The shift to 3D growth during embryogenesis of kelp species, atlas of cell division and differentiation of Saccharina latissima.

In most organisms, 3D growth takes place at the onset of embryogenesis. In some brown algae, 3D growth occurs later in development, when the organism consists of several hundred cells. We studied the cellular events that take place when 3D growth is established in the embryo of the brown alga Saccharina, a kelp species. Semi-thin sections, taken from where growth shifts from 2D to 3D, show that 3D growth first initiates from symmetrical cell division in the monolayered lamina, and then is enhanced through a series of asymmetrical cell divisions in a peripheral monolayer of cells called the meristoderm. Then, daughter cells rapidly differentiate into cortical and medullary cells, characterised by their position, size and shape. In essence, 3D growth in kelps is based on a series of differentiation steps that occur rapidly after the initiation of a bilayered lamina, followed by further growth of the established differentiated tissues. Our study depicts the cellular landscape necessary to study cell-fate programming in the context of a novel mode of 3D growth in an organism phylogenetically distant from plants and animals.

Ethylene controls three-dimensional growth involving reduced auxin levels in the moss Physcomitrium patens.

The conquest of land by plants was concomitant with, and possibly enabled by, the evolution of three-dimensional (3D) growth. The moss Physcomitrium patens provides a model system for elucidating molecular mechanisms in the initiation of 3D growth. Here, we investigate whether the phytohormone ethylene, which is believed to have been a signal before land plant emergence, plays a role in 3D growth regulation in P. patens. We report ethylene controls 3D gametophore formation, based on results from exogenously applied ethylene and genetic manipulation of PpEIN2, which is a central component in the ethylene signaling pathway. Overexpression (OE) of PpEIN2 activates ethylene responses and leads to earlier formation of gametophores with fewer gametophores produced thereafter, phenocopying ethylene-treated wild-type. Conversely, Ppein2 knockout mutants, which are ethylene insensitive, show initially delayed gametophore formation with more gametophores produced later. Furthermore, pharmacological and biochemical analyses reveal auxin levels are decreased in the OE lines but increased in the knockout mutants. Our results suggest that evolutionarily, ethylene and auxin molecular networks were recruited to build the plant body plan in ancestral land plants. This might have played a role in enabling ancient plants to acclimate to the continental surfaces of the planet.

Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit.

The determination of fruit size and shape are of considerable interest in horticulture and developmental biology. Fruit typically exhibits three-dimensional structures characterized by geometric features that are dependent on the genotype. Although minor developmental variations have been recognized, few studies have fully visualized and measured these variations throughout fruit growth. Here, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon (Diospyros kaki) cultivars with various complex shapes. We obtained 2380 3D models that fully represented fruit appearance, and enabled precise and automated measurements of shape features throughout fruit development, including horizontal and vertical grooves, length-to-width ratio, and roundness. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity was found in vertical groove development, and these grooves could be filled by tissue expansion in the carpel fusion zone during fruit development. In addition, transcriptome analysis of fruit tissues from groove and non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence of YABBY homologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. Overall, our results revealed deterministic patterns of complex shape traits in persimmon fruit and showed that different growth patterns among tissues are the main factor contributing to the shape of both vertical and horizontal grooves.

Evolution of CLE peptide signalling.

CLEs are small non-cell autonomous signalling peptides that regulate cell division rate and orientation in a variety of developmental contexts. Recent years have generated a huge amount of research on CLE function across land plants, characterising their role across the whole plant; they control stem cell division in the shoot, root and cambial meristems, balance developmental investment into symbiosis, regulate leaf development, pattern stomata and control axillary branching. They have even been co-opted by parasitic nematodes to mediate infection. This review synthesises these recent findings and embeds them in an evolutionary context, outlining the likely evolution of the CLE signalling pathway. I use this framework to infer common mechanistic themes and pose key future questions for the field.

Unprecedented Uniform 3D Growth Integration of 10-Layer Stacked Si Nanowires on Tightly Confined Sidewall Grooves.

