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Jenne A, Soong R, Downey K, Biswas RG, Decker V, Busse F, Goerling B, Haber A, Simpson MJ, Simpson AJ. Brewing alcohol 101: An undergraduate experiment utilizing benchtop NMR for quantification and process monitoring. Magn Reson Chem 2024; 62:429-438. [PMID: 38230451 DOI: 10.1002/mrc.5428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
In recent years there has been a renewed interest in benchtop NMR. Given their lower cost of ownership, smaller footprint, and ease of use, they are especially suited as an educational tool. Here, a new experiment targeted at upper-year undergraduates and first-year graduate students follows the conversion of D-glucose into ethanol at low-field. First, high and low-field data on D-glucose are compared and students learn both the Hz and ppm scales and how J-coupling is field-independent. The students then acquire their own quantitative NMR datasets and perform the quantification using an Electronic Reference To Access In Vivo Concentration (ERETIC) technique. To our knowledge ERETIC is not currently taught at the undergraduate level, but has an advantage in that internal standards are not required; ideal for following processes or with future use in flow-based benchtop monitoring. Using this quantitative data, students can relate a simple chemical process (fermentation) back to more complex topics such as reaction kinetics, bridging the gaps between analytical and physical chemistry. When asked to reflect on the experiment, students had an overwhelmingly positive experience, citing agreement with learning objectives, ease of understanding the protocol, and enjoyment. Each of the respondents recommended this experiment as a learning tool for others. This experiment has been outlined for other instructors to utilize in their own courses across institutions, with the hope that a continued expansion of low-field NMR will increase accessibility and learning opportunities at the undergraduate level.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | | | | | | | | | | | - Myrna J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
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Ratnayake A, Bansal A, Wong N, Saseetharan T, Prompiengchai S, Jenne A, Thiagavel J, Ashok A. All "wrapped" up in reflection: supporting metacognitive awareness to promote students' self-regulated learning. J Microbiol Biol Educ 2024; 25:e0010323. [PMID: 38661420 PMCID: PMC11044636 DOI: 10.1128/jmbe.00103-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/25/2023] [Indexed: 04/26/2024]
Abstract
Self-regulated learning (SRL) is the process of utilizing effective strategies to acquire knowledge or skills and is influenced by motivation, metacognitive processing, and study-related behaviors. We hypothesized that by using survey tools that allow reflection on and refinement of students' study strategies, we could nurture metacognitive skill development, encourage positive motivation and study-related behaviors, and hence promote academic success. Undergraduate students in a semester-long, second-year biology course were provided with resources to promote SRL and three survey instruments that encouraged them to create study plans and reflect on the effectiveness of their study strategies. Using a student-partnered approach, we sought to investigate the role of metacognition, motivation, and study-related behaviors on academic performance by (i) identifying the self-regulated learning strategies most utilized by students, (ii) investigating the role of reflection in enhancing metacognitive processing and academic performance, and (iii) understanding whether students created and/or modified their study strategies as an outcome of self-regulation. Survey responses allowed us to understand the repertoire of study strategies used by students. Our analyses suggest that students demonstrated metacognitive skill development through the use of the resources and reflection instruments, as they accurately reported on the effectiveness of their study strategies and indicated future plans to shift study-related behaviors from passive to active reviewing techniques. Students across the grade spectrum perceived the reflection instruments as beneficial in identifying areas of improvement and developing long-term study habits, suggesting that these instruments were effective in promoting metacognitive skill development for a variety of student learners. We conclude that supporting students with resources that promote SRL and providing opportunities for timely reflection can promote metacognitive skill development, a key feature of academic success.
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Affiliation(s)
- Ayuni Ratnayake
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Aditi Bansal
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Natalie Wong
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Theluckshan Saseetharan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Sapolnach Prompiengchai
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Amy Jenne
- Department of Chemistry, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Jeneni Thiagavel
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Aarthi Ashok
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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3
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Steiner K, Bermel W, Soong R, Lysak DH, Jenne A, Downey K, Wolff WW, Costa PM, Ronda K, Moxley-Paquette V, Pellizzari J, Simpson AJ. A simple 1H ( 12C/ 13C) filtered experiment to quantify and trace isotope enrichment in complex environmental and biological samples. J Magn Reson 2024; 361:107653. [PMID: 38471414 DOI: 10.1016/j.jmr.2024.107653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Nuclear magnetic resonance (NMR) based 13C tracing has broad applications across medical and environmental research. As many biological and environmental samples are heterogeneous, they experience considerable spectral overlap and relatively low signal. Here a 1D 1H-12C/13C is introduced that uses "in-phase/opposite-phase" encoding to simultaneously detect and discriminate both protons attached to 12C and 13C at full 1H sensitivity in every scan. Unlike traditional approaches that focus on the 12C/13C satellite ratios in a 1H spectrum, this approach creates separate sub-spectra for the 12C and 13C bound protons. These spectra can be used for both quantitative and qualitative analysis of complex samples with significant spectral overlap. Due to the presence of the 13C dipole, faster relaxation of the 1H-13C pairs results in slight underestimation compared to the 1H-12C pairs. However, this is easily compensated for, by collecting an additional reference spectrum, from which the absolute percentage of 13C can be calculated by difference. When combined with the result, 12C and 13C percent enrichment in both 1H-12C and 1H-13C fractions are obtained. As the approach uses isotope filtered 1H NMR for detection, it retains nearly the same sensitivity as a standard 1H spectrum. Here, a proof-of-concept is performed using simple mixtures of 12C and 13C glucose, followed by suspended algal cells with varying 12C /13C ratios representing a complex mixture. The results consistently return 12C/13C ratios that deviate less than 1 % on average from the expected. Finally, the sequence was used to monitor and quantify 13C% enrichment in Daphnia magna neonates which were fed a 13C diet over 1 week. The approach helped reveal how the organisms utilized the 12C lipids they are born with vs. the 13C lipids they assimilate from their diet during growth. Given the experiments simplicity, versatility, and sensitivity, we anticipate it should find broad application in a wide range of tracer studies, such as fluxomics, with applications spanning various disciplines.
