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Jakubowski HV, Agnew H, Jardine B, Sauro HM. Use of interactive mathematical simulations in Fundamentals of Biochemistry, a LibreText online educational resource, to promote understanding of dynamic reactions. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 52:426-435. [PMID: 38516799 PMCID: PMC11245375 DOI: 10.1002/bmb.21830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/09/2024] [Accepted: 03/09/2024] [Indexed: 03/23/2024]
Abstract
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities. At the same time, students struggle to understand and apply binding and kinetic analyses for the simplest reactions such as the irreversible first-order conversion of a single reactant to a product. This likely results from cognitive difficulties in combining structural, chemical, mathematical, and textual descriptions of binding and catalytic reactions. To help students better understand dynamic reactions and their analyses, we have introduced two kinds of interactive graphs and simulations into the online educational resource, Fundamentals of Biochemistry, a LibreText biochemistry book. One is available for simple binding and kinetic reactions. The other displays progress curves (concentrations vs. time) for simple reactions and complex metabolic and signal transduction pathways. Users can move sliders to change dissociation and kinetic constants as well as initial concentrations and see instantaneous changes in the graphs. They can also export data into a spreadsheet for further processing, such as producing derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial velocity (v0) versus substrate concentration.
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Affiliation(s)
- Henry V Jakubowski
- Department of Chemistry, College of Saint Benedict/Saint John's University, Saint Joseph, Minnesota, USA
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California, USA
| | - Bartholomew Jardine
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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Kunde SA, Schmerl B, von Sivers J, Ahmadyar E, Gupta T, Rademacher N, Zieger HL, Shoichet SA. JNK activity modulates postsynaptic scaffold protein SAP102 and kainate receptor dynamics in dendritic spines. J Biol Chem 2024; 300:107263. [PMID: 38582451 PMCID: PMC11081805 DOI: 10.1016/j.jbc.2024.107263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
Synapse formation depends on the coordinated expression and regulation of scaffold proteins. The JNK family kinases play a role in scaffold protein regulation, but the nature of this functional interaction in dendritic spines requires further investigation. Here, using a combination of biochemical methods and live-cell imaging strategies, we show that the dynamics of the synaptic scaffold molecule SAP102 are negatively regulated by JNK inhibition, that SAP102 is a direct phosphorylation target of JNK3, and that SAP102 regulation by JNK is restricted to neurons that harbor mature synapses. We further demonstrate that SAP102 and JNK3 cooperate in the regulated trafficking of kainate receptors to the cell membrane. Specifically, we observe that SAP102, JNK3, and the kainate receptor subunit GluK2 exhibit overlapping expression at synaptic sites and that modulating JNK activity influences the surface expression of the kainate receptor subunit GluK2 in a neuronal context. We also show that SAP102 participates in this process in a JNK-dependent fashion. In summary, our data support a model in which JNK-mediated regulation of SAP102 influences the dynamic trafficking of kainate receptors to postsynaptic sites, and thus shed light on common pathophysiological mechanisms underlying the cognitive developmental defects associated with diverse mutations.
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Affiliation(s)
- Stella-Amrei Kunde
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bettina Schmerl
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Judith von Sivers
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Elham Ahmadyar
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Taanisha Gupta
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nils Rademacher
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
| | - Hanna L Zieger
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, University of Bordeaux, Bordeaux, France
| | - Sarah A Shoichet
- Neuroscience Research Center NWFZ, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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Bandilla L. Corrigendum to "Versatile open-source fluorescence documentation system" [HardwareX 15, September (2023), e00450]. HARDWAREX 2024; 17:e00502. [PMID: 38497031 PMCID: PMC10944117 DOI: 10.1016/j.ohx.2023.e00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
[This corrects the article DOI: 10.1016/j.ohx.2023.e00450.].
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Kaste JAM, Green A, Shachar-Hill Y. Integrative teaching of metabolic modeling and flux analysis with interactive python modules. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:653-661. [PMID: 37584426 DOI: 10.1002/bmb.21777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/06/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The modeling of rates of biochemical reactions-fluxes-in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint-based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to-date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C-metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands-on computer laboratory component of a four-day metabolic modeling workshop and participant survey results showed improvements in learners' self-assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.
