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SLAS Discovery : Advancing Life... Dec 2021Well-behaved, in vitro bioassays generally produce normally distributed values in their primary (efficacy) data. Accordingly, the best practices for statistical analysis...
Well-behaved, in vitro bioassays generally produce normally distributed values in their primary (efficacy) data. Accordingly, the best practices for statistical analysis are well documented and understood. However, assays may occasionally display unusually high variability and fall outside the assumptions inherent in these standard analyses. These assays may still be in the optimization phase, in which the source of variation could be identified and addressed. They might also represent the best available option to address the biological process being examined. In these cases, the use of robust statistical methods may provide a more appropriate set of tools for both data analysis and assay optimization. This article provides guidance on best practices for the use of robust statistical methods for the analysis of bioassay data as an alternative to standard methods. Impacts on experimental design and interpretation will be discussed.
Topics: Biological Assay
PubMed: 34474612
DOI: 10.1177/24725552211038379 -
Molecules (Basel, Switzerland) Feb 2019Lipases are enzymes responsible for the conversion of triglycerides and other esterified substrates, they are involved in the basic metabolism of a wide number of... (Review)
Review
Lipases are enzymes responsible for the conversion of triglycerides and other esterified substrates, they are involved in the basic metabolism of a wide number of organisms, from a simple microorganism and to mammals. They also have broad applicability in many fields from which industrial biotechnology, the production of cleaning agents, and pharmacy are the most important. The use of lipases in analytical chemistry where it can serve as a part of biosensors or bioassays is an application of growing interest and has become another important use. This review is focused on the description of lipases chemistry, their current applications and the methods for their assay measurement. Examples of bioassays and biosensors, including their physical and chemical principles, performance for specific substrates, and discussion of their relevance, are given in this work.
Topics: Biological Assay; Biosensing Techniques; Catalysis; Electrochemical Techniques; Enzyme Activation; Hydrolysis; Lipase
PubMed: 30744203
DOI: 10.3390/molecules24030616 -
Clinical & Translational Oncology :... Sep 2014The objective of this review is to summarize recent scientific and medical literature regarding chemoresponse assays or chemotherapy sensitivity and resistance assays... (Review)
Review
The objective of this review is to summarize recent scientific and medical literature regarding chemoresponse assays or chemotherapy sensitivity and resistance assays (CSRAs), specifically as applied to epithelial ovarian cancer. A total of sixty-seven articles, identified through PubMed using the key words "in vitro chemoresponse assay," "chemo sensitivity resistance assay," "ATP," "HDRA," "EDR," "MiCK," and "ChemoFx," were reviewed. Recent publications on marker validation, including relevant clinical trial designs, were also included. Recent CSRA research and clinical studies are outlined in this review. Published findings demonstrate benefits regarding patient outcome with respect to recent CSRAs. Specifically, analytical and clinical validations, as well as clinical utility and economic benefit, of the most common clinically used CSRA in the United States support its use to aid in making effective, individualized clinical treatment selections for patients with ovarian cancer.
Topics: Biological Assay; Biomarkers, Tumor; Carcinoma, Ovarian Epithelial; Drug Resistance, Neoplasm; Female; Humans; Neoplasms, Glandular and Epithelial; Ovarian Neoplasms; Research Design
PubMed: 24986099
DOI: 10.1007/s12094-014-1192-8 -
Bioanalysis Feb 2012For every drug development program it needs to be discussed whether discrimination between free and total drug concentrations is required to accurately describe its...
For every drug development program it needs to be discussed whether discrimination between free and total drug concentrations is required to accurately describe its pharmacokinetic behavior. This perspective describes the application of mathematical simulation approaches to guide this initial decision based on available knowledge about target biology, binding kinetics and expected drug concentrations. We provide generic calculations that can be used to estimate the necessity of free drug quantification for different drug molecules. In addition, mathematical approaches are used to simulate various assay conditions in bioanalytical ligand-binding assays: it is demonstrated that due to the noncovalent interaction between the binding partners and typical assay-related interferences in the equilibrium, a correct quantification of the free drug concentration is highly challenging and requires careful design of different assay procedure steps.
Topics: Antibodies, Monoclonal; Biological Assay; Biological Availability; Computer Simulation; Humans; Ligands; Models, Biological; Research Design
PubMed: 22394139
DOI: 10.4155/bio.11.321 -
The Journal of Biological Chemistry Apr 2022Intracellular spaces are partitioned into separate compartments to ensure that numerous biochemical reactions and cellular functions take place in a spatiotemporally... (Review)
Review
Intracellular spaces are partitioned into separate compartments to ensure that numerous biochemical reactions and cellular functions take place in a spatiotemporally controlled manner. Biomacromolecules including proteins and RNAs undergo liquid-liquid phase separation and subsequent phase transition to form biological condensates with diverse material states. The material/physical properties of biological condensates are crucial for fulfilling their distinct physiological functions, and abnormal material properties can cause deleterious effects under pathological conditions. Here, we review recent studies showing the role of the material properties of biological condensates in their physiological functions. We also summarize several classic methods as well as newly emerging techniques for characterization and/or measurement of the material properties of biological condensates.
Topics: Biological Assay; Cell Physiological Phenomena; Phase Transition; Proteins; RNA
PubMed: 35245500
DOI: 10.1016/j.jbc.2022.101782 -
Free Radical Biology & Medicine Mar 2018Increased mortality and diverse morbidities are globally associated with exposure to ambient air pollution (AAP), cigarette smoke (CS), and household air pollution... (Review)
Review
Increased mortality and diverse morbidities are globally associated with exposure to ambient air pollution (AAP), cigarette smoke (CS), and household air pollution (HAP). The AAP-CS-HAP aerosols present heterogeneous particulate matter (PM) of diverse chemical and physical characteristics. Some epidemiological models have assumed the same health hazards by PM weight for AAP, CS, and HAP regardless of the composition. While others have recognized that biological activities and toxicity will vary with components, we focus particularly on oxidation because of its major role in assay outcomes. Our review of PM assays considers misinterpretations of some chemical measures used for oxidative activity. Overall, there is low consistency across chemical and cell-based assays for oxidative and inflammatory activity. We also note gaps in understanding how much airborne PM of various sizes enter cells and organs. For CS, the body burden per cigarette may be much below current assumptions. Synergies shown for health hazards of AAP and CS suggest crosstalk in detoxification pathways mediated by AHR, NF-κB, and Nrf2. These complex genomic and biochemical interactions frustrate resolution of the toxicity of specific AAP components. We propose further strategies based on targeted gene expression based on cell-type differences.
Topics: Air Pollution; Biological Assay; Humans; Particulate Matter; Smoke; Tobacco Products
PubMed: 29407794
DOI: 10.1016/j.freeradbiomed.2018.01.030 -
Assay and Drug Development Technologies Feb 2011This review describes the use of high-throughput flow cytometry for performing multiplexed cell-based and bead-based screens. With the many advances in cell-based... (Review)
Review
This review describes the use of high-throughput flow cytometry for performing multiplexed cell-based and bead-based screens. With the many advances in cell-based analysis and screening, flow cytometry has historically been underutilized as a screening tool largely due to the limitations in handling large numbers of samples. However, there has been a resurgence in the use of flow cytometry due to a combination of innovations around instrumentation and a growing need for cell-based and bead-based applications. The HTFC™ Screening System (IntelliCyt Corporation, Albuquerque, NM) is a novel flow cytometry-based screening platform that incorporates a fast sample-loading technology, HyperCyt®, with a two-laser, six-parameter flow cytometer and powerful data analysis capabilities. The system is capable of running multiplexed screening assays at speeds of up to 40 wells per minute, enabling the processing of a 96- and 384-well plates in as little as 3 and 12 min, respectively. Embedded in the system is HyperView®, a data analysis software package that allows rapid identification of hits from multiplexed high-throughput flow cytometry screening campaigns. In addition, the software is incorporated into a server-based data management platform that enables seamless data accessibility and collaboration across multiple sites. High-throughput flow cytometry using the HyperCyt technology has been applied to numerous assay areas and screening campaigns, including efflux transporters, whole cell and receptor binding assays, functional G-protein-coupled receptor screening, in vitro toxicology, and antibody screening.
Topics: Biological Assay; Cell Physiological Phenomena; Drug Evaluation, Preclinical; Equipment Design; Equipment Failure Analysis; Flow Cytometry; Flow Injection Analysis; High-Throughput Screening Assays; Microfluidic Analytical Techniques
PubMed: 21050072
DOI: 10.1089/adt.2010.0308 -
Journal of Visualized Experiments : JoVE May 2018The production of ATP by oxidative phosphorylation is the primary function of mitochondria. Mitochondria in higher eukaryotes also participate in cytosolic Ca buffering,...