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Affiliation(s)
- Katrina Steiner
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, Ettlingen 76275, Germany
| | - Ronald Soong
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - William W Wolff
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Peter M Costa
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Kiera Ronda
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Vincent Moxley-Paquette
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Jacob Pellizzari
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
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Jenne A, Soong R, Gruschke O, Bastawrous M, Monks P, Moloney C, Brougham DF, Busse F, Bermel W, Courtier-Murias D, Wu B, Simpson A. A holistic NMR framework to understand environmental impact: Examining the impacts of superparamagnetic iron oxide nanoparticles (SPIONs) in Daphnia magna via imaging, spectroscopy, and metabolomics. Magn Reson Chem 2023; 61:728-739. [PMID: 36137948 DOI: 10.1002/mrc.5315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are a contaminant of emerging interest, often used in the medical field as an imaging contrast agent, with additional uses in wastewater treatment and as food additives. Although the use of SPIONs is increasing, little research has been conducted on the toxic impacts to living organisms beyond traditional lethal concentration endpoints. Daphnia magna are model organisms for aquatic toxicity testing with a well understood metabolome and high sensitivity to SPIONs. Thus, as environmental concentrations continue to increase, it is becoming critical to understand their sub-lethal toxicity. Due to the paramagnetic nature of SPIONs, a range of potential nuclear magnetic resonance spectroscopy (NMR) experiments are possible, offering the potential to probe the physical location (via imaging), binding (via relaxation weighted spectroscopy), and the biochemical pathways impacted (via in vivo metabolomics). Results indicate binding to carbohydrates, likely chitin in the exoskeleton, along with a decrease in energy metabolites and specific biomarkers of oxidative stress. The holistic NMR framework used here helps provide a more comprehensive understanding of SPIONs impacts on D. magna and showcases NMR's versatility in providing physical, chemical, and biochemical insights.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | | | - Monica Bastawrous
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Patricia Monks
- Department of Chemistry, RCSI University of Health Sciences, Dublin, Ireland
| | - Cara Moloney
- School of Medicine, BioDiscovery Institute-3, University of Nottingham, University Park, Nottingham, UK
| | | | | | | | - Denis Courtier-Murias
- Université Gustave Eiffel, GERS-LEE, Bouguenais, France
- Institut de Recherche en Sciences et Techniques de la Ville IRSTV, CNRS, Nantes, France
| | - Bing Wu
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Andre Simpson
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
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Ghosh Biswas R, Bermel W, Jenne A, Soong R, Simpson MJ, Simpson AJ. HR-MAS DREAMTIME NMR for Slow Spinning ex Vivo and in Vivo Samples. Anal Chem 2023; 95:17054-17063. [PMID: 37934172 DOI: 10.1021/acs.analchem.3c03800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
HR-MAS NMR is a powerful tool, capable of monitoring molecular changes in intact heterogeneous samples. However, one of the biggest limitations of 1H NMR is its narrow spectral width which leads to considerable overlap in complex natural samples. DREAMTIME NMR is a highly selective technique that allows users to isolate suites of metabolites from congested spectra. This permits targeted metabolomics by NMR and is ideal for monitoring specific processes. To date, DREAMTIME has only been employed in solution-state NMR, here it is adapted for HR-MAS applications. At high spinning speeds (>5 kHz), DREAMTIME works with minimal modifications. However, spinning over 3-4 kHz leads to cell lysis, and if maintaining sample integrity is necessary, slower spinning (<2.5 kHz) is required. Very slow spinning (≤500 Hz) is advantageous for in vivo analysis to increase organism survival; however, sidebands from water pose a problem. To address this, a version of DREAMTIME, termed DREAMTIME-SLOWMAS, is introduced. Both techniques are compared at 2500, 500, and 50 Hz, using ex vivo worm tissue. Following this, DREAMTIME-SLOWMAS is applied to monitor key metabolites of anoxic stress in living shrimp at 500 Hz. Thus, standard DREAMTIME works well under MAS conditions and is recommended for samples reswollen in D2O or spun >2500 Hz. For slow spinning in vivo or intact tissue samples, DREAMTIME-SLOWMAS provides an excellent way to target process-specific metabolites while maintaining sample integrity. Overall, DREAMTIME should find widespread application wherever targeted molecular information is required from complex samples with a high degree of spectral overlap.
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Affiliation(s)
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Andre J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
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Lysak DH, Wolff WW, Soong R, Bermel W, Kupče ER, Jenne A, Biswas RG, Lane D, Gasmi-Seabrook G, Simpson A. Application of 15N-Edited 1H- 13C Correlation NMR Spectroscopy─Toward Fragment-Based Metabolite Identification and Screening via HCN Constructs. Anal Chem 2023; 95:11926-11933. [PMID: 37535003 DOI: 10.1021/acs.analchem.3c01362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Many key building blocks of life contain nitrogen moieties. Despite the prevalence of nitrogen-containing metabolites in nature, 15N nuclei are seldom used in NMR-based metabolite assignment due to their low natural abundance and lack of comprehensive chemical shift databases. However, with advancements in isotope labeling strategies, 13C and 15N enriched metabolites are becoming more common in metabolomic studies. Simple multidimensional nuclear magnetic resonance (NMR) experiments that correlate 1H and 15N via single bond 1JNH or multiple bond 2-3JNH couplings using heteronuclear single quantum coherence (HSQC) or heteronuclear multiple bond coherence are well established and routinely applied for structure elucidation. However, a 1H-15N correlation spectrum of a metabolite mixture can be difficult to deconvolute, due to the lack of a 15N specific database. In order to bridge this gap, we present here a broadband 15N-edited 1H-13C HSQC NMR experiment that targets metabolites containing 15N moieties. Through this approach, nitrogen-containing metabolites, such as amino acids, nucleotide bases, and nucleosides, are identified based on their 13C, 1H, and 15N chemical shift information. This approach was tested and validated using a [15N, 13C] enriched Daphnia magna (water flea) metabolite extract, where the number of clearly resolved 15N-containing peaks increased from only 11 in a standard HSQC to 51 in the 15N-edited HSQC, and the number of obscured peaks decreased from 59 to just 7. The approach complements the current repertoire of NMR techniques for mixture deconvolution and holds considerable potential for targeted metabolite NMR in 15N, 13C enriched systems.
