Formation Of Three-dimensional Structures Research Articles

Escarpments within Mediterranean seagrass Posidonia oceanica meadows increase habitat heterogeneity and structural complexity enhancing fish diversity and biomass

Seagrass meadows provide important ecosystem services including carbon sequestration, coastal protection from erosion, and sustained biodiversity and fisheries thereby improving the wellbeing and livelihoods of coastal communities. The erosion of millenary deposits of intertwined roots and rhizomes of Posidonia results in the formation of three-dimensional structures named escarpments that constitute a biogenic reef habitat. However, the natural history of seagrass escarpments including their formation processes and their role as habitat for reef fauna and flora remains poorly understood. This research located and characterized Posidonia oceanica escarpments in Menorca (Balearic Islands) and compared structural complexity and fish assemblages among seagrass escarpments, seagrass meadows, rocky substrates and bare sand with emphasis on its role as habitat and shelter for typical rocky fish. Fish abundance and biomass were similar between seagrass escarpments and rocky substrates (P > 0.05), but significantly lower in seagrass meadows (P < 0.001). The large number of caves found along seagrass escarpments provide shelter to fish, including species only associated to rocky substrates. Seagrass meadows form a rather homogenous habitat within their canopy, but the presence of seagrass escarpments enhances habitat heterogeneity and structural complexity along with fish abundance and biomass at the seascape level. This study enhances understanding on the ecological importance of seagrass escarpments.

Development of Au Nanoparticle Two-Dimensional Assemblies Dispersed with Au Nanoparticle-Nanostar Complexes and Surface-Enhanced Raman Scattering Activity.

We recently found that polyvinylpyrrolidone (PVP)-protected metal nanoparticles dispersed in water/butanol mixture spontaneously float to the air/water interface and form two-dimensional assemblies due to classical surface excess theory and Rayleigh-Bénard-Marangoni convection induced by butanol evaporation. In this study, we found that by leveraging this principle, a unique structure is formed where hetero gold nanospheres (AuNPs)/gold nanostars (AuNSs) complexes are dispersed within AuNP two-dimensional assemblies, obtained from a mixture of polyvinylpyrrolidone-protected AuNPs and AuNSs that interact electrostatically with the AuNPs. These structures were believed to form as a result of AuNPs/AuNSs complexes formed in the water/butanol mixture floating to the air/water interface and being incorporated into the growth of AuNP two-dimensional assemblies. These structures were obtained by optimizing the amount of mixed AuNSs, with excessive addition resulting in the formation of random three-dimensional network structures. The AuNP assemblies dispersed with AuNPs/AuNSs complexes exhibited significantly higher Raman (surface-enhanced resonance Raman scattering: SERRS) activity compared to simple AuNP assemblies, while the three-dimensional network structure did not show significant SERRS activity enhancement. These results demonstrate the excellent SERRS activity of AuNP two-dimensional assemblies dispersed with hetero AuNPs/AuNSs complexes.

4D-printing of high-temperature shape-memory polymers based on polyimide, N,N-dimethylacrylamide and photoactive cross-linkers

Thermally responsive shape memory polyimides (PIs) have attracted significant attention in the high-tech fields like aerospace industry. At the same time creating of materials and approaches to the formation of three-dimensional (3D) shape memory structures containing PIs remains an urgent task. In this work we have developed new photopolymeric compositions (PPCs) based on high-performance readily soluble PI, reactive solvent (N,N-dimethylacrylamide) and photoactive cross-linker (bisphenol A ethoxylate diacrylate (BAEDA) or tris[2-(acryloyloxy)ethyl] isocyanurate (TAI)). The resulting PPCs were used to form 3D-structures using LCD 3D-printing. It has been found that the nature of the cross-linker and post-processing temperature have a significant impact on the thermal and mechanical properties of the materials. The tensile strength has the maximum value after the thermal post-curing at 250°С for 1 h (83.3 ± 7.4 MPa and 60.8 ± 4.8 MPa for PPCs with TAI and BAEDA, respectively). Moreover, 4D-printed PI-containing materials exhibit an excellent shape memory performance at recovery temperatures >150 °C, with shape fixity ratio >99% and shape recovery ratio up to 95.6%.

Investigating Texture and Freeze-Thaw Stability of Cold-Set Gel Prepared by Soy Protein Isolate and Carrageenan Compounding.

