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151 results for “high throughput screening”
Dataset of the paper entitled methods for high-throughput screening of novel agents against the maize pest, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae)
<p>Title: Methods for high-throughput screening of novel agents against the maize pest, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) </p> <p>Authors: Sri Ita Tarigan, Gyorgy Turoczi, Jozsef Kiss, Stefan Toepfer</p> <p>Abstract: <br>The western corn rootworm, <em>Diabrotica virgifera virgifera</em> (Coleoptera: Chrysomelidae), poses a significant threat to maize crops in North America and Europe, necessitating development of novel, effective, and less disruptive crop protection agents. With recent bans on key insecticides and concerns about overuse of remaining options, there is an urgent need for accessible and comparable screening methods. We propose comparative high-throughput screening methods against the eggs, larvae and adults of this pest, emphasizing the importance of suitable positive controls tailored to the specific bioassay types. We evaluated seven common insecticides (imidacloprid, clothianidin, acetamiprid, novaluron, cypermethrin, chlorpyrifos-methyl, spinosad) against eggs, larvae, and adults as potential positive controls for each of the proposed assay methods. Dipping assays with ready-to-hatch eggs revealed several ingredients to cause mortality; but imidacloprid might be most suitable as a positive control due to its robust dose-response in reducing egg hatching and causing mortality of hatching neonates. Larval bioassays using artificial diet overlay assays revealed mortality caused by all insecticides, with imidacloprid and acetamiprid exhibiting best dose-mortality response curves as well as sublethal effects. Adult bioassays using artificial diet-core overlay assays revealed mortality caused by all insecticides, with cypermethrin or acetamiprid exhibiting best dose-mortality response curves. The provided ED <sub>50</sub>, ED <sub>80</sub> values, and dose-response equations offer valuable insight for researchers in selecting appropriate positive controls for screening new crop protection agents or assessing resistance levels against different life stages of this pest.</p> <p>Data:</p> <p>The data file is related to the screening of commercial insecticides against eggs, first instar larvae (L1) and adults of the maize pest, <em>Diabrotica virgifera virgifera</em> using standard bioassays. We are proposing comparative high-throughput screening methods against the eggs, larvae and adults of this maize pest. This includes the crucial aspect of suitable positive controls tailored to the specific bioassay type. We evaluated seven common insecticides (imidacloprid, clothianidin, acetamiprid, novaluron, cypermethrin, chlorpyrifos-methyl, spinosad) against eggs, larvae, and adults as potential positive controls for each of the proposed assay method. To access effects and dose-responses of commonly used insecticides on eggs, we applied standard screening methods under controlled semi-sterile conditions.</p> <p>For egg bioassays, eggs were transferred to the 200 ml of treatments in the eppendorf tubes and then soaked for 1 hour. Then 20µl with 10 to 20 eggs were pipetted onto a filter paper in a petri dish (150 mm×25 mm). Then 100 µl of sterilized tap water was added for moisture. The pipette tip was replaced between treatments. The eggs been transferred were counted per filter paper and dish (15± 8). The eggs were then incubated in the dishes at 23-25<sup>0</sup>C for 7 days, when the experiment was terminated. Egg hatching, mortality of newly hatching larvae, and days until start of egg hatching were observed under stereo microscope and recorded. Data were collected at 1,3, 5 and 7 days after treatments.</p> <p>To assess the effect and dose-responses of commonly used insecticides on neonates of <em>D. v. virgifera</em>, we applied artificial diet-overlay bioassays under controlled semi-sterile conditions. Each insecticide was prepared in at least six concentrations. Each bioassay consisted of 3 to 6 polystyrene plates of 96 wells each (07-6096 of Biologix Ltd., USA, or Costar 3917 of Corning Inc., USA). Each well had a volume of 330 µl, with a diameter of 5 mm, a height of 10 mm, and a surface area of 0.34 cm². 190 µl of the diet were pipetted into each 330 µl well, filling each to approximately 2/3<sup>rd </sup>of its capacity. Plates containing the diet were left to dry in a laminar flow cabinet for 45 minutes and then stored overnight at temperatures ranging from 3 to 5°C. The following day, treatments were applied. This is, 17 µl of a treatment was applied to the 0.34 cm<sup>2</sup> diet surface reaching good coverage and therefore forcing the after-placed larvae to feed through (10 to 100 µl pipette Biohit TM Proline). Each treatment was applied to 8 wells per plate. Following