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A Berlin-sided retrospective of the origins of metabolic control theory Interface Focus (IF 4.4) Pub Date : 2024-02-09 Tom A. Rapoport
Metabolic control theory (MCA) is celebrating its 50th anniversary. The theory introduced quantitative terms that describe the importance of an enzyme for the regulation of the overall flux and of metabolite concentrations. MCA was developed independently by two groups. The Berlin group included Reinhart Heinrich, Tom A. Rapoport and Samuel M. Rapoport, and the Edinburgh group Henrik Kacser and James
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Optimal enzyme profiles in unbranched metabolic pathways Interface Focus (IF 4.4) Pub Date : 2024-02-09 Elad Noor, Wolfram Liebermeister
How to optimize the allocation of enzymes in metabolic pathways has been a topic of study for many decades. Although the general problem is complex and nonlinear, we have previously shown that it can be solved by convex optimization. In this paper, we focus on unbranched metabolic pathways with simplified enzymatic rate laws and derive analytic solutions to the optimization problem. We revisit existing
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First-order ultrasensitivity in phosphorylation cycles Interface Focus (IF 4.4) Pub Date : 2024-02-09 Michael A. Kochen, Joseph L. Hellerstein, Herbert M. Sauro
Cellular signal transduction takes place through a network of phosphorylation cycles. These pathways take the form of a multi-layered cascade of cycles. This work focuses on the sensitivity of single, double and n length cycles. Cycles that operate in the zero-order regime can become sensitive to changes in signal, resulting in zero-order ultrasensitivity (ZOU). Using frequency analysis, we confirm
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Engineering DNA-based cytoskeletons for synthetic cells. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Kevin Jahnke,Kerstin Göpfrich
The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of
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Light-controlled growth of DNA organelles in synthetic cells. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Siddharth Agarwal,Mahdi Dizani,Dino Osmanovic,Elisa Franco
Living cells regulate many of their vital functions through dynamic, membraneless compartments that phase separate (condense) in response to different types of stimuli. In synthetic cells, responsive condensates could similarly play a crucial role in sustaining their operations. Here we use DNA nanotechnology to design and characterize artificial condensates that respond to light. These condensates
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Micro-compartmentalized strand displacement reactions with a random pool background. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Thomas Mayer,Louis Givelet,Friedrich C Simmel
Toehold-mediated strand displacement (TMSD) is a widely used process in dynamic DNA nanotechnology, which has been applied for the actuation of molecular devices, in biosensor applications, and for DNA-based molecular computation. Similar processes also occur in a biological context, when RNA strands invade secondary structures or duplexes of other RNA or DNA molecules. Complex reaction environments-inside
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Biomimetic construction of phospholipid membranes by direct aminolysis ligations. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Federica A Souto-Trinei,Roberto J Brea,Neal K Devaraj
Construction of artificial cells requires the development of straightforward methods for mimicking natural phospholipid membrane formation. Here we describe the use of direct aminolysis ligations to spontaneously generate biomimetic phospholipid membranes from water-soluble starting materials. Additionally, we explore the suitability of such biomimetic approaches for driving the in situ formation of
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On biochemical constructors and synthetic cells. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Sebastian J Maerkl
Is it possible to build life? More specifically, is it possible to create a living synthetic cell from inanimate building blocks? This question precipitated into one of the most significant grand challenges in biochemistry and synthetic biology, with several large research consortia forming around this endeavour in Europe (European Synthetic Cell Initiative), the USA (Build-a-Cell Initiative) and Japan
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Artificial cells eavesdropping on HepG2 cells. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Isabella Nymann Westensee,Brigitte Städler
