Optimization of Sirius Red-Based Microplate Assay to Investigate Collagen Production In Vitro

Tissue fibrosis is characterized by chronic fibroblast activation and consequently excessive accumulation of collagen-rich extracellular matrix. In vitro microplate-based assays are essential to investigate the underlying mechanism and the effect of antifibrotic drugs. In this study, in the absence of a gold-standard method, we optimized a simple, cost-effective, Sirius Red-based colorimetric measurement to determine the collagen production of fibroblasts grown on 96-well tissue culture plates. Based on our findings, the use of a serum-free medium is recommended to avoid aspecific signals, while ascorbate supplementation increases the collagen production of fibroblasts. The cell-associated collagens can be quantified by Sirius Red staining in acidic conditions followed by alkaline elution. Immature collagens can be precipitated from the culture medium by acidic Sirius Red solution, and after subsequent centrifugation and washing steps, their amount can be also measured. Increased attention has been paid to optimizing the assay procedure, including incubation time, temperature, and solution concentrations. The resulting assay shows high linearity and sensitivity and could serve as a useful tool in fibrosis-related basic research as well as in preclinical drug screening.

Development of a novel microplate for high-throughput screening and optimization of DHA producing strains based on CFD technology

Microtiter plates are suitable for screening and process development of most microorganisms. They are currently the container of choice for high-throughput and small-scale microbial culture, but require optimization for specific work. In this research, a novel type of microtiter plate was developed using computational fluid dynamics (CFD) technology. The new plate provided high oxygen supply and optimal mixing effects for the fermentation culture of docosahexaenoic acid (DHA) producing strains, surpassing the conventional method of strain screening with shake flasks, which was insufficient. The shape of the microtiter plate was modified, and baffles were introduced to improve mass transfer and oxygen supply effects in the vibrating bioreactor. CFD technology was used to model the new plate's characteristics, establishing the superiority of hexagonal microtiter plates with six baffles. Parameters in the incubation process, such as vibration frequency and liquid load, were optimized, and the final result achieved an oxygen transfer coefficient (KL a) of 0.61 s-1 and a volume power input of 2364 w m-3 , which was four to five times better than the original 96-well plate. The culture results optimized by the model were also verified. Therefore, this new microtiter plate provides a powerful tool for future high-throughput screening of strains.

A Critical Study on DNA Probes Attached to Microplate for CRISPR/Cas12 Trans-Cleavage Activity

CRISPR/Cas12-based biosensors are emerging tools for diagnostics. However, their application of heterogeneous formats needs the efficient detection of Cas12 activity. We investigated DNA probes attached to the microplate surface and cleaved by Cas12a. Single-stranded (ss) DNA probes (19 variants) and combined probes with double-stranded (ds) and ssDNA parts (eight variants) were compared. The cleavage efficiency of dsDNA-probes demonstrated a bell-shaped dependence on their length, with a cleavage maximum of 50%. On the other hand, the cleavage efficiency of ssDNA probes increased monotonously, reaching 70%. The most effective ssDNA probes were integrated with fluorescein, antibodies, and peroxidase conjugates as reporters for fluorescent, lateral flow, and chemiluminescent detection. Long ssDNA probes (120-145 nt) proved the best for detecting Cas12a trans-activity for all of the tested variants. We proposed a test system for the detection of the nucleocapsid (N) gene of SARS-CoV-2 based on Cas12 and the ssDNA-probe attached to the microplate surface; its fluorescent limit of detection was 0.86 nM. Being united with pre-amplification using recombinase polymerase, the system reached a detection limit of 0.01 fM, thus confirming the effectiveness of the chosen ssDNA probe for Cas12-based biosensors.