application, the plates were allowed to dry for a duration of 1 to 1.5 hours and were subsequently cooled for 1 hour in a refrigerator set at temperatures between 23 to 25°C. Each well received one neonate larva, carefully placed on the diet surface using a fine artist brush. A vigorous and visibly healthy larva was selected, lifted from the end of the abdomen with the brush, maneuvered towards a well surface, and allowed to crawl off the brush onto the diet. To avoid systematic errors, larvae were not arranged in treatment column order but rather in a rectangular pattern. After every 12 individual larvae, the brush was cleaned using 70% ethanol followed by sterile tap water. The filled plate was sealed with an optically clear adhesive qPCR seal sheet (#AB-1170, Termo Scientific, USA, or #BS3017000, Bioleader, USA), enabling data assessments without the need to open the plate. Four to five holes were carefully made with fine 00-insect pins into the seal per well to facilitate aeration. The plates, housing the larvae, were then incubated in a dark, ventilated incubator at a temperature of 23-25 °C and a relative humidity of 50 to 90% for a period of 5 days. We assessed mortality and stunting larvae within 3 and 5 days. </p> <p>To access the effect and dose-responses of common insecticides on <em>D.v.virgifera</em> adults, artificial diet-overlay bioassays with different doses were performed under controlled, semi-sterile conditions. Each insecticide was prepared in at least six concentrations. Active ingredients as specified on the product labels underwent serial dilutions using sterile tap water. Sterilized tap water was used as untreated control. In detail, each bioassay consisted of 6 polystyrene plates of 6 wells each (Eppendorf® 0030720016). Each treatment was applied to 3 wells of each plate per bioassay. The adult diet for a bioassay had been prepared 1-7days before treatment and adult infestation. The diet was prepared under semi-sterile conditions. The diet was poured out to 5-6 sterile 11 mm Petri dishes. The plates with diet were allowed to dry for up to 15 minutes under laminar flow cabinet then stored at 3 to 5°C overnight.The following day, a core of the diet was initially transferred to each well using flamed iron core-cutter (1 cm diameter) under a laminar flow. A core diet was placed each of the 6 wells of the plates. Approximately 40 µl of the treatments were then applied across the surface of diet core (0.34 cm<sup>3</sup>). The following day, a core of the diet was initially transferred to each well using flamed iron core-cutter (1 cm diameter) under a laminar flow. A core diet was placed each of the 6 wells of the plates. Approximately 40 µl of the treatments were then applied across the surface of diet core (0.34 cm<sup>3</sup>). Adult were subsequently transferred from the rearing cage into the wells of the 6-well plates containing the diet and treatments using a tube aspirator. For ease of transfer, the adults were cooled in a fridge for 4 to 7 minutes. Each well plate received 3 to 4 adults. Plates were sealed and incubated at 23-25<sup>0</sup>C, 50–90% r.h, L: D 12:12. Adult mortality were recorded on days 1,3, 5, 7 of experiment. </p> <p>To allow comparisons between experiments, data were standardized to the data of the corresponding negative control, usually sterilized tap water, as follows: standardized data = 100 × (data in negative control - data in treatment)/maximum (data in control or in treatment). The distributions of the data were investigated using histograms and QQ normal and detrended normal probability. Skewness and kurtosis of residuals was also observed for normality of influences of treatments on eggs, neonates, or adults. Equality of variances was assessed using Levene’s test. Multiple comparisons were performed using the Tukey HSD post hoc test for data with equal variances and the Games-Howell post hoc test for data with unequal variances. For each tested insecticide, linear and logarithmic regression models were fit to the dose-response data. In case of significant linear or logartimic relathionships, doses leading to 50% or 80% of relative effects (ED <sub>50,80</sub>) were calculated. </p> <p>The raw data as well as the standardised data are available as a csv file on zenodo. </p> <p> </p> <p> </p>
High-Throughput Density Functional Theory Screening of Double Transition Metal MXene Precursors
<p>This dataset contains density functional theory results on a set of double-transition metal MXene precursors</p>
Raw data for the article: High-throughput computational solvent screening for lignocellulosic biomass processing
<p>This data set contains the raw data for the article "High-throughput computational solvent screening for lignocellulosic biomass processing" published in <em>Chemical Engineering Journal</em>, DOI: <a href="https://doi.org/10.1016/j.cej.2022.139476">https://doi.org/10.1016/j.cej.2022.139476</a></p>
