Review
Pharmacology & Pharmacy
Jacopo Cardellini, Arianna Balestri, Costanza Montis, Debora Berti
Summary: The emergence of super-resolution microscopic techniques revolutionized the field of fluorescence microscopy, providing the scientific community with higher resolution observation tools. The application of these techniques in drug delivery has greatly expanded experimental opportunities and enhanced understanding of the behavior of drug delivery systems in biologically relevant environments.
Article
Multidisciplinary Sciences
Jagadish Sankaran, Harikrushnan Balasubramanian, Wai Hoh Tang, Xue Wen Ng, Adrian Rollin, Thorsten Wohland
Summary: This study presents an experimental strategy that optimizes spatial and temporal resolution simultaneously by implementing a GPU-supported, camera-based measurement strategy. The results demonstrate the importance of pixel-wise cross-correlation of parameters obtained from different techniques on the same data set for robust physicochemical parameter estimation and providing unique biological knowledge.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Hansen Zhao, Feng Ge, Yongyu Zhang, Zhenrong Huang, Xiangjun Shi, Bin Xiong, Xuebin Liao, Sichun Zhang, Yan He
Summary: Understanding spatiotemporal dynamics of particles in complex biological environments is crucial. SEES, a method based on historical experience vector analysis, automatically presents global trajectory patterns and local continuities without predefined models, showing greater sensitivity to rare events and multivariable observations compared to the Hidden Markov model. Application of SEES to analyze interactions between nanoparticles and PD-L1 expressing cells successfully pinpointed rare events, visualized Brownian motion, and evaluated different dynamics. These findings could help in designing highly efficient nanocargoes.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Elias Amselem, Bo Broadwater, Tora Haevermark, Magnus Johansson, Johan Elf
Summary: This study presents a 3D tracking method based on cross-entropy minimization and the true excitation point spread function, which enables sub-millisecond tracking of individual molecules in living cells. The method achieves high precision and time resolution in tracking beads and has been successfully applied to track a specific protein in living bacterial cells. However, it is still challenging to resolve state transitions based on diffusivity at this time scale.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Miguel Bernabe-Rubio, Minerva Bosch-Fortea, Miguel A. Alonso, Jorge Bernardino de la Serna
Summary: The assembly of the primary cilium in polarized epithelial cells involves the formation of the centrosome-associated membrane patch (CAMP) from the remnant-associated membrane patch (RAMP), from which the ciliary membrane stems. A correlative imaging approach has been developed to quantitatively analyze the lipid collective assembly at the plasma membrane over time and different spatial scales. These findings provide insights into the mechanisms behind the biogenesis of the ciliary membrane in polarized epithelial cells.
Article
Cell Biology
Dmytro Puchkov, Paul Markus Mueller, Martin Lehmann, Claudia Matthaeus
Summary: This study describes a novel method combining super-resolution light microscopy and platinum replica transmission electron microscopy (CLEM-PREM) for analyzing plasma membrane sheets in terms of their structural details, curvature, and associated protein composition. The implementation of super-resolution stimulated emission depletion (STED) microscopy reduces sample preparation time and technical challenges for imaging and analysis. Additionally, scanning electron microscopy (SEM) imaging overcomes technical challenges associated with replica preparation and transfer on a TEM grid.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Javier Aguirre Rivera, Jimmy Larsson, Ivan L. Volkov, A. Carolin Seefeldt, Suparna Sanyal, Magnus Johansson
Summary: Aminoglycoside drugs slow down translation elongation and decrease the number of elongation cycles per initiation event, suggesting that they do not cause severe inhibition of translocation in bacterial cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Optics
Shawn Yoshida, William Schmid, Nam Vo, William Calabrase, Lydia Kisley
Summary: This study improves the efficiency of fcsSOFI by parallelizing the least-squares curve fitting step on a GPU, implementing anomalous and two-component Brownian diffusion models, and packaging it in a user-friendly GUI. By applying fesSOFI to simulations of protein diffusion in polyacrylamide, it super-resolves locations of slower, anomalous diffusion within smaller, confined pores. These enhancements in speed, scope, and usability will facilitate the broader adoption of super-resolution correlation analysis across diverse research domains.
