Nonspecific Interactions Research Articles

Rapid assembly of mixed thiols for toll-like receptor-based electrochemical pathogen sensing.

Herein, we describe a rapid and facile fabrication of electrochemical sensors utilizing two different toll-like receptor (TLR) proteins as biorecognition elements to detect bacterial pathogen associated molecular patterns (PAMPs). Using potential-assisted self-assembly, binary mixtures of 11-mercaptoundecanoic acid (MUA) and 6-mercapto-1-hexanol (MCH), or MUA and an in-house synthesized zwitterionic sulfobetaine thiol (DPS) were assembled on a gold working electrode within 5 minutes, which is >200 times shorter than other TLR sensors' preparation time. Electrochemical methods and X-ray photoelectron microscopy were used to characterize the SAM layers. SAMs composed of the betaine terminated thiol exhibited superior resistance to nonspecific interactions, and were used to develop the TLR sensors. Biosensors containing two individually immobilized TLRs (TLR4 and TLR9) were fabricated on separate MUA-DPS SAM modified Au electrodes (MUA-DPS/Au) and tested for their response towards their respective PAMPs. The changes to electron transfer resistance in EIS of the TLR4/MUA-DPS/Au sensor showed a detection limit of 4 ng mL-1 for E. coli 0157:H7 endotoxin (lipopolysaccharide, LPS) and a dynamic range of up to 1000 ng mL-1. The TLR4-based sensor showed negligible response when tested with LPS spiked human plasma samples, showing no interference from the plasma matrix. The TLR9/MUA-DPS/Au sensor responded linearly up to 350 μg mL-1 bacterial DNA, with a detection limit of 7 μg mL-1. The rapid assembly of the TLR sensors, excellent antifouling properties of the mixed SAM assembly, small size and ease of operation of EIS hold great promise for the development of a portable and automated broad-spectrum pathogen detection and classification tool.

Three-color single-molecule localization microscopy in chromatin.

Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit of conventional optical microscopy and is particularly useful for investigating complex biological targets like chromatin. Chromatin exhibits a hierarchical organization with structural compartments and domains at different length scales, from nanometers to micrometers. Single molecule localization microscopy (SMLM) methods, such as STORM, are essential for studying chromatin at the supra-nucleosome level due to their ability to target epigenetic marks that determine chromatin organization. Multi-label imaging of chromatin is necessary to unpack its structural complexity. However, these efforts are challenged by the high-density nuclear environment, which can affect antibody binding affinities, diffusivity and non-specific interactions. Optimizing buffer conditions, fluorophore stability, and antibody specificity is crucial for achieving effective antibody conjugates. Here, we demonstrate a sequential immunolabeling protocol that reliably enables three-label studies within the dense nuclear environment. This protocol couples multiplexed localization datasets with a robust analysis algorithm, which utilizes localizations from one target as seed points for distance, density and multi-label joint affinity measurements to explore complex organization of all three targets. Applying this multi-plexed algorithm to analyze distance and joint density reveals that heterochromatin and euchromatin are not-distinct territories, but that localization of transcription and euchromatin couple with the periphery of heterochromatic clusters. This work is a crucial step in molecular imaging of the dense nuclear environment as multi-label capacity enables for investigation of complex multi-component systems like chromatin with enhanced accuracy.

Carbon dots-based dual-mode sensor for highly selective detection of nitrite in food substrates through diazo coupling reaction