Computational Analysis of Two-dimensional High-throughput Data from Large-scale RNAi Screens and Single-cell Transcriptomics
<p>This publication provides a singularity definition file to reproduce the computational environment along with the scripts to reproduce every figure or table in the revised manuscript using ZetaSuite Perl module and R package.</p> <p>First, generate a new folder and then download all the files into the folder.</p> <p>Then, uncompressed the files DataSets_part1.tar.gz,DataSets_part2.tar.gz,DataSets_part3.tar.gz,DataSets_part4.tar.gz, and scripts.tar.gz. within the folder.</p> <p>Next, move all the files in DataSets_part1 folder, DataSets_part2 folder,DataSets_part3 folder and DataSets_part4 folder to a new folder called DataSets.</p> <p>Finally, run the following scripts to generate the figures and tables in our manuscript.</p> <p>Regeneration of Figure2 and S2: singularity exec ZetaSuite.sif sh Figure2andS2.sh </p> <p>Regeneration of Figure3 and S3: singularity exec ZetaSuite.sif sh Figure3andS3.sh </p> <p>Regeneration of Figure4 and S4: singularity exec ZetaSuite.sif sh Figure4andS4.sh </p> <p>Regeneration of Figure5 and S5: singularity exec ZetaSuite.sif sh Figure5andS5.sh </p> <p>Regeneration of Figure6 and S6: singularity exec ZetaSuite.sif sh Figure6andS6.sh </p> <p>Regeneration of Figure7 and S7: singularity exec ZetaSuite.sif sh Figure7andS7.sh </p> <p> </p>
Raw data: High-throughput screening of soybean di-nitrogen fixation and seed nitrogen content using spectral sensing
<p>Symbiotic di-nitrogen fixation of grain legumes has a substantial impact on crop performance, harvest product quality, and nitrogen (N) balance of crop rotations, particularly under organic management regimes. In soybean breeding, selection for increased nitrogen fixation is desirable for improving seed protein content and N balance of cropping systems. However, the lack of high-throughput screening methods for direct measurement of N 2 fixation rates prohibits practical breeding efforts. Therefore, hyperspectral canopy reflectance measurement as a field-based phenotyping method was evaluated in three environments for indirect estimation of N fixation and uptake of soil nitrogen in a set of early maturity soybean genotypes exhibiting a wide range in seed protein content. Reflectance spectra were collected in repeated measurements during flowering and early seed filling stages. Subsequently, various spectral reflectance indices (SRIs) were calculated for characterizing nitrogen accumulation of individual genotypes. Moreover, prediction models for seed protein content as an end-of-season target trait were developed utilizing full spectral information in partial-least-square regression (PLSR) models. A number of N-related SRIs calculated from spectral reflectance data recorded at the beginning of the seed filling stage were significantly correlated to seed protein content. The best prediction of seed protein content, however, was achieved in PLSR models (validation R 2 =0.805 across all three environments). Environments lower in initial soil mineral N content appeared as more favorable selection sites in terms of prediction accuracy, because N fixation is not masked by soil N uptake in such environments. Hyperspectral reflectance data proved to be a valuable method for determining genetic variation in crop N accumulation, which might be implemented in high-throughput screening protocols for N fixation in plant breeding programs.</p>
A hydroponics based high throughput screening system for clubroot disease pathotyping
<p>Clubroot is a devastating disease affecting the canola industry and caused by the protist <em>Plasmodiophora brassicae</em>. Since the 1940s, several pathotyping systems have been developed and different classifications have been used to differentiate <em>P. brassicae</em> isolates based on their ability to infect different hosts. Unfortunately, none of previously developed pathotyping systems discriminate virulent and avirulent isolates of <em>P. brassicae</em> against the clubroot resistance profiles of commercially available canola cultivars. To try to solve this limitation we have developed a hydroponic-based bioassay using <em>P. brassicae</em> single spore isolates (SSIs), and four canola inbreed homozygous lines (CIH). These SSIs are representative of the virulence widely spread in the field, while these CIH are representative of the resistance commercially available to growers. Through this new phenotyping scheme, we have been able to connect <em>P. brassicae</em> isolates with their ability to break down clubroot resistance in canola in shorter time and economically more efficiently. This will help to tailor the selection of resistant canola varieties to use in an infested field for the longest possible time, empowering producers to make informed decisions about the best canola cultivar to use based on the <em>P. brassicae</em> diversity in their field</p>