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Affiliation(s)
- Joshua A M Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Antwan Green
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
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Sychev AV, Lavrova AI, Dogonadze MZ, Postnikov EB. Establishing Compliance between Spectral, Colourimetric and Photometric Indicators in Resazurin Reduction Test. Bioengineering (Basel) 2023; 10:962. [PMID: 37627847 PMCID: PMC10451944 DOI: 10.3390/bioengineering10080962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The resazurin reduction test is one of the basic tests for bacterial culture viability and drug resistance endorsed by the World Health Organisation. At the same time, conventional spectrophotometric and spectrofluorimetric methods demand rather bulky and expensive equipment. This induces a challenge for developing simpler approaches to sensor systems that are portable and applicable in resource-limited settings. In this work, we address two such alternative approaches, based on the colour processing of the microbiological plate's photographic images and single-channel photometry with a recently developed portable microbiological analyser. The key results consist of establishing a sequential linear correspondence between the concentration of resorufin produced due to the reduction of resazurin by viable bacteria as determined by the UV-Vis studies, the intensity of the a* channel of the CIE L*a*b* colour space and the transmitted light intensity registered by a luxmeter under the LED illumination with a yellow colour filter. This route is illustrated with the chemical system "Hydrazine hydrate - resazurin", isolating the target colour change-inducing reaction and the test of determining the minimal inhibition concentration of the antibacterial first-line drug isoniazid acting on the culture of the H37Rv strain of M. tuberculosis.
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Affiliation(s)
- Alexander V. Sychev
- Research Center for Condensed Matter Physics, Kursk State University, Radishcheva St. 33, 305000 Kursk, Russia
| | - Anastasia I. Lavrova
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky av. 2-4, 191036 Saint-Petersburg, Russia
- Faculty of Medicine, Saint-Petersburg State University, Universitetskaya emb 7-9, 199034 Saint-Petersburg, Russia
| | - Marine Z. Dogonadze
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky av. 2-4, 191036 Saint-Petersburg, Russia
| | - Eugene B. Postnikov
- Department of Theoretical Physics, Kursk State University, Radishcheva St. 33, 305000 Kursk, Russia
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Alonso SDV, González Flecha FL. Fifty years of biophysics in Argentina. Biophys Rev 2023; 15:431-438. [PMID: 37681102 PMCID: PMC10480372 DOI: 10.1007/s12551-023-01114-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
In 1972, a group of young Argentinean scientists nucleated in the so-called Membrane Club constituted the Biophysical Society of Argentina (SAB). Over the years, this Society has grown and embraced new areas of research and emerging technologies. In this commentary, we provide an overview of the early stages of biophysics development in Argentina and highlight some of the notable achievements made during the past five decades. The SAB Annual Meetings have been a platform for intense scientific discussions, and the Society has fostered numerous international connections, becoming a hallmark of SAB activities over these 50 years. Initially centered on membrane biophysics, SAB focus has since expanded to encompass diverse fields such as molecular, cellular, and systems biophysics.
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Affiliation(s)
- Silvia del V. Alonso
- Laboratorio de Bio-Nanotecnología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Grupo de Biología Estructural y Biotecnología (GBEyB), IMBICE (CONICET CCT-La Plata), La Plata, Argentina
| | - F. Luis González Flecha
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires – CONICET, Buenos Aires, Argentina
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Münch F, Purbojo A, Wenzel F, Kohl M, Dittrich S, Rauh M, Zimmermann R, Kwapil N. [Improved quality of stored packed red blood cells by mechanical rinsing]. DIE ANAESTHESIOLOGIE 2022; 71:882-892. [PMID: 35969253 PMCID: PMC9636120 DOI: 10.1007/s00101-022-01189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 07/03/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The transfusion of packed red blood cells (PRBC) is associated with various side effects, including storage damage to PRBCs. The cells change their structure, releasing potassium as well as lactate. Mechanical rinsing, available in many hospitals, is able to remove toxic substances and possibly minimizes the negative side effects of transfusion. OBJECTIVE The primary aim of our study was to improve the quality of PRBCs before transfusion. The effects of different washing solutions on PRBC quality were analyzed. MATERIAL AND METHODS This in vitro study compares 30 mechanically washed PRBCs. They were either processed with standard normal saline 0.9% (n = 15, N group) or a hemofiltration solution containing 4 mmol/l potassium (n = 15, HF group) by a mechanical rinsing device (Xtra, LivaNova, Munich, Germany). A subgroup analysis was performed based on the storage duration of the processed PRBCs (7, 14, 37 days). Samples were taken before washing (EKprä), immediately after washing (EKpost) and 10 h later (EKpost10h), after storage in the "wash medium" at room temperature. Concentrations of ATP (probability of survival in transfused erythrocytes), lactate, citrate and electrolytes (potassium, sodium, chloride, calcium) were tested. RESULTS AND CONCLUSION Mechanical rinsing improves pretransfusion quality of PRBC. Washing with a hemofiltration solution results in a more physiological electrolyte composition. Even 10 h after mechanical rinsing with a hemofiltration solution, the quality of 37-day-old PRBC is comparable to young PRBC that have been stored for 7 days and have not been washed. Washing stored PRBC increases the ATP content, which subsequently leads to an increased probability of survival of red cells after transfusion.
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Affiliation(s)
- F Münch
- Kinderherzchirurgische Abteilung, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loschgestraße 15, 91054, Erlangen, Deutschland.
| | - A Purbojo
- Kinderherzchirurgische Abteilung, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loschgestraße 15, 91054, Erlangen, Deutschland
| | - F Wenzel
- Fakultät Medical and Life Science, Hochschule Furtwangen University Campus Villingen-Schwenningen, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Deutschland
| | - M Kohl
- Fakultät Medical and Life Science, Hochschule Furtwangen University Campus Villingen-Schwenningen, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Deutschland
| | - S Dittrich
- Kinderkardiologische Abteilung, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loschgestraße 15, 91054, Erlangen, Deutschland
| | - M Rauh
- Klinisches Labor der Kinder- und Jugendklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loschgestraße 15, 91054, Erlangen, Deutschland
| | - R Zimmermann
- Transfusionsmedizinische und Hämostaseologische Abteilung, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstraße 12, 91054, Erlangen, Deutschland
| | - N Kwapil
- Kinderherzchirurgische Abteilung, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loschgestraße 15, 91054, Erlangen, Deutschland
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Campbell IJ, Atkinson JT, Carpenter MD, Myerscough D, Su L, Ajo-Franklin CM, Silberg JJ. Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion. Biochemistry 2022; 61:1337-1350. [PMID: 35687533 DOI: 10.1021/acs.biochem.2c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate the binding of MtrA to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). The EET efficiency was found to be inversely correlated with the proximity of the insertion to the heme prosthetic groups. Mutants with decreased EET efficiencies also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular cytochrome MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET efficiencies. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III) respiration conditions correlated with anode reduction. The peptide insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for the regulation of EET.
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Affiliation(s)
- Ian J Campbell
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Matthew D Carpenter
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Dru Myerscough
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Lin Su
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
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A high-throughput, cheap, and green method for determination of ethanol in cachaça and vodka using 96-well-plate images. Talanta 2022; 241:123229. [DOI: 10.1016/j.talanta.2022.123229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/22/2022]
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Intrinsic and Chemotherapeutic Stressors Modulate ABCC-Like Transport in Trypanosoma cruzi. Molecules 2021; 26:molecules26123510. [PMID: 34207619 PMCID: PMC8227891 DOI: 10.3390/molecules26123510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
Trypanosoma cruzi is the etiologic agent for Chagas disease, which affects 6-7 million people worldwide. The biological diversity of the parasite reflects on inefficiency of benznidazole, which is a first choice chemotherapy, on chronic patients. ABC transporters that extrude xenobiotics, metabolites, and mediators are overexpressed in resistant cells and contribute to chemotherapy failure. An ABCC-like transport was identified in the Y strain and extrudes thiol-conjugated compounds. As thiols represent a line of defense towards reactive species, we aimed to verify whether ABCC-like transport could participate in the regulation of responses to stressor stimuli. In order to achieve this, ABCC-like activity was measured by flow cytometry using fluorescent substrates. The present study reveals the participation of glutathione and ceramides on ABCC-like transport, which are both implicated in stress. Hemin modulated the ABCC-like efflux which suggests that this protein might be involved in cellular detoxification. Additionally, all strains evaluated exhibited ABCC-like activity, while no ABCB1-like activity was detected. Results suggest that ABCC-like efflux is not associated with natural resistance to benznidazole, since sensitive strains showed higher activity than the resistant ones. Although benznidazole is not a direct substrate, ABCC-like efflux increased after prolonged drug exposure and this indicates that the ABCC-like efflux mediated protection against cell stress depends on the glutathione biosynthesis pathway.
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Pujari I, Thomas A, Sankar Babu V. Native and non-native host assessment towards metabolic pathway reconstructions of plant natural products. ACTA ACUST UNITED AC 2021; 30:e00619. [PMID: 33996523 PMCID: PMC8091882 DOI: 10.1016/j.btre.2021.e00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 11/16/2022]
Abstract
Plant metabolic networks are highly complex. Engineering the phytochemical pathways fully in heterologous hosts is challenging. Single plant cells with amplified multiple fission enable homogeneity. Homogeneity and high cell division rate can facilitate stable product scale-up.
Plant-based biopreparations are reasonably priced and are devoid of viral, prion and endotoxin contaminants. However, synthesizing these natural plant products by chemical methods is quite expensive. The structural complexity of plant-derived natural products poses a challenge for chemical synthesis at a commercial scale. Failure of commercial-scale synthesis is the chief reason why metabolic reconstructions in heterologous hosts are inevitable. This review discusses plant metabolite pathway reconstructions experimented in various heterologous hosts, and the inherent challenges involved. Plants as native hosts possess enhanced post-translational modification ability, along with rigorous gene edits, unlike microbes. To achieve a high yield of metabolites in plants, increased cell division rate is one of the requisites. This improved cell division rate will promote cellular homogeneity. Incorporation and maintenance of plant cell synchrony, in turn, can program stable product scale-up.
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Affiliation(s)
- Ipsita Pujari
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Abitha Thomas
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vidhu Sankar Babu
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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García-Maquilón I, Rodriguez PL, Vaidya AS, Lozano-Juste J. A Luciferase Reporter Assay to Identify Chemical Activators of ABA Signaling. Methods Mol Biol 2021; 2213:113-121. [PMID: 33270197 DOI: 10.1007/978-1-0716-0954-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Plant stress tolerance relies on intricate signaling networks that are not fully understood. Several plant hormones are involved in the adaptation to different environmental conditions. Abscisic acid (ABA) has an essential role in stress tolerance, especially in the adaptation to drought. During the last years, chemical genomics has gained attention as an alternative approach to decipher complex traits. Additionally, chemical-based strategies have been very useful to untangle genetic redundancy, which is hard to address by other approaches such as classical genetics. Here, we describe the use of an ABA-inducible luciferase (LUC) reporter line for the high-throughput identification of chemical activators of the ABA signaling pathway. In this assay, seven-day-old pMAPKKK18-LUC+ seedlings are grown on 96-well plates and treated with test compounds. Next, the activity of the LUC reporter is quantified semiautomatically by image analysis. Candidate compounds able to activate the reporter are thus identified and subjected to a secondary screen by analyzing their effect on ABA-related phenotypes (e.g., inhibition of seed germination). This assay is fast, high-throughput, nondestructive, semiquantitative and can be applied to any other luciferase reporter lines, making it ideal for forward chemical genetic screenings.
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Affiliation(s)
- Irene García-Maquilón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Aditya S Vaidya
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain.
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