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Affiliation(s)
- Daniel H Lysak
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - William W Wolff
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Ronald Soong
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, Ettlingen 76275, Germany
| | | | - Amy Jenne
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Rajshree Ghosh Biswas
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Daniel Lane
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | | | - Andre Simpson
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
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7
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Ronda K, Downey K, Jenne A, Bastawrous M, Wolff WW, Steiner K, Lysak DH, Costa PM, Simpson MJ, Jobst KJ, Simpson AJ. Exploring Proton-Only NMR Experiments and Filters for Daphnia In Vivo: Potential and Limitations. Molecules 2023; 28:4863. [PMID: 37375418 DOI: 10.3390/molecules28124863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Environmental metabolomics provides insight into how anthropogenic activities have an impact on the health of an organism at the molecular level. Within this field, in vivo NMR stands out as a powerful tool for monitoring real-time changes in an organism's metabolome. Typically, these studies use 2D 13C-1H experiments on 13C-enriched organisms. Daphnia are the most studied species, given their widespread use in toxicity testing. However, with COVID-19 and other geopolitical factors, the cost of isotope enrichment increased ~6-7 fold over the last two years, making 13C-enriched cultures difficult to maintain. Thus, it is essential to revisit proton-only in vivo NMR and ask, "Can any metabolic information be obtained from Daphnia using proton-only experiments?". Two samples are considered here: living and whole reswollen organisms. A range of filters are tested, including relaxation, lipid suppression, multiple-quantum, J-coupling suppression, 2D 1H-1H experiments, selective experiments, and those exploiting intermolecular single-quantum coherence. While most filters improve the ex vivo spectra, only the most complex filters succeed in vivo. If non-enriched organisms must be used, then, DREAMTIME is recommended for targeted monitoring, while IP-iSQC was the only experiment that allowed non-targeted metabolite identification in vivo. This paper is critically important as it documents not just the experiments that succeed in vivo but also those that fail and demonstrates first-hand the difficulties associated with proton-only in vivo NMR.
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Affiliation(s)
- Kiera Ronda
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Monica Bastawrous
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - William W Wolff
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katrina Steiner
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Daniel H Lysak
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Peter M Costa
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, NL A1C 5S7, Canada
| | - Andre J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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Downey K, Michal CA, Bermel W, Jenne A, Soong R, Decker V, Busse F, Goerling B, Heumann H, Boenisch H, Gundy M, Simpson A. Targeted Compound Selection with Increased Sensitivity in 13C-Enriched Biological and Environmental Samples Using 13C-DREAMTIME in Both High-Field and Low-Field NMR. Anal Chem 2023; 95:6709-6717. [PMID: 37037008 DOI: 10.1021/acs.analchem.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Chemical characterization of complex mixtures by Nuclear Magnetic Resonance (NMR) spectroscopy is challenging due to a high degree of spectral overlap and inherently low sensitivity. Therefore, NMR experiments that reduce overlap and increase signal intensity hold immense potential for the analysis of mixtures such as biological and environmental media. Here, we introduce a 13C version of DREAMTIME (Designed Refocused Excitation And Mixing for Targets In Vivo and Mixture Elucidation) NMR, which, when analyzing 13C-enriched materials, allows the user to selectively detect only the compound(s) of interest and remove all other peaks in a 13C spectrum. Selected peaks can additionally be "focused" into sharp "spikes" to increase sensitivity. 13C-DREAMTIME is first demonstrated at high field strength (500 MHz) with simultaneous selection of eight amino acids in a 13C-enriched cell free amino acid mixture and of six metabolites in an extract of 13C-enriched green algae and demonstrated at low field strength (80 MHz) with a standard solution of 13C-d-glucose and 13C-l-phenylalanine. 13C-DREAMTIME is then applied at high-field to analyze metabolic changes in 13C-enrichedDaphnia magna after exposure to polystyrene "microplastics," as well as at low-field to track fermentation of 13C-d-glucose using wine yeast. Ultimately, 13C-DREAMTIME reduces spectral overlap as only selected compounds are recorded, resulting in the detection of analyte peaks that may otherwise not have been discernable. In combination with focusing, up to a 6-fold increase in signal intensity can be obtained for a given peak. 13C-DREAMTIME is a promising experiment type for future reaction monitoring and for tracking metabolic processes with 13C-enriched compounds.
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Affiliation(s)
- Katelyn Downey
- Environmental NMR Centre, University of Toronto, Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Carl A Michal
- Department of Physics and Astronomy, The University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto, Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Venita Decker
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | - Benjamin Goerling
- Bruker BioSpin GmbH, Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany
| | | | | | - Marcel Gundy
- Silantes GmbH, Gollierstrasse 70c, D-80339 München, Germany
| | - Andre Simpson
- Environmental NMR Centre, University of Toronto, Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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9
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Jenne A, von der Ecken S, Moxley-Paquette V, Soong R, Swyer I, Bastawrous M, Busse F, Bermel W, Schmidig D, Kuehn T, Kuemmerle R, Al Adwan-Stojilkovic D, Graf S, Frei T, Monette M, Wheeler AR, Simpson AJ. Integrated Digital Microfluidics NMR Spectroscopy: A Key Step toward Automated In Vivo Metabolomics. Anal Chem 2023; 95:5858-5866. [PMID: 36996326 DOI: 10.1021/acs.analchem.2c04201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Toxicity testing is currently undergoing a paradigm shift from examining apical end points such as death, to monitoring sub-lethal toxicity in vivo. In vivo nuclear magnetic resonance (NMR) spectroscopy is a key platform in this endeavor. A proof-of-principle study is presented which directly interfaces NMR with digital microfluidics (DMF). DMF is a "lab on a chip" method allowing for the movement, mixing, splitting, and dispensing of μL-sized droplets. The goal is for DMF to supply oxygenated water to keep the organisms alive while NMR detects metabolomic changes. Here, both vertical and horizontal NMR coil configurations are compared. While a horizontal configuration is ideal for DMF, NMR performance was found to be sub-par and instead, a vertical-optimized single-sided stripline showed most promise. In this configuration, three organisms were monitored in vivo using 1H-13C 2D NMR. Without support from DMF droplet exchange, the organisms quickly showed signs of anoxic stress; however, with droplet exchange, this was completely suppressed. The results demonstrate that DMF can be used to maintain living organisms and holds potential for automated exposures in future. However, due to numerous limitations of vertically orientated DMF, along with space limitations in standard bore NMR spectrometers, we recommend future development be performed using a horizontal (MRI style) magnet which would eliminate practically all the drawbacks identified here.