In this study, the purpose was to investigate the effects with different concentrations of carrageenan (CG, 0-0.30%) on the gel properties and freeze-thaw stability of soy protein isolate (SPI, 8%) cold-set gels. LF-NMR, MRI, and rheology revealed that CG promoted the formation of SPI-CG cold-set gel dense three-dimensional network structures and increased gel network cross-linking sites. As visually demonstrated by microstructure observations, CG contributed to the formation of stable SPI-CG cold-set gels with uniform and compact network structures. The dense gel network formation was caused when the proportion of disulfide bonds in the intermolecular interaction of SPI-CG cold-set gels increased, and the particle size and zeta potential of SPI-CG aggregates increased. SG20 (0.20% CG) had the densest gel network in all samples. It effectively hindered the migration and flow of water, which decreased the damage of freezing to the gel network. Therefore, SG20 exhibited excellent gel strength, water holding capacity, freeze-thaw stability, and steaming stability. This was beneficial for the gel having a good quality after freeze-thaw, which provided a valuable reference for the development of freeze-thaw-resistant SPI cold-set gel products.

Experimental Investigation of the Viscosity and Stability of Scleroglucan-Based Nanofluids for Enhanced Oil Recovery.

Biopolymers emerge as promising candidates for enhanced oil recovery (EOR) applications due to their molecular structures, which exhibit better stability than polyacrylamides under harsh conditions. Nonetheless, biopolymers are susceptible to oxidation and biological degradation. Biopolymers reinforced with nanoparticles could be a potential solution to the issue. The nanofluids' stability and performance depend on the nanoparticles' properties and the preparation method. The primary objective of this study was to evaluate the effect of the preparation method and the nanoparticle type (SiO2, Al2O3, and TiO2) on the viscosity and stability of the scleroglucan (SG). The thickening effect of the SG solution was improved by adding all NPs due to the formation of three-dimensional structures between the NPs and the SG chains. The stability test showed that the SG + Al2O3 and SG + TiO2 nanofluids are highly unstable, but the SG + SiO2 nanofluids are highly stable (regardless of the preparation method). According to the ANOVA results, the preparation method and standing time influence the nanofluid viscosity with a statistical significance of 95%. On the contrary, the heating temperature and NP type are insignificant. Finally, the nanofluid with the best performance was 1000 ppm of SG + 100 ppm of SiO2_120 NPs prepared by method II.

2.5D Traction Force Microscopy: Imaging three-dimensional cell forces at interfaces and biological applications.

The forces that cells, tissues, and organisms exert on the surface of a soft substrate can be measured using Traction Force Microscopy (TFM), an important and well-established technique in Mechanobiology. The usual TFM technique (two-dimensional, 2D TFM) treats only the in-plane component of the traction forces and omits the out-of-plane forces at the substrate interfaces (2.5D) that turn out to be important in many biological processes such as tissue migration and tumour invasion. Here, we review the imaging, material, and analytical tools to perform "2.5D TFM" and explain how they are different from 2D TFM. Challenges in 2.5D TFM arise primarily from the need to work with a lower imaging resolution in the z-direction, track fiducial markers in three-dimensions, and reliably and efficiently reconstruct mechanical stress from substrate deformation fields. We also discuss how 2.5D TFM can be used to image, map, and understand the complete force vectors in various important biological events of various length-scales happening at two-dimensional interfaces, including focal adhesions forces, cell diapedesis across tissue monolayers, the formation of three-dimensional tissue structures, and the locomotion of large multicellular organisms. We close with future perspectives including the use of new materials, imaging and machine learning techniques to continuously improve the 2.5D TFM in terms of imaging resolution, speed, and faithfulness of the force reconstruction procedure.