Bottom-up catalytic growth offers a high-yield, versatile, and powerful tool for the construction of versatile 3D nanocomplexes, while the major challenge is to achieve a precise location and uniformity control, as guaranteed by top-down lithography. Here, an unprecedented uniform and reliable growth integration of 10-layer stacked Si nanowires (SiNWs) has been accomplished, for the very first time, via a new groove-confined and tailored catalyst formation and guided growth upon the truncated sidewall of SiO2/SiNx multilayers. The SiNW array accomplishes a narrow diameter of Dnw = 28 ± 2.4 nm, NW-to-NW spacing of tsp = 40 nm, and extremely stable growth over Lnw > 50 µm and bending locations, which can compete with or even outperform the state-of-the-art top-down lithography and etching approaches, in terms of stacking number, channel uniformity at different levels, fabrication cost, and efficiency. These results provide a solid basis to establish a new 3D integration approach to batch-manufacture various advanced electronic and sensor applications.

Genetic mixing and demixing on expanding spherical frontiers.

Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.

Deciphering the Mechanics of Cancer Spheroid Growth in 3D Environments through Microfluidics Driven Mechanical Actuation.

Uncontrolled growth of tumor cells is a key contributor to cancer-associated mortalities. Tumor growth is a biomechanical process whereby the cancer cells displace the surrounding matrix that provides mechanical resistance to the growing cells. The process of tumor growth and remodeling is regulated by material properties of both the cancer cells and their surrounding matrix, yet the mechanical interdependency between the two entities is not well understood. Herein, this work develops a microfluidic platform that precisely positions tumor spheroids within a hydrogel and mechanically probes the growing spheroids and surrounding matrix simultaneously. By using hydrostatic pressure to deform the spheroid-laden hydrogel along with confocal imaging and finite element (FE) analysis, this work deduces the material properties of the spheroid and the matrix in situ. For spheroids embedded within soft hydrogels, decreases in the Young's modulus of the matrix are detected at discrete locations accompanied by localized tumor growth. Contrastingly, spheroids within stiff hydrogels do not significantly decrease the Young's modulus of the surrounding matrix, despite exhibiting growth. Spheroids in stiff matrices leverage their high bulk modulus to grow and display a uniform volumetric expansion. Collectively, a quantitative platform is established and new insights into tumor growth within a stiff 3D environment are provided.

Efficient Radial-Shell Model for 3D Tumor Spheroid Dynamics with Radiotherapy.

Understanding the complex dynamics of tumor growth to develop more efficient therapeutic strategies is one of the most challenging problems in biomedicine. Three-dimensional (3D) tumor spheroids, reflecting avascular microregions within a tumor, are an advanced in vitro model system to assess the curative effect of combinatorial radio(chemo)therapy. Tumor spheroids exhibit particular crucial pathophysiological characteristics such as a radial oxygen gradient that critically affect the sensitivity of the malignant cell population to treatment. However, spheroid experiments remain laborious, and determining long-term radio(chemo)therapy outcomes is challenging. Mathematical models of spheroid dynamics have the potential to enhance the informative value of experimental data, and can support study design; however, they typically face one of two limitations: while non-spatial models are computationally cheap, they lack the spatial resolution to predict oxygen-dependent radioresponse, whereas models that describe spatial cell dynamics are computationally expensive and often heavily parameterized, impeding the required calibration to experimental data. Here, we present an effectively one-dimensional mathematical model based on the cell dynamics within and across radial spheres which fully incorporates the 3D dynamics of tumor spheroids by exploiting their approximate rotational symmetry. We demonstrate that this radial-shell (RS) model reproduces experimental spheroid growth curves of several cell lines with and without radiotherapy, showing equal or better performance than published models such as 3D agent-based models. Notably, the RS model is sufficiently efficient to enable multi-parametric optimization within previously reported and/or physiologically reasonable ranges based on experimental data. Analysis of the model reveals that the characteristic change of dynamics observed in experiments at small spheroid volume originates from the spatial scale of cell interactions. Based on the calibrated parameters, we predict the spheroid volumes at which this behavior should be observable. Finally, we demonstrate how the generic parameterization of the model allows direct parameter transfer to 3D agent-based models.

Unravelling 3D growth in the moss Physcomitrium patens.