As an antioxidant and preservative agent, nitrite (NO2−) plays an essential role in the food industry to maintain freshness or inhibit microbial growth. However, excessive addition of NO2− is detrimental to health, so accurate and portable detection of NO2− is critical for food quality control. Notably, the selectivity of most carbon dots (CDs)-based fluorescence sensors was not enough due to the nonspecific interaction mechanism of hydrogen bond, electrostatic interaction and inner filter effect etc. Herein, a novel fluorescence/UV–vis absorption (FL/UV–vis) dual-mode sensor was developed on basis of mC-CDs, which were prepared by simple solvothermal treatment of m-Phenylenediamine (m-PDA) and cyanidin cation (CC). The fluorescence of these mC-CDs could be selectively responded by NO2− through the specific diazo coupling reaction between NO2− and amino groups on the surface of mC-CDs, thus effectively improving the selectivity of NO2− detection. The CDs-based fluorescence sensor possessed a low detection limit of 0.091 μM and 0.143 μM for FL and UV–vis methods and the excellent linear range of 0.0–60.0 μM. Furthermore, the mC-CDs sensor was employed to detect NO2− in real samples with a recovery rate of 97.11 %–104.15 % for quantitative addition. Moreover, the smartphone-assisted fluorescence sensing platform developed could identify the subtle color changes that could not be distinguished by the naked eye, and had the advantages of fast detection speed and intelligence. More importantly, the portable solid phase sensor based on mC-CDs had been successfully applied to the specific fluorescence identification and concentration monitoring of NO2−. Accordingly, the designed sensor provided a new strategy for the highly selective and convenient sensing of NO2− in food substrates, and paved the way for the wide application of CDs-based nanomaterials in the detection of food safety.

Comparative Analysis of QCM and Electrochemical Aptasensors for SARS-CoV-2 Detection.

The rapid and accurate detection of SARS-CoV-2, particularly its spike receptor-binding domain (S-RBD), was crucial for managing the COVID-19 pandemic. This study presents the development and optimization of two types of aptasensors: quartz crystal microbalance (QCM) and electrochemical sensors, both employing thiol-modified DNA aptamers for S-RBD detection. The QCM aptasensor demonstrated exceptional sensitivity, achieved by optimizing aptamer concentration, buffer composition, and pre-treatment conditions, with a limit of detection (LOD) of 0.07 pg/mL and a linear range from 1 pg/mL to 0.1 µg/mL, and a significant frequency change was observed upon target binding. The electrochemical aptasensor, designed for rapid and efficient preparation, utilized a one-step modification process that reduced the preparation time to 2 h while maintaining high sensitivity and specificity. Electrochemical impedance spectroscopy (EIS) enabled the detection of S-RBD concentrations as low as 132 ng/mL. Both sensors exhibited high specificity, with negligible non-specific interactions observed in the presence of competing proteins. Additionally, the QCM aptasensor's functionality and stability were verified in biological fluids, indicating its potential for real-world applications. This study highlights the comparative advantages of QCM and electrochemical aptasensors in terms of preparation time, sensitivity, and specificity, offering valuable insights for the development of rapid, sensitive, and specific diagnostic tools for the detection of SARS-CoV-2 and other viruses.

Green Solvent γ-Valerolactone (GVL) Facilitates Photocatalytic C-H Bond Activation.

Solvents can significantly influence chemical reactions in condensed phases. Their critical properties are increasingly recognized in various research domains such as organic synthesis and biomass valorization. However, in semiconductor photocatalysis, solvents are primarily viewed as mediums for dissolving and diffusing substances, with their potential beneficial effects on photocatalytic conversions often overlooked. Additionally, common photocatalysis solvents like acetonitrile (ACN) pose serious safety and environmental concerns. In this study, we demonstrate that novel and safe green solvents, such as γ-valerolactone (GVL), can significantly enhance the performance of semiconductor photocatalysis for C-H bond activation. Non-specific solvent-solute interactions are the primary contributors to increased photocatalytic activity in the self-coupling of benzylic compounds. Specifically, GVL's large dielectric constant and high refractive index lower the energy barrier for the rate-determining C-H bond activation step, facilitating a faster coupling reaction. The versatility of GVL is further demonstrated in reactions with multiple reagents and in various oxidation and reduction photocatalytic systems beyond classic C-H bond activation. This work not only pioneers the use of green solvents but also provides comprehensive insights for proper solvent selection in semiconductor photocatalysis.

Starch-based "smart" nanomicelles: Potential delivery systems for doxorubicin.

