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Utrecht University Repository: Recent submissions

  • Artificial surface labelling of Escherichia coli with StrepTagII antigen to study how monoclonal antibodies drive complement-mediated killing 
    Muts, Remy M; den Boer, Maurits A; Bardoel, Bart W; Aerts, Piet C; de Haas, Carla J C; Heck, Albert J R; Rooijakkers, Suzan H M; Heesterbeek, Dani A C (NLM (Medline), 2023-11-01)
    Antibodies play a key role in the immune defence against Gram-negative bacteria. After binding to bacterial surface antigens, IgG and IgM can activate the complement system and trigger formation of lytic membrane attack ...
  • Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants? 
    Caspi, Yaron; Pantazopoulou, Chrysoula (Chrysa); Prompers, Jeanine; Pieterse, Corné M.J.; Pol, Hilleke E. Hulshoff; Kajala, Kaisa (eLife Sciences Publications, 2023-06-20)
    Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the ...
  • Embodiment in distributed information processing: Solid plants versus liquid ant colonies 
    Van Schijndel, Laura; Snoek, Basten L.; Ten Tusscher, Kirsten (Cambridge University Press, 2022-11-28)
    Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised ...
  • GH3-mediated auxin inactivation attenuates multiple stages of lateral root development 
    Wang, Qing; De Gernier, Hugues; Duan, Xingliang; Xie, Yuanming; Geelen, Danny; Hayashi, Ken-Ishiro; Xuan, Wei; Geisler, Markus; Ten Tusscher, Kirsten; Beeckman, Tom; Vanneste, Steffen (Blackwell Publishing Ltd, 2023-12)
    Lateral root (LR) positioning and development rely on the dynamic interplay between auxin production, transport but also inactivation. Nonetheless, how the latter affects LR organogenesis remains largely uninvestigated. ...
  • Penetration of Nanobody-Dextran Polymer Conjugates through Tumor Spheroids 
    Bitsch, Peter; Baum, Eva S.; Beltrán Hernández, Irati; Bitsch, Sebastian; Harwood, Jakob; Oliveira, Sabrina; Kolmar, Harald (American Chemical Society, 2023-10)
    Here we report the generation of nanobody dextran polymer conjugates (dextraknobs) that are loaded with small molecules, i.e., fluorophores or photosensitizers, for potential applications in cancer diagnostics and therapy. ...
  • Biased cultural transmission of a social custom in chimpanzees 
    van Leeuwen, Edwin J C; Hoppitt, William (American Association for the Advancement of Science, 2023-02-15)
    Cultural transmission studies in animals have predominantly focused on identifying between-group variation in tool-use techniques, while immaterial cultures remain understudied despite their potential for highlighting ...
  • Food sharing with friends and acquaintances: A study in preschool boys and girls 
    Hallers-Haalboom, Elizabeth T; Vermande, Marjolijn M; van Leeuwen, Edwin J C; Sterck, Elisabeth H M (Frontiers Media S.A., 2023-03-09)
    INTRODUCTION: The current study examined whether preschoolers in a (semi-)natural situation shared more food with friends or acquaintances, and whether this was different between boys and girls, older and younger children, ...
  • Chimpanzee communities differ in their inter- and intrasexual social relationships 
    Rawlings, Bruce S; van Leeuwen, Edwin J C; Davila-Ross, Marina (Springer, 2023-03)
    Male and female human social bonding strategies are culturally shaped, in addition to being genetically rooted. Investigating nonhuman primate bonding strategies across sex groups allows researchers to assess whether, as ...
  • Proteomics on malignant pleural effusions reveals ERα loss in metastatic breast cancer associates with SGK1–NDRG1 deregulation 
    Mayayo-Peralta, Isabel; Debets, Donna O.; Prekovic, Stefan; Schuurman, Karianne; Beerthuijzen, Suzanne; Almekinders, Mathilde; Sanders, Joyce; Moelans, Cathy B.; Saleiro, Sandra; Wesseling, Jelle; van Diest, Paul J.; Henrique, Rui; Jerónimo, Carmen; Altelaar, Maarten; Zwart, Wilbert (John Wiley and Sons Ltd, 2024-01-04)
    Breast cancer (BCa) is a highly heterogeneous disease, with hormone receptor status being a key factor in patient prognostication and treatment decision-making. The majority of primary tumours are positive for oestrogen ...
  • PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription 
    Mayayo-Peralta, Isabel; Gregoricchio, Sebastian; Schuurman, Karianne; Yavuz, Selçuk; Zaalberg, Anniek; Kojic, Aleksandar; Abbott, Nina; Geverts, Bart; Beerthuijzen, Suzanne; Siefert, Joseph; Severson, Tesa M.; van Baalen, Martijn; Hoekman, Liesbeth; Lieftink, Cor; Altelaar, Maarten; Beijersbergen, Roderick L.; Houtsmuller, Adriaan B.; Prekovic, Stefan; Zwart, Wilbert (Oxford University Press, 2023-10-13)
    How steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, ...
  • Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity 
    Prekovic, Stefan; Chalkiadakis, Theofilos; Roest, Merel; Roden, Daniel; Lutz, Catrin; Schuurman, Karianne; Opdam, Mark; Hoekman, Liesbeth; Abbott, Nina; Tesselaar, Tanja; Wajahat, Maliha; Dwyer, Amy R.; Mayayo-Peralta, Isabel; Gomez, Gabriela; Altelaar, Maarten; Beijersbergen, Roderick; Győrffy, Balázs; Young, Leonie; Linn, Sabine; Jonkers, Jos; Tilley, Wayne; Hickey, Theresa; Vareslija, Damir; Swarbrick, Alexander; Zwart, Wilbert (Wiley-Blackwell, 2023-12-07)
    Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative ...
  • Cryptic genetic variation of expression quantitative trait locus architecture revealed by genetic perturbation in Caenorhabditis elegans 
    van Wijk, Marijke H; Riksen, Joost A G; Elvin, Mark; Poulin, Gino B; Maulana, Muhammad I; Kammenga, Jan E; Snoek, Basten L; Sterken, Mark G (Genetics Society of America, 2023-05)
    Genetic perturbation in different genetic backgrounds can cause a range of phenotypes within a species. These phenotypic differences can be the result of the interaction between the genetic background and the perturbation. ...
  • Subtype-specific kinase dependency regulates growth and metastasis of poor-prognosis mesenchymal colorectal cancer 
    Buikhuisen, Joyce Y.; Barila, Patricia M. Gomez; Cameron, Kate; Suijkerbuijk, Saskia J. E.; Lieftink, Cor; Franco, Simone di; Garcia, Ana Krotenberg; Castro, Rebeca Uceda; Lenos, Kristiaan J.; Nijman, Lisanne E.; Torang, Arezo; Longobardi, Ciro; Jong, Joan H. de; Dekker, Daniëlle; Stassi, Giorgio; Vermeulen, Louis; Beijersbergen, Roderick L.; Rheenen, Jacco van; Huveneers, Stephan; Medema, Jan Paul (BioMed Central, 2023-12)
    Background: Colorectal cancer (CRC) can be divided into four consensus molecular subtypes (CMS), each with distinct biological features. CMS4 is associated with epithelial-mesenchymal transition and stromal infiltration ...
  • Delayed abscission in animal cells – from development to defects 
    Kodba, Snježana; Chaigne, Agathe (Company of Biologists Ltd, 2023-07-01)
    Cell division involves separating the genetic material and cytoplasm of a mother cell into two daughter cells. The last step of cell division, abscission, consists of cutting the cytoplasmic bridge, a microtubule-rich ...
  • A quick, cheap, and reliable protocol for immunofluorescence of pluripotent and differentiating mouse embryonic stem cells in 2D and 3D colonies 
    Kodba, Snježana; Chaigne, Agathe (Cell Press, 2023-03-17)
    Immunofluorescent labeling is a widely used method to visualize endogenous proteins. It can be expensive and difficult to stain mouse embryonic stem cells (mESCs) because they require expensive growth media, prefer specific ...
  • Target of rapamycin signaling couples energy to oxygen sensing to modulate hypoxic gene expression in <i>Arabidopsis</i> 
    Kunkowska, Alicja Barbara; Fontana, Fabrizia; Betti, Federico; Soeur, Raphael; Beckers, Gerold; Meyer, Christian; Jaeger, Geert De; Weits, Daniël; ELENA, LORETI; Perata, Pierdomenico (National Academy of Sciences, 2023-01-17)
    Plants respond to oxygen deprivation by activating the expression of a set of hypoxia-responsive genes (HRGs). The master regulator of this process is a small group of transcription factors belonging to group VII of the ...
  • Dim artificial light at night alters gene expression rhythms and growth in a key seagrass species (Posidonia oceanica) 
    Dalle, Carbonare L; Basile, A; Rindi, Luca; Bulleri, F; Hamedeh, H; Iacopino, S; Shukla, V; Weits, DA; Lombardi, L; Sbrana, A; Benedetti-Cecchi, Lisandro; Giuntoli, B; Licausi, F; Maggi, E (NLM (Medline), 2023-06-30)
    Artificial light at night (ALAN) is a globally spreading anthropogenic stressor, affecting more than 20% of coastal habitats. The alteration of the natural light/darkness cycle is expected to impact the physiology of ...
  • Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics 
    Pantazopoulou, Chrysoula (Chrysa); Buti, Sara; Nguyen, Chi Tam; Oskam, Lisa; Weits, Daniël; Farmer, Edward; Kajala, Kaisa; Pierik, Ronald (Nature Publishing Group, 2023-12)
    Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred ...
  • Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes 
    Eme, Laura; Tamarit, Daniel; Caceres, Eva F.; Stairs, Courtney W.; Anda, Valerie De; Schön, Max E.; Seitz, Kiley W.; Dombrowski, Nina; Lewis, William H.; Homa, Felix; Saw, Jimmy H.; Lombard, Jonathan; Nunoura, Takuro; Li, Wen-Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Banfield, Jillian F.; John, Emily St; Reysenbach, Anna-Louise; Stott, Matthew B.; Schramm, Andreas; Kjeldsen, Kasper U.; Teske, Andreas P.; Baker, Brett J.; Ettema, Thijs J. G. (Nature Research, 2023-06-29)
    In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal ...
  • Necessity Entrepreneurship 
    O'Donnell, Philip; Leger, Margot; O'Gorman, Colm; Clinton, Eric (Academy of Management, 2024-01)
    Over the past two decades, necessity entrepreneurs—those who engage in entrepreneurship because of a belief that decent or desirable livelihood alternatives do not exist for them —have become increasingly visible in the ...