Key role of three-dimensional reticular interface membranes in the formation of single polysaccharide–stabilized high internal phase emulsions

Although the interfacial activity of polysaccharides is believed to be insufficient for their applications as individual emulsifying stabilizers, four single polysaccharides examined herein, namely sodium carboxymethyl cellulose (Na-CMC), sodium alginate (SA), high-methoxyl pectin (HMP), and low-methoxyl pectin (LMP) are shown to effectively stabilize high internal phase emulsions (HIPEs) at loadings as low as 0.1 wt% under acidic conditions, that is, at pH 0.5–5.2 (Na-CMC), 0.5–4.0 (SA), 1.0–4.2 (HMP), and 1.0–3.0 (LMP). Despite their structural differences, the four studied polysaccharides feature similar HIPE stabilization mechanisms that mainly involve the formation of three-dimensional reticular interface membrane structures with fiber branching chains. Within the pH range suitable for HIPE formation, the polysaccharides mainly exist as nanofiber network structures with a grid width of 50–100 nm but adopt flake-like and other structures at higher pH. Further insights are provided by the relationship between network membrane structures formed at the interface and the fiber network structures formed by polysaccharides in the original aqueous phase. In addition, the inferred emulsification and stabilization mechanisms are shown to be significantly different from those observed for mainstream Pickering HIPE stabilizers. Thus, our work expands the understanding of the interfacial activity function of polysaccharides, provides conceptual thinking reference and design rules for the development of simple, efficient, safe, and cheap polysaccharide-based HIPEs, and supplements and furthers the theory of HIPE stabilization.

Quantitative analysis on influence of secondary flow for centrifugal impeller internal flow

A comprehensive quantitative analysis of a high-loading transonic centrifugal compressor is performed under the design point. The reason for secondary flow within the impeller is examined under the approximation of boundary layer theory. Comparing the amplitudes of different terms of the Navier–Stokes (N–S) equations reveals that the acceleration that creates secondary flow within the shear layer is caused primarily by the Coriolis force difference, which has often been neglected in previous research. Migration flow on the wall surface further leads to the formation of three-dimensional secondary flow structures that occupy the entire blade passage. The vortex structure inside the impeller is visualized, and the contribution of the different vortices to the wake is clarified. The wake is ultimately composed of high-loss fluid that includes migration flow from the hub to the tip on the blade suction surface, leakage flow, and recirculating flow at the impeller outlet. By decomposing the N–S equations, it is clarified that the pressure distribution in the blade passage is mostly determined by the acceleration caused by the three-dimensional secondary flow structure, especially the momentum convection term. Therefore, the relationship between the secondary flow and the impeller loading is established. Furthermore, the natural frequency of the unsteady fluctuation of the secondary flow inside the impeller is discovered by unsteady numerical simulation, revealing the evolution of vortex structures.

Synthesis of nonthermal plasma-irradiated polyvalent manganese (hydro)oxide functionalized nanosilica for intensifying geopolymerized solidification/stabilization of thallium-contaminated soil and mechanism exploration

Thallium (Tl) enrichment in soils can cause an immeasurable ecological disaster, disturbing ecological balance and threatening human health. In this study, nonthermal plasma (NTP) irradiation was employed to synthesize polyvalent Mn-based (hydro)oxide-functionalized nanosilica (NTP-P-Mn-nSi). Mixtures of alkali-activated geopolymers and NTP-P-Mn-nSi were subsequently prepared for the efficient solidification and stabilization (S/S) of Tl-containing soils. The synthesis of NTP-P-Mn-nSi and the geopolymerization of soils were both optimized to obtain maximum adsorption capacities and achieve excellent immobilization of the matrix. The influence of the initial pH and concentration of Tl+ on NTP-P-Mn-nSi was investigated. The leaching concentration of Tl and the compressive strengths from the soil matrix were monitored. Comprehensive strategies were adopted for soils and solidified samples to investigate the vital role played by NTP-P-Mn-nSi in the geopolymers of soils. The pseudofirst-order, intraparticle, and Elovich models were suitable for evaluating the uptake dynamics of Tl+ to NTP-P-Mn-nSi. Langmuir, Freundlich, and Tempkin were all appropriate in analysing the isotherms of heterogeneous adsorption. Four maximum monolayer adsorption capacities of NTP-P-Mn-nSi responding to Tl+ ions reached 93.90, 123.00, 355.87, and 323.62 mg/g at initial pH values of 7, 9, 11, and 13, respectively. NTP-P-Mn-nSi in the geopolymer explicitly inhibited leaching and intensified the immobilization of Tl ions in the matrix with the lowest leaching concentration of 0.16 µg/L Tl from the matrix being achieved. The increase in NTP-P-Mn-nSi dosage accelerated the growth rates of nucleation, enhanced the formation of alkali-activated gelation, induced the formation of flocculent surfaces and three-dimensional structures, and intensified the elemental overlap between Mn and Tl in the geopolymerized matrix.