Vesicular nanosystems are a cornerstone to the contemporary drug delivery paradigm owing to their ability to encapsulate a variety of drug molecules, which improves the overall pharmacokinetics and bioavailability of the cargo drug. These systems have proven potential in the delivery of hydrophobic chemotherapeutic "Doxorubicin" (DOX), which faces frequent challenge relating to its nonspecific interactions, dose-limiting toxicity (myelosuppression being the most common manifestation), and short half-life (distribution half-life of 5 min, terminal half-life of 20-48 h), which limit its overall clinical effectiveness. "Smart" nanomicelles with stimuli-responsive linkages take advantage of tumor microenvironment for deploying the cargo drug at the target site, which prevents nonspecific distribution and, hence, low toxicity. Similarly, those with stealth properties evade protein response, which triggers the immunogenic response. The nanomicelles co-loaded with magnetic nanoparticles provide additional utility such as contrast enhancement agents in theranostics. Overall, the starch-based nanomicelles prove to be an excellent delivery system for overcoming the limitations associated with the conventional DOX delivery regime.

Preparation and characterization of novel polyols-based DESs and their use in efficient sequestration of radioactive iodine

The utilization of Novel DESs can be greener alternative to traditional organic solvents. In present study, four polyols-based DESs are synthesized and characterized by several techniques. The prepared DESs are used for the efficient capture of hazardous iodine. In present study by simple combination of two readily accessible, economical, and biodegradable components four polyols-based DESs have been prepared. For the creation of these DESs, a hydrogen bond donors (HBDs) (polyols) and hydrogen bond acceptors (HBAs) (BTEAC) are used, which havemelting points far lower than their respective melting points. The developed DESs were investigated for their physicochemical properties such as density, dynamic viscosity. Our results revealed distinct trends in these properties across different DES compositions, highlighting unique molecular interactions and solvation capabilities. The FTIR and NMR characterization study indicated considerable intermolecular interaction between the various component of the DES system. Further, Kamlet-Taft solvatochromic parameters were determined using Nile red dye, and other solvatochromic dyes. For synthesized DESs, the solvatochromic parameters ENT, normalized polarity parameter, π*, polarity / polarizability; β, hydrogen-bond acceptor basicity and α, hydrogen-bond donor acidity, have been determined. The ENT parameters demonstrate that both non-specific and specific interactions play a significant role in solute–solvent interactions. The synthesized DESs have been utilized for the efficient capture of the iodine. The removal efficiency of DES depends upon the mass of the DESs taken and time duration. These findings deepen our understanding of DES behavior and underscore their versatility in diverse industrial and scientific applications.

Measuring PETase enzyme kinetics by single-molecule microscopy

Polyethylene terephthalate (PET) is one of the most widely produced man-made polymers and is a significant contributor to microplastics pollution. The environmental and human health impacts of microplastics pollution have motivated a concerted effort to develop microbe- and enzyme-based strategies to degrade PET and similar plastics. A PETase derived from the bacteria Ideonella sakaiensis was previously shown to enzymatically degrade PET, triggering multidisciplinary efforts to improve the robustness and activity of this and other PETases. However, because these enzymes only erode the surface of the insoluble PET substrate, it is difficult to measure standard kinetic parameters, such as kon, koff, and kcat, complicating interpretation of the activity of mutants using traditional enzyme kinetics frameworks. To address this challenge, we developed a single-molecule microscopy assay that quantifies the landing rate and binding duration of quantum dot-labeled PETase enzymes interacting with a surface-immobilized PET film. Wild-type PETase binding durations were well fit by a biexponential with a fast population having a 2.7 s time constant, interpreted as active binding events, and a slow population interpreted as nonspecific binding interactions that last tens of seconds. A previously described hyperactive mutant, S238F/W159H had both a faster apparent on-rate and a slower off-rate than wild-type PETase, potentially explaining its enhanced activity. Because this single-molecule approach provides a more detailed mechanistic picture of PETase enzymatic activity than standard bulk assays, it should aid future efforts to engineer more robust and active PETases to combat global microplastics pollution.

Probing Phoretic Transport of Oxidative Enzyme-Bound Zn(II)-Metallomicelle in Adenosine Triphosphate Gradient via a Spatially Relocated Biocatalytic Zone.