Cellular communication is a fundamental feature to ensure the survival of cellular assemblies, such as multicellular tissue, via coordinated adaption to changes in their surroundings. Consequently, the development of integrated semi-synthetic systems consisting of artificial cells (ACs) and mammalian cells requires feedback-based interactions. Here, we illustrate that ACs can eavesdrop on HepG2 cells
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Cell mimicry: bottom-up engineering of life. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Stephen Mann
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DNA droplets for intelligent and dynamical artificial cells: from the viewpoint of computation and non-equilibrium systems. Interface Focus (IF 4.4) Pub Date : 2023-08-11 Masahiro Takinoue
Living systems are molecular assemblies whose dynamics are maintained by non-equilibrium chemical reactions. To date, artificial cells have been studied from such physical and chemical viewpoints. This review briefly gives a perspective on using DNA droplets in constructing artificial cells. A DNA droplet is a coacervate composed of DNA nanostructures, a novel category of synthetic DNA self-assembled
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Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities. Interface Focus (IF 4.4) Pub Date : 2023-06-09 Bing Guo,Dominic Frigon
A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities
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The ecology of scale: impact of volume on coalescence and function in methanogenic communities. Interface Focus (IF 4.4) Pub Date : 2023-06-09 Pawel Sierocinski,Peter Stilwell,Daniel Padfield,Florian Bayer,Angus Buckling
Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities)
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Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant. Interface Focus (IF 4.4) Pub Date : 2023-06-09 Limin Lin,Feng Ju
High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically
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Multiscale models driving hypothesis and theory-based research in microbial ecology. Interface Focus (IF 4.4) Pub Date : 2023-06-09 Eloi Martinez-Rabert,William T Sloan,Rebeca Gonzalez-Cabaleiro
Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach
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Engineering biology in the face of uncertainty. Interface Focus (IF 4.4) Pub Date : 2023-06-09 William T Sloan,Tania L Gómez-Borraz
Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering
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As without, so within: how the brain's temporo-spatial alignment to the environment shapes consciousness. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Georg Northoff,Philipp Klar,Magnus Bein,Adam Safron
Consciousness is constituted by a structure that includes contents as foreground and the environment as background. This structural relation between the experiential foreground and background presupposes a relationship between the brain and the environment, often neglected in theories of consciousness. The temporo-spatial theory of consciousness addresses the brain-environment relation by a concept
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Chiral conformity emerges from the least-time free energy consumption. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Arto Annila
The prevalence of chirally pure biological polymers is often assumed to stem from some slight preference for one chiral form at the origin of life. Likewise, the predominance of matter over antimatter is presumed to follow from some subtle bias for matter at the dawn of the universe. However, rather than being imposed from the start, handedness standards in societies emerged to make things work. Since
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Symmetry and complexity in object-centric deep active inference models. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Stefano Ferraro,Toon Van de Maele,Tim Verbelen,Bart Dhoedt
Humans perceive and interact with hundreds of objects every day. In doing so, they need to employ mental models of these objects and often exploit symmetries in the object's shape and appearance in order to learn generalizable and transferable skills. Active inference is a first principles approach to understanding and modelling sentient agents. It states that agents entertain a generative model of
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The scaling of goals from cellular to anatomical homeostasis: an evolutionary simulation, experiment and analysis. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Léo Pio-Lopez,Johanna Bischof,Jennifer V LaPalme,Michael Levin
Complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behaviour science, evolutionary developmental biology and the field of machine intelligence all seek to understand the scaling of biological cognition: what enables individual cells to integrate their activities to result in the emergence of a novel, higher-level intelligence
