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936 results on '"Pauli, Guido F."'

6. Improving natural product research translation: From source to clinical trial

Author

Sorkin, Barbara C, Kuszak, Adam J, Bloss, Gregory, Fukagawa, Naomi K, Hoffman, Freddie Ann, Jafari, Mahtab, Barrett, Bruce, Brown, Paula N, Bushman, Frederic D, Casper, Steven J, Chilton, Floyd H, Coffey, Christopher S, Ferruzzi, Mario G, Hopp, D Craig, Kiely, Mairead, Lakens, Daniel, MacMillan, John B, Meltzer, David O, Pahor, Marco, Paul, Jeffrey, Pritchett‐Corning, Kathleen, Quinney, Sara K, Rehermann, Barbara, Setchell, Kenneth DR, Sipes, Nisha S, Stephens, Jacqueline M, Taylor, D Lansing, Tiriac, Hervé, Walters, Michael A, Xi, Dan, Zappalá, Giovanna, and Pauli, Guido F

Subjects
Medical Biotechnology, Biomedical and Clinical Sciences, Complementary and Integrative Health, Clinical Research, Good Health and Well Being, Animals, Biological Products, Drug Evaluation, Preclinical, Ethnobotany, Humans, Translational Research, Biomedical, clinical predictive validity, dietary supplements, model systems, rigor and replicability, value of information, Biochemistry and Cell Biology, Physiology, Medical Physiology, Biochemistry & Molecular Biology, Biochemistry and cell biology, Medical physiology
Abstract

While great interest in health effects of natural product (NP) including dietary supplements and foods persists, promising preclinical NP research is not consistently translating into actionable clinical trial (CT) outcomes. Generally considered the gold standard for assessing safety and efficacy, CTs, especially phase III CTs, are costly and require rigorous planning to optimize the value of the information obtained. More effective bridging from NP research to CT was the goal of a September, 2018 transdisciplinary workshop. Participants emphasized that replicability and likelihood of successful translation depend on rigor in experimental design, interpretation, and reporting across the continuum of NP research. Discussions spanned good practices for NP characterization and quality control; use and interpretation of models (computational through in vivo) with strong clinical predictive validity; controls for experimental artefacts, especially for in vitro interrogation of bioactivity and mechanisms of action; rigorous assessment and interpretation of prior research; transparency in all reporting; and prioritization of research questions. Natural product clinical trials prioritized based on rigorous, convergent supporting data and current public health needs are most likely to be informative and ultimately affect public health. Thoughtful, coordinated implementation of these practices should enhance the knowledge gained from future NP research.

Published
2020

7. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Author

McAlpine, James B, Chen, Shao-Nong, Kutateladze, Andrei, MacMillan, John B, Appendino, Giovanni, Barison, Andersson, Beniddir, Mehdi A, Biavatti, Maique W, Bluml, Stefan, Boufridi, Asmaa, Butler, Mark S, Capon, Robert J, Choi, Young H, Coppage, David, Crews, Phillip, Crimmins, Michael T, Csete, Marie, Dewapriya, Pradeep, Egan, Joseph M, Garson, Mary J, Genta-Jouve, Grégory, Gerwick, William H, Gross, Harald, Harper, Mary Kay, Hermanto, Precilia, Hook, James M, Hunter, Luke, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, Rivera-Chávez, José, Robien, Wolfgang, Saunders, Carla M, Schmidt, Thomas J, Seger, Christoph, Shen, Ben, Steinbeck, Christoph, Stuppner, Hermann, Sturm, Sonja, Taglialatela-Scafati, Orazio, Tantillo, Dean J, Verpoorte, Robert, Wang, Bin-Gui, Williams, Craig M, Williams, Philip G, Wist, Julien, Yue, Jian-Min, Zhang, Chen, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Biological Products, Magnetic Resonance Spectroscopy, Reproducibility of Results, Molecular Conformation, Generic health relevance, Organic Chemistry, Chemical Sciences, Biological Sciences, Medical and Health Sciences
Abstract