A Rapid Method to Determine Growth-Limiting Nutrient Concentrations for Yeast in a Microplate Spectrophotometer

Determining the minimal concentration of a substance-whether a compound used to inhibit cell growth or a growth-limiting nutrient-can be an arduous process. Carrying out the experiment in flasks or tubes and estimating cell density in a single-sample spectrophotometer has been a routine method of choice due to the ease of measurement and standardized conversions from optical density measurements to cell concentrations. However, when dealing with dozens or more samples, several challenges arise, including increased processing time, increased risk of contamination through repeated sampling, and an increased risk of confounding one sample for another. The protocol described here details a rapid method to estimate cell concentrations for such experiments using a microplate spectrophotometer. Using a microplate spectrophotometer to measure optical density of many cultures can be automated for high throughput and benefits from a reduced risk of contamination. Since one of the caveats of a microplate spectrophotometer is its low saturation limit, we further describe how to convert optical density readings of the microplate spectrophotometer into its single-sample spectrophotometric equivalent. To further illustrate the applicability of this protocol, we compare OD₆₀₀ readings generated using a microplate spectrophotometer and a single-sample spectrophotometer for different nutrient starvations and show that the results are comparable. Overall, this method reduces the required resources, reduces the risk of contamination, and allows for faster processing of samples. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generating an equation to convert microplate spectrophotometer readings to single-sample spectrophotometric values Basic Protocol 2: Evaluating growth-limiting nutrient concentrations using a microplate spectrophotometer.

An Optimized Direct Lysis Gene Expression Microplate Assay and Applications for Disease, Differentiation, and Pharmacological Cell-Based Studies

Routine cell culture reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) gene expression analysis is limited in scalability due to minimum sample requirement and multistep isolation procedures. In this study, we aimed to optimize and apply a cost-effective and rapid protocol for directly sampling gene expression data from microplate cell cultures. The optimized protocol involves direct lysis of microplate well population followed by a reduced thermocycler reaction time one-step RT-qPCR assay. In applications for inflammation and stress-induced cell-based models, the direct lysis RT-qPCR microplate assay was utilized to detect IFN1 and PPP1R15A expression by poly(I:C) treated primary fibroblast cultures, IL6 expression by poly(I:C) iPSC-derived astrocytes, and differential PPP1R15A expression by ER-stressed vanishing white-matter disease patient induced pluripotent stem cell (iPSC)-derived astrocytes. In application for neural differentiation medium recipe optimizations, conditions were screened for SYN1 and VGLUT1 in neuronal cultures, and S100B, GFAP and EAAT1 in astrocyte cultures. The protocol provides microplate gene expression results from cell lysate to readout within ~35 min, with comparable cost to routine RT-qPCR, and it may be utilized to support laboratory cell-based assays in basic and applied scientific and medical fields of research including stem-cell differentiation, cell physiology, and drug mechanism studies.

A High-Throughput Platform for the Rapid Quantification of Phosphorylated Histone H2AX in Cell Lysates Based on Microplate Electrochemiluminescence Immunosensor Array

Sensitive detection of phosphorylated histone H2AX (γH2AX) in cells as a biomarker of DNA double-strand breaks has great significance in the field of molecular toxicology and life science research. However, current γH2AX detection methods require labor- and time-consuming steps. Here, for the first time, we designed a simple electrochemiluminescence (ECL) immunoassay integrated with a microplate-based sensor array to realize sensitive and high-throughput detection of γH2AX in cell lysates. Under the optimized conditions, this ECL immunosensor array could linearly respond to γH2AX concentrations in the range from 2 × 10² to 1 × 10⁵ pg/mL. In addition, our approach possessed excellent specificity and satisfactory reproducibility, and its practicality was verified in real cell lysates. The whole process including instrumental and manual operation was completed in no more than 3 h. This study provides a convenient and rapid alternative method for the sensitive quantification of γH2AX, which shows promising application in high-throughput screening of genotoxic chemicals and drug candidates.

Evaluation of the Use of Cold Plasma for Microtiter Plate Cleaning to Reduce Plastic Biohazard Waste

Plastic pollution is the accumulation of plastic objects in the Earth's environment and is a global problem of increasing importance. The laboratory and health care industries contribute to this problem by the widely accepted single use of plastics, including microtiter plates used for compound testing. At AstraZeneca, we predict the use of more than 45,000 384-well and more than 11,000 1536-well microtiter plates per year. IonField Systems has developed a microplate cleaning system (MCS) powered by PlasmaKnife technology that uses cold plasma to clean microtiter plates. AstraZeneca proposed the use of this system for standard ANSI (https://slas.org/resources/information/industry-standards/) microtiter plate regeneration. Here we present the results of an evaluation using a model system involving the cleaning of plates following an enzyme-based biochemical assay, as well as the software and hardware enhancements that were incorporated into the production PlasmaKnife MCS. The method involved determining the level of inhibition achieved by residual compound following different cleaning protocols and showed that cleaning achieved in about 2 min was sufficient to remove trace compound contamination. Future work will focus on assessing the number of regeneration cycles that can be reliably achieved.

A simple high-throughput protocol for the extraction and quantification of inorganic phosphate in rice leaves

PREMISE

Phosphorus (P) is an essential macronutrient that is often limited in agricultural systems. Determining inorganic phosphate (Pi) contents of plant tissues is crucial for evaluating plant P status. Here, we present a simple, high-throughput colorimetric microplate technique to measure Pi contents in rice (Oryza sativa) leaf tissues, based on the molybdenum blue reaction.

METHODS AND RESULTS

We used a hole puncher to sample small equal areas of leaf tissue for Pi extraction. We removed the leaf grinding and weighing steps, which are time-consuming and normally required to release Pi from the tissues and to measure the biomass for data normalization, respectively. We showed that the punching method yielded comparable results to the conventional grinding method for two rice cultivars grown under various levels of P supply.

CONCLUSIONS

Compared with existing techniques, this protocol is more suited to an initial screening, enabling one researcher to determine the Pi contents of thousands of rice leaf samples within a few hours.

Potential for Bacteriophage Cocktail to Complement Commercial Sanitizer Use on Produce Against Escherichia coli O157:H7

The increasing concern for food safety has created a need to evaluate novel techniques to eliminate or control pathogens, resulting in safe food. In this study, four bacteriophages of bovine origin, specific to E. coli O157:H7, were successfully isolated and characterized. A microplate reader assay demonstrated the efficacy of the bacteriophage (phage) cocktail against E. coli O157:H7 resulting in a significant reduction (p < 0.01) in the target pathogen population. The phage cocktail demonstrated significant efficacy (p < 0.05) against E. coli O157:H7 in the presence of the most utilized sanitizers in the United States, namely 100 parts per million (ppm) free chlorine and 100-ppm peroxyacetic acid. Survival in the sanitizer concentrations demonstrates the potential use of phage cocktail and sanitizer synergistically to enhance sanitation operations in the food industry.

Efficacy of Microplates versus Miniplates in the Management of Maxillofacial Fractures

Introduction:

Increased facial trauma has led to advances in techniques of internal fixation, improvements in plating system, refinements in exposure of facial skeleton fueling the rapid use of internal fixation for the management of facial fractures. Evaluating 40 patients with confirmed midfacial (Le Fort I and II) and mandibular fractures, this study presents the efficacy of microplate in comparison with miniplate in terms of load bearing capacity, stability at the fracture site and postoperative palpability.

Objectives:

To evaluate the efficacy of microplates in comparison with miniplates in maxillofacial trauma.

Materials and Methods:

Study sample consists 40 subjects, 20 each in two groups clinically and radiographically diagnosed with Group 1 (maxillary) and Group 2 (mandibular fractures) which were subdivided into 10 each treated with miniplate and microplate respectively. Postoperatively, stability of fracture, bite force, need for postop MMF, pain, infection, wound dehiscence, mouth opening, occlusion and palpability was noted. All cases have been evaluated clinically for various parameters for minimum of 3 months to assess any postoperative complications.

Results:

We found microplates are stable enough and have adequate load bearing capacity. Due to close adaptability and less hardware, postoperative palpability is less but larger sample study with long term follow up is necessary to conclude its efficacy in load bearing fracture sites.