The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening
<h1>Pan-Canadian Chemical Library</h1> <p>This Zenodo repository contains the cheap and druglike subset of the Pan-Canadian Chemical Library (PCCL) project. For more information, visit <a href="https://pccl.thesgc.org/" rel="nofollow">https://pccl.thesgc.org</a>.</p> <h2>PCCL library</h2> <p>The PCCL library is splitted by reaction, then by number of heavy atoms. Two types of files are available in zip archives:</p> <ul> <li>The SMILES format files, with the SMILES string and their product name,</li> <li>The CSV format file, with all the information generated during their enumeration: reagents, druglike properties, etc.</li> </ul> <p>Note: Purchasability is defined according to two integers: 1 for products only composed of BB-50 reagents, and 2 for products composed of BB-40 or BB-50 reagents. Read more about the meaning of these reagents groups in the article below.</p> <h2>Citation</h2> <p>If you find the PCCL useful or if you use it, please cite our paper:</p> <p>Bedart, C. <em>et al.</em> The Pan-Canadian Chemical Library: A mechanism to open academic chemistry to high-throughput virtual screening. Scientific Data 11, (2024).<br>doi: <a title="10.1038/s41597-024-03443-5" href="https://www.nature.com/articles/s41597-024-03443-5">10.1038/s41597-024-03443-5</a></p> <p> </p> <p> </p>
High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging
<p>This repository contains datasets associated with the paper titled "High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging," accepted at ACS Materials Letters Journal.</p> <p><strong>Contents:</strong></p> <ol> <li> <p><strong>Optimized XYZ Coordinates:</strong> The hydrocarbon molecules' XYZ coordinates, obtained using the B3LYP functional and the 6-31g(d,p) basis set in Gaussian 16 software, used to simulate the IR spectra (including transition energies and absorption intensities) of the molecules.</p> </li> <li> <p><strong>Broadened Molar Absorptivity IR Spectra:</strong> The dataset's IR spectra, broadened using a Lorentzian band shape with a gamma (half-width at half-height) value of 5 cm⁻¹. Molecules with imaginary frequencies have been excluded.</p> </li> <li> <p><strong>Related SMILES Strings:</strong> Contains SMILES strings for these hydrocarbons.</p> </li> <li> <p><strong>NUMBERS_SMILES.csv:</strong> Provides the associated SMILES string for each numerated XYZ coordinate.</p> </li> </ol> <p>For any inquiries, please contact Dr. Maliheh Shaban Tameh at malihe.shaban<a rel="noreferrer">@gmail.com</a></p>
UV mutagenesis conjugated to high throughput screening as a tool to generate new phenotypic diversity in wine yeast
<p><strong>The current global changes, societal and climatic, strongly challenge the wine industry. Multiple methods are applied in the development of new strains for the industry, but many are based on the existing phenotypic and genetic diversities. UV mutagenesis, as an untargeted strategy, has been successfully used for years, with significant examples on wine. Here we developed and validated a UV-mutant generation strategy coupled with a high throughput screening in wine-like conditions. This strategy led to the production of a 502 mutant’s library for which concentrations of eight primary metabolites after fermentation were assessed. This data paper presents the resulting data.</strong></p>
BARCODE: high throughput screening and analysis of soft active materials
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Development of a high-throughput small molecule screening assay for phenotypical characterization of lysosomal storage disorder-affected cells, with infantile cystinosis as a proof of principle
<p>Together with the Pivot Park Screening Centre we performed a drug screen on CTNS-/- proximal tubule cells. For this we developed an assay to evaluate LC3-II positive puncta, and which may be applied for any disease in which autophagy plays an important role. The screen was optimized by the hotel for a 384 well format, making it useful for high throughput screening. The screen was performed with 1280 compounds from the Prestwick library.</p>
High-Throughput Screening of Tribological Properties of Monolayer Films using Molecular Dynamics and Machine Learning: Supplemental Repository
<p>Supplemental repository for the "High-Throughput Screening of Tribological Properties of Monolayer Films using Molecular Dynamics and Machine Learning" article. Contains calculated tribological properties of dual-monolayer systems from Molecular Dynamics (MD) simulation and Machine Learning (ML).</p>
"Toy Data Set" referenced in the article "A deep-learning based analysis framework for ultra-high throughput screening time-series data" (https://doi.org/10.1101/2024.08.22.609110)