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Embodied cognitive morphogenesis as a route to intelligent systems. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Bradly Alicea,Richard Gordon,Jesse Parent
The embryological view of development is that coordinated gene expression, cellular physics and migration provides the basis for phenotypic complexity. This stands in contrast with the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behaviours. We aim to unite these two perspectives as embodied
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Neuromodulatory control of complex adaptive dynamics in the brain. Interface Focus (IF 4.4) Pub Date : 2023-04-14 James M Shine
How is the massive dimensionality and complexity of the microscopic constituents of the nervous system brought under sufficiently tight control so as to coordinate adaptive behaviour? A powerful means for striking this balance is to poise neurons close to the critical point of a phase transition, at which a small change in neuronal excitability can manifest a nonlinear augmentation in neuronal activity
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Reflections on the asymmetry of causation. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Jenann Ismael
The most immediately salient asymmetry in our experience of the world is the asymmetry of causation. In the last few decades, two developments have shed new light on the asymmetry of causation: clarity in the foundations of statistical mechanics, and the development of the interventionist conception of causation. In this paper, we ask what is the status of the causal arrow, assuming a thermodynamic
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The lack of temporal brain dynamics asymmetry as a signature of impaired consciousness states. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Elvira G-Guzmán,Yonatan Sanz Perl,Jakub Vohryzek,Anira Escrichs,Dragana Manasova,Başak Türker,Enzo Tagliazucchi,Morten Kringelbach,Jacobo D Sitt,Gustavo Deco
Life is a constant battle against equilibrium. From the cellular level to the macroscopic scale, living organisms as dissipative systems require the violation of their detailed balance, i.e. metabolic enzymatic reactions, in order to survive. We present a framework based on temporal asymmetry as a measure of non-equilibrium. By means of statistical physics, it was discovered that temporal asymmetries
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Emergence of common concepts, symmetries and conformity in agent groups-an information-theoretic model. Interface Focus (IF 4.4) Pub Date : 2023-04-14 Marco Möller,Daniel Polani
The paper studies principles behind structured, especially symmetric, representations through enforced inter-agent conformity. For this, we consider agents in a simple environment who extract individual representations of this environment through an information maximization principle. The representations obtained by different agents differ in general to some extent from each other. This gives rise
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Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors. Interface Focus (IF 4.4) Pub Date : 2023-02-10 S Jane Fowler,Elena Torresi,Arnaud Dechesne,Barth F Smets
Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of
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The media composition as a crucial element in high-throughput metabolic network reconstruction. Interface Focus (IF 4.4) Pub Date : 2023-02-10 Benedict Borer,Stefanía Magnúsdóttir
In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput
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Encounter rates prime interactions between microorganisms. Interface Focus (IF 4.4) Pub Date : 2023-02-10 Jonasz Słomka,Uria Alcolombri,Francesco Carrara,Riccardo Foffi,François J Peaudecerf,Matti Zbinden,Roman Stocker
Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell-cell or cell-resource encounters. Quantification and rational design of microbial interactions thus require quantification of encounter rates. Encounter rates
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Formation and emergent dynamics of spatially organized microbial systems. Interface Focus (IF 4.4) Pub Date : 2023-02-10 Kelsey Cremin,Sarah J N Duxbury,Jerko Rosko,Orkun S Soyer
Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects
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Correction to: 'Current strategies with implementation of 3D cell culture: The challenge of quantification' (2022) by Temple et al. Interface Focus (IF 4.4) Pub Date : 2023-02-10 J Temple,E Velliou,M Shehata,R Lévy,P Gupta
[This corrects the article DOI: 10.1098/rsfs.2022.0019.][This corrects the article DOI: 10.1098/rsfs.2022.0019.].
