Article
Biochemistry & Molecular Biology
Fares Saidi, Nicolas Y. Jolivet, David J. Lemon, Arnaldo Nakamura, Akeisha M. Belgrave, Anthony G. Garza, Frederic J. Veyrier, Salim T. Islam
Summary: EPS layers on bacterial cell surface play a crucial role in biofilm formation, while the secretion of a novel biosurfactant polysaccharide by Myxococcus xanthus alters the characteristics of EPS glycocalyx, impacting cell motility and aggregative capacity in groups. This modulation leads to changes in swarm biofilm structure via cell layering and contributes to the formation of internal polysaccharide architecture in swarm communities.
MOLECULAR MICROBIOLOGY
(2021)
Article
Physics, Fluids & Plasmas
Andres Delgado-Campos, Alejandro Cuetos
Summary: This study uses computer simulations to investigate the effects of homeostatic mechanisms on the geometrical and structural properties of developing bacterial microcolonies. The study examines the relationship between cellular growth time and these properties. The results suggest that these mechanisms do not have a significant impact on the properties studied, possibly due to the importance of stochastic factors in cell division and growth processes. Additionally, the study highlights the competition between cell growth and diffusion as a key aspect in explaining the structure and geometry of developing bacterial microcolonies.
Article
Biochemistry & Molecular Biology
Julia A. Schwartzman, Ali Ebrahimi, Grayson Chadwick, Yuya Sato, Benjamin R. K. Roller, Victoria J. Orphan, Otto X. Cordero
Summary: This study demonstrates how a marine bacterium, Vibrio splendidus 12B01, forms clonal multicellular groups to collectively harvest carbon under carbon-limited conditions. The groups phenotypically differentiate into two sub-populations with differential nitrogen-source availability, and populations with a high proportion of carbon-storing individuals propagate more readily on carbon polymers.
Article
Multidisciplinary Sciences
Heidi Peussa, Joose Kreutzer, Elina Mantyla, Antti-Juhana Maki, Soile Nymark, Pasi Kallio, Teemu O. Ihalainen
Summary: It is well known that mechanical cues play a crucial role in regulating cell and tissue physiology. In order to understand the mechanistic effects of these cues, precise mechanical manipulation technologies are required. This study developed an equiaxial cell compression device based on a previously published cell stretching system, aiming to improve microscopy suitability and user-friendliness. The device was capable of producing radial pre-strain and equiaxial compression, leading to morphological changes and alterations in nucleo-cytoplasmic distribution of YAP1 in epithelial cells.
Review
Cell Biology
Katharine Goodwin, Celeste M. Nelson
Summary: Mechanical forces play a crucial role in development, with both intrinsic and extrinsic signals affecting morphogenesis. Recent studies have highlighted the diversity and importance of mechanical influences during development. There are promising avenues for future research in this rapidly expanding field.
DEVELOPMENTAL CELL
(2021)
Article
Multidisciplinary Sciences
Huaxing Huang, Jiafeng Liu, Mingsen Li, Huizhen Guo, Jin Zhu, Liqiong Zhu, Siqi Wu, Kunlun Mo, Ying Huang, Jieying Tan, Chaoqun Chen, Bofeng Wang, Yankun Yu, Li Wang, Yizhi Liu, Hong Ouyang
Summary: This study investigates the regulatory network involved in the acquisition of cell fate, focusing on the induction of surface epithelium from human embryonic stem cells. By analyzing changes in morphology-related genes and the remodeling of the cytoskeleton, the study identifies grainyhead-like 3 (GRHL3) as an initiation factor that drives the commitment to surface epithelium fate. Furthermore, the study uncovers a positive feedback loop between GRHL3 and bone morphogenetic protein 4 in regulating surface epithelium fate decisions.
Review
Biochemistry & Molecular Biology
Sandra B. Lemke, Celeste M. Nelson
Summary: Cell packing, the spatial arrangement of cells, plays a crucial role in determining the shapes of organs. Investigations of various model organisms have revealed common motifs in cellular mechanisms that allow epithelial tissues to change cell packing and shapes for functional architectures. The processes of tissue elongation, folding, invagination, and branching involve cell shape changes, cell rearrangements, and oriented cell division. This understanding provides a foundation for future studies on how epithelial cell packing dynamics shape tissues.
Review
Microbiology
Susan Schlimpert, Marie A. Elliot
Summary: Streptomyces bacteria have been studied for over 80 years due to their ability to produce a wide range of antibiotics and specialized metabolites, as well as their unique fungal-like development. The investigation of model species such as Streptomyces coelicolor and Streptomyces venezuelae has led to significant understanding of their biology, metabolism, and provided tools for manipulation. The ongoing interest in these bacteria offer opportunities for future investigations.