Article
Chemistry, Multidisciplinary
Alina Sigaeva, Axel Hochstetter, Sighom Bouyim, Mayeul Chipaux, Miroslava Stejfova, Petr Cigler, Romana Schirhagl
Summary: This paper explores the use of single-particle tracking and trajectory analysis to provide intracellular context for diamond magnetometry measurements. The findings show that this method accurately describes the movement of FNDs in different environments and deduces their intracellular localization in live cells.
Article
Chemistry, Multidisciplinary
Zhi-Gang Wang, Lei Wang, Don C. Lamb, Hua-Jie Chen, Yusi Hu, Hong-Peng Wang, Dai-Wen Pang, Shu-Lin Liu
Summary: Brain diseases pose an increasing threat to human health, while understanding the transport mechanisms of drugs in live brains remains limited. Through tracking the dynamics of WGA in live brains, this study revealed influences of specific-binding molecules and ECS nature on transport dynamics, paving the way for exploring the biophysics of drug transport in live brains and identifying potential new therapeutic applications for brain diseases.
Article
Engineering, Chemical
Haichao Wu, Alexander Kanora, Daniel K. Schwartz
Summary: The study shows that internal membrane fouling consists of three stages: fouling site formation, fouling site growth, and fouling site coalescence. Larger particles are more likely to be retained initially, leading to the formation of fouling sites that gradually grow and coalesce with other particles, ultimately blocking a significant region of membrane pores. This information will assist in improving the design and optimization of filtration processes to reduce fouling and enhance our understanding of particle transport.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Optics
Colter Russell, Naibo Jiang, Paul Danehy, Zhili Zhang, Sukesh Roy
Summary: Nonintrusive three-component velocity measurements of free jet flows were conducted using stereoscopic picosecond laser electronic excitation tagging (S-PLEET) at 100 kHz. Key turbulent properties were obtained with high-frequency turbulence properties useful for turbulence modeling and validations.
Article
Biophysics
Stephen Lee Upton, Jian Wei Tay, Daniel Keith Schwartz, Marcelo Carlos Sousa
Summary: This study investigates the diffusion behavior of BAM and SecYEG proteins using super-resolution localization microscopy and single-particle tracking. The results suggest the existence of a cross-membrane assembly in E. coli cells. The tracking of BAM and SecYEG provides insights into the structure of the E. coli cell envelope.
BIOPHYSICAL JOURNAL
(2023)
Article
Multidisciplinary Sciences
Xin Wang, Zhongju Ye, Shen Lin, Lin Wei, Lehui Xiao
Summary: In this study, a nanozyme-powered cup-shaped nanomotor was developed for active cellular targeting and synergistic photodynamic/thermal therapy. The nanomotor demonstrated asymmetric propulsion force and robust catalytic activity, allowing for more efficient cellular searching and uptake, as well as the generation of reactive oxygen species during therapy.
Article
Chemistry, Applied
Jose C. Bonilla, Mathias P. Clausen
Summary: Modern research on food materials has advanced in characterizing them at both the molecular and macroscopic levels, yet there remains a gap in understanding their microscopic organization. Utilizing optical superresolution microscopy, this study shows how more detailed information about food microstructures can be obtained compared to conventional microscopy. By studying protein aggregation in egg-white using STED microscopy, it was found to provide a 5-fold increase in resolution and allowed for a more precise quantification of structures compared to confocal microscopy. This additional information from STED microscopy could be correlated with macroscopic rheological measurements to provide a more complete understanding of protein aggregation in food matrices.
FOOD HYDROCOLLOIDS
(2022)
Article
Biochemistry & Molecular Biology
Valentina Gifford, Anna Woskowicz, Noriko Ito, Stefan Balint, B. Christopher Lagerholm, Michael L. Dustin, Yoshifumi Itoh
Summary: MT1-MMP plays a crucial role in promoting cancer cell invasion. In this study, three kinesin superfamily motor proteins (KIFs), KIF3A, KIF13A, and KIF9, were identified to be involved in the transport of MT1-MMP-containing vesicles. Knockdown of KIF3A and KIF13A inhibited MT1-MMP-dependent collagen degradation and invasion, while knockdown of KIF9 increased collagen degradation and invasion. Live-cell imaging analyses revealed the coordinated transport of MT1-MMP-containing vesicles by KIF3A and KIF13A from the trans-Golgi to endosomes, and the transport of vesicles from endosomes to the plasma membrane by KIF13A alone. This study uncovers a unique interplay between three KIFs in regulating the leading edge localization of MT1-MMP and MT1-MMP-dependent cancer cell invasion.
