA enables tracking of proteins following dissociation from protein-protein complexes. A limitation of this system, however, is that it only allows for labeling and tracking of one of the proteins forming the protein-protein complex. To track both proteins forming a protein-protein complex, each protein needs to be appropriately labeled. In this study, a split SNAP-CLIP double labeling system is developed and applied for tracking of each protein forming a protein-protein complex. As a proof-of concept, FM protein for PPIs and protein kinase C alpha (PKCα) for translocation are introduced to a split SNAP-CLIP double labeling system. The results show a split SNAP-CLIP double labeling system enables labeling of both proteins in a protein-protein complex and subsequent tracking of each of the proteins following dissociation from the protein-protein complexes in living cells.

Gelatin derivative was prepared to coating titanium surface and photo-immobilize rhBMP-2 for improved osteoinduction and function. The conjugation was confirmed by 31 P and 1 H NMR. Photo-immobilization of the azide–phosphonate–gelatin (Az–P–Gel) was evaluated by micropatterning. The rate of recombinant human bone morphogenetic protein (rhBMP-2) release was evaluated for performance of Az–P–Gel as a carrier. The water contact angle was determined to characterize Ti surface coated with Az–P–Gel. Ability to induce osteogenesis of Az–P–Gel was evaluated using alkaline phosphatase (ALP) activity assay, Alizarin Red S staining, and calcium colorimetric assay. Our results demonstrate that Ti modified with Az–P–Gel and rhBMP-2 facilitates bone regeneration.

DNA-protein conjugates are useful molecules for construction of biosensors. Herein, we report the development of an enzymatically-conjugated DNA aptamer&ndash, protein hybrid molecule for use as a bioluminescence resonance energy transfer (BRET)-based biosensor. DNA aptamers were enzymatically conjugated to a fusion protein via the catalytic domain of porcine circovirus type 2 replication initiation protein (PCV2 Rep) comprising residues 14&ndash, 109 (tpRep), which was truncated from the full catalytic domain of PCV2 Rep comprising residues 1&ndash, 116 by removing the flexible regions at the N- and C-terminals. For development of a BRET-based biosensor, we constructed a fusion protein in which tpRep was positioned between NanoLuc luciferase and a fluorescent protein and conjugated to single-stranded DNA aptamers that specifically bind to either thrombin or lysozyme. We demonstrated that the BRET ratios depended on the concentration of the target molecules.

Cellular microenvironments consist of a variety of cues, such as growth factors, extracellular matrices, and intercellular interactions. These cues are well orchestrated and are crucial in regulating cell functions in a living system. Although a number of researchers have attempted to investigate the correlation between environmental factors and desired cellular functions, much remains unknown. This is largely due to the lack of a proper methodology to mimic such environmental cues in vitro, and simultaneously test different environmental cues on cells. Here, we report an integrated platform of microfluidic channels and a nanofiber array, followed by high-content single-cell analysis, to examine stem cell phenotypes altered by distinct environmental factors. To demonstrate the application of this platform, this study focuses on the phenotypes of self-renewing human pluripotent stem cells (hPSCs). Here, we present the preparation procedures for a nanofiber array and the microfluidic structure in the fabrication of a Multiplexed Artificial Cellular MicroEnvironment (MACME) array. Moreover, overall steps of the single-cell profiling, cell staining with multiple fluorescent markers, multiple fluorescence imaging, and statistical analyses, are described.

We present a characterization of chemically treated cells using atomic force microscopy (AFM) which can observe changes in morphology and elasticity of cells. Since AFM has the significant advantage that it does not require fixation of samples, the method is simple and can capture various properties of living cells. In this study, corneal epithelial and endothelial cells were examined. The topography images of the corneal cells without glutaraldehyde (GA) fixation were successfully obtained. The images showed a natural three-dimensional shape of these cells, which scanning electron microscope (SEM) images could not provide. The AFM images of GA-fixed cells were taken and compared with a SEM image reported in the literature. Our results show that longer time for GA fixation makes the surface of the corneal endothelial tissue stiffer. Also, longer treatment results in relatively large structural variation in samples. Combined with conventional histochemical methods, this approach helps us gain an overall understanding of the influence of such chemical treatment.

