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Biochemistry. Biokhimiia Dec 2017The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors.... (Review)
Review
The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.
Topics: Biological Assay; Models, Theoretical; Research; Research Design
PubMed: 29523069
DOI: 10.1134/S0006297917130119 -
Journal of Microbiology and... Feb 2016To reduce attrition in drug development, it is crucial to consider the development and implementation of translational phenotypic assays as well as decipher diverse... (Review)
Review
To reduce attrition in drug development, it is crucial to consider the development and implementation of translational phenotypic assays as well as decipher diverse molecular mechanisms of action for new molecular entities. High-throughput fluorescence and confocal microscopes with advanced analysis software have simplified the simultaneous identification and quantification of various cellular processes through what is now referred to as highcontent screening (HCS). HCS permits automated identification of modifiers of accessible and biologically relevant targets and can thus be used to detect gene interactions or identify toxic pathways of drug candidates to improve drug discovery and development processes. In this review, we summarize several HCS-compatible, biochemical, and molecular biology-driven assays, including immunohistochemistry, RNAi, reporter gene assay, CRISPR-Cas9 system, and protein-protein interactions to assess a variety of cellular processes, including proliferation, morphological changes, protein expression, localization, post-translational modifications, and protein-protein interactions. These cell-based assay methods can be applied to not only 2D cell culture but also 3D cell culture systems in a high-throughput manner.
Topics: Biological Assay; Cell Culture Techniques; Drug Discovery; Drug Evaluation, Preclinical; Genes, Reporter; High-Throughput Screening Assays; Immunohistochemistry; Protein Processing, Post-Translational; RNA Interference; Software
PubMed: 26428732
DOI: 10.4014/jmb.1508.08007 -
Molecules (Basel, Switzerland) Jan 2020Oxylipins are derivatives of polyunsaturated fatty acids and due to their important and diverse functions in the body, they have become a popular subject of studies. The... (Review)
Review
Oxylipins are derivatives of polyunsaturated fatty acids and due to their important and diverse functions in the body, they have become a popular subject of studies. The main challenge for researchers is their low stability and often very low concentration in samples. Therefore, in recent years there have been developments in the extraction and analysis methods of oxylipins. New approaches in extraction methods were described in our previous review. In turn, the old analysis methods have been replaced by new approaches based on mass spectrometry (MS) coupled with liquid chromatography (LC) and gas chromatography (GC), and the best of these methods allow hundreds of oxylipins to be quantitatively identified. This review presents comparative and comprehensive information on the progress of various methods used by various authors to achieve the best results in the analysis of oxylipins in biological samples.
Topics: Animals; Biological Assay; Humans; Oxylipins
PubMed: 31952163
DOI: 10.3390/molecules25020349 -
American Journal of Physiology. Renal... Nov 2018Investigators have for decades used mouse voiding patterns as end points for studying behavioral biology. It is only recently that mouse voiding patterns were adopted... (Review)
Review
Investigators have for decades used mouse voiding patterns as end points for studying behavioral biology. It is only recently that mouse voiding patterns were adopted for study of lower urinary tract physiology. The spontaneous void spot assay (VSA), a popular micturition assessment tool, involves placing a mouse in an enclosure lined by filter paper and quantifying the resulting urine spot pattern. The VSA has advantages of being inexpensive and noninvasive, but some investigators challenge its ability to distinguish lower urinary tract function from behavioral voiding. A consensus group of investigators who regularly use the VSA was established by the National Institutes of Health in 2015 to address the strengths and weaknesses of the assay, determine whether it can be standardized across laboratories, and determine whether it can be used as a surrogate for evaluating urinary function. Here we leverage experience from the consensus group to review the history of the VSA and its uses, summarize experiments to optimize assay design for urinary physiology assessment, and make best practice recommendations for performing the assay and analyzing its results.
Topics: Animals; Biological Assay; Disease Models, Animal; Mice; Reproducibility of Results; Time Factors; Urinary Bladder; Urination; Urination Disorders; Urodynamics
PubMed: 30156116
DOI: 10.1152/ajprenal.00350.2018 -
Scientific Reports Jun 2022Cell Painting is a high-content image-based assay applied in drug discovery to predict bioactivity, assess toxicity and understand mechanisms of action of chemical and...
Cell Painting is a high-content image-based assay applied in drug discovery to predict bioactivity, assess toxicity and understand mechanisms of action of chemical and genetic perturbations. We investigate label-free Cell Painting by predicting the five fluorescent Cell Painting channels from brightfield input. We train and validate two deep learning models with a dataset representing 17 batches, and we evaluate on batches treated with compounds from a phenotypic set. The mean Pearson correlation coefficient of the predicted images across all channels is 0.84. Without incorporating features into the model training, we achieved a mean correlation of 0.45 with ground truth features extracted using a segmentation-based feature extraction pipeline. Additionally, we identified 30 features which correlated greater than 0.8 to the ground truth. Toxicity analysis on the label-free Cell Painting resulted a sensitivity of 62.5% and specificity of 99.3% on images from unseen batches. We provide a breakdown of the feature profiles by channel and feature type to understand the potential and limitations of label-free morphological profiling. We demonstrate that label-free Cell Painting has the potential to be used for downstream analyses and could allow for repurposing imaging channels for other non-generic fluorescent stains of more targeted biological interest.
Topics: Biological Assay; Drug Discovery; Image Processing, Computer-Assisted
PubMed: 35705591
DOI: 10.1038/s41598-022-12914-x -
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 -
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 -
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 -
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 -
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