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448 results on '"Wilkinson, Barrie"'

1. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

Author

Feeney, Morgan Anne, Newitt, Jake Terry, Addington, Emily, Algora-Gallardo, Lis, Allan, Craig, Balis, Lucas, Birke, Anna S, Castaño-Espriu, Laia, Charkoudian, Louise K, Devine, Rebecca, Gayrard, Damien, Hamilton, Jacob, Hennrich, Oliver, Hoskisson, Paul A, Keith-Baker, Molly, Klein, Joshua G, Kruasuwan, Worarat, Mark, David R, Mast, Yvonne, McHugh, Rebecca E, McLean, Thomas C, Mohit, Elmira, Munnoch, John T, Murray, Jordan, Noble, Katie, Otani, Hiroshi, Parra, Jonathan, Pereira, Camila F, Perry, Louisa, Pintor-Escobar, Linamaria, Pritchard, Leighton, Prudence, Samuel MM, Russell, Alicia H, Schniete, Jana K, Seipke, Ryan F, Sélem-Mojica, Nelly, Undabarrena, Agustina, Vind, Kristiina, van Wezel, Gilles P, Wilkinson, Barrie, Worsley, Sarah F, Duncan, Katherine R, Fernández-Martínez, Lorena T, and Hutchings, Matthew I

Subjects
Microbiology, Biological Sciences, Generic health relevance, Actinobacteria, Anti-Bacterial Agents, Streptomyces, actinobacteria, antibiotics, BGCs, CRISPR, specialised metabolites, Genetics
Abstract

Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.

Published
2022

13. Heterologous Expression of the Formicamycin Biosynthetic Gene Cluster Unveils Glycosylated Fasamycin Congeners

Author

McDonald, Hannah P., primary, Alford, Abigail, additional, Devine, Rebecca, additional, Hems, Edward S., additional, Nepogodiev, Sergey A., additional, Arnold, Corinne J., additional, Rejzek, Martin, additional, Stanley-Smith, Anna, additional, Holmes, Neil A., additional, Hutchings, Matthew I., additional, and Wilkinson, Barrie, additional

Published
2023
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20. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis

Author

Ganesan, A., Aldholmi, Mohammed, Ahmad, Rizwan, Carretero-Molina, Daniel, Reyes, Fernando, Genilloud, Olga, Gefflaut, Thierry, Carlsson, Hanne, Maklakov, Alexei, Field, Robert A., O'Neill, Ellis, Wilkinson, Barrie, and O'Connell, Maria

Subjects
General Chemistry, Catalysis
Abstract

By limiting the nitrogen source to glutamic acid, we isolated cyclic peptides from Euglena gracilis containing asparagine and non-proteinogenic amino acids. Structure elucidation was accomplished through spectroscopic methods, mass spectrometry and chemical degradation. The euglenatides potently inhibit pathogenic fungi and cancer cell lines e.g., euglenatide B exhibiting IC50 values of 4.3 ?M in Aspergillus fumigatus and 0.29 ?M in MCF-7 breast cancer cells. In an unprecedented convergence of non-ribosomal peptide synthetase and polyketide synthase assembly-line biosynthesis between unicellular species and the metazoan kingdom, euglenatides bear resemblance to nemamides from Caenorhabditis elegans and inhibited both producing organisms E. gracilis and C. elegans. By molecular network analysis, we detected over forty euglenatide-like metabolites in E. gracilis, E. sanguinea and E. mutabilis, suggesting an important biological role for these natural products.