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Affiliation(s)
- Amy Jenne
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Sebastian von der Ecken
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Nicoya, B-29 King Street East, Kitchener, Ontario N2G 2K4, Canada
| | - Vincent Moxley-Paquette
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Ian Swyer
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Monica Bastawrous
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | | | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Martine Monette
- Bruker Canada Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute for Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Andre J Simpson
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
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10
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Ghosh Biswas R, Soong R, Jenne A, Bastawrous M, Simpson MJ, Simpson AJ. SASSY NMR: Simultaneous Solid and Solution Spectroscopy. Angew Chem Int Ed Engl 2023; 62:e202216105. [PMID: 36588093 DOI: 10.1002/anie.202216105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Synergism between different phases gives rise to chemical, biological or environmental reactivity, thus it is increasingly important to study samples intact. Here, SASSY (SimultAneous Solid and Solution spectroscopY) is introduced to simultaneously observe (and differentiate) all phases in multiphase samples using standard, solid-state NMR equipment. When monitoring processes, the traditional approach of studying solids and liquids sequentially, can lead to information in the non-observed phase being missed. SASSY solves this by observing the full range of materials, from crystalline solids, through gels, to pure liquids, at full sensitivity in every scan. Results are identical to running separate 13 C CP-MAS solid-state and 13 C solution-state experiments back-to-back but requires only a fraction of the spectrometer time. After its introduction, SASSY is applied to process monitoring and finally to detect all phases in a living freshwater shrimp. SASSY is simple to implement and thus should find application across all areas of research.
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Affiliation(s)
- Rajshree Ghosh Biswas
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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Ghosh Biswas R, Soong R, Jenne A, Bastawrous M, Simpson M, Simpson AJ. SASSY NMR: Simultaneous Solid and Solution spectroscopy. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202216105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Ronald Soong
- University of Toronto Scarborough Physical and Environmental Science CANADA
| | - Amy Jenne
- University of Toronto Scarborough Chemistry CANADA
| | - Monica Bastawrous
- University of Toronto Scarborough Physical and Environmental Science CANADA
| | | | - Andre J Simpson
- University of Toronto Chemistry 1265 Military Trail M1C1A4 Toronto CANADA
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12
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Ghosh Biswas R, Soong R, Ning P, Lane D, Bastawrous M, Jenne A, Schmidig D, de Castro P, Graf S, Kuehn T, Kümmerle R, Bermel W, Busse F, Struppe J, Simpson MJ, Simpson AJ. Exploring the Applications of Carbon-Detected NMR in Living and Dead Organisms Using a 13C-Optimized Comprehensive Multiphase NMR Probe. Anal Chem 2022; 94:8756-8765. [PMID: 35675504 DOI: 10.1021/acs.analchem.2c01356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Comprehensive multiphase-nuclear magnetic resonance (CMP-NMR) is a non-invasive approach designed to observe all phases (solutions, gels, and solids) in intact samples using a single NMR probe. Studies of dead and living organisms are important to understand processes ranging from biological growth to environmental stress. Historically, such studies have utilized 1H-based phase editing for the detection of soluble/swollen components and 1H-detected 2D NMR for metabolite assignments/screening. However, living organisms require slow spinning rates (∼500 Hz) to increase survivability, but at such low speeds, complications from water sidebands and spectral overlap from the modest chemical shift window (∼0-10 ppm) make 1H NMR challenging. Here, a novel 13C-optimized E-Free magic angle spinning CMP probe is applied to study all phases in ex vivo and in vivo samples. This probe consists of a two-coil design, with an inner single-tuned 13C coil providing a 113% increase in 13C sensitivity relative to a traditional multichannel single-CMP coil design. For organisms with a large biomass (∼0.1 g) like the Ganges River sprat (ex vivo), 13C-detected full spectral editing and 13C-detected heteronuclear correlation (HETCOR) can be performed at natural abundance. Unfortunately, for a single living shrimp (∼2 mg), 13C enrichment was still required, but 13C-detected HETCOR shows superior data relative to heteronuclear single-quantum coherence at low spinning speeds (due to complications from water sidebands in the latter). The probe is equipped with automatic-tuning-matching and is compatible with automated gradient shimming─a key step toward conducting multiphase screening of dead and living organisms under automation in the near future.
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Affiliation(s)
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Paris Ning
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Peter de Castro
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Jochem Struppe
- Bruker Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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Bastawrous M, Gruschke O, Soong R, Jenne A, Gross D, Busse F, Nashman B, Lacerda A, Simpson AJ. Comparing the Potential of Helmholtz and Planar NMR Microcoils for Analysis of Intact Biological Samples. Anal Chem 2022; 94:8523-8532. [DOI: 10.1021/acs.analchem.2c01560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Bastawrous
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Oliver Gruschke
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Ronald Soong
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Dieter Gross
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Ben Nashman
- Synex Medical, 2 Bloor Street E, Suite 310, Toronto, Ontario M4W 1A8, Canada
| | - Andressa Lacerda
- Synex Medical, 2 Bloor Street E, Suite 310, Toronto, Ontario M4W 1A8, Canada
| | - Andre J. Simpson
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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Jenne A, Bermel W, Michal CA, Gruschke O, Soong R, Ghosh Biswas R, Bastawrous M, Simpson AJ. DREAMTIME NMR Spectroscopy: Targeted Multi-Compound Selection with Improved Detection Limits. Angew Chem Int Ed Engl 2022; 61:e202110044. [PMID: 35170183 DOI: 10.1002/anie.202110044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/06/2022]
Abstract
NMR/MRI are critical tools for studying molecular structure and interactions but suffer from relatively low sensitivity and spectral overlap. Here, a Nuclear Magnetic Resonance (NMR) approach, termed DREAMTIME, is introduced that provides "a molecular window" inside complex systems, capable of showing only what the user desires, with complete molecular specificity. The user chooses a list of molecules of interest, and the approach detects only those targets while all other molecules are invisible. The approach is demonstrated in whole human blood and urine, small living aquatic organisms in 1D/2D NMR, and MRI. Finally, as proof-of-concept, once overlap is removed via DREAMTIME, a novel "multi-focusing" approach can be used to increase sensitivity. In human blood and urine, sensitivity increases of 7-12 fold over standard 1 H NMR are observed. Applicable even to unknowns, DREAMTIME has widespread application, from monitoring product formation in organic chemistry to monitoring/identifying suites of molecular targets in complex media or in vivo.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Strasse 23, 76275, Ettlingen, Germany
| | - Carl A Michal
- Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, BC, V6T 1Z1, Canada
| | - Oliver Gruschke
- Bruker BioSpin GmbH, Rudolf-Plank-Strasse 23, 76275, Ettlingen, Germany
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Rajshree Ghosh Biswas
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Andre J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
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Jenne A, Bermel W, Michal CA, Gruschke O, Soong R, Ghosh Biswas R, Bastawrous M, Simpson AJ. DREAMTIME NMR Spectroscopy: Targeted Multi‐Compound Selection with Improved Detection Limits. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Amy Jenne
- Environmental NMR Centre University of Toronto Scarborough 1265 Military Trail Toronto ON, M1C 1A4 Canada
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Rudolf-Plank-Strasse 23 76275 Ettlingen Germany
| | - Carl A. Michal
- Department of Physics and Astronomy University of British Columbia 6224 Agricultural Road Vancouver BC, V6T 1Z1 Canada
| | - Oliver Gruschke
- Bruker BioSpin GmbH Rudolf-Plank-Strasse 23 76275 Ettlingen Germany
| | - Ronald Soong
- Environmental NMR Centre University of Toronto Scarborough 1265 Military Trail Toronto ON, M1C 1A4 Canada
| | - Rajshree Ghosh Biswas
- Environmental NMR Centre University of Toronto Scarborough 1265 Military Trail Toronto ON, M1C 1A4 Canada
| | - Monica Bastawrous
- Environmental NMR Centre University of Toronto Scarborough 1265 Military Trail Toronto ON, M1C 1A4 Canada
| | - Andre J. Simpson
- Environmental NMR Centre University of Toronto Scarborough 1265 Military Trail Toronto ON, M1C 1A4 Canada
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16
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Ning P, Lane D, Ghosh Biswas R, Jenne A, Bastawrous M, Soong R, Schmidig D, Frei T, De Castro P, Kovacevic I, Graf S, Wegner S, Bermel W, Busse F, Kuehn T, Kuemmerle R, Struppe J, Fey M, Stronks HJ, Monette M, Simpson MJ, Simpson AJ. Expanding current applications and permitting the analysis of larger intact samples by means of a 7 mm CMP-NMR probe. Analyst 2021; 146:4461-4472. [PMID: 34136891 DOI: 10.1039/d1an00809a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Comprehensive multiphase NMR combines the ability to study and differentiate all phases (solids, gels, and liquids) using a single NMR probe. The general goal of CMP-NMR is to study intact environmental and biological samples to better understand conformation, organization, association, and transfer between and across phases/interfaces that may be lost with conventional sample preparation such as drying or solubilization. To date, all CMP-NMR studies have used 4 mm probes and rotors. Here, a larger 7 mm probehead is introduced which provides ∼3 times the volume and ∼2.4 times the signal over a 4 mm version. This offers two main advantages: (1) the additional biomass reduces experiment time, making 13C detection at natural abundance more feasible; (2) it allows the analysis of larger samples that cannot fit within a 4 mm rotor. Chicken heart tissue and Hyalella azteca (freshwater shrimp) are used to demonstrate that phase-based spectral editing works with 7 mm rotors and that the additional biomass from the larger volumes allows detection with 13C at natural abundance. Additionally, a whole pomegranate seed berry (aril) and an intact softgel capsule of hydroxyzine hydrochloride are used to demonstrate the analysis of samples too large to fit inside a conventional 4 mm CMP probe. The 7 mm version introduced here extends the range of applications and sample types that can be studied and is recommended when 4 mm CMP probes cannot provide adequate signal-to-noise (S/N), or intact samples are simply too big for 4 mm rotors.
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Affiliation(s)
- Paris Ning
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Rajshree Ghosh Biswas
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Peter De Castro
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Ivan Kovacevic
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Sebastian Wegner
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Jochem Struppe
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Michael Fey
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Henry J Stronks
- Bruker Ltd., 2800 High Point Drive, Milton, ON, L9T 6P4Canada
| | - Martine Monette
- Bruker Ltd., 2800 High Point Drive, Milton, ON, L9T 6P4Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - André J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
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17
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Tian Z, Zhao H, Peter KT, Gonzalez M, Wetzel J, Wu C, Hu X, Prat J, Mudrock E, Hettinger R, Cortina AE, Biswas RG, Kock FVC, Soong R, Jenne A, Du B, Hou F, He H, Lundeen R, Gilbreath A, Sutton R, Scholz NL, Davis JW, Dodd MC, Simpson A, McIntyre JK, Kolodziej EP. A ubiquitous tire rubber-derived chemical induces acute mortality in coho salmon. Science 2021; 371:185-189. [PMID: 33273063 DOI: 10.1126/science.abd6951] [Citation(s) in RCA: 362] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022]
Abstract
In U.S. Pacific Northwest coho salmon (Oncorhynchus kisutch), stormwater exposure annually causes unexplained acute mortality when adult salmon migrate to urban creeks to reproduce. By investigating this phenomenon, we identified a highly toxic quinone transformation product of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD), a globally ubiquitous tire rubber antioxidant. Retrospective analysis of representative roadway runoff and stormwater-affected creeks of the U.S. West Coast indicated widespread occurrence of 6PPD-quinone (<0.3 to 19 micrograms per liter) at toxic concentrations (median lethal concentration of 0.8 ± 0.16 micrograms per liter). These results reveal unanticipated risks of 6PPD antioxidants to an aquatic species and imply toxicological relevance for dissipated tire rubber residues.