The colonization of land by plants, and the greening of the terrestrial biosphere, was one of the most important events in the history of life on Earth. The transition of plants from water to land was accompanied, and largely facilitated, by the acquisition of apical cells with three or more cutting faces (3D growth). This enabled plants to develop the morphological characteristics required to survive and reproduce effectively on land and to colonize progressively drier habitats. Most plants develop in such a way that makes genetic studies of 3D growth difficult as the onset of 3D growth is established early during embryo development. On the other hand, in the moss Physcomitrium patens, the onset of 3D growth is preceded by a protracted 2D filamentous phase of the life cycle that can be continuously propagated. P. patens is an ideal model system in which to identify the genetic toolkit underpinning the 2D to 3D growth transition, and this is because 3D growth is not a pre-requisite for survival. Thus, insights into the mechanisms underpinning the formation of apical cells and the subsequent establishment and maintenance of 3D growth have largely been gained through studies in P. patens. This review summarizes the most recently published articles that have provided new and important insights into the mechanisms underpinning 3D growth in P. patens.

The Effect of Heavy Fe-Doping on 3D Growth Mode and Fe Diffusion in GaN for High Power HEMT Application.

The high electron mobility transistor (HEMT) structures on Si (111) substrates were fabricated with heavily Fe-doped GaN buffer layers by metalorganic chemical vapor deposition (MOCVD). The heavy Fe concentrations employed for the purpose of highly insulating buffer resulted in Fe segregation and 3D island growth, which played the role of a nano-mask. The in situ reflectance measurements revealed a transition from 2D to 3D growth mode during the growth of a heavily Fe-doped GaN:Fe layer. The 3D growth mode of Fe nano-mask can effectively annihilate edge-type threading dislocations and improve transfer properties in the channel layer, and consequently decrease the vertical leakage current by one order of magnitude for the applied voltage of 1000 V. Moreover, the employment of GaN:C film on GaN:Fe buffer can further reduce the buffer leakage-current and effectively suppress Fe diffusion.

Autophagy modulates growth and development in the moss Physcomitrium patens.

Physcomitrium patens apical growing protonemal cells have the singularity that they continue to undergo cell divisions as the plant develops. This feature provides a valuable tool to study autophagy in the context of a multicellular apical growing tissue coupled to development. Herein, we showed that the core autophagy machinery is present in the moss P. patens, and characterized the 2D and 3D growth and development of atg5 and atg7 loss-of-function mutants under optimal and nutrient-deprived conditions. Our results showed that 2D growth of the different morphological and functional protonemata apical growing cells, chloronema and caulonema, is differentially modulated by this process. These differences depend on the protonema cell type and position along the protonemal filament, and growth condition. As a global plant response, the absence of autophagy favors the spread of the colony through protonemata growth at the expense of a reduction of the 3D growth, such as the buds and gametophore development, and thus the adult gametophytic and reproductive phases. Altogether this study provides valuable information suggesting that autophagy has roles during apical growth with differential responses within the cell types of the same tissue and contributes to life cycle progression and thus the growth and development of the 2D and 3D tissues of P. patens.

NRG1/ERBB3/ERBB2 Axis Triggers Anchorage-Independent Growth of Basal-like/Triple-Negative Breast Cancer Cells.

ERBB3, also known as HER3, is a tyrosine kinase transmembrane receptor of the ERBB family. Upon binding to neuregulin 1 (NRG1), ERBB3 preferentially dimerizes with HER2 (ERBB2), in turn inducing aggressive features in several cancer types. The analysis of a dataset of breast cancer patients unveiled that higher ERBB3 mRNA expression correlates with shorter relapse-free survival in basal-like breast cancers, despite low ERBB3 expression in this breast cancer subtype. Administration of neuregulin 1 beta (NRG1ß) significantly affected neither cellular proliferation nor the basal migratory ability of basal-like/triple-negative quasi-normal MCF10A breast cells, cultured in mono-layer conditions. Furthermore, no significant regulation in cell morphology or in the expression of basal/myoepithelial and luminal markers was observed upon stimulation with NRG1ß. In non-adherent conditions, NRG1ß administration to MCF10A cells did not significantly influence cell survival; however, it robustly induced cell growth as spheroids (3D growth). Intriguingly, a remarkable upregulation of ERBB3 and ERBB2 protein abundance was observed in 3D compared to 2D cell cultures, and NRG1ß-induced 3D cell growth was efficiently prevented by the anti-HER2 monoclonal antibody pertuzumab. Similar results were obtained by the analysis of basal-like/triple-negative breast cancer cellular models, MDA-MB-468 and MDA-MB-231 cells, in which NRG1ß induced anchorage-independent cell growth that in turn was prevented or reduced by the simultaneous administration of anti-HER2 neutralizing antibodies. Finally, the ability of pertuzumab in suppressing NRG1ß-induced 3D growth was also evaluated and confirmed in MCF10A engineered with HER2-overexpression. We suggest that the NRG1/ERBB3/ERBB2 pathway promotes the anchorage-independent growth of basal-like breast cancer cells. Importantly, we provide evidence that ERBB2 neutralization, in particular by pertuzumab, robustly inhibits this process. Our results pave the way towards the development of novel anticancer strategies for basal-like breast cancer patients based on the interception of the NRG1/ERBB3/ERBB2 signaling axis.