Review
Food Science & Technology
Qiushuang Song, Renjie Li, Xiao Song, Mathias P. Clausen, Vibeke Orlien, Davide Giacalone
Summary: This paper provides a narrative review of sensory studies on high pressure treated fruit juices and smoothies published in the last 25 years. It concludes that a combination of high pressure processing and low temperature storage preserves the sensory properties better than thermal processing, resulting in products with 'fresh-like' quality. However, the studies often lack proper sample sizes and mismatch between test type and assessors. Future research should focus on experimental conditions, proper sensory methods, and the relationship between sensory quality and consumer perception to better understand the effect of high pressure processing on the sensory quality of fruit juices and smoothies.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Cell Biology
Thomas L. Steinacker, Siu-Shing Wong, Zsofia A. Novak, Saroj Saurya, Lisa Gartenmann, Eline J. H. van Houtum, Judith R. Sayers, B. Christoffer Lagerholm, Jordan W. Raff
Summary: In Drosophila embryos, the cytoplasmic concentrations of centriole assembly proteins remain constant throughout the assembly process, suggesting that they are not limiting factors for centriole assembly. However, the diffusion rate of Ana2/STIL increases significantly towards the end of S-phase due to the increased activity of Cdk/Cyclin. Phosphorylation of Ana2 by Cdk/Cyclin seems to reduce the efficiency of daughter centriole assembly, ensuring that they stop growing at the correct time.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Chemistry, Applied
Shaghayegh Keshanidokht, Matias Alejandro Via, Cigdem Yucel Falco, Mathias Porsmose Clausen, Jens Risbo
Summary: The aim of this research was to introduce a novel method using zein protein to stabilize an ethanol-based emulsion. The effect of ethanol concentration and zein concentration on the stability and microstructure of the emulsions was investigated.
FOOD HYDROCOLLOIDS
(2022)
Article
Chemistry, Applied
Jose C. Bonilla, Jesper L. Sorensen, Amalie S. Warming, Mathias P. Clausen
Summary: Recent advances in software development and machine learning algorithms have revolutionized the analysis and quantification of microstructures in fields like biology and neuroscience. This article demonstrates the use of a deep-learning cellular segmentation algorithm, 'Cellpose', to identify and quantify foam microstructures for the study of food structure-function relationships. The algorithm successfully identified air bubbles in a protein foam matrix and allowed for further analysis of microstructural parameters. The study examined the effects of sugar concentration and acidic conditions on the microstructural mechanisms and rheological responses of the foam. The understanding gained from the algorithm-identified microstructures provides a new approach to characterize and study food foams.
FOOD HYDROCOLLOIDS
(2022)
Article
Food Science & Technology
Qiushuang Song, Christina J. Birke Rune, Anette K. Thybo, Mathias P. Clausen, Vibeke Orlien, Davide Giacalone
Summary: High pressure processing (HPP) is an effective alternative to thermal pasteurization (TP) for extending the shelf-life and maintaining the sensory quality of fruit juices. This study investigated the effects of HPP on sensory quality and consumer perception of orange and apple juice, and found that treatment and storage conditions significantly impacted sensory quality and consumer liking. Shorter storage times and cold storage were favored by consumers, while HPP showed better sensory preservation compared to TP.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
D. M. Jeziorska, E. A. J. Tunnacliffe, J. M. Brown, H. Ayyub, J. Sloane-Stanley, J. A. Sharpe, B. C. Lagerholm, C. Babbs, A. J. H. Smith, V. J. Buckle, D. R. Higgs
Summary: The authors observed transcription dynamics during erythropoiesis and found that the pattern of transcriptional bursting changes during differentiation. Variability in individual cells is significantly reduced at the peak period of gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Food Science & Technology
Davide Giacalone, Mathias P. Clausen, Sara R. Jaeger
Summary: Plant-based meat and dairy alternatives are a growing trend in improving the sustainability of global food systems. However, these products still face challenges in replicating the sensory qualities of traditional meat and dairy. It is important to consider both sensory and non-sensory factors, as well as individual differences, in order to develop targeted approaches for different consumer groups.