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Affiliation(s)
- Zhenyu Tian
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Haoqi Zhao
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Katherine T Peter
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Melissa Gonzalez
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Jill Wetzel
- School of the Environment, Washington State University, Puyallup, WA 98371, USA
| | - Christopher Wu
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Ximin Hu
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jasmine Prat
- School of the Environment, Washington State University, Puyallup, WA 98371, USA
| | - Emma Mudrock
- School of the Environment, Washington State University, Puyallup, WA 98371, USA
| | - Rachel Hettinger
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Allan E Cortina
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Rajshree Ghosh Biswas
- Department of Chemistry, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | | | - Ronald Soong
- Department of Chemistry, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Department of Chemistry, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Bowen Du
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Fan Hou
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Huan He
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rachel Lundeen
- Center for Urban Waters, Tacoma, WA 98421, USA
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
| | - Alicia Gilbreath
- San Francisco Estuary Institute, 4911 Central Avenue, Richmond, CA 94804, USA
| | - Rebecca Sutton
- San Francisco Estuary Institute, 4911 Central Avenue, Richmond, CA 94804, USA
| | - Nathaniel L Scholz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
| | - Jay W Davis
- U.S. Fish and Wildlife Service, Washington Fish and Wildlife Office, Lacey, WA 98503, USA
| | - Michael C Dodd
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Andre Simpson
- Department of Chemistry, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Jenifer K McIntyre
- School of the Environment, Washington State University, Puyallup, WA 98371, USA
| | - Edward P Kolodziej
- Center for Urban Waters, Tacoma, WA 98421, USA.
- Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA 98421, USA
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
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18
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Ghosh Biswas R, Fortier-McGill B, Akhter M, Soong R, Ning P, Bastawrous M, Jenne A, Schmidig D, De Castro P, Graf S, Kuehn T, Busse F, Struppe J, Fey M, Heumann H, Boenisch H, Gundy M, Simpson MJ, Simpson AJ. Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR. Anal Chim Acta X 2020; 6:100051. [PMID: 33392494 PMCID: PMC7772632 DOI: 10.1016/j.acax.2020.100051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a non-invasive analytical technique which allows for the study of intact samples. Comprehensive Multiphase NMR (CMP-NMR) combines techniques and hardware from solution state and solid state NMR to allow for the holistic analysis of all phases (i.e. solutions, gels and solids) in unaltered samples. This study is the first to apply CMP-NMR to deceased, intact organisms and uses 13C enriched Daphnia magna (water fleas) as an example. D. magna are commonly used model organisms for environmental toxicology studies. As primary consumers, they are responsible for the transfer of nutrients across trophic levels, and a decline in their population can potentially impact the entire freshwater aquatic ecosystem. Though in vivo research is the ultimate tool to understand an organism’s most biologically relevant state, studies are limited by conditions (i.e. oxygen requirements, limited experiment time and reduced spinning speed) required to keep the organisms alive, which can negatively impact the quality of the data collected. In comparison, ex vivo CMP-NMR is beneficial in that; organisms do not need oxygen (eliminating air holes in rotor caps and subsequent evaporation); samples can be spun faster, leading to improved spectral resolution; more biomass per sample can be analyzed; and experiments can be run for longer. In turn, higher quality ex vivo NMR, can provide more comprehensive NMR assignments, which in many cases could be transferred to better understand less resolved in vivo signals. This manuscript is divided into three sections: 1) multiphase spectral editing techniques, 2) detailed metabolic assignments of 2D NMR of 13C enriched D. magna and 3) multiphase biological changes over different life stages, ages and generations of D. magna. In summary, ex vivo CMP-NMR proves to be a very powerful approach to study whole organisms in a comprehensive manner and should provide very complementary information to in vivo based research. Comprehensive Multiphase NMR detects all phases (solid/liquid/gel) in whole samples. Deceased organisms are not subjected to the limitations of in vivo NMR studies. 2D ex vivo NMR offer increased spectral resolution, improving metabolite assignment. Holistic analysis shows biological changes in D. magna over different life stages. Ex vivo NMR can be a complementary tool for in vivo NMR metabolomic studies.