The solubilizing ability of single-walled carbon nanotubes (SWCNTs) in water with several dispersants was investigated. Among the dispersants, including low-molecular-weight surfactants, peptides, DNA, and a water-soluble polymer, the peptide aptamer, A2 (IFRLSWGTYFS), exhibited the highest dispersion capability below the critical micelle concentration at a concentration of 0.02 w/v%. The dispersion of supernatant aqueous solution of SWCNTs containing aptamer A2 was essentially unchanged for several months after high-speed ultracentrifugation and gave rise to an efficient and stable dispersion of the SWCNTs in water. From the results of isothermal titration calorimetry and molecular dynamics simulations, the effective binding capability of A2 was due to π-π interaction between aromatic groups in the peptide aptamer and the side walls of SWCNTs. Interestingly, the peptide aptamer showed the possibility of diameter separation of semiconducting SWCNTs using a uniform density gradient ultracentrifuge. These phenomena are encouraging results toward an effective approach to the dispersion and separation of SWCNTs.

Nanoparticles are small size-controlled particles from 1 to 100 nm diameters and characterized by their structure, base material and functional units displayed on their surfaces. In this study, protein-based nanoparticles composed of a hydrophobic elastin-like peptide unit, a hydrophilic aspartic acid-rich peptide unit and displaying antibody binding domains on their surfaces, were designed and genetically synthesized. The constituent fusion proteins, termed ELP-D-C, were found to exist in monomeric form (ELP-D-C/monomer) at low temperature. Above the phase transition temperature, however, ELP-D-C was found to rapidly self-assemble to form spherical micelles (ELP-D-C/micelle) with a hydrophobic core and diameters of ∼40 nm. Furthermore, ELP-D-C/micelle were shown to display antibody binding domains on their surfaces, which allowed for immobilization of antibodies and subsequent formation of large, visually detectable complexes in the presence of target molecule (antigen), whose sizes increased in proportion to the target molecule concentration. The observed target molecule concentration-dependent complex formation suggests that ELP-D-C/micelle may be useful as base particles in applications such as homogeneous turbidity immunoassays.

Protein-protein interactions (PPIs) are important for various biological processes in living cells. Several methods have been developed for the visualization of PPIs in vivo; however, these methods are unsuitable for visualization of post-PPI events such as dissociation and translocation. In this study, we applied a split SNAP-tag system for the visualization of post-PPI events. This method enabled tracking of the protein following dissociation from the protein-protein complex. Thus, the split SNAP-tag system should prove to be a useful tool for visualization of post-PPI events.

We constructed a novel peptide-array format system for cellular toxicity analysis. In this system, a peptide was immobilized on a conventional 96-well plate bottom via a photo-cleavable linker. Once UV light irradiated the desired wells, the peptide was released from the bottom. As a result, the cytotoxic behavior of the peptide could be monitored. Immobilization and light-irradiation conditions were optimized. The immobilized peptide showed no cytotoxicity; therefore, the cells could be cultured on the peptide-immobilizing plate from the beginning of the experiment. Cell-toxicity assays with this system for three cell types were performed. All cell types showed ∼25% lowering of viability with the photo-released 5-(and-6)-carboxytetramethylrhodamine (TMR)-GKLAKLAKKLAKLAKKLAKLAKGC (TMR-KLA-C) peptide compared with the non-coated plate. This relative toxicity nearly corresponded to that of ∼10 μM TMR-KLA-C in solution, and we found that the released peptide concentration per well was ∼10 μM at 60 min irradiation. Throughout this study, we successfully immobilized peptides via the photo-cleavable linker, released them by UV irradiation spatiotemporally and conducted the cell-toxicity assay. This study implies that the peptide photo-releasing array system will allow the realization of high-throughput cell arrays for cellomics analyses and cell-based phenotypic drug screenings. A novel peptide-array format system with a photo-cleavage linker for cellular toxicity analysis was constructed. In this system, a peptide was immobilized on a commercially available plate bottom via the photo-cleavable linker. UV light irradiation on the desired wells releases the peptide from the plate bottom, and then the cytotoxic behavior of the peptide can be monitored.

A ribosome display from a diverse random library was applied for selecting peptide aptamers with high binding affinity to single-wall carbon nanotubes (SWCNTs). The selected peptide aptamer bound to and solubilized SWCNTs more strongly than did the peptide aptamer selected by a phage display method reported previously, and more strongly than other commonly used organic surfactants. The fluorescence spectrum of this aptamer showed a red shift upon interaction with SWCNTs but circular dichroism spectroscopy did not show any significant difference between the presence or absence of SWCNT binding.