Although cellular transport machinery is mostly ATP-driven and ATPase-dependent, there has been a recent surge in understanding colloidal transport processes relying on a nonspecific physical interaction with biologically significant small molecules. Herein, we probe the phoretic behavior of a biocolloid [composed of a Zn(II)-coordinated metallomicelle and enzymes horseradish peroxidase (HRP) and glucose oxidase (GOx)] when exposed to a concentration gradient of ATP under microfluidic conditions. Simultaneously, we demonstrate that an ATP-independent oxidative biocatalytic product formation zone can be modulated in the presence of a (glucose + ATP) gradient. We report that both directionality and extent of transport can be tuned by changing the concentration of the ATP gradient. This diffusiophoretic mobility of a submicrometer biocolloidal object for the spatial transposition of a biocatalytic zone signifies the ATP-mediated functional transportation without the involvement of ATPase. Additionally, the ability to analyze colloidal transport in microfluidic channels using an enzymatic fluorescent product-forming reaction could be a new nanobiotechnological tool for understanding transport and spatial catalytic patterning processes. We believe that this result will inspire further studies for the realization of elusive biological transport processes and target-specific delivery vehicles, considering the omnipresence of the ATP-gradient across the cell.

Redox conditions influence the chemical composition of iron-associated organic carbon in boreal lake sediments: A synchrotron-based NEXAFS study

The global carbon and iron cycles are intimately linked as redox-sensitive iron oxides readily bind organic carbon in a variety of environmental settings, including marine and lacustrine sediments. While these iron-organic carbon complexes sequester vast quantities of organic carbon, the composition of the organic matter within them remains unknown for lacustrine environments. Here we present C K1s and Fe L3,2 edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of surface sediments and authigenic iron complexes from adjacent basins of a pristine boreal lake located in Québec, Canada, with contrasting oxygen exposure regimes. We demonstrate differences in organic carbon speciation in sediments from both basins, as well as co-localization of organic carbon and iron on a sub-micron scale in 100 nm thick samples. Differences in redox cycling across these two basins allow for a direct comparison of the effect of oscillating redox conditions on the composition of organic carbon sequestered by iron. Our results suggest that reactive organic molecules, which may be polysaccharides, were found preferentially associated with iron in the perennially oxic sediments compared to more phenol rich organics in the seasonally anoxic sediments, highlighting the importance of iron oxides in the protection and preservation of labile organic compounds. Traces of aliphatic carbon were observed in sediments from the anoxic basin, alongside carboxyl and aromatic functionalities. This carboxyl-rich aliphatic material could possibly interact with the sediment mineral matrix either through a ligand exchange mechanism between the mineral phases and the carboxyl functionalities, or via non-specific hydrophobic interactions involving the aliphatic moieties. Finally, our work also shows that OC:Fe ratios should be used with caution when inferring a binding mechanism between OC and iron oxides.

DNA Aptamer Integrated Hydrogel Nanocomposites on Screen Printed Gold Electrodes for Point-of-Care Detection of Testosterone in Human Serum.

This work describes the development and evaluation of a novel electrochemical aptasensor for testosterone detection. The sensor utilizes a specifically designed DNA immobilized on a screen-printed gold electrode (SPGE) modified with a conductive hydrogel and gold nanoparticles (HG/NP) composite. The aptasensor exhibited a dose-dependent response to testosterone (0.05 to 50 ng/mL) with a detection limit of 0.14 ng/mL and a good sensitivity of 0.23 μA ng-1 mL cm-2. The sensor displayed excellent selectivity towards testosterone compared to structurally similar steroid hormones. Importantly, the incorporation of HG/NP not only improved the sensor's conductivity but also acted as an antifouling layer, minimizing signal interference from non-specific biomolecule interactions in complex biological samples like human serum. The results obtained from the aptasensor showed good correlation with a standard ELISA method, demonstrating its effectiveness in real-world scenarios.

Non-specific yet selective interactions contribute to small molecule condensate partitioning behavior.