Deconvolution of Luminescence Cross-Talk in High-Throughput Gene Expression Profiling

Luciferase reporters have become standard genetic tools to monitor gene expression in real time and in high-throughput using microplate readers. Compared to reporter gene assays based on fluorescence proteins, luciferase reporters have a superior signal-to-noise ratio, since they do not suffer from the high autofluorescence background of the bacterial cell. However, at the same time luciferase reporters have the drawback of constant light emission, which leads to undesired cross-talk between neighboring wells on a microplate. To overcome this limitation, we developed a computational method to correct for luminescence bleed-through and to estimate the "true" luminescence activity for each well of a microplate. As the sole input our algorithm uses the signals measured from a calibration plate, in which the light emitted from a single luminescent well serves as an estimate for the "light-spread function". We show that this light-spread function can be used to deconvolve any other measurement obtained under the same technical conditions. Our analysis demonstrates that the correction preserves low-level signals close to the background and shows that it is universally applicable to different kinds of microplate readers and plate types.

A comprehensive in vitro fluorescence anisotropy assay system for screening ligands of the jasmonate COI1-JAZ co-receptor in plants

The phytohormone (+)-7-iso-jasmonoyl-l-isoleucine regulates many developmental and stress responses in plants and induces protein-protein interactions between COI1, the F-box component of E3 ubiquitin ligase, and jasmonate ZIM domain (JAZ) repressors. These interactions cause JAZ degradation and activate jasmonate (JA), leading to plant defense responses, growth inhibition, and senescence. Thirteen JAZ subtypes are encoded in the Arabidopsis thaliana genome, but a detailed understanding of the physiological functions of these JAZ subtypes remains unclear, partially because of the genetic redundancy of JAZ genes. One strategy to elucidate the complex JA signaling pathways is to develop a reliable and comprehensive binding assay system of the ligands with all combinations of the co-receptors. Herein, we report the development of a fluorescence anisotropy-based in vitro binding assay system to screen for the ligands of the COI1-JAZ co-receptors. Our assay enabled the first quantitative analysis of the affinity values and JAZ-subtype selectivity of various endogenous JA derivatives, such as coronatine, jasmonic acid, and 12-hydroxyjasmonoyl-l-isoleucine. Because of its high signal-to-noise ratio and convenient mix-and-read assay system, our screening approach can be used in plate reader-based assays of both agonists and antagonists of COI1-JAZ co-receptors.

Design of Microplate-Compatible Illumination Panels for a Semiautomated Benchtop Pipetting System

Microplates are an essential tool used in laboratories for storing research materials and performing assays. Many types of laboratory automation exist that greatly reduce the effort needed to utilize microplates; however, there are cases where the use of such automation is not feasible or practical. In these instances, researchers must work in an environment where liquid handling operations are performed manually with handheld pipetting devices. This type of work is tedious and error-prone as it relies on researchers to manually track a significant amount of metadata, including transfer volumes, plate barcodes, well contents, and well locations. To address this challenge, we have developed an open-source, semiautomated benchtop system that facilitates manual pipetting using visual indicators. This device streamlines the process of identifying the location of wells so that the researcher can perform manual transfers in a more efficient, reliable, and accurate manner. This system utilizes a graphical user interface that allows the user to load worklists and then issues commands to illuminate wells of interest, providing a visual indicator for users to follow in real time. The software and hardware tools utilized for development, along with the implementation techniques used to produce this system, are described within.

A high-throughput method of analyzing multiple plant defensive compounds in minimized sample mass

PREMISE OF THE STUDY

Current methods for quantifying herbivore-induced alterations in plant biochemistry are often unusable by researchers due to practical constraints. We present a cost-effective, high-throughput protocol to quantify multiple biochemical responses from small plant tissue samples using spectrophotometric techniques.

METHODS AND RESULTS

Using Solanum lycopersicum and Medicago polymorpha leaves pre- and post-herbivory, we demonstrate that our protocol quantifies common plant defense responses: peroxidase production, polyphenol oxidase production, reactive oxygen species production, total protein production, and trypsin-like protease inhibition activity.

