13 Works

Multi-site assessment of reproducibility in high-content live cell imaging data

Jianjiang Hu, Xavier Serra-Picamal, Gert-Jan Bakker, Marleen Van Troys, Sabina Winograd-katz, Nil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama Clucas, Anna Dowbaj, Erik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai & Staffan Strömblad
This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data".
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental...

Data from: The clathrin adaptor complex AP-2 mediates endocytosis of BRASSINOSTEROID INSENSITIVE1 in Arabidopsis

Simone Di Rubbo, Niloufer G. Irani, Soo Youn Kim, Zheng-Yi Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, Geert Persiau, Dominique Eeckhout, Sibu Simon, Kyungyoung Song, Jürgen Kleine-Vehn, Jiří Friml, Geert De Jaeger, Daniël Van Damme, Inhwan Hwang & Eugenia Russinova
Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized....

Multi-site assessment of reproducibility in high-content live cell imaging data

Jianjiang Hu, Xavier Serra-Picamal, Gert-Jan Bakker, Marleen Van Troys, Sabina Winograd-katz, Nil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama Clucas, Anna Dowbaj, Erik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai & Staffan Strömblad
This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data".
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental...

Multi-site assessment of reproducibility in high-content live cell imaging data

Jianjiang Hu, Xavier Serra-Picamal, Gert-Jan Bakker, Marleen Van Troys, Sabina Winograd-katz, Nil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama Clucas, Anna Dowbaj, Erik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai & Staffan Strömblad
This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data".
The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental...

Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species

Canan Külahoglu, Manuel Sommer, Janina Maß, Simon Schliesky, Barbara Berckmans, Elsa Gongora-Castillo, C. Robin Buell, Rüdiger Simon, Lieven De Veylder, Andrea Bräutigam, Andreas P. M. Weber, Alisandra K. Denton & Thomas J. Wrobel
C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species,...

Data from: Fitness trade-offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa

Kristine Stepanyan, Tom Wenseleers, Edgar A. Duéñez-Guzmán, Frédéric Muratori, Bram Van Den Bergh, Natalie Verstraeten, Luc De Meester, Kevin J. Verstrepen, Maarten Fauvart & Jan Michiels
Microbial populations often contain a fraction of slow-growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels...

Data from: A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis

Ruben Vanholme, Véronique Storme, Bartel Vanholme, Lisa Sundin, Jørgen Holst Christensen, Geert Goeminne, Claire Halpin, Antje Rohde, Kris Morreel & Wout Boerjan
Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant’s response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (PAL1 , PAL2, C4H, 4CL1, 4CL2, CCoAOMT1, CCR1, F5H1,...

Data from: Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

Rahul Bhosale, Jeremy B. Jewell, Jens Hollunder, Abraham J. K. Koo, Marnik Vuylsteke, Tom Michoel, Pierre Hilson, Alain Goossens, Gregg A. Howe, John Browse & Steven Maere
Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene...

Data from: Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberley M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu … & Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient...

Data from: The origin of floral organ identity quartets

Philip Ruelens, Zhicheng Zhang, Hilda Van Mourik, Steven Maere, Kerstin Kaufmann & Koen Geuten
The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting...

Data from: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

Nicolas Blondiaux, Martin Moune, Matthieu Desroses, Rosangela Frita, Marion Flipo, Vanessa Mathys, Karine Soetaert, Mehdi Kiass, Vincent Delorme, Kamel Djaout, Vincent Trebosc, Christian Kemmer, René Wintjens, Alexandre Wohlkönig, Rudy Antoine, Ludovic Huot, David Hot, Mireia Coscolla, Julia Feldmann, Sebastien Gagneux, Camille Locht, Priscille Brodin, Marc Gitzinger, Benoit Deprez, Nicolas Willand … & Alain R. Baulard
Antibiotic resistance is one of the biggest threats to human health globally. Alarmingly, multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis have now spread worldwide. Some key antituberculosis antibiotics are prodrugs, for which resistance mechanisms are mainly driven by mutations in the bacterial enzymatic pathway required for their bioactivation. We have developed drug-like molecules that activate a cryptic alternative bioactivation pathway of ethionamide in M. tuberculosis, circumventing the classic activation pathway in which resistance mutations have now...

Data from: The role of cuticular hydrocarbons in mate recognition in Drosophila suzukii

Yannick Snellings, Beatriz Herrera, Bruna Wildemann, Melissa Beelen, Liesbeth Zwarts, Tom Wenseleers & Patrick Callaerts
Cuticular hydrocarbons (CHCs) play a central role in the chemical communication of many insects. In Drosophila suzukii, an economically important pest insect, very little is known about chemical communication and the possible role of CHCs. In this study, we identified 60 CHCs of Drosophila suzukii and studied their changes in function of age (maturation), sex and interactions with the opposite sex. We demonstrate that age (maturation) is the key factor driving changes in the CHC...

Data from: Randomized phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis

James F. Howard, Vera Bril, Ted M. Burns, Renato Mantegazza, Malgorzata Bilinska, Andrzej Szczudlik, Said Beydoun, Francisco Javier Rodriguez De Rivera Garrido, Fredrik Piehl, Mariarosa Rottoli, Philip Van Damme, Tuan Vu, Amelia Evoli, Miriam Freimer, Tahseen Mozaffar, E. Sally Ward, Torsten Dreier, Peter Ulrichts, Katrien Verschueren, Antonio Guglietta, Hans De Haard, Nicolas Leupin & Jan J. G. M. Verschuuren
Objective: To investigate safety and explore efficacy of efgartigimod (ARGX-113), an anti-neonatal Fc receptor immunoglobulin G1 Fc fragment, in patients with generalized myasthenia gravis (gMG) with a history of anti-acetylcholine receptor (AChR) autoantibodies, who were on stable standard-of-care myasthenia gravis (MG) treatment. Methods: A phase 2, exploratory, randomized, double-blind, placebo-controlled, 15-center study is described. Eligible patients were randomly assigned (1:1) to receive 4 doses over a 3-week period of either 10 mg/kg IV efgartigimod or...

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Affiliations

  • Flanders Institute for Biotechnology
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