PCR-based DNA walking is of efficacy for capturing unknown flanking genomic sequences. Here, an uracil base PCR (UB-PCR) with satisfying specificity has been devised for DNA walking. Primary UB-PCR replaces thymine base with uracil base, resulting in a primary PCR product composed of U-DNAs. A single-primer (primary nested sequence-specific primer) single-cycle amplification, using the four normal bases (adenine, thymine, cytosine, and guanine) as substrate, is then performed on the primary PCR product. Clearly, only those U-DNAs, ended by the primary nested sequence-specific primer at least at one side, will produce the corresponding normal single strands. Next, the single-cycle product undergoes uracil-DNA glycosylase treatment to destroy the U-DNAs, while the normal single strands are unaffected. Afterward, secondary even tertiary PCR is performed to exclusively enrich the target product. The feasibility of UB-PCR has been checked by obtaining unknown sequences bordering the three selected genetic sites.

In recent times, biopharmaceuticals have gained attention because of their tremendous potential to benefit millions of patients globally by treating widespread diseases such as cancer, diabetes and many rare diseases. Short peptides (SP), also termed as oligopeptides, are one such class of biopharmaceuticals, that are majorly involved in efficient functioning of biological systems. Peptide chains that are 2-20 amino acids long are considered as oligopeptides by researchers and are some of the functionally vital compounds with widespread applications including self-assembly material for drug delivery, targeting ligands for precise/specific targeting and other biological uses. Using functionalised biomacromolecules such as short chained peptides, helps in improving pharmacokinetic properties and biodistribution profile of the drug. Apart from this, functionalised SP are being employed as cell penetrating peptides and prodrug to specifically and selectively target tumor sites. In order to minimize any unwanted interaction and adverse effects, the stability and safety of SP should be ensured throughout its development from manufacturing to market. Formulation development and characterization strategies of these potential molecules are described in the following review along with various applications and details of marketed formulations.

Due to the current increase in the number of people suffering from diabetes worldwide, how to monitor the blood glucose level in the human body has become an urgent problem to be solved nowadays. The electrochemical sensor method can be used for real-time glucose monitoring due to its advantages of real-time monitoring capability and high sensitivity. Reduced graphene oxide (rGO) has great potential for application in the field of sensors due to its advantages of large specific surface area, high stability, and good electrical and thermal conductivity. Meanwhile, the synergistic effect between two-dimensional transition metal sulfides and graphene can improve the electrochemical performance of materials due to their similar mechanical flexibility and strength. This article uses flake graphite, copper sulfate, and glucose oxidase (GOx) as raw materials to prepare CuS/rGO/GOx/GCE electrodes, and explores the performance of electrode electrocatalysis for glucose. The results showed that the prepared sensor was characterized by a low detection limit (1.75 nM) and a wide linear range (0.1-100 mM) for glucose detection, displaying a good overall detection performance, and its sensing mechanism and dynamic process were also investigated. In addition, the sensor has outstanding selectivity, anti-interference, repeatability, reproducibility and practicality.

Adenosine triphosphate (ATP) is the energy currency of all living organisms and can be used as an indicator for cell proliferation and cytotoxicity. In the present work, we have developed a novel ATP detection system by combining the biotinylation reaction from archaeon Sulfolobus tokodaii with fluorescence resonance energy transfer (FRET). In biotinylation from S. tokodaii, an enzyme known as biotin protein ligase (BPL) forms a very stable complex with its product, biotinylated substrate protein (BCCP). Here, BPL and BCCP were fused to the fluorescent proteins Cerulean and Clover, respectively, and ATP detection was accomplished by monitoring the FRET signal between the two fluorescent proteins, since ATP is an essential component for biotinylation and the tight BPL-BCCP complex is formed only after biotinylation. Using this system, we have succeeded in detecting 5 nM of ATP by biotinylation reaction with 50 nM of each fusion protein. Our method has a characteristic that the signal does not decay for at least 2 h after the start of the reaction, unlike in the case of the luminescence-based assay with luciferase commonly used for the ATP detection. Thus, our system allows for ATP detection which is not significantly constrained by measurement timing.