<p>This data set, referenced as "toy data set" in the article "A deep-learning based analysis framework for ultra-high throughput screening time-series data" (<a href="Lint-to-article">https://doi.org/10.1101/2024.08.22.609110</a>), mimics a high-throughput screening data set. To demonstrate the application of our analysis framework described in the main article this toy data set was generated. It contains in total 1536000 individual transient signals, splitted in 5 batches of each 200 plates in 1536-well plate format. Five distinct signal classes were used to resemble typical shapes encountered in biological experiments. Fequency of occurrences for each class is reported in the main article.</p>
Impact of Interval Censoring on Data Accuracy and Machine Learning Performance in Biological High-Throughput Screening
<div> <h2>Overview</h2> <div>Data and Results used in the publication entitled "Impact of Interval Censoring on Data Accuracy and Machine Learning Performance in Biological High-Throughput Screening"</div> </div> <div> <h3><strong>Data</strong></h3> <div>This folder contains the raw data used during this work.</div> <div>`EvoEF.csv` contains information on the library used (sequences, number of mutations, etc.) and the fitness (energy) used as continuous mean values. `mut.csv` contains the information about the combinatorial scaling (N vs N_norm), the number of mutations (m) and the probability of each variant using different distributions (uniform and binomial) at different $p_{WT}$.</div> <div>For further details on how the fitness values were calculated and how the combinatorial scale works, please refer to our prevoius [Paper](https://arxiv.org/abs/2405.05167).</div> <div> </div> <h3><strong>Results</strong></h3> <div> <div>This folder contains the results (outputs) of all scripts used. Such results are included in the form of `.npy` and `.npz` files. To load such files with numpy you should include the option `allow_pickle=True`.</div> </div> </div>
Supplementary Information for "Semi-automated high-throughput substrate screening assay for nucleoside kinases
<p>This is the external Supplementary Information for our publication "Semi-automated high-throughput substrate screening assay for nucleoside kinases". Files are to follow soon. We apologize for the delay. Thank you for your patience.</p> <p> </p> <p>The preprint and the Supporting Information are available at ChemRxiv (https://doi.org/10.33774/chemrxiv-2021-k0w7q).</p>
High-Throughput-Methyl-Reading (HTMR) assay: A solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases
<p>Epigenetic therapy has significant potential for cancer treatment. However, few small potent molecules have been identified against DNA or RNA modification regulatory proteins. Current approaches for activity detection of DNA/RNA methyltransferases and demethylases are time-consuming and labor-intensive, making it difficult to subject them to high-throughput screening. Here, we developed a fluorescence polarization-based "High-Throughput Methyl Reading" (HTMR) assay to implement large-scale compound screening for DNA/RNA methyltransferases and demethylases-DNMTs, TETs, ALKBH5, and METTL3/METTL14. This assay is simple to perform in a mix-and-read manner by adding the methyl-binding proteins MBD1 or YTHDF1. The proteins can be used to distinguish FAM-labelled substrates or product oligonucleotides with different methylation statuses catalyzed by enzymes. Therefore, the extent of the enzymatic reactions can be coupled with the variation of FP binding signals. Furthermore, this assay can be effectively used to conduct a cofactor competition study. Based on the assay, we identified two natural products as candidate compounds for DNMT1 and ALKBH5. In summary, this study outlines a powerful homogeneous approach for high-throughput screening and evaluating enzymatic activity for DNA/RNA methyltransferases and demethylases that is cheap, easy, quick, and highly sensitive.</p>
Data from: High-throughput computational screening of bioinspired dual atom alloys for CO2 activation
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High-Throughput-Methyl-Reading (HTMR) assay: A solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases
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AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles
<p>I the present study, a novel AFM-based high throughput mechanical characterization for extracellular vesicles is presented. The method relies on the analysis of vesicles morphometry following their adsorption on surfaces. The deformation extent of the vesicle, which is representative of the vesicle stiffness, is evaluated by the calculation of the so-called vesicle contact angle. The method was applied to different etracellular vesicles (EVs) samples from different natural sources and was employed for spotting the presence of non-vesicular contaminants.</p>
Dataset "High-throughput screening of BAM inhibitors in native membrane environment"
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