Urban growth prediction with parcel based 3D urban growth model (PURGOM).

While cities grow horizontally over natural areas, they also grow vertically with high-rise construction in time. The Floor Area Ratio (FAR) is defined as the ratio of the amount of construction area on a parcel to the parcel area. FAR is one of the essential indicators for detecting and measuring 3D (three-dimensional) change. The amount and trends of change differ for each urban settlement and on its internal dynamics. This study consists of two stages: determining and modeling the variables and their weights that affect the FAR values and generating future estimates. First, the criteria affecting the growth trends between the years of 2012 and 2019 in the study area of Saray were examined as five groups at the parcel level with statistical and spatial analysis. It has been determined that the criteria; accessibility, accessibility in line with planning decisions, zoning and land-use decisions, land values, and the built environment affect the FAR value distribution. As a result of the analysis, the selected criteria were evaluated with Geographical Information Systems (GIS) and the weighted linear combination method. The probable spatial distribution of FAR coefficients of each parcel was found. The FAR coefficients obtained were calibrated by real FAR values for 2019. Future predictions for the years 2030 and 2040 were revealed according to the demand scenario. As a result, it was determined that there is a construction pressure on the urban center and near the transportation routes. The primary purpose of this study is to determine current trends by creating a 3D urban growth model based on parcel-level FAR values, making predictions, and producing decision support tools for city managers.•Determination of criteria and weights according to spatial dynamics of the study area.•Determination of the amount and type of urban growth demand specific to the study area and its compatibility with different scenarios.•Prediction of parcel-based 3D urban growth.

Beyond gold nanoparticles cytotoxicity: Potential to impair metastasis hallmarks.

Gold nanoparticle (AuNP)-based systems have been extensively investigated as diagnostic and therapeutic agents due to their tunable properties and easy surface functionalization. Upon cell uptake, AuNPs present an inherent cell impairment potential based on organelle and macromolecules damage, leading to cell death. Such cytotoxicity is concentration-dependent and completely undesirable, especially if unspecific. However, under non-cytotoxic concentrations, internalized AuNPs could potentially weaken cells and act as antitumor agents. Therefore, this study aimed to investigate the antitumor effect of ultrasmall AuNPs (~3 nm) stabilized by the anionic polysaccharide gum arabic (GA-AuNPs). Other than intrinsic cytotoxicity, the focus was downregulation of cancer hallmarks of aggressive tumors, using a highly metastatic model of melanoma. We first demonstrated that GA-AuNPs showed excellent stability under biological environment. Non-cytotoxic concentrations to seven different cell lines, including tumorigenic and non-tumorigenic cells, were determined by standard 2D in vitro assays. Gold concentrations ≤ 2.4 mg L-1 (16.5 nM AuNPs) were non-cytotoxic and therefore chosen for further analyses. Cells exposed to GA-AuNPs were uptaken by melanoma cells through endocytic processes. Next we described remarkable biological properties using non-cytotoxic concentrations of this nanomaterial. Invasion through an extracellular matrix barrier as well as 3D growth capacity (anchorage-independent colony formation and spheroids growth) were negatively affected by 2.4 mg L-1 GA-AuNPs. Additionally, exposed spheroids showed morphological changes, suggesting that GA-AuNPs could penetrate into the preformed tumor and affect its integrity. All together these results demonstrate that side effects, such as cytotoxicity, can be avoided by choosing the right concentration, nevertheless, preserving desirable effects such as modulation of key tumor cell malignancy features.

