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4. Continuous downstream processing

Author

Jungbauer, Alois, Satzer, Peter, Duerauer, Astrid, Azevedo, Ana, Aires-Barros, Raquel, Nilsson, Bernt, Farid, Suzy, Goldrick, Stephen, Ottens, Marcel, Sponchioni, Mattia, and Marcelo Fernandez Lahore, Hector

Published
2024
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8. SPRTN patient variants cause global-genome DNA-protein crosslink repair defects

Author

Pedro Weickert, Hao-Yi Li, Maximilian J. Götz, Sophie Dürauer, Denitsa Yaneva, Shubo Zhao, Jacqueline Cordes, Aleida C. Acampora, Ignasi Forne, Axel Imhof, and Julian Stingele

Subjects
Science
Abstract

Abstract DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.

Published
2023
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10. Comprehensive Comparison of Baculoviral and Plasmid Gene Delivery in Mammalian Cells

Author

Maria Toth, Manuel Reithofer, Gregory Dutra, Patricia Pereira Aguilar, Astrid Dürauer, and Reingard Grabherr

Subjects
BacMam, baculovirus, transfection, transduction, protein production, expression enhancement, Microbiology, QR1-502
Abstract

(1) Recombinant protein production in mammalian cells is either based on transient transfection processes, often inefficient and underlying high batch-to-batch variability, or on laborious generation of stable cell lines. Alternatively, BacMam, a transduction process using the baculovirus, can be employed. (2) Six transfecting agents were compared to baculovirus transduction in terms of transient and stable protein expression characteristics of the model protein ACE2-eGFP using HEK293-6E, CHO-K1, and Vero cell lines. Furthermore, process optimization such as expression enhancement using sodium butyrate and TSA or baculovirus purification was assessed. (3) Baculovirus transduction efficiency was superior to all transfection agents for all cell lines. Transduced protein expression was moderate, but an 18-fold expression increase was achieved using the enhancer sodium butyrate. Ultracentrifugation of baculovirus from a 3.5 L bioreactor significantly improved the transduction efficiency and protein expression. Stable cell lines were obtained with each baculovirus transduction, yet stable cell line generation after transfection was highly unreliable. (4) This study demonstrated the superiority of the BacMam platform to standard transfections. The baculovirus efficiently transduced an array of cell lines both transiently and stably and achieved the highest efficiency for all tested cell lines. The feasibility of the scale-up of baculovirus production was demonstrated and the possibility of baculovirus purification was successfully explored.

Published
2024
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11. A national-scale land cover reference dataset from local crowdsourcing initiatives in Indonesia

Author

Hadi, Ping Yowargana, Muhammad Thoha Zulkarnain, Fathir Mohamad, Bunga K. Goib, Paul Hultera, Tobias Sturn, Mathias Karner, Martina Dürauer, Linda See, Steffen Fritz, Adis Hendriatna, Afi Nursafingi, Dian Nuraini Melati, F. V. Astrolabe Sian Prasetya, Ita Carolita, Kiswanto, Muhammad Iqbal Firdaus, Muhammad Rosidi, and Florian Kraxner

Subjects
Science
Abstract

Measurement(s) land cover Technology Type(s) visual interpretation of satellite imagery Sample Characteristic - Location Indonesia

Published
2022
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12. Humoral immune response to SARS-CoV-2 third vaccination in patients with multiple sclerosis and healthy controls: A prospective multicenter study

Author

Krajnc, Nik, Hegen, Harald, Traxler, Gerhard, Leutmezer, Fritz, Di Pauli, Franziska, Kornek, Barbara, Rommer, Paulus, Zulehner, Gudrun, Riedl, Katharina, Dürauer, Sophie, Bauer, Angelika, Kratzwald, Sarah, Klotz, Sigrid, Winklehner, Michael, Deisenhammer, Florian, Guger, Michael, Höftberger, Romana, Berger, Thomas, and Bsteh, Gabriel

Published
2022
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14. Global forest management data for 2015 at a 100 m resolution