The production of ATP by oxidative phosphorylation is the primary function of mitochondria. Mitochondria in higher eukaryotes also participate in cytosolic Ca buffering, and the ATP production in mitochondrial can be mediated by intramitochondrial free Ca concentration. Ca retention capacity can be regarded as the capability of mitochondria to retain calcium in the mitochondrial matrix. Accumulated intracellular Ca leads to the permeability of the inner mitochondrial membrane, termed the opening of mitochondrial permeability transition pore (mPTP), which leads to the leakage of molecules with a molecular weight less than 1.5 kDa. Ca-triggered mitochondria swelling is used to indicate the mPTP opening. Here, we describe two assays to examine the Ca retention capacity and Ca-triggered mitochondrial swelling in isolated mitochondria. After certain amounts of Ca are added, all steps can be completed in one day and recorded by a microplate reader. Thus, these two simple and effective assays can be adopted to assess the Ca-related mitochondrial functions.
Topics: Biological Assay; Calcium; Humans; Mitochondrial Swelling; Protein Biosynthesis
PubMed: 29781984
DOI: 10.3791/56236 -
Biotechnology Advances 2010Commercial HIV-1 RNA viral load assays have been routinely used in developed countries to monitor antiretroviral treatment (ART). However, these assays require expensive... (Review)
Review
Commercial HIV-1 RNA viral load assays have been routinely used in developed countries to monitor antiretroviral treatment (ART). However, these assays require expensive equipment and reagents, well-trained operators, and established laboratory infrastructure. These requirements restrict their use in resource-limited settings where people are most afflicted with the HIV-1 epidemic. Inexpensive alternatives such as the Ultrasensitive p24 assay, the reverse transcriptase (RT) assay and in-house reverse transcription quantitative polymerase chain reaction (RT-qPCR) have been developed. However, they are still time-consuming, technologically complex and inappropriate for decentralized laboratories as point-of-care (POC) tests. Recent advances in microfluidics and nanotechnology offer new strategies to develop low-cost, rapid, robust and simple HIV-1 viral load monitoring systems. We review state-of-the-art technologies used for HIV-1 viral load monitoring in both developed and developing settings. Emerging approaches based on microfluidics and nanotechnology, which have potential to be integrated into POC HIV-1 viral load assays, are also discussed.
Topics: Biological Assay; Developed Countries; HIV-1; Health Resources; Humans; Point-of-Care Systems; Viral Load
PubMed: 20600784
DOI: 10.1016/j.biotechadv.2010.06.004 -
Biostatistics (Oxford, England) Jul 2020Group testing involves pooling individual specimens (e.g., blood, urine, swabs, etc.) and testing the pools for the presence of disease. When the proportion of diseased...
Group testing involves pooling individual specimens (e.g., blood, urine, swabs, etc.) and testing the pools for the presence of disease. When the proportion of diseased individuals is small, group testing can greatly reduce the number of tests needed to screen a population. Statistical research in group testing has traditionally focused on applications for a single disease. However, blood service organizations and large-scale disease surveillance programs are increasingly moving towards the use of multiplex assays, which measure multiple disease biomarkers at once. Tebbs and others (2013, Two-stage hierarchical group testing for multiple infections with application to the Infertility Prevention Project. Biometrics69, 1064-1073) and Hou and others (2017, Hierarchical group testing for multiple infections. Biometrics73, 656-665) were the first to examine hierarchical group testing case identification procedures for multiple diseases. In this article, we propose new non-hierarchical procedures which utilize two-dimensional arrays. We derive closed-form expressions for the expected number of tests per individual and classification accuracy probabilities and show that array testing can be more efficient than hierarchical procedures when screening individuals for multiple diseases at once. We illustrate the potential of using array testing in the detection of chlamydia and gonorrhea for a statewide screening program in Iowa. Finally, we describe an R/Shiny application that will help practitioners identify the best multiple-disease case identification algorithm.
Topics: Algorithms; Biological Assay; Chlamydia Infections; Communicable Diseases; Gonorrhea; Humans; Iowa; Mass Screening; Models, Theoretical
PubMed: 30371749
DOI: 10.1093/biostatistics/kxy058