Phylogenetic Constitution and Survival of Microbial Biofilms Formed on the Surface of Polyethylene Composites Protected with Polyguanidine Biocides

A series of biocide-containing polyethylene composites were obtained using novel guanidine-containing copolymers immobilized on an inert mineral carrier. Multispecies microbial communities were isolated from the surface of polyethylene samples either incubated or found in the environment, and their taxonomic composition was determined. Biofilms reconstructed using microorganisms obtained from different ecotopes were shown to intensively foul polyethylene surfaces. The presence of polyguanidine biocide suppressed the growth and survival of both binary and multispecies biofilms, with a cumulative effect during long-term incubation. When microorganisms were co-cultivated in binary biofilms, the phenomenon of a decrease in biocide effectiveness was demonstrated. This protective effect is potentially based on cooperative interactions inside the binary biofilm community. Scanning electron microscopy showed a pronounced difference in the architecture of reconstructed biofilms incubated in the presence of biocide in comparison to control samples, where biocide suppressed the formation of dense and well-organized three-dimensional structures. Biofilm disruption by immobilized biocides occurred primarily during the later stages of biofilm formation, probably caused by polycation interaction with their negatively charged extracellular components.

Solvent-Driven Self-Organization of Meso-Substituted Porphyrins: Morphological Analysis from Fluorescence Lifetime Imaging Microscopy.

A morphological analysis of different thin films of meso-tetra-p-(di-p-phenylamino)phenylporphyrin, H2T(TPA)4P, was made by fluorescence lifetime imaging microscopy (FLIM) and scanning electron microscopy (SEM). A comprehensive study of H2T(TPA)4P was undertaken through UV/vis absorption and fluorescence techniques in different solvents, solvent mixtures and in thin films. In solution, occurrence of intramolecular energy transfer from the triphenylamine (TPA) moieties to the porphyrin core, with quenching efficiencies in the order of 94-97%, is observed. The energy transfer rate constants are determined assuming Förster's dipole-dipole and Dexter's electron exchange mechanisms. In drop-cast-prepared thin films, from samples with different solvent mixtures, the photoluminescence (PL) quantum yield (ΦPL) decreases ∼1 order of magnitude compared to the solution behavior. FLIM and SEM experiments showed the self-organization and morphology of H2T(TPA)4P in thin films to be highly dependent on the solvent mixture used to prepare the film. In chloroform, the solvent's evaporation results in the formation of elongated and overlapped microrod structures. Introduction of a cosolvent, namely, a polar cosolvent, promotes changes in the morphology of the self-assembled structures, with the formation of three-dimensional spherical structures and hollow spheres. H2T(TPA)4P dispersed in a polymer matrix shows enhanced ΦPL values when compared to the drop-cast films. FLIM images showed coexistence of three different states or domains: aggregated, interface, and nonaggregated or less-aggregated states. This work highlights the importance of FLIM in the morphological characterization of heterogeneous films, together with the photophysical characterization of nano- and microdomains.

Formation of Three-Dimensional Structures by Graphite Oxide of Different Nature in the Interaction with Thiourea

Formation of Three-Dimensional Structures by Graphite Oxide of Different Nature in the Interaction with Thiourea

Pulmonary surfactant structure as solved by neutron reflectometry and atomic force microscopy.

In order to sustain breathing mechanics, the alveolar surface needs to be covered by pulmonary surfactant, a lipid/protein system that provides with the required surface tension reduction to avoid alveolar collapse at the end of expiration. Any disruption of this system could impair its function leading to severe respiratory pathologies. Pulmonary surfactant is composed by 90 % lipids and 10 % hydrophilic (SP-A and SP-D) and hydrophobic (SP-B and SP-C) proteins. After secretion, surfactant lipids form a complex structure at the alveolar air-liquid interface consisting of an adsorbed monolayer connected to a membranous reservoir in the subphase maintained thanks to the action of both hydrophobic proteins. The molecular mechanism of surfactant proteins is still not fully understood, making the finding of treatments for some respiratory pathologies a challenge. Model lipid systems mimicking pulmonary surfactant composition (DPPC/POPC/POPG 50:25:15 w:w:w) in the presence of SP-B and/or SP-C, as well as a native surfactant isolated from animal lungs, have been used as models for the study of the structure and function of pulmonary surfactant films. In this work, we have characterized these models with different biophysical technics such as neutron reflectometry and atomic force microscopy. The results point to the importance of hydrophobic proteins in the formation of three-dimensional structures associated to highly compressed surfactant films. Furthermore, a recently isolated human amniotic fluid surfactant has also been studied. This material is thought to maintain the properties of a freshly synthetized and secreted surfactant that could cover the air-liquid interface in a more efficient way, with physiological importance to develop new surfactant therapies. Here we show that amniotic fluid surfactant exhibits a similar behavior than animal-derived surfactant once it coats the interface.

