Dataset Information

When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening.

ABSTRACT: While complex sample pooling strategies have been developed for large-scale experiments with robotic liquid handling, many medium-scale experiments like mycotoxin screening by Enzyme-Linked Immunosorbent Assay (ELISA) are still conducted manually in 48- and 96-well plates. At this scale, the opportunity to save on reagent costs is offset by the increased costs of labor, materials, and risk-of-error caused by increasingly complex pooling strategies. This paper compares one-dimensional (1D), two-dimensional (2D), and Shifted Transversal Design (STD) pooling to study whether pooling affects assay accuracy and experimental cost and to provide guidance for when a human experimentalist might benefit from pooling. We approximated mycotoxin contamination in single corn kernels by fitting statistical distributions to experimental data (432 kernels for aflatoxin and 528 kernels for fumonisin) and used experimentally-validated Monte-Carlo simulation (10,000 iterations) to evaluate assay sensitivity, specificity, reagent cost, and pipetting cost. Based on the validated simulation results, assay sensitivity remains 100% for all four pooling strategies while specificity decreases as prevalence level rises. Reagent cost could be reduced by 70% and 80% in 48- and 96-well plates, with 1D and STD pooling being most reagent-saving respectively. Such a reagent-saving effect is only valid when prevalence level is < 21% for 48-well plates and < 13%-21% for 96-well plates. Pipetting cost will rise by 1.3-3.3 fold for 48-well plates and 1.2-4.3 fold for 96-well plates, with 1D pooling by row requiring the least pipetting. Thus, it is advisable to employ pooling when the expected prevalence level is below 21% and when the likely savings of up to 80% on reagent cost outweighs the increased materials and labor costs of up to 4 fold increases in pipetting.

SUBMITTER: Cheng X

PROVIDER: S-EPMC7406063 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening.

Cheng Xianbin X Chavez Ruben A RA Stasiewicz Matthew J MJ

PloS one 20200805 8

While complex sample pooling strategies have been developed for large-scale experiments with robotic liquid handling, many medium-scale experiments like mycotoxin screening by Enzyme-Linked Immunosorbent Assay (ELISA) are still conducted manually in 48- and 96-well plates. At this scale, the opportunity to save on reagent costs is offset by the increased costs of labor, materials, and risk-of-error caused by increasingly complex pooling strategies. This paper compares one-dimensional (1D), two-d ...[more]

PMID: 32756571

Similar Datasets

Project description:BackgroundA key goal of drug discovery is to increase the throughput of small molecule screens without sacrificing screening accuracy. High-throughput screening (HTS) in drug discovery involves testing a large number of compounds in a biological assay to identify active compounds. Normally, molecules from a large compound library are tested individually to identify the activity of each molecule. Usually a small number of compounds are found to be active, however the presence of false positive and negative testing errors suggests that this one-drug one-assay screening strategy can be significantly improved. Pooling designs are testing schemes that test mixtures of compounds in each assay, thereby generating a screen of the whole compound library in fewer tests. By repeatedly testing compounds in different combinations, pooling designs also allow for error-correction. These pooled designs, for specific experiment parameters, can be simply and efficiently created using the Shifted Transversal Design (STD) pooling algorithm. However, drug screening contains a number of key constraints that require specific modifications if this pooling approach is to be useful for practical screen designs.ResultsIn this paper, we introduce a pooling strategy called poolHiTS (Pooled High-Throughput Screening) which is based on the STD algorithm. In poolHiTS, we implement a limit on the number of compounds that can be mixed in a single assay. In addition, we show that the STD-based pooling strategy is limited in the error-correction that it can achieve. Due to the mixing constraint, we show that it is more efficient to split a large library into smaller blocks of compounds, which are then tested using an optimized strategy repeated for each block. We package the optimal block selection algorithm into poolHiTS. The MATLAB codes for the poolHiTS algorithm and the corresponding decoding strategy are also provided.ConclusionWe have produced a practical version of STD algorithm for pooled drug screens. This pooling strategy provides both assay compression and error-correction capabilities that can both accelerate and reduce the overall cost of HTS in drug discovery.

Project description:We unravel the out-of-equilibrium quantum dynamics of a few interacting bosonic clouds in a two-dimensional asymmetric double-well potential at the resonant tunneling scenario. At the single-particle level of resonant tunneling, particles tunnel under the barrier from, typically, the ground-state in the left well to an excited state in the right well, i.e., states of different shapes and properties are coupled when their one-particle energies coincide. In two spatial dimensions, two types of resonant tunneling processes are possible, to which we refer to as longitudinal and transversal resonant tunneling. Longitudinal resonant tunneling implies that the state in the right well is longitudinally-excited with respect to the state in the left well, whereas transversal resonant tunneling implies that the former is transversely-excited with respect to the latter. We show that interaction between bosons makes resonant tunneling phenomena in two spatial dimensions profoundly rich, and analyze these phenomena in terms of the loss of coherence of the junction and development of fragmentation, and coupling between transverse and longitudinal degrees-of-freedom and excitations. To this end, a detailed analysis of the tunneling dynamics is performed by exploring the time evolution of a few physical quantities, namely, the survival probability, occupation numbers of the reduced one-particle density matrix, and the many-particle position, momentum, and angular-momentum variances. To accurately calculate these physical quantities from the time-dependent many-boson wavefunction, we apply a well-established many-body method, the multiconfigurational time-dependent Hartree for bosons (MCTDHB), which incorporates quantum correlations exhaustively. By comparing the survival probabilities and variances at the mean-field and many-body levels of theory and investigating the development of fragmentation, we identify the detailed mechanisms of many-body longitudinal and transversal resonant tunneling in two dimensional asymmetric double-wells. In particular, we find that the position and momentum variances along the transversal direction are almost negligible at the longitudinal resonant tunneling, whereas they are substantial at the transversal resonant tunneling which is caused by the combination of the density and breathing mode oscillations. We show that the width of the interparticle interaction potential does not affect the qualitative physics of resonant tunneling dynamics, both at the mean-field and many-body levels. In general, we characterize the impact of the transversal and longitudinal degrees-of-freedom in the many-boson tunneling dynamics at the resonant tunneling scenarios.

Dataset Information

When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening.

Publications

When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets