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Tišma, M. (author), Kaljević, Jovana (author), Gruber, Stephan (author), Le, Tung B.K. (author), Dekker, C. (author)
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome...
review 2024
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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...
review 2023
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Blanch Jover, A. (author), Dekker, C. (author)
The Cdv system is the protein machinery that performs cell division and other membrane-deforming processes in a subset of archaea. Evolutionarily, the system is closely related to the eukaryotic ESCRT machinery, with which it shares many structural and functional similarities. Since its first description 15 years ago, the understanding of the...
review 2023
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Whitley, K.D. (author), Middlemiss, Stuart (author), Jukes, Calum (author), Dekker, C. (author), Holden, Séamus (author)
Light microscopy is indispensable for analysis of bacterial spatial organization, yet the sizes and shapes of bacterial cells pose unique challenges to imaging. Bacterial cells are not much larger than the diffraction limit of visible light, and many species have cylindrical shapes and so lie flat on microscope coverslips, yielding low...
review 2022
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Ying, Yi Lun (author), Hu, Zheng Li (author), Zhang, Shengli (author), Qing, Yujia (author), Fragasso, A. (author), Maglia, Giovanni (author), Meller, Amit (author), Bayley, Hagan (author), Dekker, C. (author), Long, Yi Tao (author)
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the...
review 2022
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Bharadwaj, M. (author), Bengtson, M.L. (author), Golverdingen, Mirte (author), Waling, Loulotte (author), Dekker, C. (author)
Inadequate and nonintegrated diagnostics are the Achilles' heel of global efforts to monitor, control, and eradicate neglected tropical diseases (NTDs). While treatment is often available, NTDs are endemic among marginalized populations, due to the unavailability or inadequacy of diagnostic tests that cause empirical misdiagnoses. The need of...
review 2021
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Bohländer, P.R. (author), Filius, M. (author), van Kooten, Xander F. (author), Pomorski, A.K. (author), Schmid, S. (author), Dekker, C. (author), Eelkema, R. (author), Kim, S.H. (author), Joo, C. (author)
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside...
review 2021
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Gogou, C. (author), Japaridze, A. (author), Dekker, C. (author)
The process of DNA segregation, the redistribution of newly replicated genomic material to daughter cells, is a crucial step in the life cycle of all living systems. Here, we review DNA segregation in bacteria which evolved a variety of mechanisms for partitioning newly replicated DNA. Bacterial species such as Caulobacter crescentus and...
review 2021
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Olivi, Lorenzo (author), Berger, Mareike (author), Creyghton, Ramon N.P. (author), De Franceschi, N. (author), Dekker, C. (author), Mulder, Bela M. (author), Claassens, Nico J. (author), ten Wolde, Pieter Rein (author), van der Oost, John (author)
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes...
review 2021
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Deshpande, Siddharth (author), Dekker, C. (author)
Cells organize their interior through membrane-bound organelles and through membraneless condensates that are formed by liquid–liquid phase separation (LLPS). The complex process of coacervation that is involved in LLPS is challenging to study in living cells. Hence, studying coacervation in cell-mimicking synthetic containers can yield...
review 2021
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Schmid, S. (author), Dekker, C. (author)
This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or...
review 2021
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Schmid, S. (author), Dekker, C. (author)
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing.While static 3D structures are now readily available, observing the functional cycle of proteins-involving conformational changes and...
review 2021
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Birnie, Anthony (author), Dekker, C. (author)
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics,...
review 2021
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Fragasso, A. (author), Schmid, S. (author), Dekker, C. (author)
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of...
review 2020
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Schrijvers, Jim (author), van den Noort, Josien C. (author), van der Esch, Martin (author), Dekker, Joost (author), Harlaar, J. (author)
Background: Instability of the knee joint during gait is frequently reported by patients with knee osteoarthritis or an anterior cruciate ligament rupture. The assessment of instability in clinical practice and clinical research studies mainly relies on self-reporting. Alternatively, parameters measured with gait analysis have been explored...
review 2019
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Cramer, Sophie J.E. (author), Dekker, Janneke (author), Dankelman, J. (author), Pauws, Steffen C. (author), Hooper, Stuart B. (author), te Pas, Arjan B. (author)
Apnea of prematurity (AOP) is one of the most common diagnoses in preterm infants. Severe and recurrent apneas are associated with cerebral injury and adverse neurodevelopmental outcome. Despite pharmacotherapy and respiratory support to prevent apneas, a proportion of infants continue to have apneas and often need tactile stimulation, mask,...
review 2018
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Spoelstra, W.K. (author), Deshpande, S.R. (author), Dekker, C. (author)
Recently, the bottom-up assembly of a synthetic cell has emerged as a daring novel approach that can be expected to have major impact in generating fundamental insight in the organization and function of actual biological cells, as well as in stimulating a broad range of applications from drug delivery systems to chemical nanofactories. A...
review 2018
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Restrepo Perez, L. (author), Joo, C. (author), Dekker, C. (author)
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example,...
review 2018
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Eeftens, J.M. (author), Dekker, C. (author)
Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the...
review 2017
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Wu, F. (author), Dekker, C. (author)
Nanofabricated structures and microfluidic technologies are increasingly being used to study bacteria because of their precise spatial and temporal control. They have facilitated studying many long-standing questions regarding growth, chemotaxis and cell-fate switching, and opened up new areas such as probing the effect of boundary geometries...
review 2016
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