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Multidisciplinary approaches to the Amazonian past: introduction to the theme issue Interface Focus (IF 4.4) Pub Date : 2023-02-06 Nicholas Q. Emlen, Leonardo Arias, Rik van Gijn
This theme issue presents collaborative research by anthropologists, linguists, archaeologists, geneticists, historians and biogeographers, who work across disciplinary boundaries to investigate the Amazonian past. Amazonia is a fertile ground in which to develop such multidisciplinary approaches because its relative paucity of documentary records makes other sources of evidence regarding the past
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Deriving calibrations for Arawakan using archaeological evidence Interface Focus (IF 4.4) Pub Date : 2023-02-06 Lev Michael, Fernando de Carvalho, Thiago Chacon, Konrad Rybka, Andrés Sabogal, Natalia Chousou-Polydouri, Gereon Kaiping
This paper identifies time calibration points for accurately rooting and dating the phylogeny of Arawakan, the largest Indigenous linguistic family of the Americas. We present and model a methodology for extracting calibration points from the archaeological record, based on principles of geographical overlap between archaeological sites and Arawakan peoples, and on continuity in material culture between
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Diversity, multilingualism and inter-ethnic relations in the long-term history of the Upper Rio Negro region of the Amazon Interface Focus (IF 4.4) Pub Date : 2023-02-06 Luis Cayón, Thiago Chacon
The Upper Rio Negro regional social system is made up of more than 30 languages belonging to six linguistic families. This results from socio-historical processes stretching back at least two millennia, which have built a system with different levels of autonomy and hierarchy associated with a mythical and ritual complex, and with social and linguistic exchanges. The analysis of these processes require
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Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan) Interface Focus (IF 4.4) Pub Date : 2023-02-06 Leonardo Arias, Nicholas Q. Emlen, Sietze Norder, Nora Julmi, Magdalena Lemus Serrano, Thiago Chacon, Jurriaan Wiegertjes, Austin Howard, Matheus C. B. C. Azevedo, Allison Caine, Saskia Dunn, Mark Stoneking, Rik Van Gijn
Northwestern Amazonia is home to a great degree of linguistic diversity, and the human societies in that region are part of complex networks of interaction that predate the arrival of Europeans. This study investigates the population and language contact dynamics between two languages found within this region, Yukuna and Tanimuka, which belong to the Arawakan and Tukanoan language families, respectively
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Untangling the evolution of body-part terminology in Pano: conservative versus innovative traits in body-part lexicalization Interface Focus (IF 4.4) Pub Date : 2023-02-06 Roberto Zariquiey, Javier Vera, Simon J. Greenhill, Pilar Valenzuela, Russell J. Gray, Johann-Mattis List
Although language-family specific traits which do not find direct counterparts outside a given language family are usually ignored in quantitative phylogenetic studies, scholars have made ample use of them in qualitative investigations, revealing their potential for identifying language relationships. An example of such a family specific trait are body-part expressions in Pano languages, which are
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The social lives of isolates (and small language families): the case of the Northwest Amazon Interface Focus (IF 4.4) Pub Date : 2023-02-06 Rik Van Gijn, Sietze Norder, Leonardo Arias, Nicholas Q. Emlen, Matheus C. B. C. Azevedo, Allison Caine, Saskia Dunn, Austin Howard, Nora Julmi, Olga Krasnoukhova, Mark Stoneking, Jurriaan Wiegertjes
The Americas are home to patches of extraordinary linguistic (genealogical) diversity. These high-diversity areas are particularly unexpected given the recent population of the Americas. In this paper, we zoom in on one such area, the Northwest Amazon, and address the question of how the diversity in this area has persisted to the present. We contrast two hypotheses that claim opposite mechanisms for
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Correction to 'COVID-19: the case for aerosol transmission' 2022 by Tellier. Interface Focus (IF 4.4) Pub Date : 2022-12-09 Raymond Tellier
[This corrects the article DOI: 10.1098/rsfs.2021.0072.][This corrects the article DOI: 10.1098/rsfs.2021.0072.].
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Mucus from human bronchial epithelial cultures: rheology and adhesion across length scales Interface Focus (IF 4.4) Pub Date : 2022-10-14 Myriam Jory, Dario Donnarumma, Christophe Blanc, Karim Bellouma, Aurélie Fort, Isabelle Vachier, Laura Casanellas, Arnaud Bourdin, Gladys Massiera
Mucus is a viscoelastic aqueous fluid that participates in the protective barrier of many mammals' epithelia. In the airways, together with cilia beating, mucus rheological properties are crucial for lung mucociliary function, and, when impaired, potentially participate in the onset and progression of chronic obstructive pulmonary disease (COPD). Samples of human mucus collected in vivo are inherently
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Experimental challenges in determining the rheological properties of bacterial biofilms Interface Focus (IF 4.4) Pub Date : 2022-10-14 Steffen Geisel, Eleonora Secchi, Jan Vermant
Bacterial biofilms are communities living in a matrix consisting of self-produced, hydrated extracellular polymeric substances. Most microorganisms adopt the biofilm lifestyle since it protects by conferring resistance to antibiotics and physico-chemical stress factors. Consequently, mechanical removal is often necessary but rendered difficult by the biofilm’s complex, viscoelastic response, and adhesive
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Flow simulations of rectal evacuation: towards a quantitative evaluation from video defaecography Interface Focus (IF 4.4) Pub Date : 2022-10-14 Faisal Ahmad, Stéphane Tanguy, Alain Dubreuil, Albert Magnin, Jean-Luc Faucheron, Clément de Loubens
Mechanistic understanding of anorectal (patho)physiology is missing to improve the medical care of patients suffering from defaecation disorders. Our objective is to show that complex fluid dynamics modelling of video defaecography may open new perspectives in the diagnosis of defaecation disorders. Based on standard X-ray video defaecographies, we developed a bi-dimensional patient-specific simulation
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The role of biofilm matrix composition in controlling colony expansion and morphology Interface Focus (IF 4.4) Pub Date : 2022-10-14 Samuel G. V. Charlton, Dorothee L. Kurz, Steffen Geisel, Joaquin Jimenez-Martinez, Eleonora Secchi
Biofilms are biological viscoelastic gels composed of bacterial cells embedded in a self-secreted polymeric extracellular matrix (ECM). In environmental settings, such as in the rhizosphere and phyllosphere, biofilm colonization occurs at the solid–air interface. The biofilms’ ability to colonize and expand over these surfaces depends on the formation of osmotic gradients and ECM viscoelastic properties
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Measuring the linear viscoelastic regime of MCF-7 cells with a monolayer rheometer in the presence of microtubule-active anti-cancer drugs at high concentrations Interface Focus (IF 4.4) Pub Date : 2022-10-14 Suhyang Lee, Khawaja Muhammad Imran Bashir, Dong Hee Jung, Santanu Kumar Basu, Gayeon Seo, Man-Gi Cho, Andreas Wierschem
The rheological properties of cells have vital functional implications. Depending, for instance, on the life cycle, cells show large cell-to-cell variations making it cumbersome to quantify average viscoelastic properties of cells by single-cell techniques. Microfluidic devices, typically working in the nonlinear viscoelastic range, allow fast analysis of single-cell deformation. Averaging over a large
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Red blood cell dynamics in extravascular biological tissues modelled as canonical disordered porous media Interface Focus (IF 4.4) Pub Date : 2022-10-14 Qi Zhou, Kerstin Schirrmann, Eleanor Doman, Qi Chen, Naval Singh, P. Ravi Selvaganapathy, Miguel O. Bernabeu, Oliver E. Jensen, Anne Juel, Igor L. Chernyavsky, Timm Krüger
The dynamics of blood flow in the smallest vessels and passages of the human body, where the cellular character of blood becomes prominent, plays a dominant role in the transport and exchange of solutes. Recent studies have revealed that the microhaemodynamics of a vascular network is underpinned by its interconnected structure, and certain structural alterations such as capillary dilation and blockage
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How dynamic prestress governs the shape of living systems, from the subcellular to tissue scale Interface Focus (IF 4.4) Pub Date : 2022-10-14 Alexander Erlich, Jocelyn Étienne, Jonathan Fouchard, Tom Wyatt
Cells and tissues change shape both to carry out their function and during pathology. In most cases, these deformations are driven from within the systems themselves. This is permitted by a range of molecular actors, such as active crosslinkers and ion pumps, whose activity is biologically controlled in space and time. The resulting stresses are propagated within complex and dynamical architectures