The amyloid beta (Aβ) peptide is regarded as a causative agent of Alzheimer's disease. In this study, fluorescent and luminescent fusion proteins were constructed to analyze Aβ aggregation. A system was developed to monitor changes in luminescence that provides information about Aβ aggregation. In the presence of monomeric Aβ, the fusion protein exhibits higher luminescence intensity, and the luminescence intensity is diminished after aggregation of the fusion protein and Aβ. In contrast, the fluorescence is sustained in the presence of Aβ. In the absence of Aβ, the fusion protein self-aggregates, and its luminescence and fluorescence are quenched, thus decreasing the background fluorescence and enhancing the detection of Aβ inside and outside the cells. The ratio of the luminescence intensity to the fluorescence intensity would allow the aggregation degrees of Aβ to be distinguished. This study would be a promising method for analyzing the aggregation state of a particular amyloid protein/peptide (monomer, oligomer, or fibril), as well as the distribution of the amyloid protein/peptide within and at the cell surface, by using a single fusion protein. Copyright © 2017 European Peptide Society and John WileySons, Ltd.

Artificial extracellular matrix (ECM) proteins have been designed that have strong cell-adhesive activity and active functional units that inhibit network formation among vascular endothelial cells. A laminin-derived sequence (YIGSR) that blocks migration of vascular endothelial cells was designed to incorporate into an elastin-derived structural unit. The designed ECM fusion protein also had a cell-adhesive RGDN sequence that conferred an intense migration-inhibitory effect. The resultant ECM showed cell-adhesive activity superior to that of the synthetic YIGSR peptide and it blocked the migration of vascular endothelial cells. Furthermore, the designed ECM inhibited the angiogenic activity of a collagen gel. The engineering strategy of designing multi-functional ECM proteins could be applied to support novel tissue engineering techniques.

We explored the intra- and extracellular processes governing the kinetics of extracellular ATP (ATPe) in human erythrocytes stimulated with agents that increase cAMP. Using the luciferin-luciferase reaction in off-line luminometry we found both direct adenylyl cyclase activation by forskolin and indirect activation through β-adrenergic stimulation with isoproterenol-enhanced [ATP]e in a concentration-dependent manner. A mixture (3V) containing a combination of these agents and the phosphodiesterase inhibitor papaverine activated ATP release, leading to a 3-fold increase in [ATP]e, and caused increases in cAMP concentration (3-fold for forskolin + papaverine, and 10-fold for 3V). The pannexin 1 inhibitor carbenoxolone and a pannexin 1 blocking peptide ((10)Panx1) decreased [ATP]e by 75-84%. The residual efflux of ATP resulted from unavoidable mechanical perturbations stimulating a novel, carbenoxolone-insensitive pathway. In real-time luminometry experiments using soluble luciferase, addition of 3V led to an acute increase in [ATP]e to a constant value of ∼1 pmol × (10(6) cells)(-1). A similar treatment using a surface attached luciferase (proA-luc) triggered a rapid accumulation of surface ATP levels to a peak concentration of 2.4 pmol × (10(6) cells)(-1), followed by a slower exponential decay (t(frac12;) = 3.7 min) to a constant value of 1.3 pmol × (10(6) cells)(-1). Both for soluble luciferase and proA-luc, ATP efflux was fully blocked by carbenoxolone, pointing to a 3V-induced mechanism of ATP release mediated by pannexin 1. Ecto-ATPase activity was extremely low (∼28 fmol × (10(6) cells min)(-1)), but nevertheless physiologically relevant considering the high density of erythrocytes in human blood.

Endothelial cells (ECs) release ATP in response to shear stress, a fluid mechanical force generated by flowing blood but, although its release has a crucial role in controlling a variety of vascular functions by activating purinergic receptors, the mechanism of ATP release has never been established. To analyze the dynamics of ATP release, we developed a novel chemiluminescence imaging method by using cell-surface-attached firefly luciferase and a CCD camera. Upon stimulation of shear stress, cultured human pulmonary artery ECs simultaneously released ATP in two different manners, a highly concentrated, localized manner and a less concentrated, diffuse manner. The localized ATP release occurred at caveolin-1-rich regions of the cell membrane, and was blocked by caveolin-1 knockdown with siRNA and the depletion of plasma membrane cholesterol with methyl-β-cyclodexrin, indicating involvement of caveolae in localized ATP release. Ca2+ imaging with Fluo-4 combined with ATP imaging revealed that shear stress evoked an increase in intracellular Ca2+ concentration and the subsequent Ca2+ wave that originated from the same sites as the localized ATP release. These findings suggest that localized ATP release at caveolae triggers shear-stress-dependent Ca2+ signaling in ECs.

We demonstrate examples of cellular differentiation assessments, including cellular neurite outgrowth and fat cell maturation, by measuring the degree of membrane adsorption or cellular internalization using designed peptides. Because changes in the cellular membrane and cytosol during differentiation were shown to influence membrane adsorption and cellular internalization, we could successfully evaluate the extent of differentiation simply like stain indicators.