CONCLUSIONS

Current protocols can require 500 mg of tissue, but our assays detect activity in less than 10 mg. Our protocol takes two people 6 h to run any of the assays on 300 samples in triplicate, or all of the assays on 20 samples. Our protocol enables researchers to plan complex experiments that compare local versus systemic plant responses, quantify environmental and genetic variation, and measure population-level variation.

Controllable Fabrication and Tuned Electrochemical Performance of Potassium Co-Ni Phosphate Microplates as Electrodes in Supercapacitors

Most reported pristine phosphates, such as NH₄MPO₄·H₂O (M = Co, Ni), are not very stable as supercapacitor electrodes because of their chemical properties. In this work, KCo_xNi_1-xPO₄·H₂O microplates were fabricated by a facile hydrothermal method at low temperature and used as electrodes in supercapacitors. The Co and Ni content could be adjusted, and optimal electrochemical performance was found in KCo_0.33Ni_0.67PO₄·H₂O, which also possessed superior specific capacitance, rate performance, and long-term chemical stability compared with NH₄Co_0.33Ni_0.67PO₄·H₂O because of its unique chemical composition and microstructure. Asymmetric supercapacitor cells based on KCo_0.33Ni_0.67PO₄·H₂O and active carbon were assembled, which produce specific capacitance of 34.7 mA h g^-1 (227 F g^-1) under current density of 1.5 A g^-1 and retain 82% as initial specific capacitance after charging and discharging approximately 5000 times. The assembled asymmetric supercapacitor cells (ASCs) exhibited much higher power and energy density than most previously reported transition metal phosphate ASCs. The KCo_xNi_1-xPO₄·H₂O electrodes fabricated in this work are efficient, inexpensive, and composed of naturally abundant materials, rendering them promising for energy storage device applications.

A fast and reproducible cell- and 96-well plate-based method for the evaluation of P2X7 receptor activation using YO-PRO-1 fluorescent dye

The YO-PRO-1 assay provides a quantitative estimation of P2X7 receptor activation. P2X7 receptor is associated to pathological conditions including infectious, inflammatory, neurological, musculoskeletal disorders, pain and cancer. Most primary cells and cell lines from diverse origin may be used thanks to the ubiquitous distribution of P2X7 receptor. To study the activation of P2X7 receptor by chemicals or biological agents, we established a microplate-based cytometry protocol to accurately and rapidly quantify the activation of P2X7 receptor that leads to the formation of large pores in cell membranes. The YO-PRO-1 assay is based on the ability of cells to incorporate and bind YO-PRO-1 dye to DNA after activation of P2X7 receptor through pore formation. Cells are seeded in 96-well plates and incubated with the compound being tested for the appropriate time. The microplate is then incubated for 10 min with YO-PRO-1 staining solution. After the 10 min staining time, fluorescence signal is read using a microplate reader in 1 min. This procedure is easier and requires less handling steps than flow cytometry. 96-well plate based YO-PRO-1 assay is a reproducible and fast method to study both P2X7 receptor activation by toxic agents at subnecrotic concentrations and P2X7 receptor inhibition by antagonists.

Enhancement of Fluorescence-Based Sandwich Immunoassay Using Multilayered Microplates Modified with Plasma-Polymerized Films

A functional modification of the surface of a 96-well microplate coupled with a thin layer deposition technique is demonstrated for enhanced fluorescence-based sandwich immunoassays. The plasma polymerization technique enabling the deposition of organic thin films was employed for the modification of the well surface of a microplate. A silver layer and a plasma-polymerized film were consecutively deposited on the microplate as a metal mirror and the optical interference layer, respectively. When Cy3-labeled antibody was applied to the wells of the resulting multilayered microplate without any immobilization step, greatly enhanced fluorescence was observed compared with that obtained with the unmodified one. The same effect could be also exhibited for an immunoassay targeting antigen directly adsorbed on the multilayered microplate. Furthermore, a sandwich immunoassay for the detection of interleukin 2 (IL-2) was performed with the multilayered microplates, resulting in specific and 88-fold–enhanced fluorescence detection.

