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1. Polymorphic self-assembly of helical tubules is kinetically controlled

   https://doi.org/10.1039/D2SM00679K  

   Fang, Huang; Tyukodi, Botond; Rogers, W. Benjamin; Hagan, Michael F. (September 2022, Soft Matter)

   In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly. In this article, we study an example class of self-closing assemblies: cylindrical tubules that assemble from triangular monomers. By combining kinetic Monte Carlo simulations, free energy calculations, and simple theoretical models, we show that a range of programmable size scales can be targeted by controlling the intricate balance between the preferred curvature of the monomers and their interaction strengths. However, their assembly is kinetically controlled—the tubule morphology is essentially fixed shortly after closure, resulting in a distribution of tubule widths that is significantly broader than the equilibrium distribution. We develop a simple kinetic model based on this observation and the underlying free-energy landscape of assembling tubules that quantitatively describes the distributions. Our results are consistent with recent experimental observations of tubule assembly from triangular DNA origami monomers. The modeling framework elucidates design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality. 

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2. Viscous control of cellular respiration by membrane lipid composition

   https://doi.org/10.1126/science.aat7925  

   Budin, Itay; de Rond, Tristan; Chen, Yan; Chan, Leanne Jade G.; Petzold, Christopher J.; Keasling, Jay D. (October 2018, Science)

   Lipid composition determines the physical properties of biological membranes and can vary substantially between and within organisms. We describe a specific role for the viscosity of energy-transducing membranes in cellular respiration. Engineering of fatty acid biosynthesis inEscherichia coliallowed us to titrate inner membrane viscosity across a 10-fold range by controlling the abundance of unsaturated or branched lipids. These fluidizing lipids tightly controlled respiratory metabolism, an effect that can be explained with a quantitative model of the electron transport chain (ETC) that features diffusion-coupled reactions between enzymes and electron carriers (quinones). Lipid unsaturation also modulated mitochondrial respiration in engineered budding yeast strains. Thus, diffusion in the ETC may serve as an evolutionary constraint for lipid composition in respiratory membranes. 

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3. Fluid-structure interaction modelling of neighboring tubes with primary cilium analysis

   https://doi.org/10.3934/mbe.2023172  

   Zekaj, Nerion; Ryan, Shawn D; Resnick, Andrew (January 2022, Mathematical Biosciences and Engineering)

   We have developed a numerical model of two osculating cylindrical elastic renal tubules to investigate the impact of neighboring tubules on the stress applied to a primary cilium. We hypothesize that the stress at the base of the primary cilium will depend on the mechanical coupling of the tubules due to local constrained motion of the tubule wall. The objective of this work was to determine the in-plane stresses of a primary cilium attached to the inner wall of one renal tubule subject to the applied pulsatile flow, with a neighboring renal tube filled with stagnant fluid in close proximity to the primary tubule. We used the commercial software COMSOL^Ⓡ to model the fluid-structure interaction of the applied flow and tubule wall, and we applied a boundary load to the face of the primary cilium during this simulation to produces a stress at its base. We confirm our hypothesis by observing that on average the in-plane stresses are greater at the base of the cilium when there is a neighboring renal tube versus if there is no neighboring tube at all. In combination with the hypothesized function of a cilium as a biological fluid flow sensor, these results indicate that flow signaling may also depend on how the tubule wall is constrained by neighboring tubules. Our results may be limited in their interpretation due to the simplified nature of our model geometry, and further improvements to the model may potentially lead to the design of future experiments. 

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4. Lipid Mass Tags via Aziridination for Probing Unsaturated Lipid Isomers and Accurate Relative Quantification**

   https://doi.org/10.1002/anie.202207098  

   Yang, Tingyuan; Tang, Shuli; Kuo, Syuan‐Ting; Freitas, Dallas; Edwards, Madison; Wang, Hongying; Sun, Yuxiang; Yan, Xin (August 2022, Angewandte Chemie International Edition)

   Abstract Knowing concentrations of lipids is essential for understanding their physiological functions and discovering new disease biomarkers. However, it is highly challenging to accurately quantify lipids due to structural diversity and multiple isomeric forms of lipids. To address these critical gaps, we have developed a novel aziridine‐based isobaric tag labelling strategy that allows (i) determination of lipid double‐bond positional isomers, (ii) accurate relative quantification of unsaturated lipids, and (iii) improvement of ionization efficiencies of nonpolar lipids. The power of this method is demonstrated in characterization and quantification of various categories of lipids such as fatty acids, phosphoglycerol lipids, cholesteryl esters (CE), and glycerides. 17 CE lipid isomers were identified and quantified simultaneously from Alzheimer's disease (AD) mouse serum without using lipid standards. Among them, 6 CE isomers showed significant changes in concentrations in AD serum. 

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5. Synthesis of Metal‐Modified Nanocellulose as a Biofilm Analogue for Biofilm Mimicry in Biomedical and Environmental Applications

   https://doi.org/10.1002/bip.70029  

   Taylor, Darryl_W; Jones, III, A‐Andrew_D (May 2025, Biopolymers)

   ABSTRACT Bacterial biofilms are complex, multi‐component structures consisting primarily of four key elements: polysaccharides, metal ions, proteins, and extracellular DNA. In our research, we specifically focus on the polysaccharide and metal ion components, which play a crucial role in determining the biofilm's mechanical properties. Polysaccharides provide the structural matrix, although metal ions, particularly divalent cations like calcium and cobalt, cross‐link with the polysaccharides, thereby modulating the biofilm's rigidity and viscoelastic behavior. By introducing divalent cations into nanocellulose, we can replicate this natural cross‐linking process, allowing us to finely tune the material's mechanical properties to more closely resemble those of bacterial biofilms. This approach not only enhances the accuracy of synthetic biofilm models over alginate hydrogels but also provides valuable insights into how biofilms maintain their structural integrity in various environments. Our findings indicate that nanocellulose exhibits mechanical properties closer to biofilms than alginate analogs, making it a suitable non‐living control for biofilm studies. Furthermore, divalent nickel, followed by calcium and magnesium, demonstrate a closer mechanical mimicry to biofilms. In conclusion, this research shows the potential of nanocellulose as a versatile material for bacterial biofilm mimicry. 

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