CURRENT OPINION IN FOOD SCIENCE
(2022)
Article
Chemistry, Applied
Shaghayegh Keshanidokht, Saket Kumar, Peter Waaben Thulstrup, Matias Alejandro Via, Mathias Porsmose Clausen, Jens Risbo
Summary: A series of oleogels stabilized by zein and plasticized with glycerol were investigated for their rheological and microstructural properties. The plasticized zein oleogel exhibited a weak-link regime with a protein network that became denser with increasing glycerol concentration. Higher zein concentration resulted in a denser oleogel network. The rheological behavior of the oleogels showed a reversible transition from solid-like to liquid-like upon heating, starting at 75 degrees C.
FOOD HYDROCOLLOIDS
(2023)
Article
Medicine, Research & Experimental
Suzanne E. Engelen, Francesca A. Ververs, Angela Markovska, B. Christoffer Lagerholm, Jordan M. Kraaijenhof, Laura I. E. Yousif, Yasemin-Xiomara Zurke, Can M. C. Gulersonmez, Sander Kooijman, Michael Goddard, Robert J. van Eijkeren, Peter J. Jervis, Gurdyal S. Besra, Saskia Haitjema, Folkert W. Asselbergs, Eric Kalkhoven, Hidde L. Ploegh, Marianne Boes, Vincenzo Cerundolo, G. K. Hovingh, Mariolina Salio, Edwin C. A. Stigter, Patrick C. N. Rensen, Claudia Monaco, Henk S. Schipper
Summary: This study reveals that circulating lipoproteins form complexes with lipid antigens to facilitate their transport and uptake by antigen-presenting cells, leading to enhanced iNKT cell activation. This discovery uncovers a novel mechanism of lipid antigen delivery to APCs and provides further insight into the immunological capacities of circulating lipoproteins.
Article
Biochemistry & Molecular Biology
Camilla B. Andersen, Astrid K. Lausdahl, Janni Nielsen, Mathias P. Clausen, Frans A. A. Mulder, Daniel E. Otzen, Eva C. Arnspang
Summary: Oxidative stress and the formation of cytotoxic oligomers by the natively unfolded protein & alpha;-synuclein (& alpha;-syn) are implicated in the development of Parkinson's disease. However, the specific mechanisms underlying these processes are still unclear. In this study, & alpha;-syn oligomers (& alpha;SOs) were prepared in vitro in the presence of a lipid peroxidation product, and their interaction with live cells was investigated using advanced microscopy techniques. The results demonstrate that the cytotoxic & alpha;-syn aggregates closely interact with cellular membranes and organelles, providing direct evidence for their involvement in cellular dysfunction associated with Parkinson's disease.
Article
Food Science & Technology
Christina J. Birke Rune, Davide Giacalone, Ida Steen, Lars Duelund, Morten Munchow, Mathias Porsmose Clause
Summary: Light-roast coffee beans are popular for their high acidity, but the relationship between roast level and acidity is not clear. This study tested the concentrations of acids and sugars in brewed coffee and found that the concentration of most acids either significantly decreased or increased with increasing roast degree. Only citric acid was detected above the sensory threshold, while other acids were unlikely to be individually perceived in coffee. The results question the direct relation between individual organic acids and acidity in coffee.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Chemistry, Applied
Sabrina Baether, Jasper Hartwig Seibt, Christoph Simon Hundschell, Jose C. Bonilla, Mathias Porsmose Clausen, Anja Maria Wagemans
Summary: This study investigated the phase behavior and structure formation of alginate-gelatin composite gels under different mixing ratios and temperatures. The state of gelatin, either liquid or gelled, strongly influenced the gelation velocity and strength of alginate. Different microstructures were observed in the phase-separated networks depending on the mixing ratio, which correlated with variations in the turbidity of the gels. The findings provide insights into the structure-function relationship of alginate-gelatin composite gels, potentially beneficial for the customization of specific network types for 3D bioprinting.
FOOD HYDROCOLLOIDS
(2024)
Article
Food Science & Technology
Christina J. Birke Rune, Qiushuang Song, Mathias P. Clausen, Davide Giacalone
Summary: Driven by consumer interest in sustainable diets, plant-based meat alternatives (PBMA) are gaining popularity with more products available on the market. Consumers increasingly demand clean label (CL) products free of additives and using a limited number of ingredients. This study investigated consumer understanding and interpretation of CL status in PBMA, using plant-based burger recipes as case study. The length of the ingredients list was found to be more important for consumer perception of CL status in PBMA than the presence of chemical additives.