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Affiliation(s)
- Rajshree Ghosh Biswas
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Blythe Fortier-McGill
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Mohammad Akhter
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Ronald Soong
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Paris Ning
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Monica Bastawrous
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Amy Jenne
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Daniel Schmidig
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Peter De Castro
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Stephan Graf
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Till Kuehn
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Falko Busse
- Bruker Biospin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Jochem Struppe
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Michael Fey
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Hermann Heumann
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Holger Boenisch
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Marcel Gundy
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Myrna J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - André J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
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Wu B, Ecken S, Swyer I, Li C, Jenne A, Vincent F, Schmidig D, Kuehn T, Beck A, Busse F, Stronks H, Soong R, Wheeler AR, Simpson A. Rapid Chemical Reaction Monitoring by Digital Microfluidics‐NMR: Proof of Principle Towards an Automated Synthetic Discovery Platform. Angew Chem Int Ed Engl 2019; 58:15372-15376. [DOI: 10.1002/anie.201910052] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Bing Wu
- Department of ChemistryUniversity of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Sebastian Ecken
- Department of ChemistryUniversity of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Ian Swyer
- Department of ChemistryUniversity of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Chunliang Li
- Laboratory of Physical ChemistryEindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Amy Jenne
- Department of ChemistryUniversity of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Franck Vincent
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Daniel Schmidig
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Till Kuehn
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Armin Beck
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Falko Busse
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Henry Stronks
- Bruker Canada Ltd. 2800 High Point Drive Milton Ontario L9T 6P4 Canada
| | - Ronald Soong
- Department of ChemistryUniversity of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Aaron R. Wheeler
- Department of ChemistryUniversity of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - André Simpson
- Department of ChemistryUniversity of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
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Wu B, Ecken S, Swyer I, Li C, Jenne A, Vincent F, Schmidig D, Kuehn T, Beck A, Busse F, Stronks H, Soong R, Wheeler AR, Simpson A. Rapid Chemical Reaction Monitoring by Digital Microfluidics‐NMR: Proof of Principle Towards an Automated Synthetic Discovery Platform. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bing Wu
- Department of Chemistry University of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Sebastian Ecken
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Ian Swyer
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Chunliang Li
- Laboratory of Physical Chemistry Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Amy Jenne
- Department of Chemistry University of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Franck Vincent
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Daniel Schmidig
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Till Kuehn
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Armin Beck
- Bruker BioSpin AG Industriestrasse 26 8117 Fällanden Switzerland
| | - Falko Busse
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Henry Stronks
- Bruker Canada Ltd. 2800 High Point Drive Milton Ontario L9T 6P4 Canada
| | - Ronald Soong
- Department of Chemistry University of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
| | - Aaron R. Wheeler
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - André Simpson
- Department of Chemistry University of Toronto Scarborough 1265 Military Trail Toronto ON M1C 1A4 Canada
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Swyer I, von der Ecken S, Wu B, Jenne A, Soong R, Vincent F, Schmidig D, Frei T, Busse F, Stronks HJ, Simpson AJ, Wheeler AR. Digital microfluidics and nuclear magnetic resonance spectroscopy for in situ diffusion measurements and reaction monitoring. Lab Chip 2019; 19:641-653. [PMID: 30648175 DOI: 10.1039/c8lc01214h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In recent years microcoils and related structures have been developed to increase the mass sensitivity of nuclear magnetic resonance spectroscopy, allowing this extremely powerful analytical technique to be extended to small sample volumes (<5 μl). In general, microchannels have been used to deliver the samples of interest to these microcoils; however, these systems tend to have large dead volumes and require more complex fluidic connections. Here, we introduce a two-plate digital microfluidic (DMF) strategy to interface small-volume samples with NMR microcoils. In this system, a planar microcoil is surrounded by a copper plane that serves as the counter-electrode for the digital microfluidic device, allowing for precise control of droplet position and shape. This feature allows for the user-determination of the orientation of droplets relative to the main axes of the shim stack, permitting improved shimming and a more homogeneous magnetic field inside the droplet below the microcoil, which leads to improved spectral lineshape. This, along with high-fidelity droplet actuation, allows for rapid shimming strategies (developed over decades for vertically oriented NMR tubes) to be employed, permitting the determination of reaction-product diffusion coefficients as well as quantitative monitoring of reactive intermediates. We propose that this system paves the way for new and exciting applications for in situ analysis of small samples by NMR spectroscopy.
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Affiliation(s)
- Ian Swyer
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON M5S 3H6, Canada.
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22
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Abstract
In vivo NMR (nuclear magnetic resonance) has the potential to monitor and record metabolic flux in close to real time, which is essential for better understanding the toxic mode of action of a contaminant and deciphering complex interconnected stress-induced pathways impacted inside an organism. Here, we describe how to construct and use a simple flow system to keep small aquatic organisms alive inside the NMR spectrometer. In living organisms, magnetic susceptibility distortions lead to severe broadening in conventional NMR. Two main approaches can be employed to overcome this issue: (1) use a pulse sequence to reduce the distortions, or (2) employ multidimensional NMR in combination with isotopic enrichment to provide the spectral dispersion required to separate peaks from overlapping resonances. Both approaches are discussed, and protocols for both approaches are provided here in the context of small aquatic organisms.
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Affiliation(s)
- Maryam Tabatabaei Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Daniel Lane
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada
| | - Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Amy Jenne
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada
| | - André J Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada.
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23
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Jenne A, Soong R, Bermel W, Sharma N, Masi A, Tabatabaei Anaraki M, Simpson A. Focusing on “the important” through targeted NMR experiments: an example of selective13C–12C bond detection in complex mixtures. Faraday Discuss 2019; 218:372-394. [DOI: 10.1039/c8fd00213d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here, a targeted NMR experiment is introduced which selectively detects the formation of13C–12C bonds in mixtures.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Centre
- University of Toronto
- Toronto
- Canada
| | - Ronald Soong
- Environmental NMR Centre
- University of Toronto
- Toronto
- Canada
| | | | - Nisha Sharma
- Department of Agronomy, Food, Natural Resources, Animals and the Environment
- University of Padova
- Padova
- Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and the Environment
- University of Padova
- Padova
- Italy
| | | | - Andre Simpson
- Environmental NMR Centre
- University of Toronto
- Toronto
- Canada
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Bastawrous M, Jenne A, Tabatabaei Anaraki M, Simpson AJ. In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity. Metabolites 2018; 8:E35. [PMID: 29795000 PMCID: PMC6027203 DOI: 10.3390/metabo8020035] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.
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Affiliation(s)
- Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Amy Jenne
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Maryam Tabatabaei Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - André J Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
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Freund S, Haberecht K, Wissing J, Hammerer P, Jenne A, Jänsch L. 177 Kinome analysis in renal cell carcinoma. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)70984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Jenne A, Hartig JS, Piganeau N, Tauer A, Samarsky DA, Green MR, Davies J, Famulok M. Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nat Biotechnol 2001; 19:56-61. [PMID: 11135553 DOI: 10.1038/83513] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability to rapidly identify small molecules that interact with RNA would have significant clinical and research applications. Low-molecular-weight molecules that bind to RNA have the potential to be used as drugs. Therefore, technologies facilitating the rapid and reliable identification of such activities become increasingly important. We have applied a fluorescence-based assay to screen for modulators of hammerhead ribozyme (HHR) catalysis from a small library of antibiotic compounds. Several unknown potent inhibitors of the hammerhead cleavage reaction were identified and further characterized. Tuberactinomycin A, for which positive cooperativity of inhibition in vitro was found, also reduced ribozyme cleavage in vivo. The assay is applicable to the screening of mixtures of compounds, as inhibitory activities were detected within a collection of 2,000 extracts from different actinomycete strains. This approach allows the rapid, reliable, and convenient identification and characterization of ribozyme modulators leading to insights difficult to obtain by classical methodology.
