Label-Free Protein Glycosylation Analysis Using NanoMonitor-An Ultrasensitive Electrochemical Biosensor.

Glycans (oligosaccharide chains attached to glycoproteins) are a promising class of biomarkers, found in body fluids such as serum, saliva, urine, etc., that can be used for the diagnosis of disease conditions. Subtle changes in glycans resulting from altered glycosylation machinery have been reported during various diseases, including carcinogenesis. In this article, we detail protocols for the rapid, label-free analysis of glycans using a previously developed highly sensitive and selective electrochemical impedance spectroscopy-based biosensing diagnostic platform called "NanoMonitor." The glycosensor operation is based on the specific affinity capture of the target glycans on the sensor surface by glycan-binding proteins known as lectins. This glycan-lectin binding activity modulates the impedance of the electrical double layer at the buffer-electrode interface. Protocols for the preparation of glycoprotein samples and glycosylation analysis using NanoMonitor and lectin-based ELISA are described here. The data obtained using these protocols show that NanoMonitor is capable of distinguishing between glycoform variants of the glycoprotein fetuin and glycoproteins derived from cultured human pancreatic cancer cells with high sensitivity (orders of magnitude higher than lectin-based ELISA) and selectivity. The results obtained indicate that NanoMonitor protocols can be further developed to enable use of NanoMonitor as a handheld electronic biosensor device for routine multiplexed detection of glycan biomarkers from clinical samples. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparing the NanoMonitor surface for glycan biosensing Support Protocol: Synthesis of glycoform variants of fetuin Basic Protocol 2: Performing Electrochemical Impedance Spectroscopy (EIS) for analyzing glycoprotein structures.

Development and In Vitro Evaluation of Vitamin E-Enriched Nanoemulsion Vehicles Loaded with Genistein for Chemoprevention Against UVB-Induced Skin Damage.

There is a great need for effective protection against cutaneous pathologies arising from chronic exposure to harmful solar UVB radiations. A promising pharmaceutical strategy to improve the efficacy of chemotherapeutic/preventative natural compounds (e.g., soy isoflavone Genistein, Gen) is to enhance their dermal delivery using nanoemulsion (NE) formulations. This report investigates the development of nanoemulsified tocotrienol(T3)-rich fraction of red palm oil (Tocomin®), to yield an optimal NE delivery system for dermal photoprotection (z-average size <150 nm, ζ-potential ≈ -30 mV, polydispersity index < 0.25). Physicochemical characterization and photostability studies indicate NE formulations utilizing surfactant mixture (Smix) of Solutol® HS-15 (SHS15) blended with vitamin E TPGS (TPGS) as cosurfactant was significantly superior to formulations that utilized Lutrol® F68 (LF68) as the cosurfactant. A ratio of 60:40 of SHS15-TPGS-NE was further identified as lead Tocomin® NE topical platform using in vitro pharmaceutical skin reactivity studies that assess cutaneous irritancy and cytotoxicity. Prototype Tocomin® NE loaded with the antiphotocarcinogenic molecule Gen (Gen-Tocomin® NE) showed slow-release profile in both liquid and cream forms. Gen-Tocomin® NE also showed excellent biocompatibility, and provided substantial UVB protection to cultured subcutaneous L929 fibroblasts, indicating the great potential of our Tocomin® NE warranting further prototype development as topical pharmaceutical platform for skin photoprotection applications.

Nanochannel-based electrochemical sensor for the detection of pharmaceutical contaminants in water.

Effective real-time monitoring is the key to understanding and tackling the issue of pharmaceutical contamination of water. This research demonstrates the utility of an alumina nanochannel-based electrochemical sensor platform for the detection of ibuprofen in water derived from various sources. Our results indicate that the sensor is highly sensitive with a limit of detection at 0.25 pg mL(-1). The novel sensor described here has potential for application as a simple, rapid, inexpensive and highly reliable method for real-time environmental water quality assessment.

Label-free measuring and mapping of binding kinetics of membrane proteins in single living cells.

