scholarly journals Novel method for high-throughput phenotyping of sleep in mice

2007 ◽  
Vol 28 (2) ◽  
pp. 232-238 ◽  
Author(s):  
Allan I. Pack ◽  
Raymond J. Galante ◽  
Greg Maislin ◽  
Jacqueline Cater ◽  
Dimitris Metaxas ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Time Of Day ◽  
Chemical Mutagenesis ◽  
High Throughput Phenotyping ◽  
Novel Method ◽  
Initial Implantation ◽  
Method Of Assessment ◽  
Digital Video Analysis ◽  
Electroencephalogram Eeg

Assessment of sleep in mice currently requires initial implantation of chronic electrodes for assessment of electroencephalogram (EEG) and electromyogram (EMG) followed by time to recover from surgery. Hence, it is not ideal for high-throughput screening. To address this deficiency, a method of assessment of sleep and wakefulness in mice has been developed based on assessment of activity/inactivity either by digital video analysis or by breaking infrared beams in the mouse cage. It is based on the algorithm that any episode of continuous inactivity of ≥40 s is predicted to be sleep. The method gives excellent agreement in C57BL/6J male mice with simultaneous assessment of sleep by EEG/EMG recording. The average agreement over 8,640 10-s epochs in 24 h is 92% ( n = 7 mice) with agreement in individual mice being 88–94%. Average EEG/EMG determined sleep per 2-h interval across the day was 59.4 min. The estimated mean difference (bias) per 2-h interval between inactivity-defined sleep and EEG/EMG-defined sleep was only 1.0 min (95% confidence interval for mean bias −0.06 to +2.6 min). The standard deviation of differences (precision) was 7.5 min per 2-h interval with 95% limits of agreement ranging from −13.7 to +15.7 min. Although bias significantly varied by time of day ( P = 0.0007), the magnitude of time-of-day differences was not large (average bias during lights on and lights off was +5.0 and −3.0 min per 2-h interval, respectively). This method has applications in chemical mutagenesis and for studies of molecular changes in brain with sleep/wakefulness.

scholarly journals DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

2016 ◽  
Vol 8 (1) ◽  
Author(s):  
Othman Soufan ◽  
Wail Ba-Alawi ◽  
Moataz Afeef ◽  
Magbubah Essack ◽  
Panos Kalnis ◽  
...  
Keyword(s):  
Active Learning ◽  
High Throughput ◽  
High Throughput Screening ◽  
Novel Method ◽  
Screening Assays

scholarly journals Matrix-Based Activity Pattern Classification as a Novel Method for the Characterization of Enzyme Inhibitors Derived from High-Throughput Screening

2016 ◽  
Vol 21 (10) ◽  
pp. 1075-1089 ◽  
Author(s):  
Douglas S. Auld ◽  
Marta Jimenez ◽  
Kimberley Yue ◽  
Scott Busby ◽  
Yu-Chi Chen ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Enzyme Inhibitors ◽  
Classification Method ◽  
Shift Method ◽  
Lead Selection ◽  
Small Matrix ◽  
Novel Method ◽  
Good Agreement

One of the central questions in the characterization of enzyme inhibitors is determining the mode of inhibition (MOI). Classically, this is done with a number of low-throughput methods in which inhibition models are fitted to the data. The ability to rapidly characterize the MOI for inhibitors arising from high-throughput screening in which hundreds to thousands of primary inhibitors may need to be characterized would greatly help in lead selection efforts. Here we describe a novel method for determining the MOI of a compound without the need for curve fitting of the enzyme inhibition data. We provide experimental data to demonstrate the utility of this new high-throughput MOI classification method based on nonparametric analysis of the activity derived from a small matrix of substrate and inhibitor concentrations (e.g., from a 4S × 4I matrix). Lists of inhibitors from four different enzyme assays are studied, and the results are compared with the previously described IC50-shift method for MOI classification. The MOI results from this method are in good agreement with the known MOI and compare favorably with those from the IC50-shift method. In addition, we discuss some advantages and limitations of the method and provide recommendations for utilization of this MOI classification method.

High-throughput screening of organic reactions in microdroplets using desorption electrospray ionization mass spectrometry (DESI-MS): hardware and software implementation

2020 ◽  
Vol 12 (28) ◽  
pp. 3654-3669
Author(s):  
Tiago Jose P. Sobreira ◽  
Larisa Avramova ◽  
Botond Szilagyi ◽  
David L. Logsdon ◽  
Bradley P. Loren ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Electrospray Ionization ◽  
High Throughput ◽  
Electrospray Ionization Mass Spectrometry ◽  
High Throughput Screening ◽  
Desorption Electrospray Ionization ◽  
Ionization Mass Spectrometry ◽  
Ionization Mass ◽  
Desi Ms ◽  
Novel Method

Implementation of a novel method for high-throughput screening of reactions in microdroplets. The reaction and analysis steps are performed simultaneously using desorption electrospray ionization mass spectrometry (DESI-MS) at a rate of up to 1 reaction mixture per second.

scholarly journals A novel method for mining highly imbalanced high-throughput screening data in PubChem

2009 ◽  
Vol 25 (24) ◽  
pp. 3310-3316 ◽  
Author(s):  
Qingliang Li ◽  
Yanli Wang ◽  
Stephen H. Bryant
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Novel Method

scholarly journals A Novel Method—Amenable for High-throughput Screening Purposes—to Quantify Antiviral Activity Against Viruses that Induce Limited CPE

2011 ◽  
Vol 90 (2) ◽  
pp. A33-A34
Author(s):  
Dirk Jochmans ◽  
Bernadette G. van den Hoogen ◽  
Pieter Leyssen ◽  
Ron A. Fouchier ◽  
Johan Neyts
Keyword(s):  
Antiviral Activity ◽  
High Throughput ◽  
High Throughput Screening ◽  
Novel Method

scholarly journals Droplet-Based Microfluidic High Throughput Screening of Corynebacterium glutamicum for Efficient Heterologous Protein Production and Secretion

2021 ◽  
Vol 9 ◽  
Author(s):  
Suvasini Balasubramanian ◽  
Jun Chen ◽  
Vinoth Wigneswaran ◽  
Claus Heiner Bang-Berthelsen ◽  
Peter Ruhdal Jensen
Keyword(s):  
Corynebacterium Glutamicum ◽  
High Throughput ◽  
High Throughput Screening ◽  
Protein Production ◽  
Reference Strain ◽  
Functional Enrichment ◽  
Chemical Mutagenesis ◽  
Efficient Production ◽  
Food Ingredients ◽  
Synonymous Mutations

With emerging interests in heterologous production of proteins such as antibodies, growth factors, nanobodies, high-quality protein food ingredients, etc. the demand for efficient production hosts increases. Corynebacterium glutamicum is an attractive industrial host with great secretion capacity to produce therapeutics. It lacks extracellular protease and endotoxin activities and easily achieves high cell density. Therefore, this study focuses on improving protein production and secretion in C. glutamicum with the use of droplet-based microfluidic (DBM) high throughput screening. A library of C. glutamicum secreting β-glucosidase was generated using chemical mutagenesis coupled with DBM screening of 200,000 mutants in just 20 min. Among 100 recovered mutants, 16 mutants exhibited enhanced enzyme secretion capacity, 13 of which had unique mutation profiles. Whole-genome analysis showed that approximately 50–150 SNVs had occurred on the chromosome per mutant. Functional enrichment analysis of genes with non-synonymous mutations showed overrepresentation of genes involved in protein synthesis and secretion relevant biological processes, such as DNA and ribosome RNA synthesis, protein secretion and energy turnover. Two mutants JCMT1 and JCMT8 exhibited the highest secretion with a six and a fivefold increase in the β-glucosidase activity in the supernatant, respectively, relative to the reference strain JC0190. After plasmid curing, a new plasmid with the gene encoding α-amylase was cloned into these two mutants. The new strains SB024 and SB025 also exhibited a five and a sixfold increase in α-amylase activity in the supernatant, respectively, relative to the reference strain SB023. The results demonstrate how DBM screening can serve as a powerful development tool to improve cell factories for the production and secretion of heterologous proteins.

A novel method to evaluate protein solubility using a high throughput screening approach

2009 ◽  
Vol 64 (17) ◽  
pp. 3778-3788 ◽  
Author(s):  
Matthias Wiendahl ◽  
Christiane Völker ◽  
Ilka Husemann ◽  
Janus Krarup ◽  
Arne Staby ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Protein Solubility ◽  
Screening Approach ◽  
Novel Method

scholarly journals 3D visualization and volume based quantification of rice chalkiness in vivo by using high resolution micro-CT

2020 ◽  
Author(s):  
Yi Su ◽  
Langtao Xiao
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
3D Visualization ◽  
Three Dimensional ◽  
Micro Ct ◽  
Kernel Quality ◽  
Production Practice ◽  
Phenotype Analysis ◽  
Novel Method

Abstract Background: Rice quality research attracts attention worldwide. Rice chalkiness is one of the key indexes determining rice kernel quality. The traditional rice chalkiness measurement methods are mainly based on naked-eye observation or two-dimensional (2D) image analysis and the results could not represent the three-dimensional (3D) characteristics of chalkiness in the rice kernel. These methods are neither in vivo thus are unable to provide technical support for high throughput screening of rice chalkiness phenotype. Results: Here, we introduced a novel method for 3D visualization and accurate volume-based quantification of rice chalkiness in vivo by using X-ray microcomputed tomography (micro-CT). This approach not only develops a novel method to measure the rice chalkiness index, but also provides a high throughput solution for rice chalkiness phenotype analysis. Conclusions: Our method could be a new powerful tool for rice chalkiness measurement, which would greatly help the research of rice chalkiness traits as well as the quality evaluation in rice production practice.

scholarly journals Bottlenecks and opportunities in field-based high-throughput phenotyping for heat and drought stress

2021 ◽  
Author(s):  
Nathan T Hein ◽  
Ignacio A Ciampitti ◽  
S V Krishna Jagadish
Keyword(s):  
Remote Sensing ◽  
Drought Stress ◽  
High Throughput ◽  
Complex Traits ◽  
Crop Improvement ◽  
Grain Filling ◽  
Time Of Day ◽  
Water Soluble ◽  
High Throughput Phenotyping ◽  
Improvement Programs

Abstract Flowering and grain-filling stages are highly sensitive to heat and drought stress exposure, leading to significant loss in crop yields. Therefore, phenotyping to enhance resilience to these abiotic stresses is critical for sustaining genetic gains in crop improvement programs. However, traditional methods for screening traits related to these stresses are slow, laborious, and often expensive. Remote sensing provides opportunities to introduce low-cost, less-biased, high-throughput phenotyping methods to capture large genetic diversity to facilitate enhancement of stress resilience in crops. This review focuses on four key physiological traits or processes that are critical in understanding crop responses to drought and heat stress during reproductive and grain-filling periods. Specifically, these traits include: i) time-of-day of flowering, to escape these stresses during flowering, ii) optimizing photosynthetic efficiency, iii) storage and translocation of water-soluble carbohydrates, and iv) yield and yield components to provide in-season yield estimates. An overview of current advances in remote sensing in capturing these traits, limitations with existing technology and future direction of research to develop high-throughput phenotyping approaches for these traits are discussed in this review. In the future, phenotyping these complex traits will require sensor advancement, high-quality imagery combined with machine learning methods, and efforts in transdisciplinary science to foster integration across disciplines.

Sign in / Sign up

Export Citation Format

Share Document