Author

Myroslava Lesiv, Dmitry Schepaschenko, Marcel Buchhorn, Linda See, Martina Dürauer, Ivelina Georgieva, Martin Jung, Florian Hofhansl, Katharina Schulze, Andrii Bilous, Volodymyr Blyshchyk, Liudmila Mukhortova, Carlos Luis Muñoz Brenes, Leonid Krivobokov, Stephan Ntie, Khongor Tsogt, Stephan Alexander Pietsch, Elena Tikhonova, Moonil Kim, Fulvio Di Fulvio, Yuan-Fong Su, Roma Zadorozhniuk, Flavius Sorin Sirbu, Kripal Panging, Svitlana Bilous, Sergii B. Kovalevskii, Florian Kraxner, Ahmed Harb Rabia, Roman Vasylyshyn, Rekib Ahmed, Petro Diachuk, Serhii S. Kovalevskyi, Khangsembou Bungnamei, Kusumbor Bordoloi, Andrii Churilov, Olesia Vasylyshyn, Dhrubajyoti Sahariah, Anatolii P. Tertyshnyi, Anup Saikia, Žiga Malek, Kuleswar Singha, Roman Feshchenko, Reinhard Prestele, Ibrar ul Hassan Akhtar, Kiran Sharma, Galyna Domashovets, Seth A. Spawn-Lee, Oleksii Blyshchyk, Oleksandr Slyva, Mariia Ilkiv, Oleksandr Melnyk, Vitalii Sliusarchuk, Anatolii Karpuk, Andrii Terentiev, Valentin Bilous, Kateryna Blyshchyk, Maxim Bilous, Nataliia Bogovyk, Ivan Blyshchyk, Sergey Bartalev, Mikhail Yatskov, Bruno Smets, Piero Visconti, Ian Mccallum, Michael Obersteiner, and Steffen Fritz

Subjects
Science
Abstract

Measurement(s) forest management type Technology Type(s) Geo-Wiki toolbox

Published
2022
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15. Drivers of tropical forest loss between 2008 and 2019

Author

Juan Carlos Laso Bayas, Linda See, Ivelina Georgieva, Dmitry Schepaschenko, Olga Danylo, Martina Dürauer, Hedwig Bartl, Florian Hofhansl, Roman Zadorozhniuk, Maksym Burianchuk, Flavius Sirbu, Brigitte Magori, Kateryna Blyshchyk, Volodymyr Blyshchyk, Ahmed Harb Rabia, Chandra Kant Pawe, Yuan-Fong Su, Merajuddin Ahmed, Kripal Panging, Oleksandr Melnyk, Olesia Vasylyshyn, Roman Vasylyshyn, Andrii Bilous, Svitlana Bilous, Krishna Das, Reinhard Prestele, Ana Pérez-Hoyos, Khangsembou Bungnamei, Andrii Lashchenko, Maryna Lakyda, Ivan Lakyda, Oleksandr Serediuk, Galyna Domashovets, Yuriy Yurchuk, Michèle Koper, and Steffen Fritz

Subjects
Science
Abstract

Measurement(s) drivers of tree loss Technology Type(s) visual inspection of very high resolution satellite imagery Sample Characteristic - Organism trees Sample Characteristic - Environment Forests Sample Characteristic - Location Tropics and subtropics

Published
2022
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16. Global forest management data for 2015 at a 100 m resolution

Author

Lesiv, Myroslava, Schepaschenko, Dmitry, Buchhorn, Marcel, See, Linda, Dürauer, Martina, Georgieva, Ivelina, Jung, Martin, Hofhansl, Florian, Schulze, Katharina, Bilous, Andrii, Blyshchyk, Volodymyr, Mukhortova, Liudmila, Brenes, Carlos Luis Muñoz, Krivobokov, Leonid, Ntie, Stephan, Tsogt, Khongor, Pietsch, Stephan Alexander, Tikhonova, Elena, Kim, Moonil, Di Fulvio, Fulvio, Su, Yuan-Fong, Zadorozhniuk, Roma, Sirbu, Flavius Sorin, Panging, Kripal, Bilous, Svitlana, Kovalevskii, Sergii B., Kraxner, Florian, Rabia, Ahmed Harb, Vasylyshyn, Roman, Ahmed, Rekib, Diachuk, Petro, Kovalevskyi, Serhii S., Bungnamei, Khangsembou, Bordoloi, Kusumbor, Churilov, Andrii, Vasylyshyn, Olesia, Sahariah, Dhrubajyoti, Tertyshnyi, Anatolii P., Saikia, Anup, Malek, Žiga, Singha, Kuleswar, Feshchenko, Roman, Prestele, Reinhard, Akhtar, Ibrar ul Hassan, Sharma, Kiran, Domashovets, Galyna, Spawn-Lee, Seth A., Blyshchyk, Oleksii, Slyva, Oleksandr, Ilkiv, Mariia, Melnyk, Oleksandr, Sliusarchuk, Vitalii, Karpuk, Anatolii, Terentiev, Andrii, Bilous, Valentin, Blyshchyk, Kateryna, Bilous, Maxim, Bogovyk, Nataliia, Blyshchyk, Ivan, Bartalev, Sergey, Yatskov, Mikhail, Smets, Bruno, Visconti, Piero, Mccallum, Ian, Obersteiner, Michael, and Fritz, Steffen

Published
2022
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17. Drivers of tropical forest loss between 2008 and 2019

Author

Laso Bayas, Juan Carlos, See, Linda, Georgieva, Ivelina, Schepaschenko, Dmitry, Danylo, Olga, Dürauer, Martina, Bartl, Hedwig, Hofhansl, Florian, Zadorozhniuk, Roman, Burianchuk, Maksym, Sirbu, Flavius, Magori, Brigitte, Blyshchyk, Kateryna, Blyshchyk, Volodymyr, Rabia, Ahmed Harb, Pawe, Chandra Kant, Su, Yuan-Fong, Ahmed, Merajuddin, Panging, Kripal, Melnyk, Oleksandr, Vasylyshyn, Olesia, Vasylyshyn, Roman, Bilous, Andrii, Bilous, Svitlana, Das, Krishna, Prestele, Reinhard, Pérez-Hoyos, Ana, Bungnamei, Khangsembou, Lashchenko, Andrii, Lakyda, Maryna, Lakyda, Ivan, Serediuk, Oleksandr, Domashovets, Galyna, Yurchuk, Yuriy, Koper, Michèle, and Fritz, Steffen

Published
2022
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22. Sensors and chemometrics in downstream processing.

Author

Dürauer, Astrid, Jungbauer, Alois, and Scharl, Theresa

Abstract

The biopharmaceutical industry is still running in batch mode, mostly because it is highly regulated. In the past, sensors were not readily available and in‐process control was mainly executed offline. The most important product parameters are quantity, purity, and potency, in addition to adventitious agents and bioburden. New concepts using disposable single‐use technologies and integrated bioprocessing for manufacturing will dominate the future of bioprocessing. To ensure the quality of pharmaceuticals, initiatives such as Process Analytical Technologies, Quality by Design, and Continuous Integrated Manufacturing have been established. The aim is that these initiatives, together with technology development, will pave the way for process automation and autonomous bioprocessing without any human intervention. Then, real‐time release would be realized, leading to a highly predictive and robust biomanufacturing system. The steps toward such automated and autonomous bioprocessing are reviewed in the context of monitoring and control. It is possible to integrate real‐time monitoring gradually, and it should be considered from a soft sensor perspective. This concept has already been successfully implemented in other industries and requires relatively simple model training and the use of established statistical tools, such as multivariate statistics or neural networks. This review describes a scenario for integrating soft sensors and predictive chemometrics into modern process control. This is exemplified by selective downstream processing steps, such as chromatography and membrane filtration, the most common unit operations for separation of biopharmaceuticals. [ABSTRACT FROM AUTHOR]

Published
2024
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25. A Continental Assessment of the Drivers of Tropical Deforestation With a Focus on Protected Areas

Author

Steffen Fritz, Juan Carlos Laso Bayas, Linda See, Dmitry Schepaschenko, Florian Hofhansl, Martin Jung, Martina Dürauer, Ivelina Georgieva, Olga Danylo, Myroslava Lesiv, and Ian McCallum

