Recently added

DSpace/Manakin Repository

UMC Repository: Recent submissions

  • Cellular communication in a 'virtual lab': going beyond the classical ligand-receptor interaction 
    Gladka, Monika M (Oxford University Press, 2020-06-01)
  • An optimized dissociation protocol for FACS-based isolation of rare cell types from Caenorhabditis elegans L1 larvae 
    Fernandes Póvoa, Euclides E; Ebbing, Annabel L P; Betist, Marco C; van der Veen, Christa; Korswagen, Hendrik C (Elsevier, 2020)
    Single-cell isolation and transcriptomic analysis of a specific cell type or tissue offers the possibility of studying cell function and heterogeneity in time-dependent processes with remarkable resolution. The reduced ...
  • An in vitro model of early anteroposterior organization during human development 
    Moris, Naomi; Anlas, Kerim; van den Brink, Susanne C; Alemany, Anna; Schröder, Julia; Ghimire, Sabitri; Balayo, Tina; van Oudenaarden, Alexander; Martinez Arias, Alfonso (Nature Research, 2020-06-18)
    The body plan of the mammalian embryo is shaped through the process of gastrulation, an early developmental event that transforms an isotropic group of cells into an ensemble of tissues that is ordered with reference to ...
  • Single-Cell Resolution Three-Dimensional Imaging of Intact Organoids 
    van Ineveld, Ravian L; Ariese, Hendrikus C R; Wehrens, Ellen J; Dekkers, Johanna F; Rios, Anne C (MYJoVE Corporation, 2020-06-05)
    Organoid technology, in vitro 3D culturing of miniature tissue, has opened a new experimental window for cellular processes that govern organ development and function as well as disease. Fluorescence microscopy has played ...
  • Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment 
    Eckersley-Maslin, Mélanie A; Parry, Aled; Blotenburg, Marloes; Krueger, Christel; Ito, Yoko; Franklin, Valar Nila Roamio; Narita, Masashi; D'Santos, Clive S; Reik, Wolf (Nature Research, 2020-08)
    How the epigenetic landscape is established in development is still being elucidated. Here, we uncover developmental pluripotency associated 2 and 4 (DPPA2/4) as epigenetic priming factors that establish a permissive ...
  • Phosphatidic acid-dependent localization and basal de-phosphorylation of RA-GEFs regulate lymphocyte trafficking 
    Ishihara, Sayaka; Sato, Tsuyoshi; Du, Guangwei; Guardavaccaro, Daniele; Nakajima, Akihiko; Sawai, Satoshi; Kataoka, Tohru; Katagiri, Koko (BioMed Central Ltd., 2020-06-29)
    BACKGROUND: Lymphocytes circulate between peripheral lymphoid tissues via blood and lymphatic systems, and chemokine-induced migration is important in trafficking lymphocytes to distant sites. The small GTPase Rap1 is ...
  • Pharmaceutical-Grade Rigosertib Is a Microtubule-Destabilizing Agent 
    Jost, Marco; Chen, Yuwen; Gilbert, Luke A; Horlbeck, Max A; Krenning, Lenno; Menchon, Grégory; Rai, Ankit; Cho, Min Y; Stern, Jacob J; Prota, Andrea E; Kampmann, Martin; Akhmanova, Anna; Steinmetz, Michel O; Tanenbaum, Marvin E; Weissman, Jonathan S (Cell Press, 2020-07-02)
    We recently used CRISPRi/a-based chemical-genetic screens and cell biological, biochemical, and structural assays to determine that rigosertib, an anti-cancer agent in phase III clinical trials, kills cancer cells by ...
  • mRNA structural dynamics shape Argonaute-target interactions 
    Ruijtenberg, Suzan; Sonneveld, Stijn; Cui, Tao Ju; Logister, Ive; de Steenwinkel, Dion; Xiao, Yao; MacRae, Ian J; Joo, Chirlmin; Tanenbaum, Marvin E (Nature Research, 2020-09)
    Small interfering RNAs (siRNAs) promote RNA degradation in a variety of processes and have important clinical applications. siRNAs direct cleavage of target RNAs by guiding Argonaute2 (AGO2) to its target site. Target site ...
  • Intestinal organoids as tools for enriching and studying specific and rare cell types: advances and future directions 
    Boonekamp, Kim E; Dayton, Talya L; Clevers, Hans (Oxford University Press, 2020-08-01)
  • Temporal precision of molecular events with regulation and feedback 
    Gupta, Shivam; Fancher, Sean; Korswagen, Hendrik C; Mugler, Andrew (American Physical Society, 2020-06-26)
    Cellular behaviors such as migration, division, and differentiation rely on precise timing, and yet the molecular events that govern these behaviors are highly stochastic. We investigate regulatory strategies that decrease ...
  • Thermal proteome profiling in zebrafish reveals effects of napabucasin on retinoic acid metabolism 
    Leijten, Niels M; Bakker, Petra; Spaink, Herman P; den Hertog, Jeroen; Lemeer, Simone (American Society for Biochemistry and Molecular Biology Inc., 2021-02)
    Thermal proteome profiling (TPP) allows for the unbiased detection of drug–target protein engagements in vivo. Traditionally, 1 cell type is used for TPP studies, with the risk of missing important differentially expressed ...
  • Relationship Between Early Functional and Structural Brain Developments and Brain Injury in Preterm Infants 
    De Wel, O; Van Huffel, S; Lavanga, M; Jansen, K; Dereymaeker, A; Dudink, J; Gui, L; Hüppi, P S; de Vries, L S; Naulaers, G; Benders, M J N L; Tataranno, M L (Springer New York, 2021-08)
    BACKGROUND: Recent studies explored the relationship between early brain function and brain morphology, based on the hypothesis that increased brain activity can positively affect structural brain development and that ...
  • An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells 
    Lamers, Mart M; van der Vaart, Jelte; Knoops, Kèvin; Riesebosch, Samra; Breugem, Tim I; Mykytyn, Anna Z; Beumer, Joep; Schipper, Debby; Bezstarosti, Karel; Koopman, Charlotte D; Groen, Nathalie; Ravelli, Raimond B G; Duimel, Hans Q; Demmers, Jeroen A A; Verjans, Georges M G M; Koopmans, Marion P G; Muraro, Mauro J; Peters, Peter J; Clevers, Hans; Haagmans, Bart L (Springer Science and Business Media Deutschland GmbH, 2021-03-01)
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which may result in acute respiratory distress syndrome (ARDS), multiorgan failure, and death. The alveolar epithelium ...
  • SIRT1 inhibitors mitigate radiation-induced GI syndrome by enhancing intestinal-stem-cell survival 
    Fu, Guoxiang; Chen, Shengzhi; Liang, Liping; Li, Xiaomeng; Tang, Peiyuan; Rao, Xinxin; Pan, Mengxue; Xu, Xiaoya; Li, Yuanchuang; Yao, Ye; Zhou, Yi; Gao, Jun; Mo, Shaobo; Cai, Sanjun; Peng, Junjie; Zhang, Zhen; Clevers, Hans; Gao, Jianjun; Hua, Guoqiang (Elsevier Ireland Ltd, 2021-03-31)
    High-dose radiation exposure induces gastrointestinal (GI) stem cell death, resulting in denudation of the intestinal mucosa and lethality from GI syndrome, for which there is currently no effective therapy. Studying an ...
  • Attach and stretch: Emerging roles for genome-lamina contacts in shaping the 3D genome 
    Rullens, Pim M J; Kind, Jop (Elsevier Limited, 2021-06)
    A large proportion of the metazoan genome is spatially segregated at the nuclear periphery through genomic contacts with the nuclear lamina, a thin meshwork of lamin filaments that lines the inner-nuclear membrane. ...
  • Establishment of Pancreatic Organoids from Normal Tissue and Tumors 
    Driehuis, Else; Gracanin, Ana; Vries, Robert Gerhardus Jacob; Clevers, Hans; Boj, Sylvia Fernández (Cell Press, 2020-12-18)
    Establishment of patient-derived adult stem cell-based pancreatic (tumor) organoids was first described in 2015. Since then, multiple laboratories have demonstrated the robustness of this method. We recently described the ...
  • BAZ2A safeguards genome architecture of ground-state pluripotent stem cells 
    Dalcher, Damian; Tan, Jennifer Yihong; Bersaglieri, Cristiana; Peña-Hernández, Rodrigo; Vollenweider, Eva; Zeyen, Stefan; Schmid, Marc W; Bianchi, Valerio; Butz, Stefan; Roganowicz, Marcin; Kuzyakiv, Rostyslav; Baubec, Tuncay; Marques, Ana Claudia; Santoro, Raffaella (Springer Science and Business Media Deutschland GmbH, 2020-12-01)
    Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison ...
  • L-Cell Differentiation Is Induced by Bile Acids Through GPBAR1 and Paracrine GLP-1 and Serotonin Signaling 
    Lund, Mari Lilith; Sorrentino, Giovanni; Egerod, Kristoffer Lihme; Kroone, Chantal; Mortensen, Brynjulf; Knop, Filip Krag; Reimann, Frank; Gribble, Fiona M; Drucker, Daniel J; de Koning, Eelco J P; Schoonjans, Kristina; Bäckhed, Fredrik; Schwartz, Thue W; Petersen, Natalia (American Diabetes Association Inc., 2020-04)
    Glucagon-like peptide 1 (GLP-1) mimetics are effective drugs for treatment of type 2 diabetes, and there is consequently extensive interest in increasing endogenous GLP-1 secretion and L-cell abundance. Here we identify ...
  • Publisher Correction: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids 
    van den Brink, Susanne C; Alemany, Anna; van Batenburg, Vincent; Moris, Naomi; Blotenburg, Marloes; Vivié, Judith; Baillie-Johnson, Peter; Nichols, Jennifer; Sonnen, Katharina F; Martinez Arias, Alfonso; van Oudenaarden, Alexander (Nature Research, 2020-03-19)
    In this Article, owing to errors during the production process, the text ‘n = 25,202’ was erroneously obscuring the top left of Figs. 1a and 2a (in Fig. 1a, this text was duplicated, and in Fig. 2a, this text was inadvertently ...
  • Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr+ Progenitors 
    Wang, Daisong; Wang, Jingqiang; Bai, Lanyue; Pan, Hong; Feng, Hua; Clevers, Hans; Zeng, Yi Arial (Elsevier, 2020-03-19)
    It has generally proven challenging to produce functional β cells in vitro. Here, we describe a previously unidentified protein C receptor positive (Procr+) cell population in adult mouse pancreas through single-cell RNA ...