Mesenchymal Stem/Stromal Cells in Three-Dimensional Cell Culture: Ion Homeostasis and Ouabain-Induced Apoptosis.

This study describes the changes in ion homeostasis of human endometrial mesenchymal stem/stromal cells (eMSCs) during the formation of three-dimensional (3D) cell structures (spheroids) and investigates the conditions for apoptosis induction in 3D eMSCs. Detached from the monolayer culture, (2D) eMSCs accumulate Na+ and have dissipated transmembrane ion gradients, while in compact spheroids, eMSCs restore the lower Na+ content and the high K/Na ratio characteristic of functionally active cells. Organized as spheroids, eMSCs are non-proliferating cells with an active Na/K pump and a lower K+ content per g cell protein, which is typical for quiescent cells and a mean lower water content (lower hydration) in 3D eMSCs. Further, eMSCs in spheroids were used to evaluate the role of K+ depletion and cellular signaling context in the induction of apoptosis. In both 2D and 3D eMSCs, treatment with ouabain (1 µM) results in inhibition of pump-mediated K+ uptake and severe K+ depletion as well as disruption of the mitochondrial membrane potential. In 3D eMSCs (but not in 2D eMSCs), ouabain initiates apoptosis via the mitochondrial pathway. It is concluded that, when blocking the Na/K pump, cardiac glycosides prime mitochondria to apoptosis, and whether a cell enters the apoptotic pathway depends on the cell-specific signaling context, which includes the type of apoptotic protein expressed.

Preparation of polyether amine-bridged lignosulfonate for utilization as a nano dye dispersant

The long-term stability of nano disperse dye slurry is a problem in industry. In this work, high molecular-weight polyether amine-bridged lignosulfonates (PEABLs) were prepared to improve the adsorption strength of dispersants on dye surfaces, and thus the stability of nano disperse dyes. Specifically, the molecular simulation software was firstly used to analyze the adsorption of PEABL on dye surfaces. Then, PEABLs with different molecular weights were synthesized and characterized by adjusting the addition of polyether amine. Next, nano disperse dyes were prepared using PEABLs and the optimum grinding conditions were explored and obtained. Finally, PEABL3 was determined to the optimum dispersant, having a smallest particle size (168 nm) and highest stability, comparable to the commercial Reax 85A dispersant and basically satisfying the demand of nano disperse dyes required in digital transfer printing technology. Quartz crystal microbalance (QCM), atomic force microscopy (AFM) and zeta potential results showed as the molecular weight of PEABL increased, the adsorption amount, adsorbed layer rigidity, adsorption force and absolute zeta potential value all firstly increased due to the enhanced hydrophobic interaction, and then decreased due to the formation of complicated three-dimensional network structures caused by the crosslink of lignosulfonate molecules. A maximum was observed for PEABL3.

Polarization-sensitive direct laser patterning of azopolymer thin films with vortex beams.

Laser patterning of thin films of materials is widely used for the fabrication of one-, two- and three-dimensional functional nanomaterials. Using structured laser beams with a complex structure of amplitude, phase, and polarization distributions allows one to significantly simplify and speed up the procedure of manufacturing nano- and microstructures with a complex shape, such as a spiral structure. Here, we demonstrate the use of vortex laser beams with a helical wavefront for the realization of spiral mass transfer in azopolymer films. The polarization sensitivity of this material allows us to demonstrate the formation of different three-dimensional structures in the case of linearly or circularly polarized vortex beams of different orders. The presented theoretical analysis shows that the profile of the fabricated structures is defined by the structure of the longitudinal component of the incident radiation, and thus can be easily controlled with the polarization state of the radiation without the need to change the amplitude-phase structure of the beam.

