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1. 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

2. 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, 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

5. Genome Mining and Metabolomics Unveil Pseudonochelin: A Siderophore Containing 5-Aminosalicylate from a Marine-Derived Pseudonocardia sp. Bacterium

Author

Zhang, Fan, primary, Ramos Alvarenga, René F., additional, Throckmorton, Kurt, additional, Chanana, Shaurya, additional, Braun, Doug R., additional, Fossen, Jen, additional, Zhao, Miao, additional, McCrone, Sue, additional, Harper, Mary Kay, additional, Rajski, Scott R., additional, Rose, Warren E., additional, Andes, David R., additional, Thomas, Michael G., additional, and Bugni, Tim S., additional

Published
2022
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10. Topsentinol L Trisulfate, a new Marine Natural Product, that Targets Basal-like and Claudin-low Breast Cancers

Author

El-Chaar, Nader N., primary, Smith, Thomas E., additional, Shrestha, Gajendra, additional, Piccolo, Stephen R., additional, Harper, Mary Kay, additional, Van Wagoner, Ryan M., additional, Lu, Zhenyu, additional, Venancio, Ashlee R., additional, Ireland, Chris M., additional, Bild, Andrea H., additional, and Moos, Philip J., additional

Published
2020
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12. Additional file 5 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Abstract

Additional file 5: Figure S5. Validation of the screening method by interfering with auxins. Per treatment, 1 µM of NAA, 2,4-D, IAA, and NPA was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”). The root data for the 2,4-D treatment are not available, because the root system was unmeasurable. The picture shows the harvested rice seedling treated with 1 µM 2,4-D with the “stumpy” root phenotype. Scale bar, 1 cm.

Published
2020
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14. Additional file 4 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Subjects
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Abstract

Additional file 4: Figure S4. Graphical User Interface of Plength and its interference functionalities. Top panel: GUI with an uploaded image. Information on the file directory and image size are displayed. Bottom panel: Interference functionalities. (A) The four settings that can be changed, i.e. plant type, coleoptile or seedling, scale bar position and length, and minimum detection area. (B) Preprocessing. Before the analysis, the image can be cropped and the detected areas can be checked. (top) cropping tool; (bottom) color thresholding tool. (C) Postprocessing. The display after analysis completion. Detected regions are framed and numbered and the leaves are traced. For each detected area, the shoot, internode and leaf lengths are given.

Published
2020
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15. Additional file 6 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Abstract

Additional file 6: Figure S6. Validation of the screening method by interfering with cytokinins. Per treatment, 1 µM of kinetin, 2iP, and trans-zeatin was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”).

Published
2020
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16. Additional file 3 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Abstract

Additional file 3: Figure S3. Theoretical example of the analysis of artificial plants with three or four leaves. Detected regions are numbered and framed. Leaves are traced in yellow.

Published
2020
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17. Additional file 8 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Abstract

Additional file 8: Figure S8. Validation of the screening method by interference with the ethylene pathway. Per treatment, 1 µM of ACC and AgNO3 was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”).

Published
2020
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18. Additional file 2 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Subjects
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Abstract

Additional file 2: Figure S2. Extra information about the image processing pipeline in Plength. Top panel: Smoothing improving thresholding by homogenizing the colors, removal of the noise, and connection of edges. Middle panel: Segmentation, i.e. thresholding and partitioning of the image into individual plants. Bottom panel: Prior to feature extraction, skeletonization of the contour, conversion to a graph, and pruning. The red and green dots indicate nodes and connecting edges, respectively. Note that the initial graph consists of nine nodes, but the pruned graph of only of seven.

Published
2020
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19. Additional file 9 of Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Author

Vlaminck, Lena, Chananchida Sang-Aram, Botterman, Deborah, Uy, Christine Jewel C., Harper, Mary Kay, Inzé, Dirk, Gheysen, Godelieve, and Depuydt, Stephen

Abstract

Additional file 9: Figure S9. Validation of the screening method by means of a concentration range of NaCl in Oryza sativa (L.) cv. Chucheongbyeo. Also 1 µM GA3 was added in the test tubes. Mock_DMSO corresponds to GA3 as this is also dissolved in DMSO, while NaCl is dissolved in sterile dH2O. The shoot parameters (in mm) are lengths of total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between the treatments (see “Methods”).

Published
2020
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24. Deoxyamphimedine, a new pyridoacridine alkaloid from two tropical Xestospongia sponges

Author

Tasdemir, Deniz, Marshall, Kathryn M., Mangalindan, Gina C., Concepcion, Gisela P., Barrows, Louis R., Harper, Mary Kay, and Ireland, Chris M.

Subjects
Chemistry, Organic -- Research, Alkaloids -- Physiological aspects, Enzymes -- Analysis, Toxins -- Physiological aspects, Biological sciences, Chemistry
Abstract

Research has been conducted on the pyridoacridine alkaloids, a class of marine-derived heteroaromatic pigments with cytotoxic activity. The study of the the deoxyamphimedine, a new pyridoacridine alkaloid, has been carried out in a purified enzyme system along with amphimedine and neoamphimedine and the results are discussed.

Published
2001

25. Neoamphimedine: a new pyridoacridine topoisomerase II inhibitor which catenates DNA

Author

Guzman, Florecita S. de, Carte, Brad, Troupe, Nelson, Faulkner, D. John, Harper, Mary Kay, Concepcion, Gisela P., Mangalindan, Gina C., Matsumoto, Sandra S., Barrows, Louis R., and Ireland, Chris M.