Membrane proteins mediate a variety of cellular responses to extracellular signals. Although membrane proteins are studied intensively for their values as disease biomarkers and therapeutic targets, in situ investigation of the binding kinetics of membrane proteins with their ligands has been a challenge. Traditional approaches isolate membrane proteins and then study them ex situ, which does not reflect accurately their native structures and functions. We present a label-free plasmonic microscopy method to map the local binding kinetics of membrane proteins in their native environment. This analytical method can perform simultaneous plasmonic and fluorescence imaging, and thus make it possible to combine the strengths of both label-based and label-free techniques in one system. Using this method, we determined the distribution of membrane proteins on the surface of single cells and the local binding kinetic constants of different membrane proteins. Furthermore, we studied the polarization of the membrane proteins on the cell surface during chemotaxis.

Single cells and intracellular processes studied by a plasmonic-based electrochemical impedance microscopy.

Electrochemical impedance spectroscopy is a crucial tool for the detection and study of various biological substances, from DNA and proteins to viruses and bacteria. It does not require any labelling species, and methods based on it have been developed to study cellular processes (such as cell spreading, adhesion, invasion, toxicology and mobility). However, data have so far lacked spatial information, which is essential for investigating heterogeneous processes and imaging high-throughput microarrays. Here, we report an electrochemical impedance microscope based on surface plasmon resonance that resolves local impedance with submicrometre spatial resolution. We have used an electrochemical impedance microscope to monitor the dynamics of cellular processes (apoptosis and electroporation of individual cells) with millisecond time resolution. The high spatial and temporal resolution makes it possible to study individual cells, but also resolve subcellular structures and processes without labels, and with excellent detection sensitivity (~2 pS). We also describe a model that simulates cellular and electrochemical impedance microscope images based on local dielectric constant and conductivity.

NanoMonitor: a miniature electronic biosensor for glycan biomarker detection.

AIM: The goal of our research is to develop an ultrasensitive diagnostic platform called 'NanoMonitor' to enable rapid label-free analysis of a highly promising class of biomarkers called glycans (oligosaccharide chains attached to proteins) with high sensitivity and selectivity. The glycosylation of fetuin - a serum protein - and extracts from a human pancreatic cancer line was analyzed to demonstrate the capabilities of the NanoMonitor. MATERIAL & METHODS: The NanoMonitor device consists of a silicon chip with an array of gold electrodes forming multiple sensor sites and works on the principle of electrochemical impedance spectroscopy. Each sensor site is overlaid with a nanoporous alumina membrane that forms a high density of nanowells on top of each electrode. Lectins (proteins that bind to and recognize specific glycan structures) are conjugated to the surface of the electrode. When specific glycans from a test sample bind to lectins at the base of each nanowell, a perturbation of electrical double-layer occurs, which results in a change in the impedance. Using the lectins Sambucs nigra agglutinin (SNA) and Maackia amurensis agglutinin (MAA), subtle variations to the glycan chains of fetuin were investigated. Protein extracts from BXPC-3, a cultured human pancreatic cancer cell line were also analyzed for binding to SNA and MAA lectins. The performance of the NanoMonitor was compared to a conventional laboratory technique: lectin-based enzyme linked immunosorbent assay (ELISA). RESULTS & DISCUSSION: The NanoMonitor was used to identify glycoform variants of fetuin and global differences in glycosylation of protein extracts from cultured human pancreatic cancerous versus normal cells. While results from NanoMonitor correlate very well with results from lectin-based ELISA, the NanoMonitor is rapid, completely label free, requires just 10 microl of sample, is approximately five orders of magnitude more sensitive and highly selective over a broad dynamic range of glycoprotein concentrations. CONCLUSION: Based on its performance metrics, the NanoMonitor has excellent potential for development as a point-of-care handheld electronic biosensor device for routine detection of glycan biomarkers from clinical samples.

Piezoelectric printing and probing of Lectin NanoProbeArrays for glycosylation analysis.

Glycans have great potential as disease biomarkers and therapeutic targets. However, the major challenge for glycan biomarker identification from clinical samples is the low abundance of key glycosylated proteins. To demonstrate the potential for glycan analysis with nanoliter amounts of glycoprotein, we have developed a new technology (Lectin NanoProbeArray) based on piezoelectric liquid dispensing for non-contact printing and probing of a lectin array. Instead of flooding the glycoprotein probe on the lectin array surface, as in conventional microarray screening, a piezoelectric printer is used to dispense nanoliters of fluorescently labeled glycoprotein probe over the lectin spots on the array. As a proof-of-concept, the ability of Lectin NanoProbeArrays to precisely identify and reliably distinguish between the closely related glycoforms of fetuin is illustrated here. Sensitivity levels comparable to lectin arrays that use evanescent-field scanners was achieved along with several orders of magnitude reduction in the amount of probe required for glycosylation analysis.