Published
2022

21. Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Author

Cramer, Estee Y., primary, Ray, Evan L., additional, Lopez, Velma K., additional, Bracher, Johannes, additional, Brennen, Andrea, additional, Castro Rivadeneira, Alvaro J., additional, Gerding, Aaron, additional, Gneiting, Tilmann, additional, House, Katie H., additional, Huang, Yuxin, additional, Jayawardena, Dasuni, additional, Kanji, Abdul H., additional, Khandelwal, Ayush, additional, Le, Khoa, additional, Mühlemann, Anja, additional, Niemi, Jarad, additional, Shah, Apurv, additional, Stark, Ariane, additional, Wang, Yijin, additional, Wattanachit, Nutcha, additional, Zorn, Martha W., additional, Gu, Youyang, additional, Jain, Sansiddh, additional, Bannur, Nayana, additional, Deva, Ayush, additional, Kulkarni, Mihir, additional, Merugu, Srujana, additional, Raval, Alpan, additional, Shingi, Siddhant, additional, Tiwari, Avtansh, additional, White, Jerome, additional, Abernethy, Neil F., additional, Woody, Spencer, additional, Dahan, Maytal, additional, Fox, Spencer, additional, Gaither, Kelly, additional, Lachmann, Michael, additional, Meyers, Lauren Ancel, additional, Scott, James G., additional, Tec, Mauricio, additional, Srivastava, Ajitesh, additional, George, Glover E., additional, Cegan, Jeffrey C., additional, Dettwiller, Ian D., additional, England, William P., additional, Farthing, Matthew W., additional, Hunter, Robert H., additional, Lafferty, Brandon, additional, Linkov, Igor, additional, Mayo, Michael L., additional, Parno, Matthew D., additional, Rowland, Michael A., additional, Trump, Benjamin D., additional, Zhang-James, Yanli, additional, Chen, Samuel, additional, Faraone, Stephen V., additional, Hess, Jonathan, additional, Morley, Christopher P., additional, Salekin, Asif, additional, Wang, Dongliang, additional, Corsetti, Sabrina M., additional, Baer, Thomas M., additional, Eisenberg, Marisa C., additional, Falb, Karl, additional, Huang, Yitao, additional, Martin, Emily T., additional, McCauley, Ella, additional, Myers, Robert L., additional, Schwarz, Tom, additional, Sheldon, Daniel, additional, Gibson, Graham Casey, additional, Yu, Rose, additional, Gao, Liyao, additional, Ma, Yian, additional, Wu, Dongxia, additional, Yan, Xifeng, additional, Jin, Xiaoyong, additional, Wang, Yu-Xiang, additional, Chen, YangQuan, additional, Guo, Lihong, additional, Zhao, Yanting, additional, Gu, Quanquan, additional, Chen, Jinghui, additional, Wang, Lingxiao, additional, Xu, Pan, additional, Zhang, Weitong, additional, Zou, Difan, additional, Biegel, Hannah, additional, Lega, Joceline, additional, McConnell, Steve, additional, Nagraj, V. P., additional, Guertin, Stephanie L., additional, Hulme-Lowe, Christopher, additional, Turner, Stephen D., additional, Shi, Yunfeng, additional, Ban, Xuegang, additional, Walraven, Robert, additional, Hong, Qi-Jun, additional, Kong, Stanley, additional, van de Walle, Axel, additional, Turtle, James A., additional, Ben-Nun, Michal, additional, Riley, Steven, additional, Riley, Pete, additional, Koyluoglu, Ugur, additional, DesRoches, David, additional, Forli, Pedro, additional, Hamory, Bruce, additional, Kyriakides, Christina, additional, Leis, Helen, additional, Milliken, John, additional, Moloney, Michael, additional, Morgan, James, additional, Nirgudkar, Ninad, additional, Ozcan, Gokce, additional, Piwonka, Noah, additional, Ravi, Matt, additional, Schrader, Chris, additional, Shakhnovich, Elizabeth, additional, Siegel, Daniel, additional, Spatz, Ryan, additional, Stiefeling, Chris, additional, Wilkinson, Barrie, additional, Wong, Alexander, additional, Cavany, Sean, additional, España, Guido, additional, Moore, Sean, additional, Oidtman, Rachel, additional, Perkins, Alex, additional, Kraus, David, additional, Kraus, Andrea, additional, Gao, Zhifeng, additional, Bian, Jiang, additional, Cao, Wei, additional, Lavista Ferres, Juan, additional, Li, Chaozhuo, additional, Liu, Tie-Yan, additional, Xie, Xing, additional, Zhang, Shun, additional, Zheng, Shun, additional, Vespignani, Alessandro, additional, Chinazzi, Matteo, additional, Davis, Jessica T., additional, Mu, Kunpeng, additional, Pastore y Piontti, Ana, additional, Xiong, Xinyue, additional, Zheng, Andrew, additional, Baek, Jackie, additional, Farias, Vivek, additional, Georgescu, Andreea, additional, Levi, Retsef, additional, Sinha, Deeksha, additional, Wilde, Joshua, additional, Perakis, Georgia, additional, Bennouna, Mohammed Amine, additional, Nze-Ndong, David, additional, Singhvi, Divya, additional, Spantidakis, Ioannis, additional, Thayaparan, Leann, additional, Tsiourvas, Asterios, additional, Sarker, Arnab, additional, Jadbabaie, Ali, additional, Shah, Devavrat, additional, Della Penna, Nicolas, additional, Celi, Leo A., additional, Sundar, Saketh, additional, Wolfinger, Russ, additional, Osthus, Dave, additional, Castro, Lauren, additional, Fairchild, Geoffrey, additional, Michaud, Isaac, additional, Karlen, Dean, additional, Kinsey, Matt, additional, Mullany, Luke C., additional, Rainwater-Lovett, Kaitlin, additional, Shin, Lauren, additional, Tallaksen, Katharine, additional, Wilson, Shelby, additional, Lee, Elizabeth C., additional, Dent, Juan, additional, Grantz, Kyra H., additional, Hill, Alison L., additional, Kaminsky, Joshua, additional, Kaminsky, Kathryn, additional, Keegan, Lindsay T., additional, Lauer, Stephen A., additional, Lemaitre, Joseph C., additional, Lessler, Justin, additional, Meredith, Hannah R., additional, Perez-Saez, Javier, additional, Shah, Sam, additional, Smith, Claire P., additional, Truelove, Shaun A., additional, Wills, Josh, additional, Marshall, Maximilian, additional, Gardner, Lauren, additional, Nixon, Kristen, additional, Burant, John C., additional, Wang, Lily, additional, Gao, Lei, additional, Gu, Zhiling, additional, Kim, Myungjin, additional, Li, Xinyi, additional, Wang, Guannan, additional, Wang, Yueying, additional, Yu, Shan, additional, Reiner, Robert C., additional, Barber, Ryan, additional, Gakidou, Emmanuela, additional, Hay, Simon I., additional, Lim, Steve, additional, Murray, Chris, additional, Pigott, David, additional, Gurung, Heidi L., additional, Baccam, Prasith, additional, Stage, Steven A., additional, Suchoski, Bradley T., additional, Prakash, B. Aditya, additional, Adhikari, Bijaya, additional, Cui, Jiaming, additional, Rodríguez, Alexander, additional, Tabassum, Anika, additional, Xie, Jiajia, additional, Keskinocak, Pinar, additional, Asplund, John, additional, Baxter, Arden, additional, Oruc, Buse Eylul, additional, Serban, Nicoleta, additional, Arik, Sercan O., additional, Dusenberry, Mike, additional, Epshteyn, Arkady, additional, Kanal, Elli, additional, Le, Long T., additional, Li, Chun-Liang, additional, Pfister, Tomas, additional, Sava, Dario, additional, Sinha, Rajarishi, additional, Tsai, Thomas, additional, Yoder, Nate, additional, Yoon, Jinsung, additional, Zhang, Leyou, additional, Abbott, Sam, additional, Bosse, Nikos I., additional, Funk, Sebastian, additional, Hellewell, Joel, additional, Meakin, Sophie R., additional, Sherratt, Katharine, additional, Zhou, Mingyuan, additional, Kalantari, Rahi, additional, Yamana, Teresa K., additional, Pei, Sen, additional, Shaman, Jeffrey, additional, Li, Michael L., additional, Bertsimas, Dimitris, additional, Skali Lami, Omar, additional, Soni, Saksham, additional, Tazi Bouardi, Hamza, additional, Ayer, Turgay, additional, Adee, Madeline, additional, Chhatwal, Jagpreet, additional, Dalgic, Ozden O., additional, Ladd, Mary A., additional, Linas, Benjamin P., additional, Mueller, Peter, additional, Xiao, Jade, additional, Wang, Yuanjia, additional, Wang, Qinxia, additional, Xie, Shanghong, additional, Zeng, Donglin, additional, Green, Alden, additional, Bien, Jacob, additional, Brooks, Logan, additional, Hu, Addison J., additional, Jahja, Maria, additional, McDonald, Daniel, additional, Narasimhan, Balasubramanian, additional, Politsch, Collin, additional, Rajanala, Samyak, additional, Rumack, Aaron, additional, Simon, Noah, additional, Tibshirani, Ryan J., additional, Tibshirani, Rob, additional, Ventura, Valerie, additional, Wasserman, Larry, additional, O’Dea, Eamon B., additional, Drake, John M., additional, Pagano, Robert, additional, Tran, Quoc T., additional, Ho, Lam Si Tung, additional, Huynh, Huong, additional, Walker, Jo W., additional, Slayton, Rachel B., additional, Johansson, Michael A., additional, Biggerstaff, Matthew, additional, and Reich, Nicholas G., additional

Published
2022
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22. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis

Author

Aldholmi, Mohammed, primary, Ahmad, Rizwan, additional, Carretero‐Molina, Daniel, additional, Pérez‐Victoria, Ignacio, additional, Martín, Jesús, additional, Reyes, Fernando, additional, Genilloud, Olga, additional, Gourbeyre, Léa, additional, Gefflaut, Thierry, additional, Carlsson, Hanne, additional, Maklakov, Alexei, additional, O'Neill, Ellis, additional, Field, Robert A., additional, Wilkinson, Barrie, additional, O'Connell, Maria, additional, and Ganesan, A., additional

Published
2022
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23. Recombinant strains for the enhanced production of bioengineered rapalogs

Author

Kendrew, Steven G., Petkovic, Hrvoje, Gaisser, Sabine, Ready, Sarah J., Gregory, Matthew A., Coates, Nigel J., Nur-e-Alam, Mohammad, Warneck, Tony, Suthar, Dipen, Foster, Teresa A., McDonald, Leonard, Schlingman, Gerhard, Koehn, Frank E., Skotnicki, Jerauld S., Carter, Guy T., Moss, Steven J., Zhang, Ming-Qiang, Martin, Christine J., Sheridan, Rose M., and Wilkinson, Barrie

Published
2013
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24. The United States COVID-19 Forecast Hub dataset

Author

US COVID-19 Forecast Hub Consortium, Cramer, Estee Y., Huang, Yuxin, Wang, Yijin, Ray, Evan L., Cornell, Matthew, Bracher, Johannes, Brennen, Andrea, Rivadeneira, Alvaro J. Castro, Gerding, Aaron, House, Katie, Jayawardena, Dasuni, Kanji, Abdul Hannan, Khandelwal, Ayush, Le, Khoa, Mody, Vidhi, Mody, Vrushti, Niemi, Jarad, Stark, Ariane, Shah, Apurv, Wattanchit, Nutcha, Zorn, Martha W., Reich, Nicholas G., Gneiting, Tilmann, Mühlemann, Anja, Gu, Youyang, Chen, Yixian, Chintanippu, Krishna, Jivane, Viresh, Khurana, Ankita, Kumar, Ajay, Lakhani, Anshul, Mehrotra, Prakhar, Pasumarty, Sujitha, Shrivastav, Monika, You, Jialu, Bannur, Nayana, Deva, Ayush, Jain, Sansiddh, Kulkarni, Mihir, Merugu, Srujana, Raval, Alpan, Shingi, Siddhant, Tiwari, Avtansh, White, Jerome, Adiga, Aniruddha, Hurt, Benjamin, Lewis, Bryan, Marathe, Madhav, Peddireddy, Akhil Sai, Porebski, Przemyslaw, Venkatramanan, Srinivasan, Wang, Lijing, Dahan, Maytal, Fox, Spencer, Gaither, Kelly, Lachmann, Michael, Meyers, Lauren Ancel, Scott, James G., Tec, Mauricio, Woody, Spencer, Srivastava, Ajitesh, Xu, Tianjian, Cegan, Jeffrey C., Dettwiller, Ian D., England, William P., Farthing, Matthew W., George, Glover E., Hunter, Robert H., Lafferty, Brandon, Linkov, Igor, Mayo, Michael L., Parno, Matthew D., Rowland, Michael A., Trump, Benjamin D., Chen, Samuel, Faraone, Stephen V., Hess, Jonathan, Morley, Christopher P., Salekin, Asif, Wang, Dongliang, Zhang-James, Yanli, Baer, Thomas M., Corsetti, Sabrina M., Eisenberg, Marisa C., Falb, Karl, Huang, Yitao, Martin, Emily T., McCauley, Ella, Myers, Robert L., Schwarz, Tom, Gibson, Graham Casey, Sheldon, Daniel, Gao, Liyao, Ma, Yian, Wu, Dongxia, Yu, Rose, Jin, Xiaoyong, Wang, Yu-Xiang, Yan, Xifeng, Chen, YangQuan, Guo, Lihong, Zhao, Yanting, Chen, Jinghui, Gu, Quanquan, Wang, Lingxiao, Xu, Pan, Zhang, Weitong, Zou, Difan, Chattopadhyay, Ishanu, Huang, Yi, Lu, Guoqing, Pfeiffer, Ruth, Sumner, Timothy, Wang, Dongdong, Wang, Liqiang, Zhang, Shunpu, Zou, Zihang, Biegel, Hannah, Lega, Joceline, Hussain, Fazle, Khan, Zeina, Van Bussel, Frank, McConnell, Steve, Guertin, Stephanie L., Hulme-Lowe, Christopher, Nagraj, V. P., Turner, Stephen D., Bejar, Benjamín, Choirat, Christine, Flahault, Antoine, Krymova, Ekaterina, Lee, Gavin, Manetti, Elisa, Namigai, Kristen, Obozinski, Guillaume, Sun, Tao, Thanou, Dorina, Ban, Xuegang, Shi, Yunfeng, Walraven, Robert, Hong, Qi-Jun, Van De Walle, Axel, Ben-Nun, Michal, Riley, Steven, Riley, Pete, Turtle, James, Cao, Duy, Galasso, Joseph, Cho, Jae H., Jo, Areum, DesRoches, David, Forli, Pedro, Hamory, Bruce, Koyluoglu, Ugur, Kyriakides, Christina, Leis, Helen, Milliken, John, Moloney, Michael, Morgan, James, Nirgudkar, Ninad, Ozcan, Gokce, Piwonka, Noah, Ravi, Matt, Schrader, Chris, Shakhnovich, Elizabeth, Siegel, Daniel, Spatz, Ryan, Stiefeling, Chris, Wilkinson, Barrie, Wong, Alexander, Cavany, Sean, España, Guido, Moore, Sean, Oidtman, Rachel, Perkins, Alex, Ivy, Julie S., Mayorga, Maria E., Mele, Jessica, Rosenstrom, Erik T., Swann, Julie L., Kraus, Andrea, Kraus, David, Bian, Jiang, Cao, Wei, Gao, Zhifeng, Ferres, Juan Lavista, Li, Chaozhuo, Liu, Tie-Yan, Xie, Xing, Zhang, Shun, Zheng, Shun, Chinazzi, Matteo, Vespignani, Alessandro, Xiong, Xinyue, Davis, Jessica T., Mu, Kunpeng, Piontti, Ana Pastore Y, Baek, Jackie, Farias, Vivek, Georgescu, Andreea, Levi, Retsef, Sinha, Deeksha, Wilde, Joshua, Zheng, Andrew, Lami, Omar Skali, Bennouna, Amine, Ndong, David Nze, Perakis, Georgia, Singhvi, Divya, Spantidakis, Ioannis, Thayaparan, Leann, Tsiourvas, Asterios, Weisberg, Shane, Jadbabaie, Ali, Sarker, Arnab, Shah, Devavrat, Celi, Leo A., Penna, Nicolas D., Sundar, Saketh, Berlin, Abraham, Gandhi, Parth D., McAndrew, Thomas, Piriya, Matthew, Chen, Ye, Hlavacek, William, Lin, Yen Ting, Mallela, Abhishek, Miller, Ely, Neumann, Jacob, Posner, Richard, Wolfinger, Russ, Castro, Lauren, Fairchild, Geoffrey, Michaud, Isaac, Osthus, Dave, Wolffram, Daniel, Karlen, Dean, Panaggio, Mark J., Kinsey, Matt, Mullany, Luke C., Rainwater-Lovett, Kaitlin, Shin, Lauren, Tallaksen, Katharine, Wilson, Shelby, Brenner, Michael, Coram, Marc, Edwards, Jessie K., Joshi, Keya, Klein, Ellen, Hulse, Juan Dent, Grantz, Kyra H., Hill, Alison L., Kaminsky, Kathryn, Kaminsky, Joshua, Keegan, Lindsay T., Lauer, Stephen A., Lee, Elizabeth C., Lemaitre, Joseph C., Lessler, Justin, Meredith, Hannah R., Perez-Saez, Javier, Shah, Sam, Smith, Claire P., Truelove, Shaun A., Wills, Josh, Gardner, Lauren, Marshall, Maximilian, Nixon, Kristen, Burant, John C., Budzinski, Jozef, Chiang, Wen-Hao, Mohler, George, Gao, Junyi, Glass, Lucas, Qian, Cheng, Romberg, Justin, Sharma, Rakshith, Spaeder, Jeffrey, Sun, Jimeng, Xiao, Cao, Gao, Lei, Gu, Zhiling, Kim, Myungjin, Li, Xinyi, Wang, Yueying, Wang, Guannan, Wang, Lily, Yu, Shan, Jain, Chaman, Bhatia, Sangeeta, Nouvellet, Pierre, Barber, Ryan, Gaikedu, Emmanuela, Hay, Simon, Lim, Steve, Murray, Chris, Pigott, David, Reiner, Robert C., Baccam, Prasith, Gurung, Heidi L., Stage, Steven A., Suchoski, Bradley T., Fong, Chung-Yan, Yeung, Dit-Yan, Adhikari, Bijaya, Cui, Jiaming, Prakash, B. Aditya, Rodríguez, Alexander, Tabassum, Anika, Xie, Jiajia, Asplund, John, Baxter, Arden, Keskinocak, Pinar, Oruc, Buse Eylul, Serban, Nicoleta, Arik, Sercan O., Dusenberry, Mike, Epshteyn, Arkady, Kanal, Elli, Le, Long T., Li, Chun-Liang, Pfister, Tomas, Sinha, Rajarishi, Tsai, Thomas, Yoder, Nate, Yoon, Jinsung, Zhang, Leyou, Wilson, Daniel, Belov, Artur A., Chow, Carson C., Gerkin, Richard C., Yogurtcu, Osman N., Ibrahim, Mark, Lacroix, Timothee, Le, Matthew, Liao, Jason, Nickel, Maximilian, Sagun, Levent, Abbott, Sam, Bosse, Nikos I., Funk, Sebastian, Hellewell, Joel, Meakin, Sophie R., Sherratt, Katharine, Kalantari, Rahi, Zhou, Mingyuan, Karimzadeh, Morteza, Lucas, Benjamin, Ngo, Thoai, Zoraghein, Hamidreza, Vahedi, Behzad, Wang, Zhongying, Pei, Sen, Shaman, Jeffrey, Yamana, Teresa K., Bertsimas, Dimitris, Li, Michael L., Soni, Saksham, Bouardi, Hamza Tazi, Adee, Madeline, Ayer, Turgay, Chhatwal, Jagpreet, Dalgic, Ozden O., Ladd, Mary A., Linas, Benjamin P., Mueller, Peter, Xiao, Jade, Bosch, Jurgen, Wilson, Austin, Zimmerman, Peter, Wang, Qinxia, Wang, Yuanjia, Xie, Shanghong, Zeng, Donglin, Bien, Jacob, Brooks, Logan, Green, Alden, Hu, Addison J., Jahja, Maria, McDonald, Daniel, Narasimhan, Balasubramanian, Politsch, Collin, Rajanala, Samyak, Rumack, Aaron, Simon, Noah, Tibshirani, Ryan J., Tibshirani, Rob, Ventura, Valerie, Wasserman, Larry, Drake, John M., O’Dea, Eamon B., Abu-Mostafa, Yaser, Bathwal, Rahil, Chang, Nicholas A., Chitta, Pavan, Erickson, Anne, Goel, Sumit, Gowda, Jethin, Jin, Qixuan, Jo, HyeongChan, Kim, Juhyun, Kulkarni, Pranav, Lushtak, Samuel M., Mann, Ethan, Popken, Max, Soohoo, Connor, Tirumala, Kushal, Tseng, Albert, Varadarajan, Vignesh, Vytheeswaran, Jagath, Wang, Christopher, Yeluri, Akshay, Yurk, Dominic, Zhang, Michael, Zlokapa, Alexander, Pagano, Robert, Jain, Chandini, Tomar, Vishal, Ho, Lam, Huynh, Huong, Tran, Quoc, Lopez, Velma K., Walker, Jo W., Slayton, Rachel B., Johansson, Michael A., and Biggerstaff, Matthew

Subjects
ddc:510, Mathematics
Abstract

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages.

Published
2022

25. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis

Author

Ganesan, A, primary, Aldholmi, Mohammed, additional, Ahmad, Rizwan, additional, Carretero-Molina, Daniel, additional, Pérez-Victoria, Ignacio, additional, Martín, Jesús, additional, Reyes, Fernando, additional, Genilloud, Olga, additional, Gourbeyre, Léa, additional, Gefflaut, Thierry, additional, Carlsson, Hanne, additional, Maklakov, Alexei, additional, Field, Robert A., additional, O'Neill, Ellis, additional, Wilkinson, Barrie, additional, and O'Connell, Maria, additional

Published
2022
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26. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate

Author

Andexer, Jennifer N., Kendrew, Steven G., Nur-e-Alam, Mohammad, Lazos, Orestis, Foster, Teresa A., Zimmermann, Anna-Sophie, Warneck, Tony D., Suthar, Dipen, Coates, Nigel J., Koehn, Frank E., Skotnicki, Jerauld S., Carter, Guy T., Gregory, Matthew A., Martin, Christine J., Moss, Steven J., Leadlay, Peter F., Wilkinson, Barrie, and Demain, Arnold L.

Published
2011

27. Formicamycin biosynthesis involves a unique reductive ring contraction† †Electronic supplementary information (ESI) available: General remarks; full experimental details; Fig. S1–S60 and Tables S1–S5. See DOI: 10.1039/d0sc01712d

Author

Qin, Zhiwei, Devine, Rebecca, Booth, Thomas J., Farrar, Elliot H. E., Grayson, Matthew N., Hutchings, Matthew I., and Wilkinson, Barrie

Subjects
Chemistry
Abstract

Using a combination of biomimetic chemistry and molecular genetics we demonstrate that formicamycin biosynthesis proceeds via reductive Favorskii-like reaction., Fasamycin natural products are biosynthetic precursors of the formicamycins. Both groups of compounds are polyketide natural products that exhibit potent antibacterial activity despite displaying different three-dimensional topologies. We show here that transformation of fasamycin into formicamycin metabolites requires two gene products and occurs via a novel two-step ring expansion-ring contraction pathway. Deletion of forX, encoding a flavin dependent monooxygenase, abolished formicamycin production and leads to accumulation of fasamycin E. Deletion of the adjacent gene forY, encoding a flavin dependent oxidoreductase, also abolished formicamycin biosynthesis and led to the accumulation of new lactone metabolites that represent Baeyer–Villiger oxidation products of the fasamycins. These results identify ForX as a Baeyer–Villiger monooxygenase capable of dearomatizing ring C of the fasamycins. Through in vivo cross feeding and biomimetic semi-synthesis experiments we showed that these lactone products represent biosynthetic intermediates that are reduced to formicamycins in a unique reductive ring contraction reaction catalyzed by ForY.

Published
2020

28. The Biosynthesis of Aliphatic Polyketides

Author

Staunton, James, Wilkinson, Barrie, de Meijere, Armin, editor, Houk, K. N., editor, Lehn, Jean-Marie, editor, Ley, Steven V., editor, Thiem, Joachim, editor, Trost, Barry M., editor, Vögtle, Fritz, editor, Yamamoto, Hisashi, editor, Leeper, Finian J., editor, and Vederas, John C., editor

Published
1998
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29. The Biochemistry Of the Particulate Methane Monooxygenase

Author

Nguyen, Hiep-Hoa A. T., Zhu, Mei, Elliott, Sean J., Nakagawa, Kent H., Hedman, Britt, Costello, Andria M., Peeples, Tonya L., Wilkinson, Barrie, Morimoto, Hiromi, Williams, Philip G., Floss, Heinz G., Lidstrom, Mary E., Hodgson, Keith O., Chan, Sunney I., Lidstrom, Mary E., editor, and Tabita, F. Robert, editor

Published
1996
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30. Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus

Author

Gomez-Escribano, Juan Pablo, primary, Algora Gallardo, Lis, additional, Bozhüyük, Kenan A. J., additional, Kendrew, Steven G., additional, Huckle, Benjamin D., additional, Crowhurst, Nicola A., additional, Bibb, Mervyn J., additional, Collis, Andrew J., additional, Micklefield, Jason, additional, Herron, Paul R., additional, and Wilkinson, Barrie, additional

Published
2021
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32. Additional file 1 of Competition-based screening helps to secure the evolutionary stability of a defensive microbiome

Author

Worsley, Sarah F., Innocent, Tabitha M., Holmes, Neil A., Al-Bassam, Mahmoud M., Schiøtt, Morten, Wilkinson, Barrie, Murrell, J. Colin, Boomsma, Jacobus J., Yu, Douglas W., and Hutchings, Matthew I.

Abstract

Additional file 1: Supplemental tables, figures and methods referenced in the text. Fig. S1. Overview of methodology used for RNA stable isotope probing; Fig. S2. Fluorescent microscopy images of glucose water diet treatment; Fig. S3. The relationship between RNA-SIP fraction number and buoyant density; Fig. S4. 16S rRNA gene copy number across different fractions of buoyant density gradients, as determined via qPCR; Fig. S5. The atom percentage of 13C in ants, as determined by Isotope Ratio Mass Spectrometry (IRMS) analysis; Fig. S6. The expression of Kegg orthology pathway categories in Pseudonocardia symbiont strains; Fig. S7. The bioactivity of Pseudonocardia isolates against the specialized fungus-garden pathogen Escovopsis weberi; Fig. S8. Individual growth-rate experiments of Acromyrmex-resident, non-producer strains; Fig. S9. Antibiotic resistance profiles for producer, non-producer, and resident non-producer strains; Table S1. Details of ant colonies, bacterial and fungal strains, reference genomes and primers used in experiments; Table S2. Details RNA-sequencing reads from ant propleural plate samples; Table S3. Secondary metabolite BGCs in the Pseudonocardia mutualist genomes (table adapted from [32]); Table S4. Media recipes and antibiotics used in this study.

Published
2021
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37. Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US

Author

Cramer, Estee Y, primary, Ray, Evan L, additional, Lopez, Velma K, additional, Bracher, Johannes, additional, Brennen, Andrea, additional, Castro Rivadeneira, Alvaro J, additional, Gerding, Aaron, additional, Gneiting, Tilmann, additional, House, Katie H, additional, Huang, Yuxin, additional, Jayawardena, Dasuni, additional, Kanji, Abdul H, additional, Khandelwal, Ayush, additional, Le, Khoa, additional, Mühlemann, Anja, additional, Niemi, Jarad, additional, Shah, Apurv, additional, Stark, Ariane, additional, Wang, Yijin, additional, Wattanachit, Nutcha, additional, Zorn, Martha W, additional, Gu, Youyang, additional, Jain, Sansiddh, additional, Bannur, Nayana, additional, Deva, Ayush, additional, Kulkarni, Mihir, additional, Merugu, Srujana, additional, Raval, Alpan, additional, Shingi, Siddhant, additional, Tiwari, Avtansh, additional, White, Jerome, additional, Abernethy, Neil F, additional, Woody, Spencer, additional, Dahan, Maytal, additional, Fox, Spencer, additional, Gaither, Kelly, additional, Lachmann, Michael, additional, Meyers, Lauren Ancel, additional, Scott, James G, additional, Tec, Mauricio, additional, Srivastava, Ajitesh, additional, George, Glover E, additional, Cegan, Jeffrey C, additional, Dettwiller, Ian D, additional, England, William P, additional, Farthing, Matthew W, additional, Hunter, Robert H, additional, Lafferty, Brandon, additional, Linkov, Igor, additional, Mayo, Michael L, additional, Parno, Matthew D, additional, Rowland, Michael A, additional, Trump, Benjamin D, additional, Zhang-James, Yanli, additional, Chen, Samuel, additional, Faraone, Stephen V, additional, Hess, Jonathan, additional, Morley, Christopher P, additional, Salekin, Asif, additional, Wang, Dongliang, additional, Corsetti, Sabrina M, additional, Baer, Thomas M, additional, Eisenberg, Marisa C, additional, Falb, Karl, additional, Huang, Yitao, additional, Martin, Emily T, additional, McCauley, Ella, additional, Myers, Robert L, additional, Schwarz, Tom, additional, Sheldon, Daniel, additional, Gibson, Graham Casey, additional, Yu, Rose, additional, Gao, Liyao, additional, Ma, Yian, additional, Wu, Dongxia, additional, Yan, Xifeng, additional, Jin, Xiaoyong, additional, Wang, Yu-Xiang, additional, Chen, YangQuan, additional, Guo, Lihong, additional, Zhao, Yanting, additional, Gu, Quanquan, additional, Chen, Jinghui, additional, Wang, Lingxiao, additional, Xu, Pan, additional, Zhang, Weitong, additional, Zou, Difan, additional, Biegel, Hannah, additional, Lega, Joceline, additional, McConnell, Steve, additional, Nagraj, VP, additional, Guertin, Stephanie L, additional, Hulme-Lowe, Christopher, additional, Turner, Stephen D, additional, Shi, Yunfeng, additional, Ban, Xuegang, additional, Walraven, Robert, additional, Hong, Qi-Jun, additional, Kong, Stanley, additional, van de Walle, Axel, additional, Turtle, James A, additional, Ben-Nun, Michal, additional, Riley, Steven, additional, Riley, Pete, additional, Koyluoglu, Ugur, additional, DesRoches, David, additional, Forli, Pedro, additional, Hamory, Bruce, additional, Kyriakides, Christina, additional, Leis, Helen, additional, Milliken, John, additional, Moloney, Michael, additional, Morgan, James, additional, Nirgudkar, Ninad, additional, Ozcan, Gokce, additional, Piwonka, Noah, additional, Ravi, Matt, additional, Schrader, Chris, additional, Shakhnovich, Elizabeth, additional, Siegel, Daniel, additional, Spatz, Ryan, additional, Stiefeling, Chris, additional, Wilkinson, Barrie, additional, Wong, Alexander, additional, Cavany, Sean, additional, España, Guido, additional, Moore, Sean, additional, Oidtman, Rachel, additional, Perkins, Alex, additional, Kraus, David, additional, Kraus, Andrea, additional, Gao, Zhifeng, additional, Bian, Jiang, additional, Cao, Wei, additional, Ferres, Juan Lavista, additional, Li, Chaozhuo, additional, Liu, Tie-Yan, additional, Xie, Xing, additional, Zhang, Shun, additional, Zheng, Shun, additional, Vespignani, Alessandro, additional, Chinazzi, Matteo, additional, Davis, Jessica T, additional, Mu, Kunpeng, additional, y Piontti, Ana Pastore, additional, Xiong, Xinyue, additional, Zheng, Andrew, additional, Baek, Jackie, additional, Farias, Vivek, additional, Georgescu, Andreea, additional, Levi, Retsef, additional, Sinha, Deeksha, additional, Wilde, Joshua, additional, Perakis, Georgia, additional, Bennouna, Mohammed Amine, additional, Nze-Ndong, David, additional, Singhvi, Divya, additional, Spantidakis, Ioannis, additional, Thayaparan, Leann, additional, Tsiourvas, Asterios, additional, Sarker, Arnab, additional, Jadbabaie, Ali, additional, Shah, Devavrat, additional, Penna, Nicolas Della, additional, Celi, Leo A, additional, Sundar, Saketh, additional, Wolfinger, Russ, additional, Osthus, Dave, additional, Castro, Lauren, additional, Fairchild, Geoffrey, additional, Michaud, Isaac, additional, Karlen, Dean, additional, Kinsey, Matt, additional, Mullany, Luke C., additional, Rainwater-Lovett, Kaitlin, additional, Shin, Lauren, additional, Tallaksen, Katharine, additional, Wilson, Shelby, additional, Lee, Elizabeth C, additional, Dent, Juan, additional, Grantz, Kyra H, additional, Hill, Alison L, additional, Kaminsky, Joshua, additional, Kaminsky, Kathryn, additional, Keegan, Lindsay T, additional, Lauer, Stephen A, additional, Lemaitre, Joseph C, additional, Lessler, Justin, additional, Meredith, Hannah R, additional, Perez-Saez, Javier, additional, Shah, Sam, additional, Smith, Claire P, additional, Truelove, Shaun A, additional, Wills, Josh, additional, Marshall, Maximilian, additional, Gardner, Lauren, additional, Nixon, Kristen, additional, Burant, John C., additional, Wang, Lily, additional, Gao, Lei, additional, Gu, Zhiling, additional, Kim, Myungjin, additional, Li, Xinyi, additional, Wang, Guannan, additional, Wang, Yueying, additional, Yu, Shan, additional, Reiner, Robert C, additional, Barber, Ryan, additional, Gakidou, Emmanuela, additional, Hay, Simon I., additional, Lim, Steve, additional, Murray, Chris J.L., additional, Pigott, David, additional, Gurung, Heidi L, additional, Baccam, Prasith, additional, Stage, Steven A, additional, Suchoski, Bradley T, additional, Prakash, B. Aditya, additional, Adhikari, Bijaya, additional, Cui, Jiaming, additional, Rodríguez, Alexander, additional, Tabassum, Anika, additional, Xie, Jiajia, additional, Keskinocak, Pinar, additional, Asplund, John, additional, Baxter, Arden, additional, Oruc, Buse Eylul, additional, Serban, Nicoleta, additional, Arik, Sercan O, additional, Dusenberry, Mike, additional, Epshteyn, Arkady, additional, Kanal, Elli, additional, Le, Long T, additional, Li, Chun-Liang, additional, Pfister, Tomas, additional, Sava, Dario, additional, Sinha, Rajarishi, additional, Tsai, Thomas, additional, Yoder, Nate, additional, Yoon, Jinsung, additional, Zhang, Leyou, additional, Abbott, Sam, additional, Bosse, Nikos I, additional, Funk, Sebastian, additional, Hellewell, Joel, additional, Meakin, Sophie R, additional, Sherratt, Katharine, additional, Zhou, Mingyuan, additional, Kalantari, Rahi, additional, Yamana, Teresa K, additional, Pei, Sen, additional, Shaman, Jeffrey, additional, Li, Michael L, additional, Bertsimas, Dimitris, additional, Lami, Omar Skali, additional, Soni, Saksham, additional, Bouardi, Hamza Tazi, additional, Ayer, Turgay, additional, Adee, Madeline, additional, Chhatwal, Jagpreet, additional, Dalgic, Ozden O, additional, Ladd, Mary A, additional, Linas, Benjamin P, additional, Mueller, Peter, additional, Xiao, Jade, additional, Wang, Yuanjia, additional, Wang, Qinxia, additional, Xie, Shanghong, additional, Zeng, Donglin, additional, Green, Alden, additional, Bien, Jacob, additional, Brooks, Logan, additional, Hu, Addison J, additional, Jahja, Maria, additional, McDonald, Daniel, additional, Narasimhan, Balasubramanian, additional, Politsch, Collin, additional, Rajanala, Samyak, additional, Rumack, Aaron, additional, Simon, Noah, additional, Tibshirani, Ryan J, additional, Tibshirani, Rob, additional, Ventura, Valerie, additional, Wasserman, Larry, additional, O’Dea, Eamon B, additional, Drake, John M, additional, Pagano, Robert, additional, Tran, Quoc T, additional, Tung Ho, Lam Si, additional, Huynh, Huong, additional, Walker, Jo W, additional, Slayton, Rachel B, additional, Johansson, Michael A, additional, Biggerstaff, Matthew, additional, and Reich, Nicholas G, additional

Published
2021
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38. Roles of rapH and rapG in positive regulation of rapamycin biosynthesis in Streptomyces hygroscopicus

Author

Kuscer, Enej, Coates, Nigel, Challis, Iain, Gregory, Matt, Wilkinson, Barrie, Sheridan, Rose, and Petkovic, Hrvoje

Subjects
Rapamycin -- Research, Biosynthesis -- Research, Streptomyces -- Genetic aspects, Streptomyces -- Research, Biological sciences
Abstract

Rapamycin is an important macrocyclic polyketide produced by Streptoyces hygroscopicus and showing immunosuppressive, antifungal, and antitumor activities as well as displaying anti-inflammatory and neuroregenerative properties. The immense pharmacological potential of rapamycin has led to the production of an array of analogues, including through genetic engineering of the rapamycin biosynthetic gene cluster. This cluster contains several putative regulatory, genes. Based on DNA sequence analysis, the products of genes rapH and rapG showed high similarities with two different families of transcriptional activators, LAL and AraC, respectively. Overexpression of either gene resulted in a substantial increase in rapamycin biosynthesis, confirming their positive regulator role, while deletion of both from the chromosome of S. hygroscopicus resulted in a complete loss of antibiotic production. Complementation studies indicated an essential role of the RapG regulator for rapamycin biosynthesis and a supportive role of RapH. A direct effect of rapH and rapG gene products on the promoter of the rapamycin polyketide synthase operon, rapA-rapB, was observed using the chalcone synthase gene rppA as a reporter system.

Published
2007

39. An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotransferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics

Author

Neary, Joanne M., Powell, Amanda, Gordon, Lyndsey, Milne, Claire, Flett, Fiona, Wilkinson, Barrie, Smith, Colin P., and Micklefield, Jason

Subjects
Asparagine -- Research, Biosynthesis -- Research, Calpain -- Research, Phosphotransferases -- Research, Biological sciences
Abstract

Nonribosomal peptides contain a wide range of unusual non-proteinogenic amino acid residues. As a result, these complex natural products are amongst the most structurally diverse secondary metabolites in nature, and possess a broad spectrum of biological activities. [beta]-Hydroxylation of amino acid precursors or peptidyl residues and their subsequent processing by downstream tailoring enzymes are some of the most common themes in the biosynthetic diversification of these therapeutically important peptides. Identification and characterization of the biosynthetic intermediates and enzymes involved in these processes are thus pivotal in understanding nonribosomal peptide assembly and modification. To this end, the putative asparaginyl oxygenase- and 3-hydroxyasparaginyl phosphotransferase-encoding genes hasP and asnO were separately deleted from the calcium-dependent antibiotic (CDA) biosynthetic gene cluster of Streptomyces coelicolor. Whilst the parent strains produce a number of 3-hydroxyasparagine- and 3-phosphohydroxyasparagine-containing CDAs, the [DELTA]hasP mutants produce exclusively non-phosphorylated CDAs. On the other hand, [DELTA] asnO mutants produce several new Asn-containing CDAs not present in the wild-type, which retain calcium-dependent antimicrobial activity. This confirms that AsnO and HasP are required for the [beta]-hydroxylation and phosphorylation of the Asn residue within CDA.

Published
2007

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