Article
Multidisciplinary Sciences
Sabrina Meindlhumer, Fridtjof Brauns, Jernej Rudi Finzgar, Jacob Kerssemakers, Cees Dekker, Erwin Frey
Summary: Meindlhumer et al. have conducted a combined theoretical and experimental study on how the propagation direction of Min protein patterns can be changed by a bulk flow of solution. They demonstrate that the direction of in vitro Min protein patterns can be controlled by hydrodynamic flow, with downstream propagation for low concentration ratios of MinE:MinD, upstream propagation for large ratios, and multistability in between. Their study reveals the potential of using flow to probe molecular features and constrain mathematical models for pattern formation systems.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Nicolas Sundqvist, Sebastian Sten, Peter Thompson, Benjamin Jan Andersson, Maria Engstrom, Gunnar Cedersund
Summary: This study presents a new model that integrates MRS and BOLD data to describe the neurovascular and neurometabolic couplings in the brain. The model can simultaneously describe BOLD data and predict expected metabolic responses in experiments where metabolism has not been measured.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematics
Jingyu Li, Linlin Su, Xuefeng Wang, Yantao Wang
Summary: This paper discusses recursive reaction-diffusion models between bulk and membrane, obtaining two effective models as the membrane thickness approaches zero. The crucial factors for these effective models are appropriate transmission conditions at the interface and optimal alignment of the diffusion tensor in the membrane.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2021)
Article
Physics, Multidisciplinary
Sabrina Meindlhumer, Jacob Kerssemakers, Cees Dekker
Summary: The Min protein system is a highly studied model system for biological pattern formation. This paper presents a methodology for quantitatively analyzing Min patterns, providing definitions for pattern features and introducing the use of autocorrelation analysis and flow-field analysis to extract global and local parameters, respectively. Practical implementation guidance and Python code are also provided.
FRONTIERS IN PHYSICS
(2022)
Article
Geosciences, Multidisciplinary
Suqin Q. Q. Duan, Kirsten I. L. Findell, Stephan A. A. Fueglistaler
Summary: This study reveals changes in tropical land hydroclimate following CO2-induced global warming, with organized patterns in the AI/SM phase space. The transformation from geographical space to process-oriented phase space allows for the interpretation of local mechanistic relationships between hydroclimatic variables. The results show coherent changes aligning with established soil-moisture/evapotranspiration regimes and the position of critical soil moisture values.
GEOPHYSICAL RESEARCH LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Xiaotong Ma, Mingbo Li, Xuefei Xu, Chao Sun
Summary: This study investigates the coupling effects of ionic surfactants and electrolytes on the stability of bulk nanobubbles. Experimental results show that ionic surfactants not only reduce the surface tension but also promote the accumulation of net charges, which facilitate the nucleation and stabilization of bulk nanobubbles.
Review
Chemistry, Physical
Jiahao Wu, To Ngai
Summary: This review article discusses the assembly process of fibrinogen to a fibrin network and the structure-property relationship of fibrin mechanics at different scales. The influence of surface properties, including surface charge, wettability, and surface morphology, on network formation is also examined. Advanced characterization techniques are needed to further understand the structural origin and in-vivo implications of fibrin mechanics. The study of fibrin clots on material surfaces also holds great potential for future research.
CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
(2023)
Article
Pharmacology & Pharmacy
Ashkan Karbasi, Anahita Abbasifard, Farzin Firouzian, Sara Soleimani Asl, Zahra Azizi, Akram Ranjbar
Summary: The toxicity of PQ nanoparticles (PQNPs) and their impact on acute lung injury were evaluated in this study. The results showed that PQNPs exhibited lower cell cytotoxicity compared to bulk PQ and resulted in lower levels of oxidative damage in the lungs. Overall, PQ loaded in chitosan-alginate particles offers safer characteristics than bulk PQ.