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Frustrated ‘run and tumble’ of swimming Escherichia coli bacteria in nematic liquid crystals Interface Focus (IF 4.4) Pub Date : 2022-10-14 Martyna Goral, Eric Clement, Thierry Darnige, Teresa Lopez-Leon, Anke Lindner
In many situations, bacteria move in complex environments, as soils, oceans or the human gut-track, where carrier fluids show complex structures associated with non-Newtonian rheology. Many fundamental questions concerning the ability to navigate in such environments remain unsolved. Recently, it has been shown that the kinetics of bacterial motion in structured fluids as liquid crystals (LCs) is constrained
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Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo Interface Focus (IF 4.4) Pub Date : 2022-10-14 Sarah Lecinski, Jack W. Shepherd, Kate Bunting, Lara Dresser, Steven D. Quinn, Chris MacDonald, Mark C. Leake
In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalized in
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Hyperelastic continuum models for isotropic athermal fibrous networks Interface Focus (IF 4.4) Pub Date : 2022-10-14 Dawei Song, Assad A. Oberai, Paul A. Janmey
Many biological materials contain fibrous protein networks as their main structural components. Understanding the mechanical properties of such networks is important for creating biomimicking materials for cell and tissue engineering, and for developing novel tools for detecting and diagnosing disease. In this work, we develop continuum models for isotropic, athermal fibrous networks by combining a
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Semen rheology and its relation to male infertility Interface Focus (IF 4.4) Pub Date : 2022-10-14 Giovanna Tomaiuolo, Fiammetta Fellico, Valentina Preziosi, Stefano Guido
Infertility affects 15% of couples of reproductive age worldwide. In spite of many advances in understanding and treating male infertility, there is still a number of issues that need further investigation and translation to the clinic. Here, we review the current knowledge and practice concerning semen rheology and its relation with pathological states affecting male infertility. Although it is well
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Correction to 'Mathematical modelling of oxygen transport in a muscle-on-chip device' (2022) by Hardman et al. Interface Focus (IF 4.4) Pub Date : 2022-10-14 David Hardman,Manh-Louis Nguyen,Stéphanie Descroix,Miguel O Bernabeu
[This corrects the article DOI: 10.1098/rsfs.2022.0020.][This corrects the article DOI: 10.1098/rsfs.2022.0020.].
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Current strategies with implementation of three-dimensional cell culture: the challenge of quantification Interface Focus (IF 4.4) Pub Date : 2022-08-12 Jonathan Temple, Eirini Velliou, Mona Shehata, Raphaël Lévy
From growing cells in spheroids to arranging them on complex engineered scaffolds, three-dimensional cell culture protocols are rapidly expanding and diversifying. While these systems may often improve the physiological relevance of cell culture models, they come with technical challenges, as many of the analytical methods used to characterize traditional two-dimensional (2D) cells must be modified
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An insight into the iPSCs-derived two-dimensional culture and three-dimensional organoid models for neurodegenerative disorders Interface Focus (IF 4.4) Pub Date : 2022-08-12 Anushka Bhargava, Ana M. Sandoval Castellanos, Sonali Shah, Ke Ning
The use of induced pluripotent stem cells (iPSCs) is a promising approach when used as models to study neurodegenerative disorders (NDDs) in vitro. iPSCs have been used in in vitro two-dimensional cultures; however, these two-dimensional cultures do not mimic the physiological three-dimensional cellular environment. The use of iPSCs-derived three-dimensional organoids has risen as a powerful alternative
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Mathematical modelling of oxygen transport in a muscle-on-chip device Interface Focus (IF 4.4) Pub Date : 2022-08-12 David Hardman, Manh-Louis Nguyen, Stéphanie Descroix, Miguel O. Bernabeu
Muscle-on-chip devices aim to recapitulate the physiological characteristics of in vivo muscle tissue and so maintaining levels of oxygen transported to cells is essential for cell survival and for providing the normoxic conditions experienced in vivo. We use finite-element method numerical modelling to describe oxygen transport and reaction in a proposed three-dimensional muscle-on-chip bioreactor
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‘Cloudbuster’: a Python-based open source application for three-dimensional reconstruction and quantification of stacked biological imaging samples Interface Focus (IF 4.4) Pub Date : 2022-08-12 A. Rohwedder, S. Knipp, F. O. Esteves, M. Hale, S. E. Ketchen, D. Treanor, A. Brüning-Richardson
