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1. Computational Approaches and Observer Variation in the 3D Musculoskeletal Modeling of the Heads of Anolis

   https://doi.org/10.1093/iob/obae009  

   Lagorio, A D; McGechie, F R; Fields, M G; Fortner, J; Mackereth, E; Perez, C; Wilken, A T; Leal, M; Ward, C V; Middleton, K M; et al (January 2024, Integrative Organismal Biology)

   Synopsis High-resolution imaging, 3D modeling, and quantitative analyses are equipping evolutionary biologists with new approaches to understanding the variation and evolution of the musculoskeletal system. However, challenges with interpreting DiceCT data and higher order use of modeled muscles have not yet been fully explored, and the error in and accuracy of some digital methods remain unclear. West Indian Anolis lizards are a model clade for exploring patterns in functional adaptation, ecomorphology, and sexual size dimorphism in vertebrates. These lizards possess numerous jaw muscles with potentially different anatomies that sculpt the adductor chamber of the skull. Here we test approaches to quantifying the musculoskeletal shape of the heads of two species of Anolis: A. pulchellus and A. sagrei. We employ comparative approaches such as DiceCT segmentation of jaw muscles, 3D surface attachment mapping, and 3D landmarking with the aim of exploring muscle volumes, 3D muscle fiber architecture, and sexual dimorphism of the skull. We then compare sources of measurement error in these 3D analyses while also presenting new 3D musculoskeletal data from the Anolis feeding apparatus. These findings demonstrate the accessibility and repeatability of these emerging techniques as well as provide details regarding the musculoskeletal anatomy of the heads of A. pulchellus and A. sagrei which show potential for further research of comparative biomechanics and evolution in the clade. 

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2. habtools : An R package to calculate 3D metrics for surfaces and objects

   https://doi.org/10.1111/2041-210X.70027  

   Schiettekatte, Nina; Asbury, Mollie; Chen, Guanyan Keelung; Dornelas, Maria; Reichert, Jessica; Torres‐Pulliza, Damaris; Zawada, Kyle_J A; Madin, Joshua S (May 2025, Methods in Ecology and Evolution)

   Abstract Technological advances in three imaging techniques have opened the door to advanced morphological analyses and habitat mapping for biologists and ecologists.At the same time, the challenge of translating complex 3D data into meaningful metrics that can be used in conjunction with biological data currently hinders progress and accessibility.We introducehabtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow.We expect the functionality ofhabtoolsto continue to expand as new metrics and faster methods become available, and we welcome new contributions and ideas. 

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3. 3D printing of superhydrophobic and multifunctional objects via simple and inexpensive vat photopolymerization

   https://doi.org/10.1039/d4nr05135a  

   Rather, Adil Majeed; Barrubeeah, Mohammed; Zarei, Mohammad Javad; Kim, Young Jae; Vallabhuneni, Sravanthi; Kota, Arun Kumar (January 2025, Nanoscale)

   We fabricated superhydrophobic and multifunctional objects using a simple and inexpensive vat photopolymerization 3D printer with a 2-component ink and a 2-step process. 

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4. Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum

   https://doi.org/10.1094/MPMI-05-23-0068-R  

   Regmi, Kamesh C; Ghosh, Suchismita; Koch, Benjamin; Neumann, Ulla; Stein, Barry; O'Connell, Richard J; Innes, Roger W (April 2024, Molecular Plant-Microbe Interactions®)

   We used serial block-face scanning electron microscopy (SBF-SEM) to study the host–pathogen interface between Arabidopsis cotyledons and the hemibiotrophic fungus Colletotrichum higginsianum. By combining high-pressure freezing and freeze-substitution with SBF-SEM, followed by segmentation and reconstruction of the imaging volume using the freely accessible software IMOD, we created 3D models of the series of cytological events that occur during the Colletotrichum–Arabidopsis susceptible interaction. We found that the host cell membranes underwent massive expansion to accommodate the rapidly growing intracellular hypha. As the fungal infection proceeded from the biotrophic to the necrotrophic stage, the host cell membranes went through increasing levels of disintegration culminating in host cell death. Intriguingly, we documented autophagosomes in proximity to biotrophic hyphae using transmission electron microscopy (TEM) and a concurrent increase in autophagic flux between early to mid/late biotrophic phase of the infection process. Occasionally, we observed osmiophilic bodies in the vicinity of biotrophic hyphae using TEM only and near necrotrophic hyphae under both TEM and SBF-SEM. Overall, we established a method for obtaining serial SBF-SEM images, each with a lateral ( x-y) pixel resolution of 10 nm and an axial ( z) resolution of 40 nm, that can be reconstructed into interactive 3D models using the IMOD. Application of this method to the Colletotrichum–Arabidopsis pathosystem allowed us to more fully understand the spatial arrangement and morphological architecture of the fungal hyphae after they penetrate epidermal cells of Arabidopsis cotyledons and the cytological changes the host cell undergoes as the infection progresses toward necrotrophy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . 

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5. Reproducible 3D bioprinting of Streptococcus mutans to create model oral biofilms

   https://doi.org/10.1128/spectrum.00935-25  

   Rocha, Guilherme Roncari; Benoit, Danielle_S W; Meyer, Anne S (November 2025, Microbiology Spectrum)

   Kolodkin-Gal, Ilana (Ed.)

   ABSTRACT Novel approaches are needed to study relationships between oral biofilm strains, enable three-dimensional oral biofilm deposition, and hasten the rigor and pace of basic and translational biofilm studies. Previously, 3D-bioprinters were leveraged to deposit spatially patterned biofilms onto sugar-rich agar surfaces to study how the underlying spatial organization of various microbes impacts biofilm persistence and virulence. Herein, we have developed a new method to adapt this process from limited, soft agar surfaces to biomimetic solid substrates submerged in aqueous solutions for studying oral biofilmsin vitro. Streptococcus mutansUA159 was used to compare standardin vitrobiofilm development with our new 3D-printed bio-ink hydrogels on hydroxyapatite disks, which mimic tooth surfaces. Biofilms formed using the bio-ink methodology showed minimal quantitative differences in virulence factors, including environmental pH, biomass, and cell density, compared to biofilms formed using the standardin vitromethodology. The bio-ink technique resulted in higher exopolysaccharide deposition, a key virulence factor for biofilm cohesion and protection, as well as more homogeneous spatial distribution of bacterial microcolonies. Our newly developed technique produces 3D-printable model biofilms that match the virulence benchmarks of the standard method, opening possibilities to print biofilms onto any substrate and a new way to study multidimensional biofilm dynamics.IMPORTANCEDental caries is the most common oral disease caused by biofilms in humans with cost limitations. Changes in the human diet have increased the exposure to sugar-rich processed food, increasing the incidence and severity of dental caries and creating greater rationale for understanding biofilm deposition, microbial interactions, and maintenance of quiescence of the oral microbiota. Recent 3D-printing techniques have been leveraged to develop the first model biofilms, providing spatial control over microbe deposition and enabling unprecedented investigation of the impact of cell-cell interactions and spatial organizationupon biofilm persistence, sensitivity to drugs, and virulence. Here, we have developed new methods to extend bioprinting to oral biofilms using cariogenicStreptococcus mutans. Our technique is an attempt to establish an alternative method for oral biofilm formationin vitrothat uses 3D-printing tools, preserving the virulence of standardin vitrobiofilms while amplifying the availability and versatility of methods for understanding the microbiome. 

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