MicroRNA-204/CREB5 axis regulates vasculogenic mimicry in breast cancer cells.

Vasculogenic mimicry (VM) is characterized by formation of three-dimensional (3D) channels-like structures by tumor cells, supplying the nutrients needed for tumor growth. VM is stimulated by hypoxic tumor microenvironment, and it has been associated with increased metastasis and clinical poor outcome in cancer patients. cAMP responsive element (CRE)-binding protein 5 (CREB5) is a hypoxia-activated transcription factor involved in tumorigenesis. However, CREB5 functions in VM and if its regulated by microRNAs remains unknown in breast cancer. We aim to study the functional relationships between VM, CREB5 and microRNA-204-5p (miR-204) in breast cancer cells. CREB5 expression was evaluated by mining the public databases, and using RT-qPCR and Western blot assays. CREB5 expression was silenced using short-hairpin RNAs in MDA-MB-231 and MCF-7 breast cancer cells. VM formation was analyzed using matrigel-based cultures in hypoxic conditions. MiR-204 expression was restored in cancer cells by transfection of RNA mimics. Luciferase reporter assays were performed to evaluate the binding of miR-204 to 3'UTR of CREB5. Our data showed that CREB5 mRNA expression was upregulated in a set of breast cancer cell lines and clinical tumors, and it was positively associated with poor prognosis in lymph nodes positive and grade 3 basal breast cancer patients. Silencing of CREB5 impaired the hypoxia-induced formation of 3D channels-like structures representative of the early stages of VM in MDA-MB-231 cells. In contrast, VM formation was not observed in MCF-7 cells. Interestingly, we found that CREB5 expression was negatively regulated by miR-204 mimics in breast cancer cells. Functional analysis confirmed that miR-204 binds to CREB5 3'-UTR indicating that it's an ulterior effector. Our findings suggested that CREB5 could be a potential biomarker of disease progression in basal subtype of breast cancer, and that perturbations of the miR-204/CREB5 axis plays an important role in VM development in breast cancer cells.

Degradation of Flame-Retardant Cross-Linked Polyethylene Caused by Heat, Gamma-Rays, and Steam

Various kinds of polymers are used for electrical insulation in nuclear power plants. They are subjected to thermal and radioactive stresses, depending on their locations. They are also subjected to high-temperature steam in the event of an accident. Regarding this, sheets of flame-retardant cross-linked polyethylene (FR-XLPE) were subjected to heat, gamma-rays, and steam exposure, and their infrared absorption spectra, stress-strain relations, indenter moduli, and permittivity spectra were measured. As a result, we have made clear various degradation-induced property changes of FR-XLPE. In addition, it has also become clear that cross-linked structures are formed by the gamma-ray irradiation in FR-XLPE. In this regard, some aspects of degradation due to subsequent steam exposure are suppressed by the formation of firm three-dimensional cross-linked structures.

Shutdown corner, a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish.

Morphogenesis, the formation of three-dimensional organ structures, requires precise coupling of genetic regulation and complex cell behaviors. The genetic networks governing many morphogenetic systems, including that of the embryonic eye, are poorly understood. In zebrafish, several forward genetic screens have sought to identify factors regulating eye development. These screens often look for eye defects at stages after the optic cup is formed and when retinal neurogenesis is under way. This approach can make it difficult to identify mutants specific for morphogenesis, as opposed to neurogenesis. To this end, we carried out a forward genetic, small-scale haploid mutagenesis screen in zebrafish (Danio rerio) to identify factors that govern optic cup morphogenesis. We screened ∼100 genomes and isolated shutdown corner (sco), a mutant that exhibits multiple tissue defects and harbors a ∼10-Mb deletion that encompasses 89 annotated genes. Using a combination of live imaging and antibody staining, we found cell proliferation, cell death, and tissue patterning defects in the sco optic cup. We also observed other phenotypes, including paralysis, neuromuscular defects, and ocular vasculature defects. To date, the largest deletion mutants reported in zebrafish are engineered using CRISPR-Cas9 and are less than 300 kb. Because of the number of genes within the deletion interval, shutdown corner [Df(Chr05:sco)z207] could be a useful resource to the zebrafish community, as it may be helpful for gene mapping, understanding genetic interactions, or studying many genes lost in the mutant.

Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.

A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present 'Origami', a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia.