Establishing a high throughput screening method for large scale phenotyping of castor genotypes for resistance to Fusarium wilt disease

A restriction endonuclease (RE) is an enzyme that can recognize a specific DNA sequence and cleave that DNA into fragments with double-stranded breaks. This sequence-specific cleaving ability and its ease of use have made REs commonly used tools in molecular biology since their first isolation and characterization in 1970s. While artificial REs still face many challenges in large-scale synthesis and precise activity control for practical use, searching for new REs in natural samples remains a viable route for expanding the RE pool for fundamental research and industrial applications. In this paper, we propose a new strategy to search for REs in an efficient fashion. Briefly, we construct a host bacterial cell to link the RE genotype to the phenotype of β-galactosidase expression based on the bacterial SOS response, and use a high-throughput microfluidic platform to isolate, detect and sort the REs. We employ this strategy to screen for the XbaI gene from constructed libraries of varied sizes. In single round of sorting, a 30-fold target enrichment was obtained within 1 h. The direct screening approach we propose shows potential for efficient search of desirable REs in natural samples compared to the conventional RE-screening method, and is amenable to being adapted to high-throughput screening of other genotoxic targets.

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A fluorescence-based high-throughput screening method for cytokinin translocation mutants

Plant Methods ◽

10.1186/s13007-020-00676-4 ◽

2020 ◽

Vol 16 (1) ◽

Author(s):

Mengyuan Zhang ◽

Bingli Ding ◽

Jiangzhe Zhao ◽

Penghong Zhang ◽

Yujia Li ◽

...

Keyword(s):

High Throughput ◽

Stress Responses ◽

High Throughput Screening ◽

Large Scale ◽

Fluorescent Protein ◽

Imaging System ◽

Screening Method ◽

Cytokinin Signaling ◽

Phenotypic Analysis ◽

Long Distance

Abstract Background Cytokinins are one kind of phytohormones essential for plant growth, development and stress responses. In the past half century, significant progresses have been made in the studies of cytokinin signal transduction and metobolic pathways, but the mechanism of cytokinin translocation is poorly understood. Arabidopsis (Arabidopsis thaliana) response regulator 5 (ARR5) is a type-A response factor in cytokinin signaling which is induced by cytokinins and has been used as a reporter gene for the endogenous cytokinins in Arabidopsis. Here, we report a fluorescence-based high-throughput method to screen cytokinin translocation mutants using an ethyl methyl sulfone (EMS) mutagenesis library generated with ARR5::eGFP transgenic plants. Results The seedlings with enhanced green fluorescent protein (GFP) signal in roots were screened in a luminescence imaging system (LIS) in large scale to obtain mutants with over-accumulated cytokinins in roots. The selected mutants were confirmed under a fluorescence microscopy and then performed phenotypic analysis. In this way, we obtained twelve mutants with elevated GFP signal in the roots and further found three of them displayed reduced GFP signal in the aerial tissues. Two of the mutants were characterized and proved to be the atabcg14 allelic mutants which are defective in the long-distance translocation of root-synthesized cytokinins. Conclusions We provide a strategy for screening mutants defective in cytokinin translocation, distribution or signaling. The strategy can be adapted to establish a system for screening mutants defective in other hormone transporters or signaling components using a fluorescence reporter.

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Efficient online-group-screening designs for agent identification

10.1101/220863 ◽

2017 ◽

Author(s):

Tianxiang Gao ◽

Omri Finkel ◽

Jeff Dangl ◽

Vladimir Jojic

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Screening Method ◽

Screening Strategy ◽

Online Version ◽

Worst Case ◽

Screening Designs ◽

Complex Agent ◽

Online Group

AbstractIdentifying significant causal agents among a large number of candidates is challenging. When experimental resources are limited, exhaustively screening a large number of agents for the desired effect could incur a large cost and take a substantial amount of time. However, in many large scale experiments, such as high-throughput screening (HTS), the ratio of causal to non-causal agents is usually very low.In this paper, we introduce a group-screening strategy to efficiently screen causal agents by grouping them into treatments. Our analysis shows that when a large number of candidates factors are screened and true agent percentage is very low (less than 1%), even in the worst case we could save up to 80% of the experiment runs. In the case where experiments span many rounds, we provide an online version of the group-screening that can determine the best strategy automatically based on the existing results. We applied this method to a real HTS experiment with 50,000 candidates that would require 9 rounds to finish in an exhaustive case. Our analysis showed that by applying the online-group-screening method, in the worst case, we can use 3 rounds and 19.7% (9828/50000) total tests to identify all the agents.Finally, we show that with minor modifications, this framework extends to more complex agent discovery problems.

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Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining

10.26434/chemrxiv.7670903.v1 ◽

2019 ◽

Author(s):

Mohammad Atif Faiz Afzal ◽

Mojtaba Haghighatlari ◽

Sai Prasad Ganesh ◽

Chong Cheng ◽

Johannes Hachmann

Keyword(s):

Data Mining ◽

Refractive Index ◽

High Throughput ◽

First Principles ◽

High Throughput Screening ◽

Large Scale ◽

Computational Study ◽

High Refractive Index ◽

Structural Features ◽

Learning Program

<div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div>

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Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity

10.26434/chemrxiv.9791162 ◽

2019 ◽

Author(s):

Huifang Xu ◽

Weinan Liang ◽

Linlin Ning ◽

Yuanyuan Jiang ◽

Wenxia Yang ◽

...

Keyword(s):

Catalytic Activity ◽

Fatty Acid ◽

Directed Evolution ◽

High Throughput ◽

High Throughput Screening ◽

Colorimetric Detection ◽

Screening Method ◽

Random Mutagenesis ◽

Direct Production ◽

Consumption Activity

P450 fatty acid decarboxylases (FADCs) have recently been attracting considerable attention owing to their one-step direct production of industrially important 1-alkenes from biologically abundant feedstock free fatty acids under mild conditions. However, attempts to improve the catalytic activity of FADCs have met with little success. Protein engineering has been limited to selected residues and small mutant libraries due to lack of an effective high-throughput screening (HTS) method. Here, we devise a catalase-deficient Escherichia coli host strain and report an HTS approach based on colorimetric detection of H2O2-consumption activity of FADCs. Directed evolution enabled by this method has led to effective identification for the first time of improved FADC variants for medium-chain 1-alkene production from both DNA shuffling and random mutagenesis libraries. Advantageously, this screening method can be extended to other enzymes that stoichiometrically utilize H2O2 as co-substrate.

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DETERMINATION OF HETEROSIS, GENE ACTION AND THE NATURE OF RESISTANCE TO FUSARIUM WILT DISEASE (FUSARIUM OXYSPORUM F.SP CAPSICI ) IN SWEET PEPPER HYBRIDS

Menoufia Journal of Plant Production ◽

10.21608/mjppf.2017.126962 ◽

2017 ◽

Vol 2 (6) ◽

pp. 515-535

Author(s):

Abeer A. El. Soliman ◽

Eman Y. Khafagi

Keyword(s):

Fusarium Oxysporum ◽

Fusarium Wilt ◽

Gene Action ◽

Sweet Pepper ◽

Wilt Disease ◽

Fusarium Wilt Disease

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Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents

Current Drug Discovery Technologies ◽

10.2174/1570163816666190603095521 ◽

2020 ◽

Vol 17 (5) ◽

pp. 716-724

Author(s):

Yan A. Ivanenkov ◽

Renat S. Yamidanov ◽

Ilya A. Osterman ◽

Petr V. Sergiev ◽

Vladimir A. Aladinskiy ◽

...

Keyword(s):

Antibacterial Activity ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Antibacterial Agents ◽

Sos Response ◽

Luciferase Assay ◽

Translational Machinery ◽

E Coli ◽

New Class

Background: The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. Methods: We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. Results: In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. Conclusion: The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.

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Reaction and growth of cucumber hybrids grafted on hybrid squash in response to infection with Fusarium wilt disease

Arab Journal Of Plant Protection ◽

10.22268/ajpp-035.1.027035 ◽

2017 ◽

Vol 35 (1) ◽

pp. 027-035

Author(s):

Alaa Ibrahim ◽

◽

Omar Hmmoudi ◽

George Asmar ◽

Naser Sheikh Suleiman ◽

...

Keyword(s):

Fusarium Wilt ◽

Wilt Disease ◽

Fusarium Wilt Disease

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Identification of a juvenile-hormone signaling inhibitor via high-throughput screening of a chemical library

Scientific Reports ◽

10.1038/s41598-020-75386-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Takumi Kayukawa ◽

Kenjiro Furuta ◽

Keisuke Nagamine ◽

Tetsuro Shinoda ◽

Kiyoaki Yonesu ◽

...

Keyword(s):

Juvenile Hormone ◽

Cell Line ◽

Signaling Pathway ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Ex Vivo ◽

Agricultural Field ◽

Chemical Library ◽

Field Development

Abstract Insecticide resistance has recently become a serious problem in the agricultural field. Development of insecticides with new mechanisms of action is essential to overcome this limitation. Juvenile hormone (JH) is an insect-specific hormone that plays key roles in maintaining the larval stage of insects. Hence, JH signaling pathway is considered a suitable target in the development of novel insecticides; however, only a few JH signaling inhibitors (JHSIs) have been reported, and no practical JHSIs have been developed. Here, we established a high-throughput screening (HTS) system for exploration of novel JHSIs using a Bombyx mori cell line (BmN_JF&AR cells) and carried out a large-scale screening in this cell line using a chemical library. The four-step HTS yielded 69 compounds as candidate JHSIs. Topical application of JHSI48 to B. mori larvae caused precocious metamorphosis. In ex vivo culture of the epidermis, JHSI48 suppressed the expression of the Krüppel homolog 1 gene, which is directly activated by JH-liganded receptor. Moreover, JHSI48 caused a parallel rightward shift in the JH response curve, suggesting that JHSI48 possesses a competitive antagonist-like activity. Thus, large-scale HTS using chemical libraries may have applications in development of future insecticides targeting the JH signaling pathway.

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Development of a Novel High-Throughput Screen and Identification of Small-Molecule Inhibitors of the Gα–RGS17 Protein–Protein Interaction Using AlphaScreen

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057111410427 ◽

2011 ◽

Vol 16 (8) ◽

pp. 869-877 ◽

Cited By ~ 13

Author(s):

Duncan I. Mackie ◽

David L. Roman

Keyword(s):

Small Molecule ◽

High Throughput ◽

Protein Interaction ◽

High Throughput Screening ◽

Drug Targets ◽

Screening Method ◽

Fold Increase ◽

Rgs Proteins ◽

High Throughput Screen ◽

Protein Protein Interaction

In this study, the authors used AlphaScreen technology to develop a high-throughput screening method for interrogating small-molecule libraries for inhibitors of the Gαo–RGS17 interaction. RGS17 is implicated in the growth, proliferation, metastasis, and the migration of prostate and lung cancers. RGS17 is upregulated in lung and prostate tumors up to a 13-fold increase over patient-matched normal tissues. Studies show RGS17 knockdown inhibits colony formation and decreases tumorigenesis in nude mice. The screen in this study uses a measurement of the Gαo–RGS17 protein–protein interaction, with an excellent Z score exceeding 0.73, a signal-to-noise ratio >70, and a screening time of 1100 compounds per hour. The authors screened the NCI Diversity Set II and determined 35 initial hits, of which 16 were confirmed after screening against controls. The 16 compounds exhibited IC50 <10 µM in dose–response experiments. Four exhibited IC50 values <6 µM while inhibiting the Gαo–RGS17 interaction >50% when compared to a biotinylated glutathione-S-transferase control. This report describes the first high-throughput screen for RGS17 inhibitors, as well as a novel paradigm adaptable to many other RGS proteins, which are emerging as attractive drug targets for modulating G-protein-coupled receptor signaling.

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