Biomolecular condensates are essential in various cellular processes, and their mis-regulation has been demonstrated to be underly disease. Small molecules that modulate condensate stability and material properties offer promising therapeutic approaches, but mechanistic insights into their interactions with condensates remain largely lacking. We employ a multiscale approach to enable long-time, equilibrated all-atom simulations of various condensate-ligand systems. Systematic characterization of the ligand binding poses reveals that condensates can form diverse and heterogeneous chemical environments with one or multiple chains to bind small molecules. Unlike traditional protein-ligand interactions, these chemical environments are dominated by non-specific hydrophobic interactions. Nevertheless, the chemical environments feature unique amino acid compositions and physicochemical properties that favor certain small molecules over others, resulting in varied ligand partitioning coefficients within condensates. Notably, different condensates share similar sets of chemical environments but at different populations. This population shift drives ligand selectivity towards specific condensates. Our approach can enhance the interpretation of experimental screening data and may assist in the rational design of small molecules targeting specific condensates.

Lysine methylation: A strategy to improve in-cell NMR spectroscopy of proteins

BackgroundIn-cell NMR is a valuable technique for investigating protein structure and function in cellular environments. However, challenges arise due to highly crowded cellular environment, where nonspecific interactions between the target protein and other cellular components can lead to signals broadening or disappearance in NMR spectra. ResultsWe implemented chemical reduction methylation to selectively modify lysine residues on protein surfaces aiming to weaken charge interactions and recover obscured NMR signals. This method was tested on six proteins varying in molecular size and lysine content. While methylation did not disrupt the protein's native conformation, it successful restored some previously obscured in-cell NMR signals, particularly for proteins with high isoelectric points that decreased post-methylation. SignificanceThis study affirms lysine methylation as a feasible approach to enhance the sensitivity of in-cell NMR spectra for protein studies. By mitigating signal loss due to nonspecific interactions, this method expands the utility of in-cell NMR for investigating proteins in their natural cellular environment, potentially leading to more accurate structural and functional insights.

A Zwitterionic Anti-Fouling Coating Promotes Electrochemical Biosensing in Complex Media

Biofoulants present in complex media, such as blood, plasma, saliva, etc., can cause an increase in the background of the signal or a reduction in signal-to-noise ratio, due to which most biosensors require a sample processing step. One of the major interactions for biofouling in biosensing platforms is non-specific hydrophobic interactions, which can be prevented using hydrophilic polymeric coatings [1], [2]. However, most hydrophilic polymers are not conductive enough to provide a strong electrochemical current signal, whereas the existing conductive polymers are often hydrophobic. To avoid this, zwitterionic polymers that are both ionically conductive [3] and hydrophilic [3] can be used as anti-fouling polymers for electrochemical biosensing. Additionally, these polymers are highly effective at preventing fouling by electrostatically-induced water structuring [4]. Herein, we report a zwitterionic polymer (bearing thiols, aldehydes and carboxylic acid groups) that forms a thin conductive and hydrophilic layer on the electrodes, while also housing biorecognition layers for capturing target analytes of interest.The polymer was synthesized by free radical copolymerization and coated on gold electrodes to form a thin coating (16 nm when dry), which upon hydration results in a hydrophilic interface (contact angle <15 degrees). Anti-fouling properties were validated by determining the adsorption of radiolabeled human serum albumin (HSA) protein (spiked in plasma) on polymer-coated electrodes. The polymer-coated electrodes showed a ~67% reduction in protein adsorption relative to bare gold electrodes. Additionally, no significant change in anodic current was observed when 1% HSA was incubated on polymer-coated electrodes for 1 hour; whereas an 83% decrease in anodic current was observed on bare-gold electrodes under the same conditions. The polymer-modified electrode was used in detecting redox-labeled DNA sequences with a LOD of 11 nM in buffer and unprocessed plasma. The coating was also utilized to detect COVID-19, where the prepared setup detected 104 cp/mL of SARS-CoV-2 pseudovirus spiked in 50% unprocessed saliva. Similar coatings created from poly(ethylene glycol) (PEG) were unresponsive toward SARS-CoV-2 spiked in 50% saliva [5]. The anti-fouling polymer coatings developed herein show enhanced performance compared to previously reported strategies, based on self-assembled monolayers, in detecting target analytes in complex media, demonstrating the potential for use in clinical diagnostics.

Diclofenac Interacts with Photosynthetic Apparatus: Isolated Spinach Chloroplasts and Thylakoids as a Model System.