Subjects
deforestation, crowdsourcing, drivers of deforestation, remote sensing, deforestation in protected areas, Geo-Wiki, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Deforestation contributes to global greenhouse gas emissions and must be reduced if the 1.5°C limit to global warming is to be realized. Protected areas represent one intervention for decreasing forest loss and aiding conservation efforts, yet there is intense human pressure on at least one-third of protected areas globally. There have been numerous studies addressing the extent and identifying drivers of deforestation at the local, regional, and global level. Yet few have focused on drivers of deforestation in protected areas in high thematic detail. Here we use a new crowdsourced data set on drivers of tropical forest loss for the period 2008–2019, which has been collected using the Geo-Wiki crowdsourcing application for visual interpretation of very high-resolution imagery by volunteers. Extending on the published data on tree cover and forest loss from the Global Forest Change initiative, we investigate the dominant drivers of deforestation in tropical protected areas situated within 30° north and south of the equator. We find the deforestation rate in protected areas to be lower than the continental average for the Latin Americas (3.4% in protected areas compared to 5.4%) and Africa (3.3% compared to 3.9%), but it exceeds that of unprotected land in Asia (8.5% compared to 8.1%). Consistent with findings from foregoing studies, we also find that pastures and other subsistence agriculture are the dominant deforestation driver in the Latin Americas, while forest management, oil palm, shifting cultivation and other subsistence agriculture dominate in Asia, and shifting cultivation and other subsistence agriculture is the main driver in Africa. However, we find contrasting results in relation to the degree of protection, which indicate that the rate of deforestation in Latin America and Africa in strictly protected areas might even exceed that of areas with no strict protection. This crucial finding highlights the need for further studies based on a bottom up crowdsourced, data collection approach, to investigate drivers of deforestation both inside and outside protected areas.

Published
2022
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26. Bending the curve of terrestrial biodiversity needs an integrated strategy

Author

Leclère, David, Obersteiner, Michael, Barrett, Mike, Butchart, Stuart H. M., Chaudhary, Abhishek, De Palma, Adriana, DeClerck, Fabrice A. J., Di Marco, Moreno, Doelman, Jonathan C., Dürauer, Martina, Freeman, Robin, Harfoot, Michael, Hasegawa, Tomoko, Hellweg, Stefanie, Hilbers, Jelle P., Hill, Samantha L. L., Humpenöder, Florian, Jennings, Nancy, Krisztin, Tamás, Mace, Georgina M., Ohashi, Haruka, Popp, Alexander, Purvis, Andy, Schipper, Aafke M., Tabeau, Andrzej, Valin, Hugo, van Meijl, Hans, van Zeist, Willem-Jan, Visconti, Piero, Alkemade, Rob, Almond, Rosamunde, Bunting, Gill, Burgess, Neil D., Cornell, Sarah E., Di Fulvio, Fulvio, Ferrier, Simon, Fritz, Steffen, Fujimori, Shinichiro, Grooten, Monique, Harwood, Thomas, Havlík, Petr, Herrero, Mario, Hoskins, Andrew J., Jung, Martin, Kram, Tom, Lotze-Campen, Hermann, Matsui, Tetsuya, Meyer, Carsten, Nel, Deon, Newbold, Tim, Schmidt-Traub, Guido, Stehfest, Elke, Strassburg, Bernardo B. N., van Vuuren, Detlef P., Ware, Chris, Watson, James E. M., Wu, Wenchao, and Young, Lucy

Published
2020
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33. Lessons learned in developing reference data sets with the contribution of citizens: the Geo-Wiki experience

Author

Linda See, Juan Carlos Laso Bayas, Myroslava Lesiv, Dmitry Schepaschenko, Olga Danylo, Ian McCallum, Martina Dürauer, Ivelina Georgieva, Dahlia Domian, Dilek Fraisl, Gerid Hager, Santosh Karanam, Inian Moorthy, Tobias Sturn, Anto Subash, and Steffen Fritz

Subjects
remote sensing, reference data, citizen science, crowdsourcing, land cover, environmental monitoring, Environmental technology. Sanitary engineering, TD1-1066, Environmental sciences, GE1-350, Science, Physics, QC1-999
Abstract