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Published
2019

8. Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Author

McAlpine, James B, Chen, Shao-Nong, Kutateladze, Andrei, MacMillan, John B, Appendino, Giovanni, Barison, Andersson, Beniddir, Mehdi A, Biavatti, Maique W, Bluml, Stefan, Boufridi, Asmaa, Butler, Mark S, Capon, Robert J, Choi, Young H, Coppage, David, Crews, Phillip, Crimmins, Michael T, Csete, Marie, Dewapriya, Pradeep, Egan, Joseph M, Garson, Mary J, Genta-Jouve, Grégory, Gerwick, William H, Gross, Harald, Harper, Mary Kay, Hermanto, Precilia, Hook, James M, Hunter, Luke, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, Rivera-Chávez, José, Robien, Wolfgang, Saunders, Carla M, Schmidt, Thomas J, Seger, Christoph, Shen, Ben, Steinbeck, Christoph, Stuppner, Hermann, Sturm, Sonja, Taglialatela-Scafati, Orazio, Tantillo, Dean J, Verpoorte, Robert, Wang, Bin-Gui, Williams, Craig M, Williams, Philip G, Wist, Julien, Yue, Jian-Min, Zhang, Chen, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Organic Chemistry, Chemical Sciences, Clinical Research, Biological Sciences, Medical and Health Sciences, Medicinal and biomolecular chemistry, Traditional, complementary and integrative medicine
Abstract

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

Published
2019

13. Medicinal Plant Microbiomes: Factors Affecting Bacterial and Fungal Community Composition.

Author

Zagal, Daniel, Graham, James G., Bisson, Jonathan, Green, Stefan J., and Pauli, Guido F.

Abstract

This exploratory study was designed to identify factors implicating microbial influence on medicinal plant metabolomes. Utilizing a whole-microbiome approach, amplicon sequencing was used to identify the makeup of fungal and bacterial assemblages from endophytic (interior) and epiphytic (external) environments in two different sets of congeneric host-plant pairs, with collection of multiple samples of two medicinal plant species (Actaea racemosa, Rhodiola rosea) and two generic analogs (Actaea rubra, Rhodiola integrifolia). Diversity analysis of microbial assemblages revealed the influence of three primary factors driving variance in microbial community composition: host-plant taxonomy, the compartmentalization of microbial communities within discrete plant parts, and the scale of distance (microhabitat heterogeneity) between sampling locations. These three factors accounted for ~ 60% of variance within and between investigated microbiomes. Across all our collections, bacterial populations were more diverse than fungi (per compartment), and microbial density in epiphytic compartments (aerial parts, rhizosphere) were higher than those of endophytes (leaf and root). These comparative data point to key loci associated with variation between congeneric pairs and plant genera, providing insight into the complex and contrasting relationships found within this multi-kingdom coevolutionary relationship. Although reflective of only a limited set of botanical source materials, these data document the richness of a relatively unexplored component of the plant world and highlight the relevance of a whole-microbiome ecology-driven approach to botanical research and directed natural product investigations. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

Author

Pauli, Guido F, Niemitz, Matthias, Bisson, Jonathan, Lodewyk, Michael W, Soldi, Cristian, Shaw, Jared T, Tantillo, Dean J, Saya, Jordy M, Vos, Klaas, Kleinnijenhuis, Roel A, Hiemstra, Henk, Chen, Shao-Nong, McAlpine, James B, Lankin, David C, and Friesen, J Brent

Subjects
Inorganic Chemistry, Chemical Sciences, Bridged Bicyclo Compounds, Crystallography, X-Ray, Deuterium, Magnetic Resonance Spectroscopy, Molecular Structure, Protons, Sesquiterpenes, Medicinal and Biomolecular Chemistry, Organic Chemistry, Medicinal and biomolecular chemistry, Organic chemistry
Abstract

The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

Published
2016

27. Modulatory role of terminal monomeric flavan‐3‐ol units in the viscoelasticity of dentin.

Author

Reis‐Havlat, Mariana, Alania, Yvette, Zhou, Bin, Jing, Shu‐Xi, McAlpine, James B., Chen, Shao‐Nong, Pauli, Guido F., and Bedran‐Russo, Ana K.

