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1. Inferring local molecular dynamics from the global actin network structure: A case study of 2D synthetic branching actin networks

   https://doi.org/10.1016/j.jtbi.2023.111613  

   Rostami, Minghao W; Bannish, Brittany E; Gasior, Kelsey; Pinals, Rebecca L; Copos, Calina; Dawes, Adriana T (November 2023, Journal of theoretical biology)

   Cells rely on their cytoskeleton for key processes including division and directed motility. Actin filaments are a primary constituent of the cytoskeleton. Although actin filaments can create a variety of network architectures linked to distinct cell functions, the microscale molecular interactions that give rise to these macroscale structures are not well understood. In this work, we investigate the microscale mechanisms that produce different branched actin network structures using an iterative classification approach. First, we employ a simple yet comprehensive agent-based model that produces synthetic actin networks with precise control over the microscale dynamics. Then we apply machine learning techniques to classify actin networks based on measurable network density and geometry, identifying key mechanistic processes that lead to particular branched actin network architectures. Extensive computational experiments reveal that the most accurate method uses a combination of supervised learning based on network density and unsupervised learning based on network symmetry. This framework can potentially serve as a powerful tool to discover the molecular interactions that produce the wide variety of actin network configurations associated with normal development as well as pathological conditions such as cancer. 

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2. Cell motility dependence on adhesive wetting

   https://doi.org/10.1039/C8SM01832D  

   Cao, Yuansheng; Karmakar, Richa; Ghabache, Elisabeth; Gutierrez, Edgar; Zhao, Yanxiang; Groisman, Alex; Levine, Herbert; Camley, Brian A.; Rappel, Wouter-Jan (February 2019, Soft Matter)

   Adhesive cell–substrate interactions are crucial for cell motility and are responsible for the necessary traction that propels cells. These interactions can also change the shape of the cell, analogous to liquid droplet wetting on adhesive substrates. To address how these shape changes affect cell migration and cell speed we model motility using deformable, 2D cross-sections of cells in which adhesion and frictional forces between cell and substrate can be varied separately. Our simulations show that increasing the adhesion results in increased spreading of cells and larger cell speeds. We propose an analytical model which shows that the cell speed is inversely proportional to an effective height of the cell and that increasing this height results in increased internal shear stress. The numerical and analytical results are confirmed in experiments on motile eukaryotic cells. 

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3. Mechanical shear controls bacterial penetration in mucus

   https://doi.org/10.1038/s41598-019-46085-z  

   Figueroa-Morales, Nuris; Dominguez-Rubio, Leonardo; Ott, Troy L.; Aranson, Igor S. (July 2019, Scientific Reports)

   Abstract Mucus plays crucial roles in higher organisms, from aiding fertilization to protecting the female reproductive tract. Here, we investigate how anisotropic organization of mucus affects bacterial motility. We demonstrate by cryo electron micrographs and elongated tracer particles imaging, that mucus anisotropy and heterogeneity depend on how mechanical stress is applied. In shallow mucus films, we observe bacteria reversing their swimming direction without U-turns. During the forward motion, bacteria burrowed tunnels that last for several seconds and enable them to swim back faster, following the same track. We elucidate the physical mechanism of direction reversal by fluorescent visualization of the flagella: when the bacterial body is suddenly stopped by the mucus structure, the compression on the flagellar bundle causes buckling, disassembly and reorganization on the other side of the bacterium. Our results shed light into motility of bacteria in complex visco-elastic fluids and can provide clues in the propagation of bacteria-born diseases in mucus. 

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4. Systematic analysis of proximal midgut‐ and anorectal‐originating contractions in larval zebrafish using event feature detection and supervised machine learning algorithms

   https://doi.org/10.1111/nmo.14675  

   Cassidy, Ryan M.; Flores, Erika M.; Trinh Nguyen, Anh K.; Cheruvu, Sai S.; Uribe, Rosa A.; Krachler, Anne Marie; Odem, Max A. (September 2023, Neurogastroenterology & Motility)

   Abstract BackgroundZebrafish larvae are translucent, allowing in vivo analysis of gut development and physiology, including gut motility. While recent progress has been made in measuring gut motility in larvae, challenges remain which can influence results, such as how data are interpreted, opportunities for technical user error, and inconsistencies in methods. MethodsTo overcome these challenges, we noninvasively introduced Nile Red fluorescent dye to fill the intraluminal gut space in zebrafish larvae and collected serial confocal microscopic images of gut fluorescence. We automated the detection of fluorescent‐contrasted contraction events against the median‐subtracted signal and compared it to manually annotated gut contraction events across anatomically defined gut regions. Supervised machine learning (multiple logistic regression) was then used to discriminate between true contraction events and noise. To demonstrate, we analyzed motility in larvae under control and reserpine‐treated conditions. We also used automated event detection analysis to compare unfed and fed larvae. Key ResultsAutomated analysis retained event features for proximal midgut‐originating retrograde and anterograde contractions and anorectal‐originating retrograde contractions. While manual annotation showed reserpine disrupted gut motility, machine learning only achieved equivalent contraction discrimination in controls and failed to accurately identify contractions after reserpine due to insufficient intraluminal fluorescence. Automated analysis also showed feeding had no effect on the frequency of anorectal‐originating contractions. Conclusions & InferencesAutomated event detection analysis rapidly and accurately annotated contraction events, including the previously neglected phenomenon of anorectal contractions. However, challenges remain to discriminate contraction events based on intraluminal fluorescence under treatment conditions that disrupt functional motility. 

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5. Evaporation Rate Measurement at Multiple Scales Using Temperature-Sensitive Fluorescence Dyes

   https://doi.org/10.1115/IPACK2019-6372  

   Suh, Youngjoon; Lin, Cheng-Hui; Gowda, Hamsa; Won, Yoonjin (October 2019, InterPACK 2019)

   Abstract As modern electronics continuously exceed their performance limits, there is an urgent need to develop new cooling devices that balance the increasing power demands. To meet this need, cutting-edge cooling devices often utilize microscale structures that facilitate two-phase heat transfer. However, it has been difficult to understand how microstructures trigger enhanced evaporation performances through traditional experimental methods due to low spatial resolution. The previous methods can only provide coarse interpretations on how physical properties such as permeability, thermal conduction, and effective surface areas interact at the microscale to effectively dissipate heat. This motivates researchers to develop new methods to observe and analyze local evaporation phenomena at the microscale. Herein, we present techniques to characterize submicron to macroscale evaporative phenomena of microscale structures using micro laser induced fluorescence (μLIF). We corroborate the use of unsealed temperature-sensitive dyes by systematically investigating their effects on temperature, concentration, and liquid thickness on the fluorescence intensity. Considering these factors, we analyze the evaporative performances of microstructures using two approaches. The first approach characterizes local or overall evaporation rates by measuring the solution drying time. The second method employs an intensity-to-temperature calibration curve to convert temperature-sensitive fluorescence signals to surface temperatures. Then, submicron-level evaporation rates are calculated by employing a species transport equation for vapor at the liquid-vapor interface. Using these methods, we reveal that capillary-assisted liquid feeding dominates evaporation phenomena on microstructured surfaces. This study will enable engineers to decompose the key thermofluidic parameters contributing to the evaporative performance of microscale structures. 

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