Lectins are widely employed for the assessment of protein glycosylation as their carbohydrate binding specificities have been well characterized. In glycosylation assays, lectins are often conjugated with biotin tags, which interact with streptavidin to functionalize biosensing surfaces or recruit signal generating molecules, depending on the assay configuration. We here demonstrate that a high degree of biotin conjugation can limit total capture to streptavidin functionalized SPR surfaces due to multipoint binding, and can additionally bias the reported kinetic evaluations when measuring the interaction between lectins and glycoproteins by SPR. For microplate assays using different configurations, high biotinylation ratios can effectively amplify the signal obtained when using Streptavidin conjugates for detection, in some cases significantly lowering the limit of detection. The cumulative results express the importance of customizing the ligand biotinylation ratios for different assay configurations, as commercially obtained pre-biotinylated lectins are not necessarily optimized for different assay configurations.

Urinary N, N-diacetylspermine (DAS) is a known biomarker for colorectal cancer (CRC). However, DAS levels in both healthy and CRC patients' urine samples are extremely low and often challenging to quantify. Complex and expensive methods do exist to detect DAS in urine, but simpler, less expensive methods to detect DAS are needed, especially in low resource settings. Here we describe a highly efficient, fast, precise, and inexpensive colorimetric assay to detect low levels of DAS in human urine samples. We used recombinant diacetylspermine oxidase (rDAS Ox), expressed and extracted from E. coli, to oxidize DAS, producing three products including hydrogen peroxide (HO). The level of DAS present, which correlates with HO levels, was measured using horseradish peroxidase (HRP), which together with HO, oxidized Amplex™ Red to produce the pink-colored resorufin. The concentration of resorufin is directly proportional to HO (and DAS) levels. As urine contains metabolites which interfere with these oxidation reactions, we developed a simple two column-based protocol using ion exchange resins to remove these compounds and concentrate the DAS. With this novel cleaning and concentrating method, DAS was concentrated 15 times (confirmed by nuclear magnetic resonance (NMR) spectroscopy) and <1 μM DAS could be detected. Correlation graphs of urine samples spiked with known DAS concentrations versus assay-determined DAS concentrations had high coefficients of determination (R) for 0-10 μM DAS (0.94) and for 0-1 μM DAS (0.91), clearly demonstrating the excellent performance of the two-column protocol with the rDAS Ox reaction mixture. To the best of our knowledge, this is first reported colorimetric enzymatic assay that quantitates DAS in urine.

Early detection of Reactive oxygen species (ROS) concentration is very important in cancer diagnosis, pathological examinations, and health screening. Studies show that changes in ROS concentration occurs in a short time, causing irreparable damage to living cells and organs. Miniaturized sensors and microelectrodes are capable of online monitoring of electrochemical reactions both in vitro and in vivo. In this study, an enzymatic biosensor based on an electrochemically roughened gold microneedle electrode (RAuME) has been developed to measure superoxide anion released from prostate cancer cells. A uniform layer of reduced graphene oxide (rGO) was deposited onto the gold microelectrode through electrochemical reduction, followed by electrodeposition of yttrium hexacyanoferrate (YHCF) nanoparticles. The deposited layers improved the current response of the microneedle electrode in CV, Impedance, and Amperometric analysis. Furthermore, chitosan was utilized to superoxide dismutase (SOD) immobilization. The presence of chitosan maintained the catalytic properties of the SOD enzyme. The developed microsensor monitored the superoxide anion in a wide linear range from 0.304 to 314 μM with detection limit of 17 nm. According to the physiological concentration of the superoxide anion (10-100 nm), we hypothesized that the developed micro-biosensor can mediate a fast monitoring of ROS that facilitates early-stage cancer diagnosis and treatment.

There is an urgent demand for a simple yet extremely accurate biosensor to analyze tumorigenesis. Herein, we present a novel fluorescent and enzyme-free approach for detecting p53 gene cascading proximity ligation-mediated catalytic hairpin assembly and DNAzyme-assisted signal reaction. When the target p53 gene is present, the interaction between p53 and L1 and L2 chains initiates catalytic hairpin assembly and subsequently exposes DNAzyme in the P3 probe. The exposed DNAzyme binds with the loop region of the P4 probe and generates a nicking site, resulting in the release of a significant amount of ATMND that is conjugated in the stem section of P4. This leads to an amplified fluorescence response, which serves as a fluorescence signal for the detection of the p53 gene. This method allows for the accurate and sensitive identification of the p53 gene, exhibiting a linear reaction range of 1 fM to 1 nM, with a limit of detection as low as 0.23 fM. Furthermore, this fluorescent method has been utilized for the examination of clinical samples with a favorable recovery rate. Crucially, this versatile platform may be expanded to analyze different targets by changing the corresponding recognition unit, showing great potential for point-of-care testing in tumorigenesis analysis.

Dysregulations of blood clot breakdown (fibrinolysis) during vascular trauma can lead to excessive blood loss. Tranexamic acid (TXA) is an inhibitor of fibrinolysis that works by blocking the interaction between plasminogen and fibrin degradation products (FDPs) - a key step in fibrinolysis. Despite the widespread usage, there are no tests available in a clinical setting to monitor TXA levels. We developed a fluorescence resonance energy transfer (FRET)-based assay to quantify TXA concentrations in plasma by using 1) fluorescently labeled plasminogen, and 2) FDPs labeled with a fluorescence quencher. Once plasminogen binds the FDPs, the fluorescent signal is quenched. TXA causes plasminogen to dissociate from the FDPs, thus increasing fluorescence signal in a dose-dependent manner. The dose response was sensitive between 1 and 100 μM (0.16 and 15.7 mg/L). The intraassay and interassay variabilities were determined to be 5.7 % and 3.0 %, respectively. Limit of detection was estimated to be 0.28 μM (0.044 mg/L). When tested for measuring known levels of TXA added to plasma samples, the ratio between measured and expected TXA concentration was 1.0151. Our study demonstrates a novel assay that can rapidly quantify TXA concentrations in plasma samples, thus demonstrating its potential as an in-hospital tool.

Hypertension is a leading cause of cardiovascular mortality, often accompanied by complications such as arrhythmia and stroke. This silent killer requires a multifaceted pharmacological approach for effective management. This article presents new, environmentally friendly spectrophotometric methods for simultaneous quantification of telmisartan (TER) and metoprolol succinate (MTR) in laboratory prepared mixtures and pharmaceutical formulations. The suggested methodologies include the following: area under the curve method (AUC) utilizing area at specific wavelength ranges 228-233 nm (λ - λ) and 240-245 nm (λ - λ) for each analyte and Fourier self-deconvolution method (FD) depending on built-in function to address spectral interferences. In addition, the induced dual wavelength method (IDWL) employing equality factors to obtain absorbance differences at designated wavelengths, ratio difference method (RD) utilizing divisor-based ratio spectra where the utilized divisors were TER 40 μg/mL and MTR 90 μg/mL, and ratio derivative method (RDV) generating spectra through first derivative application that was measured at 266 nm and 246 nm for TER and MTR, respectively. These methods offer green alternatives for the accurate and precise determination of TER and MTR with exceptional linearity of 3-45, and 15-200 μg/mL for TER and MTR, respectively. Furthermore, the methods showed a coefficient of determination exceeding 0.9995 and good detection and quantification levels. A comprehensive greenness assessment, employing five distinct evaluation tools, confirmed the reduced environmental impact of the proposed methods in terms of waste generation, chemical consumption, and instrument safety. Successful analysis of pharmaceutical formulations and laboratory prepared mixtures containing different TER and MTR ratios confirmed the validity of the proposed methods. Standard addition studies further supported these findings, and the statistical results were comparable to those obtained using a reference method.