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Affiliation(s)
- A Jenne
- Kekulé-Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Str. 1, 35121, Bonn, Germany
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27
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Sengle G, Jenne A, Arora PS, Seelig B, Nowick JS, Jäschke A, Famulok M. Synthesis, incorporation efficiency, and stability of disulfide bridged functional groups at RNA 5'-ends. Bioorg Med Chem 2000; 8:1317-29. [PMID: 10896110 DOI: 10.1016/s0968-0896(00)00080-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Modified guanosine monophosphates have been employed to introduce various functional groups onto RNA 5'-ends. Applications of modified RNA 5'-ends include the generation of functionalized RNA libraries for in vitro selection of catalytic RNAs, the attachment of photoaffinity-tags for mapping RNA-protein interactions or active sites in catalytic RNAs, or the nonradioactive labeling of RNA molecules with fluorescent groups. While in these and in similar applications a stable linkage is desired, in selection experiments for generating novel catalytic RNAs it is often advantageous that a functional group is introduced reversibly. Here we give a quantitative comparison of the different strategies that can be applied to reversibly attach functional groups via disulfide bonds to RNA 5'-ends. We report the preparation of functional groups with disulfide linkages, their incorporation efficiency into an RNA library, and their stability under various conditions.
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Affiliation(s)
- G Sengle
- Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Germany
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28
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Weisshart K, Taneja P, Jenne A, Herbig U, Simmons DT, Fanning E. Two regions of simian virus 40 T antigen determine cooperativity of double-hexamer assembly on the viral origin of DNA replication and promote hexamer interactions during bidirectional origin DNA unwinding. J Virol 1999; 73:2201-11. [PMID: 9971803 PMCID: PMC104465 DOI: 10.1128/jvi.73.3.2201-2211.1999] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation of simian virus 40 large tumor (T) antigen on threonine 124 is essential for viral DNA replication. A mutant T antigen (T124A), in which this threonine was replaced by alanine, has helicase activity, assembles double hexamers on viral-origin DNA, and locally distorts the origin DNA structure, but it cannot catalyze origin DNA unwinding. A class of T-antigen mutants with single-amino-acid substitutions in the DNA binding domain (class 4) has remarkably similar properties, although these proteins are phosphorylated on threonine 124, as we show here. By comparing the DNA binding properties of the T124A and class 4 mutant proteins with those of the wild type, we demonstrate that mutant double hexamers bind to viral origin DNA with reduced cooperativity. We report that T124A T-antigen subunits impair the ability of double hexamers containing the wild-type protein to unwind viral origin DNA, suggesting that interactions between hexamers are also required for unwinding. Moreover, the T124A and class 4 mutant T antigens display dominant-negative inhibition of the viral DNA replication activity of the wild-type protein. We propose that interactions between hexamers, mediated through the DNA binding domain and the N-terminal phosphorylated region of T antigen, play a role in double-hexamer assembly and origin DNA unwinding. We speculate that one surface of the DNA binding domain in each subunit of one hexamer may form a docking site that can interact with each subunit in the other hexamer, either directly with the N-terminal phosphorylated region or with another region that is regulated by phosphorylation.
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Affiliation(s)
- K Weisshart
- Institute for Molecular Biotechnology, 07745 Jena, Germany
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Affiliation(s)
- A Jenne
- Institut für Biochemie der LMU München-Genzentrum, Germany
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30
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Abstract
In vitro selection of combinatorial nucleic acid libraries leads to specific target-binding molecules--RNA, single stranded DNA, modified RNA or modified DNA, commonly designated as aptamers--and to novel catalytic nucleic acids. The current state of aptamer and ribozyme technology is such that it establishes itself as a means of obtaining useful tools for molecular biology, diagnostics, molecular medicine and bio-organic chemistry.
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Affiliation(s)
- M Famulok
- Institut für Biochemie, LMU München, Germany.
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31
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Abstract
BACKGROUND The 'RNA world' hypothesis proposes that the early history of life on earth consisted of a period in which chemical transformations were catalyzed exclusively by ribozymes. Ribozymes that act as acyl transferases, or catalyze the formation of amide or peptide bonds seem particularly attractive candidates to link the RNA world to the modern protein-nucleic acid world. The central role played by aminoacylated RNAs in today's processes of translating RNA into protein suggests that aminoacyl transfer reactions catalyzed by RNA might have facilitated the development and optimization of the translation apparatus during early evolution. RESULTS We describe the isolation and characterization of a novel ribozyme that catalyzes the transfer of an amino-acid ester from an aminoacyl donor substrate onto the ribozyme itself. The site of aminoacylation was determined to be at an internal 2'-OH group of a cytosine residue. The aminoacylation depends on the presence of Mg2+ and can be competitively inhibited by the AMP moiety of the aminoacyl donor substrate, suggesting that there is a specific binding pocket for this substrate. The originally selected ribozyme was engineered to act as intermolecular catalyst that transfers the amino acid onto an external 28-residue oligonucleotide. The aminoacylated oligonucleotide was further used to quantify the reverse reaction catalyzed by the ribozyme. CONCLUSIONS The ribozyme we have isolated is an example of a catalytic RNA with ester transferase activity which uses a substrate that is not templated by Watson-Crick-pairing hydrogen bonds. The reaction catalyzed by the ribozyme expands the scope of RNA catalysis to include acyl transferase activity from an RNA 3' end to an internal 2' position and the reverse. Ribozymes with such activity have been postulated to be evolutionary precursors of ribosomal RNA.
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Affiliation(s)
- A Jenne
- Institut für Biochemie der LMU München-Genzentrum, Germany
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