Sucrose regulated expression of a Ca2+-dependent protein kinase (TaCDPK1) gene in excised leaves of wheat.

Sucrose (Suc) can influence the expression of a large number of genes and thereby regulates many metabolic and developmental processes. However, the Suc sensing and the components of the ensuing signaling transduction pathway leading to the regulation of gene expression are not fully understood. We have shown that protein kinases and phosphatases are involved in the Suc induced expression of fructosyltransferase (FT) genes and fructan accumulation by an hexokinase independent pathway in wheat (Triticum aestivum). In the present study, using an RT-PCR based strategy, we have cloned a calcium-dependent protein kinase (TaCDPK1) cDNA that is upregulated during Suc treatment of excised wheat leaves. The deduced amino-acid sequence of CDPK1 has high sequence similarity (>70%) to known CDPKs from both monocots and dicots. Based on sequence homology, TaCDPK1 sequence shows a variable domain preceding a catalytic domain, an autoinhibitory function domain, and a C-terminal calmodulin-domain containing 4 EF-hand calcium-binding motifs, along with a N-myristoylation motif in the N-terminal variable domain. The recombinant Escherichia coli expressed TaCDPK1 was able to phosphorylate histone III-S in a calcium dependent manner in in vitro assays. The TaCDPK1 gene expression, as determined by quantitative RT-PCR, is induced by Suc and this effect is repressed by the inhibitors of the putative components of the Suc signal transduction pathway (calcium, Ser/Thr protein kinases and protein phosphatases). We propose that TaCDPK1 is involved in the Suc induced signaling pathway in wheat leaves.

Knowledge-based framework for hypothesis formation in biochemical networks.

MOTIVATION: The current knowledge about biochemical networks is largely incomplete. Thus biologists constantly need to revise or extend existing knowledge. The revision and/or extension are first formulated as theoretical hypotheses, then verified experimentally. Recently, biological data have been produced in great volumes and in diverse formats. It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge. The majority of the systems help in finding 'pattern' in data and leave the reasoning to biologists. A few systems have tried to automate the reasoning process of hypothesis formation. These systems generate hypotheses from a knowledge base and given observations. A main drawback of these knowledge-based systems is the knowledge representation formalisms they use. These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about biochemical networks. RESULTS: We present a knowledge-based framework for hypothesis formation for biochemical networks. The framework has been implemented by extending BioSigNet-RR-a knowledge based system that supports elaboration-tolerant representation and non-monotonic reasoning. Features of the extended system are illustrated by a case study of the p53 signal network. AVAILABILITY: http://www.biosignet.org

Distinct regulation of sucrose: sucrose-1-fructosyltransferase (1-SST) and sucrose: fructan-6-fructosyltransferase (6-SFT), the key enzymes of fructan synthesis in barley leaves: 1-SST as the pacemaker.

• Previously we have cloned sucrose: fructan-6-fructosyltransferase (6-SFT) from barley (Hordeum vulgare) and proposed that synthesis of fructans in grasses depends on the concerted action of two main enzymes: sucrose: sucrose-1-fructosyltransferase (1-SST), as in other fructan producing plants, and 6-SFT, found only in grasses. • Here we report the cloning of barley 1-SST, verifying the activity of the encoded protein by expression in Pichia pastoris. As expected, the barley 1-SST is homologous to invertases and fructosyltransferases, and in particular to barley 6-SFT. • The gene expression pattern of 1-SST and 6-SFT, along with the corresponding enzyme activities and fructan levels, were investigated in excised barley leaves subjected to a light-dark regime known to sequentially induce fructan accumulation and mobilization. The turnover of transcripts and enzyme activities of 1-SST and 6-SFT was compared, using appropriate inhibitors. • We found the 1-SST transcripts and enzymatic activity respond quickly, being subject to a rapid turnover. By contrast, the 6-SFT transcripts and enzymatic activity were found to be much more stable. The much higher responsiveness of 1-SST to regulatory processes, as compared with 6-SFT, clearly indicates that 1-SST plays the role of the pacemaker enzyme of fructan synthesis in barley leaves.