Hsp70 prevents protein aggregation and is cytoprotective, but sustained Hsp70 overexpression is problematic. Therefore, we characterized small molecule agonists that augment Hsp70 activity. Because cumbersome assays were required to assay agonists, we developed cell-based and in vivo assays in which disease-associated consequences of Hsp70 activation can be quantified. One assay uses an optogenetic system in which the formation of TDP-43 inclusions can be controlled, and the second assay employs a zebrafish model for acute kidney injury (AKI). These complementary assays will facilitate future work to identify new Hsp70 agonists as well as optimized agonist derivatives.

Lysine β-hydroxybutyrylation (Kbhb) is newly discovered β-hydroxybutyrylate-derived histone modification which has been associated with the pathogenesis of many human diseases. To further elucidate the biological significance and molecular mechanism of Kbhb, it is necessary to accurately identify the Kbhb sites from protein sequences. In this study, a novel computational model named iBhb-Lys is developed for the identification of Kbhb sites. Four types of features are combined to encode each Kbhb site as a 3266-dimensional feature vector. And the autoencoder network is used to reduce the dimensionality of feature space, due to the high dimensionality of the combined features. In addition, to effectively reduce the influence of noise and outlier on classification, a new fuzzy support vector machine algorithm is proposed by incorporating the density around the sample into the fuzzy membership function. As illustrated by independent test, the AUC value of iBhb-Lys has increased by 2.22 % compared to the existing predictor KbhbXG. Feature analysis shows that some amino acid composition features, such as the occurrence frequency of leucine and histidine residues around Kbhb sites, contribute profoundly to the identification of Kbhb sites. The conclusions drawn in this study may provide useful reference for studying the molecular mechanism of Kbhb.

When stressed, cells synthesize di-adenosine polyphosphates (ApA), and cellular organisms also express proteins that degrade these compounds to release ATP. Most of these proteins are members of the nudix hydrolase superfamily, and several are involved in bacterial pathogenesis, neurodevelopment, and cancer. The goal of this project is to assist in the discovery of inhibitors of these enzymes that could be used to study ApA function and the cellular role of these nudix enzymes. Because these enzymes cleave ApA and ApA to produce ATP, two standard ATP detection techniques were optimized and compared here for their suitability for high throughput screening. In the first assay, cleavage is monitored by coupling to a reaction catalyzed by firefly luciferase. In the second assay, cleavage is detected by coupling to hexokinase, glucose 6-phosphate dehydrogenase, and diaphorase. Although the former assay was more sensitive, the latter was more reproducible, linear, and suitable for screening and kinetic analyses. The assays were used to characterize the kinetics of reactions catalyzed by various nudix enzymes isolated from E. coli, humans, and Mycobacterium tuberculosis, the bacterium that causes tuberculosis. Results reveal subtle differences between the proteins that might be exploited to identify specific small molecule inhibitors.

Hydrogen sulfide (HS) acts as a messenger molecule and can mediate a variety of physiological functions. Conventional methods are seldom used to detect endogenous HS and present some difficulties in selective and accurate detection. Reaction-based recognition of endogenous HS by organic small molecule probes with good specificity and biocompatibility. To address this challenge, we developed a novel HS fluorescent probe 4-(2-(6-hydroxy-2-naphthyl) ethyl)-1-methylpyridinium (DSNP) that triggers a thiolysis reaction through a strong electron withdrawing group, releasing a fluorescent molecule. The simple probe DSNP not only have good selectivity, large Stokes shifts and biocompatibility, but also demonstrated a detection limit as low as 28.4 nM and reaction times as quick as 30 min. Moreover, it has been successfully applied to imaging intracellular HS in myeloma cells and zebrafish. This study opens new insights to help push this probe forward for its applicability for detailed HS localization studies in osteosarcoma.