The interaction between proteins and ligands was evaluated by T7 RNA polymerase transcription with a DNA-modified ligand. The principle of this method is suppression of T7 RNA polymerase transcription by binding of a protein to small ligand modified by conjugation with a T7 RNA polymerase promoter. To demonstrate proof of principle, biotin or antifolate methotrexate was modified by covalent attachment of a T7 RNA promoter. Using these T7 RNA promoter-modified ligands, T7 RNA polymerase transcriptions were performed in the presence or absence of an anti-biotin antibody or recombinant human dihydrofolate reductase, respectively. Transcription was suppressed in the presence of each binding protein plus its modified ligand, but not in the absence of the binding protein.

We report the assembly of seven different antibodies (and two antigens) into functional supramolecular structures that are specifically designed to facilitate integration into devices using entirely biologically based bottom-up fabrication. This is enabled by the creation of an engineered IgG-binding domain (HG3T) with an N-terminal hexahistidine tag that facilitates purification and a C-terminal enzyme-activatable pentatyrosine “pro-tag” that facilitates covalent coupling to the pH stimuli-responsive polysaccharide, chitosan. Because we confer pH-stimuli responsiveness to the IgG-binding domain, it can be electrodeposited or otherwise assembled into many configurations. Importantly, we demonstrate the loading of both HG3T and antibodies can be achieved in a linear fashion so that quantitative assessment of antibodies and antigens is feasible. Our demonstration formats include: conventional multiwell plates, micropatterned electrodes, and fiber networks. We believe biologically based fabrication (i.e., biofabrication) provides bottom-up hierarchical assembly of a variety of nanoscale components for applications that range from point-of-care diagnostics to smart fabrics. Biotechnol. Bioeng. 2009;103: 231–240. © 2008 Wiley Periodicals, Inc.

Binary catalyst nickel oxides (NiO) and manganese oxides (MnO) were prepared individually via hydrothermal route. The catalysts were characterized by scanning electron microscope (SEM), Brunauer-Emmett-Teller (BET) analysis, cyclic voltammetry (CV), and amperometry. Morphology studies revealed physical structure of nanowires nickel oxide and spherical manganese oxide with estimated length of 0.3–2.3 μm and diameter of 0.2–0.8 μm, respectively. Surface areas obtained for nickel oxide and manganese oxide were 68.9 m2 g−1and 45.2 m2 g−1, respectively. Cyclic voltammetry exhibits electrochemical responses corresponding to the electrode surfaces. The linear responses of the binary catalyst modified gold electrodes with NiO-MnO were observed in the concentration range from 31.8 μM to 0.5 mM with the detection limit of 62.5 μM.

Although molecular recognitions between membrane receptors and their soluble ligands have been analyzed using their soluble proteins in bulk solutions, molecular recognitions of membrane receptors should be studied on lipid membranes considering their orientation and dynamics on membrane surfaces. We employed Staphylococcal Protein A (SpA) oligo B domains with long trialkyl-tags from E. coli (LppBx, x = 1, 2, and 5) and immobilized LppBx on lipid layers using hydrophobic interactions from the trialkyl-tag, while maintaining the orientation of B domain-chains on a 27 MHz quartz-crystal microbalance (QCM; AT-cut shear mode). The binding of IgG Fc regions to LppBx on lipid layers was detected by frequency decreases (mass increases) on the QCM. The maximum amount bound (Delta m(max)), association constants (K(a)), association and dissociation rate constants (k(1) and k(-1), respectively) were obtained. Binding kinetics of IgG to LppB2 and LppB5 were quite similar, showing a simple 1:1 binding of the IgG Fc region to the B domain, when the surface coverage of LppB2 and LppB5 on the lipid surface is low (1.4%). When LppB5 was immobilized at the high surface coverage of 3.5%, the complex bindings of IgG such as one IgG bound to one or two LppB5 on the membrane could be observed. IgG-LppB1 binding was largely restricted because of steric hindrance on lipid surfaces. This gives a suggestion why Protein A has five IgG binding domains.

A novel protein for controlling cellular functions was constructed by combining functional units of various proteins. The Arg-Gly-Asp (RGD) sequence functioning as a cell adhesive function, an epidermal growth factor (EGF) as a cell growth function, and a hydrophobic sequence (E12) as an efficient assembling function, were combined and incorporated into one molecule. The fusion protein, designated ERE-EGF, was produced in Escherichia coli and purified with affinity chromatography using a His-tag. The ERE-EGF coated on an unmodified hydrophobic surface of a cell-culture plate (through the hydrophobic E12 moiety) retained both cell adhesive activity (through the RGD sequence) and cell growth activity (through the EGF moiety).