Three-dimensional (3D) spheroid cultures are generating increasing interest in cancer research, e.g. for the evaluation of pharmacological effects of novel small molecule inhibitors. This is mainly due to the fact that such 3D structures reflect physiological characteristics of tumours and the cellular microenvironments they reside in more faithfully than two-dimensional (2D) cell cultures; in addition
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Potential of stem cell seeded three-dimensional scaffold for regeneration of full-thickness skin wounds Interface Focus (IF 4.4) Pub Date : 2022-08-12 Irfan Khan, Marium Naz Siddiqui, Fatima Jameel, Rida-e-Maria Qazi, Asmat Salim, Shazmeen Aslam, Midhat Batool Zaidi
Hypoxic wounds are tough to heal and are associated with chronicity, causing major healthcare burden. Available treatment options offer only limited success for accelerated and scarless healing. Traditional skin substitutes are widely used to improve wound healing, however, they lack proper vascularization. Mesenchymal stem cells (MSCs) offer improved wound healing; however, their poor retention, survival
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Dynamical landscapes of cell fate decisions Interface Focus (IF 4.4) Pub Date : 2022-06-10 M. Sáez, J. Briscoe, D. A. Rand
The generation of cellular diversity during development involves differentiating cells transitioning between discrete cell states. In the 1940s, the developmental biologist Conrad Waddington introduced a landscape metaphor to describe this process. The developmental path of a cell was pictured as a ball rolling through a terrain of branching valleys with cell fate decisions represented by the branch
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Time-keeping and decision-making in the cell cycle Interface Focus (IF 4.4) Pub Date : 2022-06-10 John J. Tyson, Béla Novák
Cell growth, DNA replication, mitosis and division are the fundamental processes by which life is passed on from one generation of eukaryotic cells to the next. The eukaryotic cell cycle is intrinsically a periodic process but not so much a ‘clock’ as a ‘copy machine’, making new daughter cells as warranted. Cells growing under ideal conditions divide with clock-like regularity; however, if they are
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Quantitative models for building and growing fated small cell networks Interface Focus (IF 4.4) Pub Date : 2022-06-10 Rocky Diegmiller, Hayden Nunley, Stanislav Y. Shvartsman, Jasmin Imran Alsous
Small cell clusters exhibit numerous phenomena typically associated with complex systems, such as division of labour and programmed cell death. A conserved class of such clusters occurs during oogenesis in the form of germline cysts that give rise to oocytes. Germline cysts form through cell divisions with incomplete cytokinesis, leaving cells intimately connected through intercellular bridges that
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Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo Interface Focus (IF 4.4) Pub Date : 2022-06-10 Corentin Robert, Francisco Prista von Bonhorst, Yannick De Decker, Geneviève Dupont, Didier Gonze
During development, cells from a population of common progenitors evolve towards different fates characterized by distinct levels of specific transcription factors, a process known as cell differentiation. This evolution is governed by gene regulatory networks modulated by intercellular signalling. In order to evolve towards distinct fates, cells forming the population of common progenitors must display
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The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems Interface Focus (IF 4.4) Pub Date : 2022-06-10 Kee-Myoung Nam, Rosa Martinez-Corral, Jeremy Gunawardena
The linear framework uses finite, directed graphs with labelled edges to model biomolecular systems. Graph vertices represent biochemical species or molecular states, edges represent reactions or transitions and labels represent rates. The graph yields a linear dynamics for molecular concentrations or state probabilities, with the graph Laplacian as the operator, and the labels encode the nonlinear
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Time-keeping and decision-making in living cells: Part I Interface Focus (IF 4.4) Pub Date : 2022-04-15 John J. Tyson, Attila Csikasz-Nagy, Didier Gonze, Jae Kyoung Kim, Silvia Santos, Jana Wolf
To survive and reproduce, a cell must process information from its environment and its own internal state and respond accordingly, in terms of metabolic activity, gene expression, movement, growth, division and differentiation. These signal–response decisions are made by complex networks of interacting genes and proteins, which function as biochemical switches and clocks, and other recognizable in