Subjects
Organic compounds -- Research, Enzyme inhibitors -- Research, DNA -- Research, DNA topoisomerase II -- Research, Biological sciences, Chemistry
Abstract

The pyridoacridines neoamphimedine and amphimedine were isolated from Xestospongia sp. from the Philippines and Xestospongia cf. carbonaria from Micronesia. The chemical formula, chemical shifts and proton coupling pattern for amphimedine is the same as for amphimedine isolated by Schmitz and colleagues. Neoamphimedine was found to be cytotoxic to normal CHO AAS cells. It was also observed that neoamphimedine stimulates topoisomerase II dependent cleavage 3% above controls compared to etoposide, which stimulates 38% cleavage at the same concentration.

Published
1999

28. Fibrosterol sulfates from the Philippine sponge Lissodendoryx (Acanthodoryx) fibrosa: sterol dimers that inhibit PKC[zeta]

Author

Whitson, Emily L., Bugni, Tim S., Chockalingam, Priya S., Concepcion, Gisela P., Xidong Feng, Guixian Jin, Harper, Mary Kay, Mangalindan, Gina C., McDonald, Leonard A., and Ireland, Chris M.

Subjects
Nuclear magnetic resonance spectroscopy -- Usage, Sterols -- Chemical properties, Sterols -- Structure, Sulfates -- Chemical properties, Sulfates -- Structure, Biological sciences, Chemistry
Abstract

The isolation of three new sulfated sterol dimers, fibrosterol sulfates A-C from the sponge Lissodendoryx (Acanthodoryx) fibrosa, collected in the Philippines is reported. The results offer insight into the structures assigned on the basis of extensive 1D and 2D NMR studies and the inhibition of PKC[zeta] with I[C.sub.50] values of 16.4 and 5.6 [mu]M, respectively.

Published
2009

29. Isolation, structure elucidation, and synthesis of eudistomides A and B, lipopeptides from a Fijian ascidian Eudistoma sp

Author

Whitson, Emily L., Ratnayake, Anokha S., Bugni, Tim S., Harper, Mary Kay, and Ireland, Chris M.

Subjects
Spectrum analysis -- Usage, Cyclic compounds -- Chemical properties, Peptides -- Chemical properties, Methyl ether -- Chemical properties, Biological sciences, Chemistry
Abstract

A combination of spectroscopic and chemical methods was employed to perform structural characterization of two new cyclic peptides, Eudistomides A and B isolated from a Fijian ascidian Eudistoma sp. The five-residue cystine-linked peptides are found to be flanked by a C-terminal methyl ester and a 12-oxo- and 12-hydroxy-tetradecanoyl moiety.

Published
2009

31. Chemical Metagenomics of an Anti-HIV Compound From Uncultivated Symbionts

Author

Smith, Thomas E., primary, Pond, Christopher D., additional, Pierce, Elizabeth, additional, Harmer, Zachary P., additional, Kwan, Jason, additional, Zachariah, Malcom M., additional, Harper, Mary Kay, additional, Wyche, Thomas P., additional, Matainaho, Teatulohi K., additional, Bugni, Tim S., additional, Barrows, Louis R., additional, Ireland, Chris M., additional, and Schmidt, Eric W., additional

Published
2018
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32. Accessing chemical diversity from the uncultivated symbionts of small marine animals

Author

Smith, Thomas E, primary, Pond, Christopher D, additional, Pierce, Elizabeth, additional, Harmer, Zachary P, additional, Kwan, Jason, additional, Zachariah, Malcolm M, additional, Harper, Mary Kay, additional, Wyche, Thomas P, additional, Matainaho, Teatulohi K, additional, Bugni, Tim S, additional, Barrows, Louis R, additional, Ireland, Chris M, additional, and Schmidt, Eric W, additional

Published
2018
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34. Microcionamides A and B, bioactive peptides from the philippine sponge clathria(thalysias) abietina

Author

Davis, Rohan A., Mangalindan, Gina C.;, Ireland, Chris M., Carter, Guy T., Bojo, Zenaida P., Antemano, Rowena R., Rodriguez, Nell O., Concepcion, Gisela P., Samson, Shiela C., de Guzman, Dennis, Cruz, Lourdes J., Tasdemir, Deniz, Feng, Xidong, and Harper, Mary Kay

Subjects
Stereochemistry -- Analysis, Peptides -- Properties, Peptides -- Analysis, Biological sciences, Chemistry
Abstract

The new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. The total structures including absolute stereochemistry, are determined by a combination of spectral and chemical methods.

Published
2004

45. WLS-dependent secretion of WNT3A requires Ser209 acylation and vacuolar acidification

Author

Coombs, Gary S., primary, Yu, Jia, additional, Canning, Claire A., additional, Veltri, Charles A., additional, Covey, Tracy M., additional, Cheong, Jit K., additional, Utomo, Velani, additional, Banerjee, Nikhil, additional, Zhang, Zong Hong, additional, Jadulco, Raquel C., additional, Concepcion, Gisela P., additional, Bugni, Tim S., additional, Harper, Mary Kay, additional, Mihalek, Ivana, additional, Jones, C. Michael, additional, Ireland, Chris M., additional, and Virshup, David M., additional

Published
2010
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50. Carteriosulfonic Acids A−C, GSK-3β Inhibitors from a Carteriospongia sp.

Author

McCulloch, Malcolm W. B., primary, Bugni, Tim S., additional, Concepcion, Gisela P., additional, Coombs, Gary S., additional, Harper, Mary Kay, additional, Kaur, Simran, additional, Mangalindan, Gina C., additional, Mutizwa, Misha M., additional, Veltri, Charles A., additional, Virshup, David M., additional, and Ireland, Chris M., additional

Published
2009
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