Diclofenac, often detected in environmental samples, poses a potential hazard to the aquatic environment. The present study aimed to understand the effect of this drug on photosynthetic apparatus, which is a little-known aspect of its phytotoxicity. Chloroplasts and thylakoids isolated from spinach (Spinacia oleracea) were used for this study and treated with various concentrations of diclofenac (from 125 to 4000 μM). The parameters of chlorophyll a fluorescence (the OJIP test) as measurements for both the intact chloroplasts and the thylakoid membranes revealed that isolated thylakoids showed greater sensitivity to the drug than chloroplasts. The relatively high concentration of diclofenac that is required to inhibit chloroplast and thylakoid functions suggests a narcotic effect of that drug on photosynthetic membranes, rather than a specific interaction with a particular element of the electron transport chain. Using confocal microscopy, we confirmed the degradation of the chloroplast structure after DCF treatment, which has not been previously reported in the literature. In conclusion, it can be assumed that diclofenac's action originated from a non-specific interaction with photosynthetic membranes, leading to the disruption in the function of the electron transport chain. This, in turn, decreases the efficiency of photosynthesis, transforming part of the PSII reaction centers into heat sinks and enhancing non-photochemical energy dissipation.

Quenched Zwitterionic Cyclic Arg-Gly-Asp-Containing Pentapeptide Probe for Real-Time Brain Tumor Imaging.

The efficacy of glioblastoma treatment is closely associated with complete tumor resection. However, conventional surgical techniques often result in incomplete removal, leading to poor prognosis. A major challenge is the accurate delineation of tumor margins from healthy tissues. Imaging-guided surgery, particularly using fluorescent probes, is a promising solution for intraoperative guidance. The recently developed 'always-on' types of targeted fluorescence probes generate signals irrespective of their presence in tumor cells or in blood circulation, hampering their effectiveness. Here, we propose a novel activatable fluorescence imaging probe, Q-cRGD, that targets glioma cells via the specific binding of the cyclic Arg-Gly Asp-containing pentapeptide (cRGD) to integrins. The Q-cRGD probe was synthesized by conjugating a near-infrared (NIR) dye to a tryptophan quencher via a disulfide linkage, including a cRGD-targeting ligand. This activatable probe remained inactive until the redox-responsive cleavage of the disulfide linkage occurred within the target cell. The zwitterionic nature of NIR dyes minimizes nonspecific interactions with serum proteins, thereby enhancing the tumor-to-background signal ratio (TBR). An in vivo fluorescence imaging study demonstrated a TBR value of 2.65 within 3 h of the intravenous injection of Q-cRGD, confirming its potential utility in imaging-guided brain cancer surgery.

Single-Domain Antibodies as Antibody-Drug Conjugates: From Promise to Practice-A Systematic Review.

Antibody-drug conjugates (ADCs) represent potent cancer therapies that deliver highly toxic drugs to tumor cells precisely, thus allowing for targeted treatment and significantly reducing off-target effects. Despite their effectiveness, ADCs can face limitations due to acquired resistance and potential side effects. This study focuses on advances in various ADC components to improve both the efficacy and safety of these agents, and includes the analysis of several novel ADC formats. This work assesses whether the unique features of VHHs-such as their small size, enhanced tissue penetration, stability, and cost-effectiveness-make them a viable alternative to conventional antibodies for ADCs and reviews their current status in ADC development. Following PRISMA guidelines, this study focused on VHHs as components of ADCs, examining advancements and prospects from 1 January 2014 to 30 June 2024. Searches were conducted in PubMed, Cochrane Library, ScienceDirect and LILACS using specific terms related to ADCs and single-domain antibodies. Retrieved articles were rigorously evaluated, excluding duplicates and non-qualifying studies. The selected peer-reviewed articles were analyzed for quality and synthesized to highlight advancements, methods, payloads, and future directions in ADC research. VHHs offer significant advantages for drug conjugation over conventional antibodies due to their smaller size and structure, which enhance tissue penetration and enable access to previously inaccessible epitopes. Their superior stability, solubility, and manufacturability facilitate cost-effective production and expand the range of targetable antigens. Additionally, some VHHs can naturally cross the blood-brain barrier or be easily modified to favor their penetration, making them promising for targeting brain tumors and metastases. Although no VHH-drug conjugates (nADC or nanoADC) are currently in the clinical arena, preclinical studies have explored various conjugation methods and linkers. While ADCs are transforming cancer treatment, their unique mechanisms and associated toxicities challenge traditional views on bioavailability and vary with different tumor types. Severe toxicities, often linked to compound instability, off-target effects, and nonspecific blood cell interactions, highlight the need for better understanding. Conversely, the rapid distribution, tumor penetration, and clearance of VHHs could be advantageous, potentially reducing toxicity by minimizing prolonged exposure. These attributes make single-domain antibodies strong candidates for the next generation of ADCs, potentially enhancing both efficacy and safety.