Article
Nanoscience & Nanotechnology
Hamidreza Daghigh Shirazi, Yujiao Dong, Jukka Niskanen, Chiara Fedele, Arri Priimagi, Ville P. Jokinen, Jaana Vapaavuori
Summary: A simple hierarchical surface patterning method is proposed by combining buckling instability and azopolymer-based surface relief grating inscription, allowing for the fabrication of surfaces with different length scales and the tuning of wetting properties. The demonstrated fine-tuning of the surface patterns may be useful in optimizing material properties related to surfaces and producing substrates of potential interest in mechanobiology and tissue engineering.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Pharmacology & Pharmacy
Andrew Otte, Frederick Damen, Craig Goergen, Kinam Park
Summary: This study investigated the impact of rodent housing conditions (climate) on the in vivo performance of PLGA microspheres, finding that housing temperature had some effect on subcutaneous temperature but minimal impact on the injected microparticles. Significant differences were observed in vitro release profiles across different temperatures, with lower temperatures potentially representing in vivo conditions more accurately. Future studies will assess the effects of temperature and co-housing on the in vivo performance of injectable polymeric microparticles based on observed in vitro release profile differences.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Biotechnology & Applied Microbiology
Zhuhong Zhang, Laien Zhao, Yuanyuan Ma, Jia Liu, Yanmei Huang, Xiaoxuan Fu, Shengjun Peng, Xiaojie Wang, Yun Yang, Xiaoyan Zhang, Wanru Ding, Jinguo Yu, Yanping Zhu, Hua Yan, Shubin Yang
Summary: The 15-nm silica nanoparticles induce size-dependent retinal toxicity, with glial cell activation and ROS generation contributing to this toxicity.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Engineering, Biomedical
Bin Wang, Wei Liu, Jiao Jiao Li, Senlin Chai, Dan Xing, Hongsheng Yu, Yuanyuan Zhang, Wenjin Yan, Zhihong Xu, Bin Zhao, Yanan Du, Qing Jiang
Summary: In the treatment of osteoarthritis, delivering low doses of MSCs through microcarriers can achieve similar reparative effects as repeated high doses. Mechanistic investigations reveal that 3D growth of MSCs reduces inflammatory factors, enhances early chondrogenesis and extracellular matrix interactions, and maintains the phenotype of co-cultured chondrocytes.
BIOACTIVE MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Ainaz Mihanfar, Saber Ghazizadeh Darband, Shirin Sadighparvar, Mojtaba Kaviani, Mohammad Mirza-Aghazadeh-Attari, Bahman Yousefi, Maryam Majidinia
Summary: This study demonstrates the inhibitory effects of syringic acid on proliferation and induction of apoptosis in human colorectal cancer cells, as well as its reduction of tumor volume and incidence in a rat model of colorectal cancer.
CHEMICO-BIOLOGICAL INTERACTIONS
(2021)
Article
Mathematics, Interdisciplinary Applications
Robert Altmann, Barbara Verfuerth
Summary: This paper introduces a multiscale method for parabolic problems with heterogeneous dynamic boundary conditions. By decoupling the discretization of bulk and surface dynamics and combining multiscale methods on the boundary with standard Lagrangian schemes in the interior, the method proves convergence and quantifies explicit rates for low-regularity solutions independent of the heterogeneities' oscillatory behavior, allowing for consideration of coarse discretization parameters. The theoretical findings are supported by numerical experiments with dynamic boundary conditions and random diffusion coefficients.
MULTISCALE MODELING & SIMULATION
(2021)
Review
Environmental Sciences
Hui Chen, Brian G. Oliver, Anushriya Pant, Annabel Olivera, Philip Poronnik, Carol A. Pollock, Sonia Saad
Summary: Airborne particulate matter (PM) is a mixture of solid and liquid particles that can cause oxidative stress and inflammation when inhaled. These changes can occur both in the lungs and throughout the body due to the ability of small-sized PM (PM2.5) to enter and circulate in the bloodstream. In 2016, airborne PM was responsible for approximately 4.2 million premature deaths worldwide. Acute exposure to high levels of PM, such as during wildfires, can worsen existing illnesses like asthma and coronary heart disease, leading to hospitalization. Prolonged exposure to PM can also increase the risk of chronic non-communicable diseases affecting various organs, although the research on kidney diseases is limited. Understanding the mechanisms behind PM-induced disorders is crucial, and in-vitro and in-vivo studies can provide valuable insights. This article focuses on the acute and long-term health effects of PM exposure, including inflammation and oxidative stress, and highlights the importance of developing effective treatments to mitigate the adverse health effects of PM exposure.
ENVIRONMENTAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Chenyu Wen, Eva Bertosin, Xin Shi, Cees Dekker, Sonja Schmid
Summary: In this study, we achieved strong trapping and extended observation of single proteins using site specific cholesterol functionalization on a lipid-coated nanopore. This greatly enhances the trapping capacity and extends the observation time.
Article
Chemistry, Physical
Alfredo Sciortino, Lukas J. Neumann, Timo Krueger, Ivan Maryshev, Tetsuhiko F. Teshima, Bernhard Wolfrum, Erwin Frey, Andreas R. Bausch
Summary: This study demonstrates the use of passive nematic materials to control the pattern formation process of active fluids by introducing and controlling defects. It shows that defects in the passive material can guide the flow of active microtubules and lead to the formation of macroscopic polar patterns, opening up new possibilities for shaping active materials using passive defects.