JOURNAL OF BACTERIOLOGY
(2023)
Review
Biophysics
Feyza Nur Arslan, Julia Eckert, Thomas Schmidt, Carl-Philipp Heisenberg
Summary: This review article focuses on the importance and research status of cell-cell adhesion, including descriptions and regulations at different levels, as well as discussions on the molecular and cellular mechanisms of cell-cell adhesion.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Mandi Mazaheri, Jens Ehrig, Alexey Shkarin, Vasily Zaburdaev, Vahid Sandoghdar
Article
Cell Biology
Damla Kaptan, Sider Penkov, Xingyu Zhang, Vamshidhar R. Gade, Bharath Kumar Raghuraman, Roberta Galli, Julio L. Sampaio, Robert Haase, Edmund Koch, Andrej Shevchenko, Vasily Zaburdaev, Teymuras Kurzchalia
Article
Physics, Multidisciplinary
Hui-Shun Kuan, Wolfram Poenisch, Frank Juelicher, Vasily Zaburdaev
Summary: Studying the dynamics of dense, active cellular aggregates is important in biology due to their prevalence. The continuum theory presented in the study helps us better understand the formation and merging processes of cellular aggregates, providing a general framework for studying their rheology and nonequilibrium dynamics.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Julicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw
Summary: This study observed the dynamics of euchromatin organization in pluripotent zebrafish cells during transcription initiation, revealing that accumulation of RNA induces the formation of transcriptionally active regions that tend to separate from transcriptionally inactive euchromatin, forming smaller scale microphases.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert
Summary: This research used STED super-resolution imaging and the concept of multiplicative cascades to describe the hierarchical packing of chromatin, which can be fully specified using only four parameters. The study found that this description is particularly effective in characterizing euchromatin organization and proposed that this concept can be applied to images of other chromatin types as well.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Developmental Biology
Toby G. R. Andrews, Wolfram Ponisch, Ewa K. Paluch, Benjamin J. Steventon, Elia Benito-Gutierrez
Summary: This study used a quantitative approach to investigate the dynamic relationship between cell shape and growth in the process of notochord morphogenesis in amphioxus, revealing significant variations in developmental timing and trajectory topology in different regions.
Review
Biochemistry & Molecular Biology
Charles Gwellem Anchang, Cong Xu, Maria Gabriella Raimondo, Raja Atreya, Andreas Maier, Georg Schett, Vasily Zaburdaev, Simon Rauber, Andreas Ramming
Summary: The increasing incidence rates of immune-mediated inflammatory diseases (IMIDs) are concerning, as current standard immunotherapies only have a 40-60% response rate. Moreover, these therapies require lifelong usage and cannot achieve true disease cure. The development of various OMICs technologies offers hope for improving IMIDs treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Multidisciplinary Sciences
Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Juelicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Wolfram Poenisch, Vasily Zaburdaev
Summary: This study presents a computational model of a micron-sized turbine powered by bacteria, showing that the turbine can rotate persistently by the collective dynamics of multiple pili, and can rotate permanently in the same direction by altering the pili binding to the turbine surface.
FRONTIERS IN PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Mai P. Tran, Rakesh Chatterjee, Yannik Dreher, Julius Fichtler, Kevin Jahnke, Lennart Hilbert, Vasily Zaburdaev, Kerstin Gopfrich
Summary: The construction of an artificial cell requires cell division. Although significant progress has been made in achieving reliable compartment division, mechanisms for segregating DNA-encoded information are still in the early stages. In this study, DNA droplets are formed through liquid-liquid phase separation using DNA Y-motifs. The segregation of DNA droplets is achieved by cleaving the connecting components between two populations of DNA Y-motifs. Enzymatic cleavage and photolabile sites are used to control the segregation process in both bulk solutions and cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). The speed of segregation is slower under confinement compared to bulk conditions. The ionic strength of the solution and the nucleobase sequences are utilized to regulate the segregation dynamics. The experimental results are validated by a lattice-based theoretical model that simulates the interactions between DNA Y-motif populations. Overall, the engineered DNA droplets reconstituted in GUVs provide a strategy for DNA segregation within bottom-up assembled synthetic cells.
Meeting Abstract
Immunology
Jennifer J. Luhr, Nils Alex, Lukas Amon, Martin Kraeter, Marketa Kubankova, Erdinc Sezgin, Christian H. K. Lehmann, Lukas Heger, Gordon F. Heidkamp, Ana Suncana Smith, Vasily Zaburdaev, Rainer A. Boeckmann, Ilya Levental, Michael L. Dustin, Christian Eggeling, Jochen Guck, Diana Dudziak
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Physics, Fluids & Plasmas
Judit Clopes, Jaeoh Shin, Marcus Jahnel, Stephan W. Grill, Vasily Zaburdaev
Summary: Recent research has shown that the EEA1 protein switches from a rigid to a flexible conformation upon binding a signaling protein, allowing it to generate a motor-like force to move vesicles. The binding-induced signal may propagate through the protein chain, leading to conformational changes.
Article
Biochemistry & Molecular Biology
Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Summary: In eukaryotes, the recruitment and pause release of RNA polymerase II (Pol II) are associated with liquid-phase condensation, where regulatory chromatin regions provide surfaces for condensation at concentrations that are too low for canonical liquid-liquid phase separation. Studies using live and super-resolution microscopy in zebrafish embryos have revealed Pol II clusters with various shapes, shedding light on a new theoretical model.
MOLECULAR SYSTEMS BIOLOGY
(2021)