Article
Biochemistry & Molecular Biology
Rui Shao, Banushree Kumar, Katja Lidschreiber, Michael Lidschreiber, Patrick Cramer, Simon J. Elsasser
Summary: This study uses transient transcriptome sequencing and RNA polymerase II occupancy profiling to investigate the pluripotent states of mouse embryonic stem cells. It reveals that RNA synthesis and turnover rates are globally reduced in the ground and paused states, accompanied by a decrease in polymerase elongation velocity and alterations in the Pol II termination window. The findings suggest that transcription activity plays a crucial role in determining mRNA levels, and changes in transcription kinetics lead to different pluripotent states.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Immunology
Jiyoon Park, Min-Ji Son, Chun-Chang Ho, Su-Hyeon Lee, Yuna Kim, Jaekyeung An, Sang-Kyou Lee
Summary: This study demonstrates that ndSTAT1-TMD can modulate the functions of Th1 and Th17 cells, making it a potential new therapeutic agent for Th1/17 cell-mediated autoimmune diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Lin Zhao, Wenxin Zhang, Fengming Luan, Xi Chen, Honghai Wu, Qiaojun He, Qinjie Weng, Ling Ding, Bo Yang
Summary: PD-L1 plays a critical role in tumor immune escape and can be targeted by blocking antibodies or suppressing its expression. Butein, a natural compound, has been shown to reduce PD-L1 expression and enhance the killing ability of CD8+ T cells, offering a potential strategy for anti-tumor therapy.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Hematology
Mehmet Emrah Selli, Jack H. Landmann, Marina Terekhova, John Lattin, Amanda Heard, Yu-Sung Hsu, Tien-Ching Chang, Jufang Chang, John Warrington, Helen Ha, Natalie Kingston, Graham Hogg, Michael Slade, Melissa M. Berrien-Elliott, Mark Foster, Samantha Kersting-Schadek, Agata Gruszczynska, David DeNardo, Todd A. Fehniger, Maxim Artyomov, Nathan Singh
Summary: In this study, an in vitro model was developed to induce T-cell dysfunction through chronic CAR activation, and the impact of CAR costimulatory domains on T-cell failure was investigated. The study found that chronic activation of CD28-based CARs resulted in T-cell exhaustion and dysfunction. In contrast, 41BB-based CARs activated a different molecular program and led to the differentiation of T cells into a novel cell state.
Article
Multidisciplinary Sciences
Weibing Yang, Sandra Cortijo, Niklas Korsbo, Pawel Roszak, Katharina Schiessl, Aram Gurzadyan, Raymond Wightman, Henrik Jonsson, Elliot Meyerowitz
Summary: Mitogens trigger cell division in animals, while in plants, cytokinins derived from adenine stimulate cell proliferation. Cytokinin signaling in Arabidopsis SAM is shown to regulate cell division by promoting nuclear shuttling of MYB3R4, a transcription factor activating mitotic gene expression. Rapid nuclear accumulation of MYB3R4 at G2-to-M transition, associated with a peak in cytokinin concentration, initiates a transcriptional cascade driving mitosis and cytokinesis, mimicking the effects of enhanced cell proliferation and meristem growth.
Article
Immunology
Rahul Sharma, Ryan M. Smolkin, Priyanka Chowdhury, Keith Conrad Fernandez, Youngjun Kim, Montserrat Cols, William Alread, Wei-Feng Yen, Wei Hu, Zhong-Min Wang, Sara Violante, Ronan Chaligne, Ming O. Li, Justin R. Cross, Jayanta Chaudhuri
Summary: Sharma et al. identify an early metabolic checkpoint dependent upon lactate dehydrogenase for newly activated B cells to enter germinal centers. The metabolic requirements of naive and activated B cells differ and are regulated by niche and cellular interactions.
Article
Multidisciplinary Sciences
Francois G. C. Blot, Joshua J. White, Amy van Hattem, Licia Scotti, Vaishnavi Balaji, Youri Adolfs, R. Jeroen Pasterkamp, Chris I. De Zeeuw, Martijn Schonewille
Summary: The classification of neuronal subpopulations has advanced, but its impact on behavior is uncertain. The flocculus of the cerebellum is a suitable model for studying neuronal subpopulations. Through genetic targeting, the study demonstrates separate micromodules within the flocculus that involve distinct subpopulations of Purkinje cells. Furthermore, optogenetic excitation of these subpopulations produces movements with different kinematic profiles. These findings highlight the importance of subpopulations in mediating specific aspects of cerebellar behavior.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Izabel Patik, Naresh S. Redhu, Alal Eran, Bin Bao, Anubhab Nandy, Ying Tang, Shorouk El Sayed, Zeli Shen, Jonathan Glickman, James G. Fox, Scott B. Snapper, Bruce H. Horwitz
Summary: Loss of IL-10R function leads to severe early onset colitis and the accumulation of immature inflammatory colonic macrophages. IL-10R inhibits STAT1 signaling in newly recruited colonic macrophages, thereby interfering with the development of an inflammatory phenotype. Additionally, IL-10R inhibits the generation of cell extrinsic signals that promote the accumulation of immature macrophages.
MUCOSAL IMMUNOLOGY
(2022)
Article
Cell Biology
Shaili D. D. Patel, Deepti Anand, Hozumi Motohashi, Fumiki Katsuoka, Masayuki Yamamoto, Salil A. A. Lachke
Summary: Deficiency of Mafg and Mafk proteins causes lens development defects and abnormal cell morphology. Loss of Mafg and Mafk leads to multilayered lens epithelium and misexpression of genes associated with cytoskeleton, cell cycle, and extracellular matrix.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Jennifer Hammelman, Tulsi Patel, Michael Closser, Hynek Wichterle, David Gifford
Summary: This study compares nine computational methods for identifying reprogramming factors for cell differentiation. The researchers found that methods using chromatin accessibility performed the best, with an average identification rate of 50-60% of reprogramming factors in the top ten candidates. Among the chromatin accessibility methods, DeepAccess and diffTF showed the highest correlation with the ranked significance of transcription factor candidates. AME and diffTF were identified as optimal methods for transcription factor recovery, allowing for systematic prioritization of candidates in the design of new reprogramming protocols.
Article
Multidisciplinary Sciences
Marco D. Carpenter, Delaney K. Fischer, Shuo Zhang, Allison M. Bond, Kyle S. Czarnecki, Morgan T. Woolf, Hongjun Song, Elizabeth A. Heller
Summary: The authors optimized a hybrid protocol, ICuRuS, to profile epigenetic features in neuronal subtypes from a single mouse. This method allows for robust epigenetic profiling at cell-type specific resolution.
NATURE COMMUNICATIONS
(2022)
Article
Developmental Biology
Izumi Oda-Ishii, Deli Yu, Yutaka Satou
Summary: The study reveals that Zic-r.a activates the posterior fate-related gene Tbx6-r.b by binding to non-canonical motifs, distinct from the typical motif. These non-canonical motifs have weaker affinity for Zic-r.a and only activate Tbx6-r.b in cells with abundant Zic-r.a expression. Additionally, Zic-r.a activates two sets of genes at different timepoints by recognizing two distinct motifs.
Article
Oncology
Ruizhen Ren, Yuanna Du, Xing Niu, Rukun Zang
Summary: In thyroid cancer, ZFPM2-AS1 acts as an oncogene mediated by STAT1, weakening the inhibitory effect of miR-515-5p on TUSC3 and promoting cancer progression. Thus, ZFPM2-AS1 may serve as a potential biomarker for thyroid cancer.
Review
Immunology
Hiroyuki Hosokawa, Ellen Rothenberg
Summary: Transcription factors play essential roles in early thymic development to establish T cell lineage identity by controlling the activities of specific genomic loci. The interactions between inherited epigenetic states, transcription factor-DNA binding affinity thresholds, and influences of given transcription factors on other factors in the same cells determine T cell identity and make the lineage choice irreversible.
NATURE REVIEWS IMMUNOLOGY
(2021)
Article
Immunology
Gloria Yiu, Tue Kruse Rasmussen, Brandon L. Tsai, Vivian K. Diep, David J. Haddon, Jennifer Tsoi, Gopika D. Miller, Begona Comin-Anduix, Bent Deleuran, Gay M. Crooks, Paul J. Utz
Summary: This study investigates the role of interferon (IFN) signaling in systemic lupus erythematosus (SLE). The results show a correlation between IFN signaling and clinical manifestations as well as immune factors in SLE, suggesting potential targets for future therapeutic approaches.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sarah Kube, Nils Hersch, Elena Naumovska, Thomas Gensch, Johnny Hendriks, Arne Franzen, Lisa Landyogt, Jan-Peter Siebrasse, Ulrich Kubitscheck, Bernd Hoffmann, Rudolf Merkel, Agnes Csiszar
Article
Multidisciplinary Sciences
Jonas Doerr, Martin Karl Schwarz, Dirk Wiedermann, Anke Leinhaas, Alina Jakobs, Florian Schloen, Inna Schwarz, Michael Diedenhofen, Nils Christian Braun, Philipp Koch, Daniel A. Peterson, Ulrich Kubitscheck, Mathias Hoehn, Oliver Bruestle
NATURE COMMUNICATIONS
(2017)
Letter
Multidisciplinary Sciences
Andreas Begitt, James Cavey, Mathias Droescher, Uwe Vinkemeier
NATURE COMMUNICATIONS
(2018)
Article
Biochemical Research Methods
Lisa Landvogt, Jan Andreas Ruland, Christian Montellese, Jan Peter Siebrasse, Ulrike Kutay, Ulrich Kubitscheck
Article
Neurosciences
Jana Buergers, Irina Pavlova, Juan E. Rodriguez-Gatica, Christian Henneberger, Marc Oeller, Jan A. Ruland, Jan P. Siebrasse, Ulrich Kubitscheck, Martin K. Schwarz
Article
Neurosciences
Bhuvaneswari Nagarajan, Alexander Harder, Anna Japp, Felix Haeberlein, Enrico Mingardo, Henning Kleinert, Oeznur Yilmaz, Angelika Zoons, Birgit Rau, Andrea Christ, Ulrich Kubitscheck, Britta Eiberger, Roger Sandhoff, Matthias Eckhardt, Dieter Hartmann, Benjamin Odermatt
Article
Optics
Anne Stockhausen, Jana Buergers, Juan Eduardo Rodriguez-Gatica, Jens Schweihoff, Rudolf Merkel, Jens Markus Prigge, Martin Karl Schwarz, Ulrich Kubitscheck
Article
Multidisciplinary Sciences
Fabian Grein, Anna Mueller, Katharina M. Scherer, Xinliang Liu, Kevin C. Ludwig, Anna Kloeckner, Manuel Strach, Hans-Georg Sahl, Ulrich Kubitscheck, Tanja Schneider
NATURE COMMUNICATIONS
(2020)
Article
Urology & Nephrology
Annika Moller-Kerutt, Juan E. Rodriguez-Gatica, Karin Wacker, Rohan Bhatia, Jan-Peter Siebrasse, Nanda Boon, Veerle Van Marck, Peter Boor, Ulrich Kubitscheck, Jan Wijnholds, Hermann Pavenstadt, Thomas Weide
Summary: Mutations in the CRB2 gene can cause SRNS, and CRB2 is an essential component of podocyte slit diaphragm, interacting with Nephrin. Crb2(podKO) mice exhibit proteinuria, disordered foot processes, and increased renal injury and inflammatory markers.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Review
Biochemistry & Molecular Biology
Martin K. Schwarz, Ulrich Kubitscheck
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jan Andreas Ruland, Annika Marie Krueger, Kerstin Doerner, Rohan Bhatia, Sabine Wirths, Daniel Poetes, Ulrike Kutay, Jan Peter Siebrasse, Ulrich Kubitscheck
Summary: The study visualizes the export of single pre-60S particles through nuclear pore complexes using super-resolution confocal microscopy and single molecule tracking. They found that successful export events show maximum particle accumulation in the center of the pore, while unsuccessful export terminates within the nuclear basket. The export process has a single rate-limiting step and lasts approximately 24 milliseconds, with only about 1/3 of attempted export events being successful.
NATURE COMMUNICATIONS
(2021)
Article
Developmental Biology
Juan Eduardo Rodriguez-Gatica, Vira Iefremova, Liubov Sokhranyaeva, Si Wah Christina Au Yeung, Yannik Breitkreuz, Oliver Brustle, Martin Karl Schwarz, Ulrich Kubitscheck
Summary: Organoids, derived from stem cells, provide a new approach to model human development and disease. By using light-sheet fluorescence expansion microscopy, cellular and subcellular structural details of organoids can be observed in three dimensions, allowing for qualitative and quantitative assessment in developmental and disease-related studies.
Article
Anatomy & Morphology
Alexander Harder, Bhuvaneswari Nagarajan, Benjamin Odermatt, Ulrich Kubitscheck
Summary: Light sheet fluorescence microscopy (LSFM) is an essential tool in developmental biology for improving image contrast. This study presents an automatic synchronization method between excitation laser and detector, which does not require additional hardware components. A specific noise-tolerant focus metric was developed for calculating relative displacement, and an image analysis approach was used to determine laser tilt.
MICROSCOPY RESEARCH AND TECHNIQUE
(2023)
Article
Optics
Anne Stockhausen, Juan Eduardo Rodriguez-Gatica, Jens Schweihoff, Martin Karl Schwarz, Ulrich Kubitscheck
Summary: Traditional light sheet microscopy has a trade-off between the width of the light sheet and the usable field of view. To overcome this, low-diverging Airy beams have been introduced, but they suffer from side lobes that degrade image contrast. In this study, an Airy beam light sheet microscope was constructed, and a deep learning image deconvolution method was developed to remove the effects of side lobes. The combination of Airy beam light sheet microscopy and deep learning deconvolution allows for rapid and high-quality imaging of large volumes.
Article
Multidisciplinary Sciences
Jan -Samuel Puls, Dominik Brajtenbach, Tanja Schneider, Ulrich Kubitscheck, Fabian Grein
Summary: Bacterial cell wall biosynthesis is an important target of antibiotics, and its coordination with cell division is crucial. However, the role of peptidoglycan synthesis in cell division and the impact of antibiotics on this coordination are not fully understood. By visualizing key proteins in Staphylococcus aureus, we found that antibiotics targeting peptidoglycan synthesis can arrest cell division within minutes. Our work identifies cell division as a key target of these antibiotics and shows that peptidoglycan synthesis is essential for septum constriction throughout cell division of S. aureus.