Article
Multidisciplinary Sciences
Sabrina Meindlhumer, Fridtjof Brauns, Jernej Rudi Finzgar, Jacob Kerssemakers, Cees Dekker, Erwin Frey
Summary: Meindlhumer et al. have conducted a combined theoretical and experimental study on how the propagation direction of Min protein patterns can be changed by a bulk flow of solution. They demonstrate that the direction of in vitro Min protein patterns can be controlled by hydrodynamic flow, with downstream propagation for low concentration ratios of MinE:MinD, upstream propagation for large ratios, and multistability in between. Their study reveals the potential of using flow to probe molecular features and constrain mathematical models for pattern formation systems.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Iain F. Davidson, Roman Barth, Maciej Zaczek, Jaco van der Torre, Wen Tang, Kota Nagasaka, Richard Janissen, Jacob Kerssemakers, Gordana Wutz, Cees Dekker, Jan-Michael Peters
Summary: CTCF is a DNA-binding protein that establishes topologically associating domains (TADs) by blocking the diffusion and loop extrusion of cohesin. CTCF functions asymmetrically and is dependent on DNA tension. Moreover, CTCF regulates cohesin's loop-extrusion activity by changing its direction and inducing loop shrinkage. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.
Article
Physics, Multidisciplinary
Meifang Fu, Tom Burkart, Ivan Maryshev, Henri G. Franquelim, Adrian Merino-Salomon, Maria Reverte-Lopez, Erwin Frey, Petra Schwille
Summary: Through a mechanochemical feedback loop involving Min proteins of Escherichia coli, liposomes start to move, which may help to design motile artificial cells.
Article
Physics, Multidisciplinary
Leonardo Demarchi, Andriy Goychuk, Ivan Maryshev, Erwin Frey
Summary: Enzyme-enriched condensates can regulate the distribution of their substrates and induce enzyme fluxes through feedback interactions. Weak feedback leads to condensate movement towards the center of a confined domain, while above a threshold, self-propulsion and oscillatory dynamics occur. Enzyme-driven fluxes can also result in interrupted coarsening and condensate division, leading to equidistant positioning.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Zihang Wang, M. Cristina Marchetti, Fridtjof Brauns
Summary: Orientational order, encoded in anisotropic fields, is important in organism development. The study focuses on the freshwater polyp Hydra and its muscle fiber orientation defects. A minimal model is introduced to study the interaction between muscle fiber orientation, morphogen gradients, and body shape. The model successfully reproduces experimentally observed reorganization of orientational order on curved surfaces mimicking Hydra's morphologies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Ian C. C. Nova, Justas Ritmejeris, Henry Brinkerhoff, Theo J. R. Koenig, Jens H. H. Gundlach, Cees Dekker
Summary: Drawing peptides through a nanopore allows for the detection of individual phosphorylation sites; Current methods cannot measure single molecules or differentiate between closely spaced phosphorylation sites; We can detect cancer-associated post-translational modifications at the single-molecule level by controlling the peptide's movement through a nanopore; With individual reads of single molecules, we can discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy.
NATURE BIOTECHNOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Laeschkir Wuerthner, Andriy Goychuk, Erwin Frey
Summary: Intracellular protein patterns play a crucial role in regulating important cellular processes and their dynamics are influenced by changes in cell shape. To understand the underlying mechanisms, a conceptual model for cell polarity on a dynamic one-dimensional manifold is explored. The dynamics of the membrane shape induce pattern-forming instabilities and can also suppress pattern formation and shift existing patterns.
Article
Biochemistry & Molecular Biology
Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
Summary: Transcription-coupled supercoiling of DNA plays a crucial role in chromosome compaction and the regulation of genetic processes. This study experimentally validates the twin-supercoiled-domain model and demonstrates that RNA polymerase can generate up- and downstream supercoils simultaneously during transcription. These findings provide insight into the mechanistic cause of supercoil generation by RNA polymerase in transcription.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Pauline J. Kolbeck, Milos Tisma, Brian T. Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Summary: In this article, the authors propose a quantitative model for the modulation of DNA binding by DNA topology and demonstrate its accuracy through experiments. They focus on the binding of fluorescent intercalators to DNA and directly observe the impact of different intercalator densities on DNA through single-molecule assays. The model has wide implications for the detection and quantification of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Timo Krueger, Ivan Maryshev, Erwin Frey
Summary: Topological defects play a central role in the formation and organization of various biological systems. In this paper, agent-based simulations are used to study phase-separated active nematics and the formation of -1/2 defects. The authors investigate the morphology and characteristics of these defects, as well as observe and characterize lateral arc-like structures separating from nematic bands. The study also introduces a hydrodynamic theory that explains the emergence of defects and arcs.
Article
Physics, Fluids & Plasmas
Tom Burkart, Jan Willeke, Erwin Frey
Summary: This article investigates how periodic temporal environmental variation can affect the composition and biodiversity of an ecosystem. By using a population dynamics model and timescale separation, the study shows that the impact of environmental changes on species coexistence and stability depends on the timescale of the changes.