Development of Immunoassay for Detection of Engineered Endolysin LysAm24-SMAP

Abstract In recent years modified bacteriophage lysins have widely been investigated for the purposes of development of antibacterial therapy. Thus, effective and precise methods for the quantitative analysis of these enzymes are in high demand. The enzyme-linked immunosorbent assay (ELISA) method has been developed for the detection of recombinant modified endolysin LysAm24-SMAP in biological samples. The optimal parameters for protein detection were determined, in particular, the influence of salt and the composition of the buffer system for preparation of the samples was studied. The applicability of the immunodetection system of the genetically engineered endolysin LysAm24-SMAP in various biological samples with enzyme concentrations from 0.4 ng/mL was demonstrated. In addition, the influence of matrix effects in samples of animal organs and tissue homogenates and producer strain lysates and their individual components during the analysis was assessed and it was shown that 0.65 M NaCl addition in the ELISA buffer is crucial for achieving correct results and reduces nonspecific interactions in the case of LysAm24-SMAP. The effectiveness of the developed system in the immunochemical control of the bacteriolytic enzyme was confirmed.

Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction.

Network inference or reconstruction algorithms play an integral role in successfully analyzing and identifying causal relationships between omics hits for detecting dysregulated and altered signaling components in various contexts, encompassing disease states and drug perturbations. However, accurate representation of signaling networks and identification of context-specific interactions within sparse omics datasets in complex interactomes pose significant challenges in integrative approaches. To address these challenges, we present pyPARAGON (PAgeRAnk-flux on Graphlet-guided network for multi-Omic data integratioN), a novel tool that combines network propagation with graphlets. pyPARAGON enhances accuracy and minimizes the inclusion of nonspecific interactions in signaling networks by utilizing network rather than relying on pairwise connections among proteins. Through comprehensive evaluations on benchmark signaling pathways, we demonstrate that pyPARAGON outperforms state-of-the-art approaches in node propagation and edge inference. Furthermore, pyPARAGON exhibits promising performance in discovering cancer driver networks. Notably, we demonstrate its utility in network-based stratification of patient tumors by integrating phosphoproteomic data from 105 breast cancer tumors with the interactome and demonstrating tumor-specific signaling pathways. Overall, pyPARAGON is a novel tool for analyzing and integrating multi-omic data in the context of signaling networks. pyPARAGON is available at https://github.com/netlab-ku/pyPARAGON.

In Situ Measurement of Nanoparticle-Blood Protein Adsorption and Its Heterogeneity with Single-Nanoparticle Resolution via Dual Fluorescence Quantification.

The formation of a protein corona gives nanomedicines a distinct biological identity, profoundly influencing their fate in the body. Nonspecific nanoparticle-protein interactions are typically highly heterogeneous, which can lead to unique biological behaviors and in vivo fates for individual nanoparticles that remain underexplored. To address this, we have established an in situ approach that allows quantitative examination of nanoparticle-protein adsorption at the individual nanoparticle level. This method integrates dual fluorescence quantification techniques, wherein the nanoparticles are first individually analyzed via nanoflow cytometry to detect fluorescent signals from adsorbed proteins. The obtained fluorescence intensity is then translated into protein quantities through calibration with microplate reader quantification. Consequently, this approach enables analysis of interparticle heterogeneity of nano-protein interactions, as well as in situ monitoring of protein adsorption kinetics and nanoparticle aggregation status in blood serum, preconditioning for a comprehensive understanding of nano-bio interactions, and predicting in vivo fate of nanomedicines.