Subjects
DENTIN, DYNAMIC mechanical analysis, VISCOELASTICITY, DAMPING capacity, INFRARED spectroscopy
Abstract

Flavan‐3‐ol monomers are the building blocks of proanthocyanidins (PACs), natural compounds from plants shown to mediate specific biologic activities on dentin. While the stereochemistry of the terminal flavan‐3‐ols, catechin (C) versus epicatechin (EC), impacts the biomechanical properties of the dentin matrix treated with oligomeric PACs, structure–activity relationships driving this bioactivity remain elusive. To gain insights into the modulatory role of the terminal monomers, two highly congruent trimeric PACs from Pinus massoniana only differing in the stereochemistry of the terminal unit (Trimer‐C vs. Trimer‐EC) were prepared to evaluate their chemical characteristics as well as their effects on the viscoelasticity and biostability of biomodified dentin matrices via infrared spectroscopy and multi‐scale dynamic mechanical analyses. The subtle alteration of C versus EC as terminal monomers lead to distinct immediate PAC‐trimer biomodulation of the dentin matrix. Nano‐ and micro‐dynamic mechanical analyses revealed that Trimer‐EC increased the complex moduli (0.51 GPa) of dentin matrix more strongly than Trimer‐C (0.26 GPa) at the nanoscale length (p < 0.001), whereas the reverse was found at the microscale length (p <.001). The damping capacity (tan δ) of dentin matrix decreased by 70% after PAC treatment at the nano‐length scale, while increased values were found at the micro‐length scale (~0.24) compared to the control (0.18 ; p <.001). An increase in amide band intensities and a decrease of complex moduli was observed after storage in simulated body fluid for both Trimer‐C and Trimer‐EC modified dentin. The stereochemical configuration of the terminal monomeric units, C and EC, did not impact the chemo‐mechanical stability of dentin matrix. [ABSTRACT FROM AUTHOR]

Published
2024
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30. Supplementary Figures 1-3 from Hops (Humulus lupulus) Inhibits Oxidative Estrogen Metabolism and Estrogen-Induced Malignant Transformation in Human Mammary Epithelial cells (MCF-10A)

Author

Hemachandra, L.P., primary, Madhubhani, P., primary, Chandrasena, R., primary, Esala, P., primary, Chen, Shao-Nong, primary, Main, Matthew, primary, Lankin, David C., primary, Scism, Robert A., primary, Dietz, Birgit M., primary, Pauli, Guido F., primary, Thatcher, Gregory R.J., primary, and Bolton, Judy L., primary

Published
2023
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31. Data from Hops (Humulus lupulus) Inhibits Oxidative Estrogen Metabolism and Estrogen-Induced Malignant Transformation in Human Mammary Epithelial cells (MCF-10A)

Author

Hemachandra, L.P., primary, Madhubhani, P., primary, Chandrasena, R., primary, Esala, P., primary, Chen, Shao-Nong, primary, Main, Matthew, primary, Lankin, David C., primary, Scism, Robert A., primary, Dietz, Birgit M., primary, Pauli, Guido F., primary, Thatcher, Gregory R.J., primary, and Bolton, Judy L., primary

Published
2023
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41. New Rufomycins from Streptomyces atratus MJM3502 Expand Anti-Mycobacterium tuberculosis Structure–Activity Relationships

Author

Zhou, Bin, primary, Shetye, Gauri, additional, Wolf, Nina M., additional, Chen, Shao-Nong, additional, Qader, Mallique, additional, Ray, G. Joseph, additional, Lankin, David C., additional, Cho, Sanghyun, additional, Cheng, Jinhua, additional, Suh, Joo-Won, additional, Franzblau, Scott G., additional, McAlpine, James B., additional, and Pauli, Guido F., additional

Published
2022
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48. The LOTUS initiative for open knowledge management in natural products research

Author

Rutz, Adriano, Sorokina, Maria, Galgonek, Jakub, Mietchen, Daniel, Willighagen, Egon, Gaudry, Arnaud, Graham, James G, Stephan, Ralf, Page, Roderic, Vondrášek, Jiří, Steinbeck, Christoph, Pauli, Guido F, Wolfender, Jean-Luc, Bisson, Jonathan, Allard, Pierre-Marie, Bioinformatica, and RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health

Abstract

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.

Published
2022

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