Organic precipitation of proteins with acetonitrile demonstrated complete protein recovery and improved chromatography of human plasma proteins. The separation of 25 μL of human plasma into 22 fractions on a QA SAX resin facilitated more effective protein discovery despite the limited sample size. Micro chromatography of plasma proteins over quaternary amine (QA) strong anion exchange (SAX) resins performed best, followed by diethylaminoethyl (DEAE), heparin (HEP), carboxymethyl cellulose (CMC), and propyl sulfate (PS) resins. Two independent statistical methods, Monte Carlo comparison with random MS/MS spectra and the rigorous X!TANDEM goodness of fit algorithm protein p-values corrected to false discovery rate q-values (q ≤ 0.01) agreed on at least 12,000 plasma proteins, each represented by at least three fully tryptic corrected peptide observations. There was qualitative agreement on 9393 protein/gene symbols between the linear quadrupole versus orbital ion trap but also quantitative agreement with a highly significant linear regression relationship between log observation frequency (F value 4,173, p-value 2.2e-16). The use of a QA resin showed nearly perfect replication of all the proteins that were also found using DEAE-, HEP-, CMC-, and PS-based chromatographic methods combined and together estimated the size of the size of the plasma proteome as ≥12,000 gene symbols.

The escalating global incidence of allergy patients illustrates the growing impact of allergic issues on global health. Allergens are small molecule antigens that trigger allergic reactions. A widely recognized strategy for allergy prevention involves identifying allergens and avoiding re-exposure. However, the laboratory methods to identify allergenic proteins are often time-consuming and resource-intensive. There is a crucial need to establish efficient and reliable computational approaches for the identification of allergenic proteins. In this study, we developed a novel allergenic proteins predictor named Alg-MFDL, which integrates pre-trained protein language models (PLMs) and traditional handcrafted features to achieve a more complete protein representation. First, we compared the performance of eight pre-trained PLMs from ProtTrans and ESM-2 and selected the best-performing one from each of the two groups. In addition, we evaluated the performance of three handcrafted features and different combinations of them to select the optimal feature or feature combination. Then, these three protein representations were fused and used as inputs to train the convolutional neural network (CNN). Finally, the independent validation was performed on benchmark datasets to evaluate the performance of Alg-MFDL. As a result, Alg-MFDL achieved an accuracy of 0.973, a precision of 0.996, a sensitivity of 0.951, and an F1 value of 0.973, outperforming the most of current state-of-the-art (SOTA) methods across all key metrics. We anticipated that the proposed model could be considered a useful tool for predicting allergen proteins.

The identification of Drug-Target Interaction (DTI) is an important step in drug discovery and drug repositioning, and has high application value in multiple fields such as drug discovery, drug repositioning, and repurposing. However, the high cost of experimental validation limits its identification. In contrast, computation-based approaches are both economical and efficient. This review first synthesizes existing chemical genomic approaches, provides a comprehensive summary of prevalent databases for predicting DTIs, and categorizes the feature encodings from recent years. This is followed by an overview and brief description of the methods currently in use for predicting DTIs. The strengths and weaknesses of newly proposed prediction methods in the last five years (2020-2024), including those based on network representation learning and graph neural networks, are then discussed in detail, evaluating the performance of the different methods on a wide range of datasets. Finally, this review explores potential directions for future DTI research, emphasizing how to improve prediction accuracy and efficiency by combining big data and emerging computing technologies.

Detection of Salmonella in food is topical due to known cases of salmonellosis epidemics. Immunochemical methods including ELISA are widely used for Salmonella detection. Traditionally, commercial ELISA kits are based on sandwich technique and detect lipopolysaccharide (LPS), which is considered to be the component of the outer membrane of Gram-negative bacteria. Our aim was elaboration of competitive ELISA test for Salmonella detection in food with improved parameters. It was shown that in the Salmonella culture after the standard sample preparation procedure LPS is present mainly outside cells as a component of outer membrane vesicles. Improved sample preparation procedure includes separation of bacteria from the medium and analysis of the medium, which increases analytical sensitivity. Immobilization of the bovine serum albumin (BSA)-LPS conjugate in microplate wells allows to obtain a more homogeneous coating than immobilization of LPS itself. Thus, we have developed test system for Salmonella detection in food by competitive ELISA of LPS secreted into the culture medium with the immobilized BSA-LPS conjugate and monoclonal antibodies (mAb) to LPS core in the liquid phase. New competitive ELISA test is high sensitive, give reproducible results, allows the detection of any Salmonella serotype and is important for the protection of human health.

