High-throughput 3D modelling of plants for phenotypic analysis

2012 ◽  
Author(s):  
Pankaj Kumar ◽  
Jinhai Cai ◽  
Stan Miklavcic
Keyword(s):  
High Throughput ◽  
3D Modelling ◽  
Phenotypic Analysis

scholarly journals High‐throughput 3D modelling to dissect the genetic control of leaf elongation in barley ( Hordeum vulgare )

2019 ◽  
Vol 98 (3) ◽  
pp. 555-570 ◽  
Author(s):  
Ben Ward ◽  
Chris Brien ◽  
Helena Oakey ◽  
Allison Pearson ◽  
Sónia Negrão ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Genetic Control ◽  
High Throughput ◽  
3D Modelling ◽  
Leaf Elongation

scholarly journals High Throughput Phenotypic Analysis of Mycobacterium tuberculosis and Mycobacterium bovis Strains' Metabolism Using Biolog Phenotype Microarrays

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e52673 ◽  
Author(s):  
Bhagwati Khatri ◽  
Mark Fielder ◽  
Gareth Jones ◽  
William Newell ◽  
Manal Abu-Oun ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Bovis ◽  
High Throughput ◽  
Phenotypic Analysis ◽  
Phenotype Microarrays

scholarly journals Cellular Phenotypic Analysis of Macrophage Activation Unveils Kinetic Responses of Agents Targeting Phosphorylation

2016 ◽  
Vol 22 (1) ◽  
pp. 51-57
Author(s):  
Qian Cao ◽  
Junlin Yao ◽  
Heyuan Li ◽  
Bo Tao ◽  
Yibo Cai ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Macrophage Activation ◽  
Protein Tyrosine Kinase ◽  
Interferon Γ ◽  
Host Immune System ◽  
Phenotypic Analysis ◽  
Dependent Cell ◽  
Pathogen Clearance ◽  
Dose Dependent

Macrophages are highly plastic cells, which serve as sentinels of the host immune system due to their ability to recognize and respond to microbial products rapidly and dynamically. Appropriate regulation of macrophage activation is essential for pathogen clearance or preventing autoimmune diseases. However, regularly used endpoint assays for analyzing macrophage functions have the limitations of being static and non–high throughput. In this study, we introduced a real-time and convenient method based on changes in cellular impedance that are detected by microelectronic biosensors. This new method can record the time/dose-dependent cell response profiles (TCRPs) of macrophages in real time and generates physiologically relevant data. The TCRPs generated from classically interferon-γ/lipopolysaccharide-activated macrophages showed considerable consistency with the data generated from standard endpoint assays. We further explored this approach by using it for global screening of a library of protein tyrosine kinase/phosphatase (PTK/PTP) inhibitors to investigate their impact on macrophage activation. Collectively, our findings suggest that the cellular impedance-based assay provides a promising approach for dynamically monitoring macrophage functions in a convenient and high-throughput manner.

scholarly journals High-Throughput Identification of Antibacterials Against Pseudomonas aeruginosa

2020 ◽  
Vol 11 ◽  
Author(s):  
Shijia Li ◽  
Pengfei She ◽  
Linying Zhou ◽  
Xianghai Zeng ◽  
Lanlan Xu ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Throughput ◽  
High Throughput Screening ◽  
Combined Therapy ◽  
Drug Repurposing ◽  
Antimicrobial Activities ◽  
Health Concern ◽  
Phenotypic Analysis ◽  
Screening Assay ◽  
High Throughput Screening Assay

Antibiotic resistance is a growing public health concern, though the constant development of new antibiotics. The combination of high-throughput screening and drug repurposing is an effective way to develop new therapeutic uses of drugs. In this study, we screened a drug library consisting of 1,573 drugs already approved by the Food and Drug Administration and 903 drugs from the natural product library, to identify antimicrobials against Pseudomonas aeruginosa. A high-throughput screening assay based on microtiter plate was used to screen 39 drugs that inhibit the planktonic or biofilm formation of P. aeruginosa while most of them are antibiotics. The antimicrobial activities of these drugs were evaluated by phenotypic analysis. Further studies showed the combined therapy of tetracycline antibiotics demeclocycline hydrochloride (DMCT) and the novel antimicrobial peptide SAAP-148 has an effective synergistic antibacterial effect on P. aeruginosa PAO1 and P. aeruginosa ATCC27853. Moreover, the time-kill curve assay and murine model of cutaneous abscesses further confirmed the synergistic effect. In addition, the combination of DMCT and SAAP-148 has the potential to combat clinically isolated multidrug-resistant (MDR) P. aeruginosa strains. Our results clearly indicate that DMCT and SAAP-148 combined therapy could be an effective method to combat MDR P. aeruginosa-related infections.

scholarly journals Towards a Systems Approach in the Genetic Analysis of Archaea: Accelerating Mutant Construction and Phenotypic Analysis inHaloferax volcanii

Archaea ◽  
2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Ian K. Blaby ◽  
Gabriela Phillips ◽  
Crysten E. Blaby-Haas ◽  
Kevin S. Gulig ◽  
Basma El Yacoubi ◽  
...  
Keyword(s):  
High Throughput ◽  
Gene Deletion ◽  
Systems Approach ◽  
Essential Gene ◽  
Gene Knockout ◽  
Deletion Mutants ◽  
Mutant Library ◽  
Phenotypic Analysis ◽  
Genome Wide ◽  
A Genome

With the availability of a genome sequence and increasingly sophisticated genetic tools,Haloferax volcaniiis becoming a model for both Archaea and halophiles. In order forH. volcaniito reach a status equivalent toEscherichia coli, Bacillus subtilis, orSaccharomyces cerevisiae, a gene knockout collection needs to be constructed in order to identify the archaeal essential gene set and enable systematic phenotype screens. A streamlined gene-deletion protocol adapted for potential automation was implemented and used to generate 22H. volcaniideletion strains and identify several potentially essential genes. These gene deletion mutants, generated in this and previous studies, were then analyzed in a high-throughput fashion to measure growth rates in different media and temperature conditions. We conclude that these high-throughput methods are suitable for a rapid investigation of anH. volcaniimutant library and suggest that they should form the basis of a larger genome-wide experiment.

scholarly journals Benchmarking of Multivariate Similarity Measures for High-Content Screening Fingerprints in Phenotypic Drug Discovery

2013 ◽  
Vol 18 (10) ◽  
pp. 1284-1297 ◽  
Author(s):  
Felix Reisen ◽  
Xian Zhang ◽  
Daniela Gabriel ◽  
Paul Selzer
Keyword(s):  
Feature Selection ◽  
Drug Discovery ◽  
High Throughput ◽  
Similarity Measures ◽  
Cellular Responses ◽  
Image Features ◽  
High Content Screening ◽  
Selection Methods ◽  
Phenotypic Analysis ◽  
Kendall’S Τ

High-content screening (HCS) is a powerful tool for drug discovery being capable of measuring cellular responses to chemical disturbance in a high-throughput manner. HCS provides an image-based readout of cellular phenotypes, including features such as shape, intensity, or texture in a highly multiplexed and quantitative manner. The corresponding feature vectors can be used to characterize phenotypes and are thus defined as HCS fingerprints. Systematic analyses of HCS fingerprints allow for objective computational comparisons of cellular responses. Such comparisons therefore facilitate the detection of different compounds with different phenotypic outcomes from high-throughput HCS campaigns. Feature selection methods and similarity measures, as a basis for phenotype identification and clustering, are critical for the quality of such computational analyses. We systematically evaluated 16 different similarity measures in combination with linear and nonlinear feature selection methods for their potential to capture biologically relevant image features. Nonlinear correlation-based similarity measures such as Kendall’s τ and Spearman’s ρ perform well in most evaluation scenarios, outperforming other frequently used metrics (such as the Euclidian distance). We also present four novel modifications of the connectivity map similarity that surpass the original version, in our experiments. This study provides a basis for generic phenotypic analysis in future HCS campaigns.

scholarly journals A Method for Obtaining Field Wheat Freezing Injury Phenotype Based on RGB Camera and Software Control

2021 ◽  
Author(s):  
xiuqing fu ◽  
Yang Bai ◽  
Jing Zhou ◽  
Hongwen Zhang ◽  
Jieyu Xian
Keyword(s):  
High Throughput ◽  
Wheat Breeding ◽  
Image Features ◽  
Seedling Stage ◽  
Freezing Stress ◽  
Freezing Injury ◽  
Data Management System ◽  
Phenotypic Analysis ◽  
Phenotypic Data ◽  
Wheat Varieties

Abstract Low temperature freezing stress has adverse effects on wheat seedling growth and final yield. The traditional method to evaluate the wheat injury caused by the freezing stress is by visual observations, which is time-consuming and laborious. Therefore, to effectively and efficiently quantify the wheat freezing injury in the field environments, a high-throughput phenotyping system was developed in this paper , namely, RGB FREEZING INJURY SYSTEM. The system is able to automatically collect, processing, and analyze the wheat images collected using a mobile phenotype cabin in the field conditions. A data management system was also developed to store and manage the original images and the calculated phenotypic data in the system. A group of 128 wheat varieties were planted with replicates under a freezing environment. Canopy images of the wheat were collected at the seedling stage and three image features were extracted for each wheat samples, including ExG, ExR and ExV. The results show that the developed methods can clearly distinguish wheat samples with different wheat freezing injury scores. The automatic phenotypic analysis method of freezing injury provides a solution for high-throughput phenotypic analysis of field wheat and can quantify the stress caused by freezing injury at the seedling stage. The method has a certain guiding significance for wheat breeding.

scholarly journals HIGH THROUGHPUT PHENOTYPING OF PHYSIOLOGICAL GROWTH DYNAMICS FROM UAS-BASED 3D MODELING IN SOYBEAN

2019 ◽  
Vol XLII-2/W13 ◽  
pp. 357-361 ◽  
Author(s):  
M. Herrero-Huerta ◽  
K. M. Rainey
Keyword(s):  
High Throughput ◽  
Digital Camera ◽  
Growth Dynamics ◽  
Cost Effective ◽  
Growing Season ◽  
3D Modelling ◽  
Crop Genetics ◽  
High Throughput Phenotyping ◽  
Research And Education ◽  
Selection Of

<p><strong>Abstract.</strong> Nowadays, an essential tool to improve the efficiency of crop genetics is automated, precise and cost-effective phenotyping of the plants. The aim of this study is to generate a methodology for high throughput phenotyping the physiological growth dynamics of soybeans by UAS-based 3D modelling. During the 2018 growing season, a soybean experiment was performed at the Agronomy Center for Research and Education (ACRE) in West-Lafayette (Indiana, USA). Periodic images were acquired by G9X Canon compact digital camera on board senseFly eBee. The study area is reconstructed in 3D by Image-based modelling. Algorithms and techniques were combined to analyse growth dynamics of the crop via height variations and to quantify biomass. Results provide practical information for the selection of phenotypes for breeding.</p>

Growth Stage-Based Phenotypic Analysis of Arabidopsis: A Model for High Throughput Functional Genomics in Plants

2001 ◽  
Vol 13 (7) ◽  
pp. 1499 ◽  
Author(s):  
Douglas C. Boyes ◽  
Adel M. Zayed ◽  
Robert Ascenzi ◽  
Amy J. McCaskill ◽  
Neil E. Hoffman ◽  
...  
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Growth Stage ◽  
Phenotypic Analysis
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