High-resolution α-amylase assay combined with high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy for expedited identification of α-amylase inhibitors: proof of concept and α-amylase inhibitor in cinnamon

Type 2 diabetes affects millions of people worldwide, and new improved drugs or functional foods containing selective α-amylase inhibitors are needed for improved management of blood glucose. In this article the development of a microplate-based high-resolution α-amylase inhibition assay with direct photometric measurement of α-amylase activity is described. The inhibition assay is based on porcine pancreatic α-amylase with 2-chloro-4-nitrophenyl-α-D-maltotriose as substrate, which this gives a stable, sensitive, and cheap inhibition assay as requested for high-resolution purposes. In combination with HPLC-HRMS-SPE-NMR, this provides an analytical platform that allows simultaneous chemical and biological profiling of α-amylase inhibitors in plant extracts. Proof-of-concept with an artificial mixture of six compounds-of which three are known α-amylase inhibitors-showed that the high-resolution α-amylase inhibition profiles allowed detection of sub-microgram amounts of the α-amylase inhibitors. Furthermore, the high-resolution α-amylase inhibition assay/HPLC-HRMS-SPE-NMR platform allowed identification of cinnamaldehyde as the α-amylase inhibitor in cinnamon (Cinnamomum verum Presl.).

Efficient assay for total antioxidant capacity in human plasma using a 96-well microplate

In the present study, we tried to establish an efficient assay for total antioxidant capacity (TAC) in human plasma using a 96-well microplate. TAC was assessed using lag time by antioxidants against the myoglobin-induced oxidation of 2,2'-azino-di(3-ethylbenzthiazoline-6-sulfonic acid (ABTS) with hydrogen peroxide, and expressed as Trolox equivalent. The linearity of the calibration curve with Trolox was maintained with the Trolox concentration range from 2.5 µM to 25 µM (R² = 0.997). The assay was applied to the measurement of TAC in healthy human plasma. Coefficient of variation in intraday assay was 2.4%. Difference was not observed in interday assay. Plasma TAC of men ((569 ± 41) µM Trolox equivalent; n = 6) was higher than that of women ((430 ± 28) µM Trolox equivalent; n = 4). After the vegetable juice was drunk for 1 week, the increase in plasma TAC was observed in almost all the volunteers. In summary, we developed the efficient assay for plasma TAC using a 96-well microplate.

Effects of van der Waals Force and Thermal Stresses on Pull-in Instability of Clamped Rectangular Microplates

We study the influence of von Karman nonlinearity, van der Waals force, and a athermal stresses on pull-in instability and small vibrations of electrostatically actuated mi-croplates. We use the Galerkin method to develop a tractable reduced-order model for elec-trostatically actuated clamped rectangular microplates in the presence of van der Waals forcesand thermal stresses. More specifically, we reduce the governing two-dimensional nonlineartransient boundary-value problem to a single nonlinear ordinary differential equation. For thestatic problem, the pull-in voltage and the pull-in displacement are determined by solving apair of nonlinear algebraic equations. The fundamental vibration frequency corresponding toa deflected configuration of the microplate is determined by solving a linear algebraic equa-tion. The proposed reduced-order model allows for accurately estimating the combined effectsof van der Waals force and thermal stresses on the pull-in voltage and the pull-in deflectionprofile with an extremely limited computational effort.

Rapid kinetic microassay for catalase activity

Catalase is a commonly assayed enzyme found in many bacteria and eukaryotes. In this report, we examined the applicability of a kinetic microassay to quantify catalase from two different sources. The assay was found to be linear over a wide range (0.1-1.0 units), but was limited at high values (>1 unit) by oxygen evolution. Nonetheless, the microassay allows simultaneous evaluation of many samples (up to 96) in a short time (<5 min) and is thus well-suited to applications, such as high-throughput screening, where many parallel assays are required.