A voltammetric immunosensor for the detection of Newcastle disease virus (NDV) has been developed by employing polyclonal antibody targeting NDV (anti-NDV) as a bioreceptor. Anti-NDV was immobilized on polyethylene glycol (PEG)-containing self-assembled monolayer (SAM) which was activated with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimidehydrochloride (EDC) and N-hydroxy succinimide (NHS) coupling on screen-printed gold electrode (SPGE). The introduction of PEG-containing SAM on the SPGE allowed the bioreceptor to covalently bound to the electrode surface whilst still providing a hydrophilic layer on the electrode which is important to greatly reduce non-specific bindings. The bioreceptor functionalized electrode was then allowed to be incubated with NDV-spiked samples. The electrode surface modification with PEG-containing SAM, immobilization of anti-NDV as bioreceptor, up to the detection of NDV were characterized electrochemically through differential pulse voltammetry (DPV) analysis in [Fe(CN)] as the redox probe. Decrement of anodic current peak (I) of [Fe(CN)] was seen as the concentration of NDV increased from 0.156 to 20 HA μL with the limit of detection (LoD) of 1.50 HA μL at 3σ m. The detection of NDV in HA μL unit in this study would ease interlaboratory interpretation as it was the same unit used in hemagglutination (HA) assay of conventional NDV diagnosis. The specificity of anti-NDV used as bioreceptor towards NDV was confirmed through western blot analysis, whilst the selectivity of the bioreceptor-functionalized electrode has been tested with allantoic fluid as the negative control in which no apparent changes of anodic peak (I) has been seen. This simple, fast, and less laborious electrochemical detection method could become an alternative to the conventional method for NDV detection.

Heliotropium bacciferum plant is very important and has been used for medicinal values since ancient times. The present study deals with the extraction of essential oil (0.14 w/w) of this plant and its GC-MS analysis, anti-inflammatory, and anti-bacterial activities evaluation. GC analysis of essential oil confirmed 76 compounds with 49 terpenes and oxygenated hydrocarbons. The main components of this essential oil are agarospirol (15.15 %), rosifoliol (9.41 %), elemol (8.96 %), tau.-cadinol (8.05 %), linalool (5.37 %), shyobunol (5.36 %) cyclohexylmethyl tridecyl ester of oxalic acid (4.74 %), respectively. The essential oil showed quite good anti-inflammatory activity while this oil indicated excellent anti-bacterial activity against 3 g-positive pathogenic bacteria (Bacillus subtilusATCC 6633, Entrococcus faecalis ATCC 29212, and Bacillus cereusATCC 11778). The essential oil of Heliotropium bacciferum showed great potential as an anti-inflammatory and anti-bacterial agent. Therefore, the reported extraction and GC-MS analysis methods are useful to extract the essential oil and determine the composition of other plants. The extracted essential oil may be used to treat several diseases.

Determination of Varicella vaccine's potency; containing live attenuated strain (Oka) of Varicella Zoster virus, has been limited to in vitro cell culture methods. In this study, a label free potentiometric biosensor has been developed for the first time and optimized to determine the content of varicella zoster virus. A passive ion-flux sensing platform has been developed using an anti-varicella monoclonal antibody and tetrabutyl ammonium bromide as a marker ion. The immunosensor has been optimized with respect to membrane diameter and concentration of the immobilized antibody. Linearity was achieved over a concentration range of 2.5-3.2 log PFU/dose with a LOD of 1.9 log PFU/dose. Potentiometric results were compared to the plaque-forming assay using the cell culture technique. The developed immunosensor was superior with respect to analysis time and cost without affecting critical analytical performance characteristics. Furthermore, in order to evaluate the stability indicating ability of the immunosensor, the effect of pH and temperature was investigated. Vaccine samples were subjected to forced degradation conditions; pH and elevated temperatures. Stability results showed the ability of immunosensor to differentiate between intact and degraded viral content. This would demonstrate the reliability of the immunosensor for evaluating the efficacy and stability of the vaccine.