The development of remotely sensed products such as land cover requires large amounts of high-quality reference data, needed to train remote sensing classification algorithms and for validation. However, due to the lack of sharing and the high costs associated with data collection, particularly ground-based information, the amount of reference data available has not kept up with the vast increase in the availability of satellite imagery, e.g. from Landsat, Sentinel and Planet satellites. To fill this gap, the Geo-Wiki platform for the crowdsourcing of reference data was developed, involving visual interpretation of satellite and aerial imagery. Here we provide an overview of the crowdsourcing campaigns that have been run using Geo-Wiki over the last decade, including the amount of data collected, the research questions driving the campaigns and the outputs produced such as new data layers (e.g. a global map of forest management), new global estimates of areas or percentages of land cover/land use (e.g. the amount of extra land available for biofuels) and reference data sets, all openly shared. We demonstrate that the amount of data collected and the scientific advances in the field of land cover and land use would not have been possible without the participation of citizens. A relatively conservative estimate reveals that citizens have contributed more than 5.3 years of the data collection efforts of one person over short, intensive campaigns run over the last decade. We also provide key observations and lessons learned from these campaigns including the need for quality assurance mechanisms linked to incentives to participate, good communication, training and feedback, and appreciating the ingenuity of the participants.

Published
2022
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37. Comprehensive Comparison of Baculoviral and Plasmid Gene Delivery in Mammalian Cells.

Author

Toth, Maria, Reithofer, Manuel, Dutra, Gregory, Pereira Aguilar, Patricia, Dürauer, Astrid, and Grabherr, Reingard

Subjects
SODIUM butyrate, CELL lines, CHO cell, PROTEIN expression, RECOMBINANT proteins, TISSUE arrays
Abstract

(1) Recombinant protein production in mammalian cells is either based on transient transfection processes, often inefficient and underlying high batch-to-batch variability, or on laborious generation of stable cell lines. Alternatively, BacMam, a transduction process using the baculovirus, can be employed. (2) Six transfecting agents were compared to baculovirus transduction in terms of transient and stable protein expression characteristics of the model protein ACE2-eGFP using HEK293-6E, CHO-K1, and Vero cell lines. Furthermore, process optimization such as expression enhancement using sodium butyrate and TSA or baculovirus purification was assessed. (3) Baculovirus transduction efficiency was superior to all transfection agents for all cell lines. Transduced protein expression was moderate, but an 18-fold expression increase was achieved using the enhancer sodium butyrate. Ultracentrifugation of baculovirus from a 3.5 L bioreactor significantly improved the transduction efficiency and protein expression. Stable cell lines were obtained with each baculovirus transduction, yet stable cell line generation after transfection was highly unreliable. (4) This study demonstrated the superiority of the BacMam platform to standard transfections. The baculovirus efficiently transduced an array of cell lines both transiently and stably and achieved the highest efficiency for all tested cell lines. The feasibility of the scale-up of baculovirus production was demonstrated and the possibility of baculovirus purification was successfully explored. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Global reference data set for validating ESA WorldCereal temporary cropland extent

Author

Lesiv, M., Dürauer, M., Georgieva, I., Bilous, A., Laso Bayas, J.C., Fritz, S., Lesiv, M., Dürauer, M., Georgieva, I., Bilous, A., Laso Bayas, J.C., and Fritz, S.

Abstract

IIASA team has created a new validation data set, which is completely independent from all other existing maps or reference data sets, and which is in line with the cropland definitions and mapping period of the WorldCereal products. To decide if this is an active cropland in each period, the experts looked at very high-resolution Google historical imagery and Google Street level images, Microsoft Bing images, ESRI imagery, Planet historical data, Sentinel-2 time series, and Modis NDVI time series. The experts were asked to label 5 by 5 Sentinel pixels (each pixel 10m by 10m) either as winter crops, or as summer crops, or as maize (if this was possible), or as active crops (where it was not possible to confirm a growing season, e.g. overlap between seasons was too big or crop fields were too small in size), or as no crops, or as not sure where was too little information available for 2021. There was additional question on irrigation system, either circle, or other irrigation, or rainfed, or not sure.

Published
2023

42. Validation data set on land cover changes for RapidAI4EO project

Author

Lesiv, M., Bun, H., Dürauer, M., Lesiv, M., Bun, H., and Dürauer, M.

Abstract

This is a reference data set collected for validation of the monthly land cover maps at a 3m and at a 10m resolution produced in the WP5. The reference data set has been collected by using Geo-Wiki toolbox for visual interpretation of very high-resolution images, including Planet data and Google maps. The data set has been collected over 3 AOIs. Each reference sample site corresponds to a 30m-by-30m box and includes information about monthly land cover type over the period 2018-2020. Land cover legend is the same as in ESA WorldCover map at a 10m resolution (https://worldcover2021.esa.int/).

Published
2023

45. Explainable deep learning for improved real-time monitoring of a chromatographic protein A capture step

Author

Theresa Scharl, Matthias Medl, Friedrich Leisch, and Astrid Dürauer

Abstract

Model-based real-time monitoring of biopharmaceutical production is a major step towards Quality-by-Design in this field and the fundament for model predictive control. Data-driven models have been proven a viable option to model bioprocesses. In the high stakes setting of biopharmaceutical manufacturing it is essential to ensure high model accuracy, robustness and explainability. That is only possible when (i) the data used for modeling is of high quality, (ii) state-of-the-art modeling algorithms are employed and (iii) the input-output mapping of the model has been characterized. In this study we evaluate the accuracy of multiple data-driven models in predicting the monoclonal antibody concentration, dsDNA concentration, host cell protein concentration, and high molecular weight impurity content during elution from a protein A chromatography capture step. We demonstrate how permutation/occlusion-based methods can be used to gain understanding on dependencies learned by of one of the most complex data-driven models; convolutional neural network ensembles. Finally, we present a workflow to test the model behavior in case of simulated sensor fouling and failure. This study represents a major step towards improved viability of data-driven models in biopharmaceutical manufacturing.

Published
2023
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49. Development of a global hybrid forest mask through the synergy of remote sensing, crowdsourcing and FAO statistics

Author

Schepaschenko, Dmitry, See, Linda, Lesiv, Myroslava, McCallum, Ian, Fritz, Steffen, Salk, Carl, Moltchanova, Elena, Perger, Christoph, Shchepashchenko, Maria, Shvidenko, Anatoly, Kovalevskyi, Sergii, Gilitukha, Dmytro, Albrecht, Franziska, Kraxner, Florian, Bun, Andriy, Maksyutov, Shamil, Sokolov, Alexander, Dürauer, Martina, Obersteiner, Michael, Karminov, Viktor, and Ontikov, Petr

Published
2015
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50. Monitoring Product Quantity, Purity and Potency of Biopharmaceuticals in Real-time by Predictive Chemometrics and Soft sensors

Author

Astrid Dürauer, Alois Jungbauer, and Theresa Scharl

Abstract

The biopharmaceutical industry is still running in batch mode, mostly because it is a highly regulated industry sector. In the past, sensors were not readily available and in-process control was mainly executed off-line. The most important product parameters are quantity, purity and potency besides adventitious agents and bioburden. There is increasing economic pressure on time-to-market and also on the environmental sustainability of biopharmaceutical manufacturing. New concepts for manufacturing using disposable single-use technologies and integrated bioprocessing will dominate the future of bioprocessing. In order to ensure the quality of pharmaceuticals initiatives such as Process Analytical Technologies, Quality by Design and Continuous Integrated Manufacturing have been established. The vision must be that these initiatives together with technology development pave the way for process automation and autonomous bioprocessing without any human intervention. Then a real-time release would be realized leading to a highly predictive and robust biomanufacturing system. The steps toward such automated and autonomous bioprocessing are reviewed in context of monitoring and control. Starting from statistical treatment of single and multiple sensors, establishing soft sensors with predictive chemometrics and hybrid models. A scenario is described how to integrate soft sensors and predictive chemometrics into modern process control. This will be exemplified by selective downstream processing steps such as chromatography and membrane filtration, the most common unit operations for separation of biopharmaceuticals.

Published
2023
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