Dexamethasone Inhibits Spheroid Formation of Thyroid Cancer Cells Exposed to Simulated Microgravity.

Detachment and the formation of spheroids under microgravity conditions can be observed with various types of intrinsically adherent human cells. In particular, for cancer cells this process mimics metastasis and may provide insights into cancer biology and progression that can be used to identify new drug/target combinations for future therapies. By using the synthetic glucocorticoid dexamethasone (DEX), we were able to suppress spheroid formation in a culture of follicular thyroid cancer (FTC)-133 cells that were exposed to altered gravity conditions on a random positioning machine. DEX inhibited the growth of three-dimensional cell aggregates in a dose-dependent manner. In the first approach, we analyzed the expression of several factors that are known to be involved in key processes of cancer progression such as autocrine signaling, proliferation, epithelial-mesenchymal transition, and anoikis. Wnt/ß-catenin signaling and expression patterns of important genes in cancer cell growth and survival, which were further suggested to play a role in three-dimensional aggregation, such as NFKB2, VEGFA, CTGF, CAV1, BCL2(L1), or SNAI1, were clearly affected by DEX. Our data suggest the presence of a more complex regulation network of tumor spheroid formation involving additional signal pathways or individual key players that are also influenced by DEX.

CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants.

How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane orientation is shared between Physcomitrella and Arabidopsis. We report that roles for CLAVATA in regulating cell proliferation and cell fate are also shared and that CLAVATA-like peptides act via conserved receptor components in Physcomitrella. Our results suggest that CLAVATA was a genetic novelty enabling the morphological innovation of 3D growth in land plants.

Invadosomes are coming: new insights into function and disease relevance.

Invadopodia and podosomes are discrete, actin-based molecular protrusions that form in cancer cells and normal cells, respectively, in response to diverse signaling pathways and extracellular matrix cues. Although they participate in a host of different cellular processes, they share a common functional theme of controlling pericellular proteolytic activity, which sets them apart from other structures that function in migration and adhesion, including focal adhesions, lamellipodia, and filopodia. In this review, we highlight research that explores the function of these complex structures, including roles for podosomes in embryonic and postnatal development, in angiogenesis and remodeling of the vasculature, in maturation of the postsynaptic membrane, in antigen sampling and recognition, and in cell-cell fusion mechanisms, as well as the involvement of invadopodia at multiple steps of the metastatic cascade, and how all of this may apply in the treatment of human disease states. Finally, we explore recent research that implicates a novel role for exosomes and microvesicles in invadopodia-dependent and invadopodia-independent mechanisms of invasion, respectively.

Obtaining and doping of InAs-QD/GaAs(001) nanostructures by ion beam sputtering.

The features of InAs quantum dots obtained on GaAs(001) single-crystal substrates by ion-beam sputtering were investigated. It has been shown that in the range of ion energies of 150 to 200 eV at a temperature of 500 °C and a beam current of 120 µA InAs quantum dots with average dimensions below 15 nm and a surface density of 1011 cm-2 are formed. The technique of controlled doping of InAs/GaAs nanostructures using a SnTe solid-state source was proposed. It has been established that a maximum donor concentration of 8.7·1018 cm-3 in the GaAs spacer layer is reached at an evaporation temperature of 415 °Ð¡. At the same time, impurity accumulation in the growth direction was observed. We have shown that increasing the impurity doping of the GaAs barrier layer increases the intensity of photoluminescence peaks of the ground state and the first excited state of the InAs quantum dots.

Insight into Nanoparticle Charging Mechanism in Nonpolar Solvents To Control the Formation of Pt Nanoparticle Monolayers by Electrophoretic Deposition.

We report on the formation of Pt nanoparticle monolayers by electrophoretic deposition from nonpolar solvents. First, the growth kinetics of Pt nanoparticles prepared by the reverse micelle technique are described in detail. Second, a model of nanoparticle charging in nonpolar media is discussed and methods to control the nanoparticle charging are proposed. Finally, essential parameters of the electrophoretic deposition process to control the deposition of nanoparticle monolayers are discussed and mechanisms of their formation are analyzed.

Reprogramming mediated radio-resistance of 3D-grown cancer cells.

In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of ß-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell-like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell-like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine.