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Ahmed S, Naqvi SMZA, Hussain F, Awais M, Ren Y, Wu J, Zhang H, Zang Y, Hu J. Quantifying Plant Signaling Pathways by Integrating Luminescence-Based Biosensors and Mathematical Modeling. BIOSENSORS 2024; 14:378. [PMID: 39194607 DOI: 10.3390/bios14080378] [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: 06/30/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Plants have evolved intricate signaling pathways, which operate as networks governed by feedback to deal with stressors. Nevertheless, the sophisticated molecular mechanisms underlying these routes still need to be comprehended, and experimental validation poses significant challenges and expenses. Consequently, computational hypothesis evaluation gains prominence in understanding plant signaling dynamics. Biosensors are genetically modified to emit light when exposed to a particular hormone, such as abscisic acid (ABA), enabling quantification. We developed computational models to simulate the relationship between ABA concentrations and bioluminescent sensors utilizing the Hill equation and ordinary differential equations (ODEs), aiding better hypothesis development regarding plant signaling. Based on simulation results, the luminescence intensity was recorded for a concentration of 47.646 RLUs for 1.5 μmol, given the specified parameters and model assumptions. This method enhances our understanding of plant signaling pathways at the cellular level, offering significant benefits to the scientific community in a cost-effective manner. The alignment of these computational predictions with experimental results emphasizes the robustness of our approach, providing a cost-effective means to validate mathematical models empirically. The research intended to correlate the bioluminescence of biosensors with plant signaling and its mathematical models for quantified detection of specific plant hormone ABA.
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Affiliation(s)
- Shakeel Ahmed
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Syed Muhammad Zaigham Abbas Naqvi
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Fida Hussain
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Muhammad Awais
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Junfeng Wu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Hao Zhang
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Yiheng Zang
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Jiandong Hu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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2
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Raza A, Tabassum J, Mubarik MS, Anwar S, Zahra N, Sharif Y, Hafeez MB, Zhang C, Corpas FJ, Chen H. Hydrogen sulfide: an emerging component against abiotic stress in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:540-558. [PMID: 34870354 DOI: 10.1111/plb.13368] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2021] [Indexed: 05/05/2023]
Abstract
As a result of climate change, abiotic stresses are the most common cause of crop losses worldwide. Abiotic stresses significantly impair plants' physiological, biochemical, molecular and cellular mechanisms, limiting crop productivity under adverse climate conditions. However, plants can implement essential mechanisms against abiotic stressors to maintain their growth and persistence under such stressful environments. In nature, plants have developed several adaptations and defence mechanisms to mitigate abiotic stress. Moreover, recent research has revealed that signalling molecules like hydrogen sulfide (H2 S) play a crucial role in mitigating the adverse effects of environmental stresses in plants by implementing several physiological and biochemical mechanisms. Mainly, H2 S helps to implement antioxidant defence systems, and interacts with other molecules like nitric oxide (NO), reactive oxygen species (ROS), phytohormones, etc. These molecules are well-known as the key players that moderate the adverse effects of abiotic stresses. Currently, little progress has been made in understanding the molecular basis of the protective role of H2 S; however, it is imperative to understand the molecular basis using the state-of-the-art CRISPR-Cas gene-editing tool. Subsequently, genetic engineering could provide a promising approach to unravelling the molecular basis of stress tolerance mediated by exogenous/endogenous H2 S. Here, we review recent advances in understanding the beneficial roles of H2 S in conferring multiple abiotic stress tolerance in plants. Further, we also discuss the interaction and crosstalk between H2 S and other signal molecules; as well as highlighting some genetic engineering-based current and future directions.
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Affiliation(s)
- A Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - J Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - M S Mubarik
- Department of Biotechnology, University of Narowal (UON), Narowal, 51600, Pakistan
| | - S Anwar
- Department of Agronomy, University of Florida, Gainesville, USA
| | - N Zahra
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Y Sharif
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - M B Hafeez
- College of Agronomy, Northwest A&F University, Yangling, China
| | - C Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - F J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council, CSIC, Granada, Spain
| | - H Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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3
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Lucas M. Future Challenges in Plant Systems Biology. Methods Mol Biol 2022; 2395:325-337. [PMID: 34822161 DOI: 10.1007/978-1-0716-1816-5_16] [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] [Indexed: 06/13/2023]
Abstract
Plant systems biology is currently facing several important challenges, whose nature depend on the considered frame of reference and associated scale. This review covers some of the issues associated respectively with the molecular, tissue, and whole-plant scales, as well as discusses the potential for latest advances in synthetic biology and machine-learning methods to be of use in the future of plant systems biology.
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Affiliation(s)
- Mikaël Lucas
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France.
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4
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Andres J, Zurbriggen MD. Genetically Encoded Biosensors for the Quantitative Analysis of Auxin Dynamics in Plant Cells. Methods Mol Biol 2022; 2379:183-195. [PMID: 35188663 DOI: 10.1007/978-1-0716-1791-5_11] [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] [Indexed: 06/14/2023]
Abstract
Plants, as sessile organisms, possess complex and intertwined signaling networks to react and adapt their behavior toward different internal and external stimuli. Due to this high level of complexity, the implementation of quantitative molecular tools in planta remains challenging. Synthetic biology as an ever-growing interdisciplinary field applies basic engineering principles in life sciences. A plethora of synthetic switches, circuits, and even higher order networks has been implemented in different organisms, such as bacteria and mammalian cells, and facilitates the study of signaling and metabolic pathways. However, the application of such tools in plants lags behind, and thus only a few genetically encoded biosensors and switches have been engineered toward the quantitative investigation of plant signaling. Here, we present a protocol for the quantitative analysis of auxin signaling in Arabidopsis thaliana protoplasts. We implemented genetically encoded, ratiometric, degradation-based luminescent biosensors and applied them for studying auxin perception dynamics. For this, we utilized three different Aux/IAAs as sensor modules and analyzed their degradation behavior in response to auxin. Our experimental approach requires simple hardware and experimental reagents and can thus be implemented in every plant-related or cell culture laboratory. The system allows for the analysis of auxin perception and signaling aspects on various levels and can be easily expanded to other hormones, as for example strigolactones. In addition, the modular sensor design enables the implementation of sensor modules in a straightforward and time-saving approach.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany.
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5
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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6
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Wang L, Zou Y, Kaw HY, Wang G, Sun H, Cai L, Li C, Meng LY, Li D. Recent developments and emerging trends of mass spectrometric methods in plant hormone analysis: a review. PLANT METHODS 2020; 16:54. [PMID: 32322293 PMCID: PMC7161177 DOI: 10.1186/s13007-020-00595-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 04/04/2020] [Indexed: 05/18/2023]
Abstract
Plant hormones are naturally occurring small molecule compounds which are present at trace amounts in plant. They play a pivotal role in the regulation of plant growth. The biological activity of plant hormones depends on their concentrations in the plant, thus, accurate determination of plant hormone is paramount. However, the complex plant matrix, wide polarity range and low concentration of plant hormones are the main hindrances to effective analyses of plant hormone even when state-of-the-art analytical techniques are employed. These factors substantially influence the accuracy of analytical results. So far, significant progress has been realized in the analysis of plant hormones, particularly in sample pretreatment techniques and mass spectrometric methods. This review describes the classic extraction and modern microextraction techniques used to analyze plant hormone. Advancements in solid phase microextraction (SPME) methods have been driven by the ever-increasing requirement for dynamic and in vivo identification of the spatial distribution of plant hormones in real-life plant samples, which would contribute greatly to the burgeoning field of plant hormone investigation. In this review, we describe advances in various aspects of mass spectrometry methods. Many fragmentation patterns are analyzed to provide the theoretical basis for the establishment of a mass spectral database for the analysis of plant hormones. We hope to provide a technical guide for further discovery of new plant hormones. More than 140 research studies on plant hormone published in the past decade are reviewed, with a particular emphasis on the recent advances in mass spectrometry and sample pretreatment techniques in the analysis of plant hormone. The potential progress for further research in plant hormones analysis is also highlighted.
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Affiliation(s)
- Liyuan Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Yilin Zou
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Han Yeong Kaw
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Gang Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Huaze Sun
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Long Cai
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Chengyu Li
- State Key Laboratory of Application of Rare Earth Resources, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Long-Yue Meng
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
- Department of Environmental Science, Yanbian University, Yanji, 133002 China
| | - Donghao Li
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
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7
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Gratz R, Brumbarova T, Ivanov R, Trofimov K, Tünnermann L, Ochoa-Fernandez R, Blomeier T, Meiser J, Weidtkamp-Peters S, Zurbriggen MD, Bauer P. Phospho-mutant activity assays provide evidence for alternative phospho-regulation pathways of the transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR. THE NEW PHYTOLOGIST 2020; 225:250-267. [PMID: 31487399 PMCID: PMC6916400 DOI: 10.1111/nph.16168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/16/2019] [Indexed: 05/03/2023]
Abstract
The key basic helix-loop-helix (bHLH) transcription factor in iron (Fe) uptake, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), is controlled by multiple signaling pathways, important to adjust Fe acquisition to growth and environmental constraints. FIT protein exists in active and inactive protein pools, and phosphorylation of serine Ser272 in the C-terminus, a regulatory domain of FIT, provides a trigger for FIT activation. Here, we use phospho-mutant activity assays and study phospho-mimicking and phospho-dead mutations of three additional predicted phosphorylation sites, namely at Ser221 and at tyrosines Tyr238 and Tyr278, besides Ser 272. Phospho-mutations at these sites affect FIT activities in yeast, plant, and mammalian cells. The diverse array of cellular phenotypes is seen at the level of cellular localization, nuclear mobility, homodimerization, and dimerization with the FIT-activating partner bHLH039, promoter transactivation, and protein stability. Phospho-mimicking Tyr mutations of FIT disturb fit mutant plant complementation. Taken together, we provide evidence that FIT is activated through Ser and deactivated through Tyr site phosphorylation. We therefore propose that FIT activity is regulated by alternative phosphorylation pathways.
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Affiliation(s)
- Regina Gratz
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Tzvetina Brumbarova
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Department of Biosciences-Plant Biology, Saarland University, 66123, Saarbruecken, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Department of Biosciences-Plant Biology, Saarland University, 66123, Saarbruecken, Germany
| | - Ksenia Trofimov
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Laura Tünnermann
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Johannes Meiser
- Department of Biosciences-Plant Biology, Saarland University, 66123, Saarbruecken, Germany
- Department of Oncology, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | | | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Department of Biosciences-Plant Biology, Saarland University, 66123, Saarbruecken, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, 40225, Düsseldorf, Germany
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8
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Abstract
A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.
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Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA. .,Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA.
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