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How a developing organ robustly coordinates the cellular mechanics and growth to reach a final size and shape remains poorly understood. Through iterations between experiments and model simulations that include a mechanistic description of interkinetic nuclear migration, we show that the local curvature, height, and nuclear positioning of cells in the Drosophila wing imaginal disc are defined by the concurrent patterning of actomyosin contractility, cell-ECM adhesion, ECM stiffness, and interfacial membrane tension. We show that increasing cell proliferation via different growth-promoting pathways results in two distinct phenotypes. Triggering proliferation through insulin signaling increases basal curvature, but an increase in growth through Dpp signaling and Myc causes tissue flattening. These distinct phenotypic outcomes arise from differences in how each growth pathway regulates the cellular cytoskeleton, including contractility and cell-ECM adhesion. The coupled regulation of proliferation and cytoskeletal regulators is a general strategy to meet the multiple context-dependent criteria defining tissue morphogenesis.

Thrombospondin-4 (TSP-4) belongs to the extracellular matrix glycoprotein family of thrombospondins (TSPs). The multidomain, pentameric structure of TSP-4 allows its interactions with numerous extracellular matrix components, proteins and signaling molecules that enable its modulation to various physiological and pathological processes. Characterization of TSP-4 expression under development and pathogenesis of disorders has yielded important insights into mechanisms underlying the unique role of TSP-4 in mediating various processes including cell-cell, cell-extracellular matrix interactions, cell migration, proliferation, tissue remodeling, angiogenesis, and synaptogenesis. Maladaptation of these processes in response to pathological insults and stress can accelerate the development of disorders including skeletal dysplasia, osteoporosis, degenerative joint disease, cardiovascular diseases, tumor progression/metastasis and neurological disorders. Overall, the diverse functions of TSP-4 suggest that it may be a potential marker or therapeutic target for prognosis, diagnosis, and treatment of various pathological conditions upon further investigations. This review article highlights recent findings on the role of TSP-4 in both physiological and pathological conditions with a focus on what sets it apart from other TSPs.

The development of ectodermal organs begins with the formation of a stratified epithelial placode that progressively invaginates into the underlying mesenchyme as the organ takes its shape. Signaling by secreted molecules is critical for epithelial morphogenesis, but how that information leads to cell rearrangement and tissue shape changes remains an open question. Using the mouse dentition as a model, we first establish that non-muscle myosin II is essential for dental epithelial invagination and show that it functions by promoting cell-cell adhesion and persistent convergent cell movements in the suprabasal layer. Shh signaling controls these processes by inducing myosin II activation via AKT. Pharmacological induction of AKT and myosin II can also rescue defects caused by the inhibition of Shh. Together, our results support a model in which the Shh signal is transmitted through myosin II to power effective cellular rearrangement for proper dental epithelial invagination.

The Hedgehog (Hh) pathway plays a crucial role in embryonic development, acting both as a morphogenic signal that organizes tissue formation and a potent mitogenic signal driving cell proliferation. Dysregulated Hh signaling leads to various developmental defects in the brain. This article aims to review the roles of Hh signaling in the development of the neocortex in the mammalian brain, focusing on its regulation of neural progenitor proliferation and neuronal production. The review will summarize studies on genetic mouse models that have targeted different components of the Hh pathway, such as the ligand Shh, the receptor Ptch1, the GPCR-like transducer Smo, the intracellular transducer Sufu, and the three Gli transcription factors. As key insights into the Hh signaling transduction mechanism were obtained from mouse models displaying neural tube defects, this review will also cover some studies on Hh signaling in neural tube development. The results from these genetic mouse models suggest an intriguing hypothesis that elevated Hh signaling may play a role in the gyrification of the brain in certain species. Additionally, the distinctive production of GABAergic interneurons in the dorsal cortex in the human brain may also be linked to the extension of Hh signaling from the ventral to the dorsal brain region. Overall, these results suggest key roles of Hh signaling as both a morphogenic and mitogenic signal during the forebrain development and imply the potential involvement of Hh signaling in the evolutionary expansion of the neocortex.

Large-scale cell flow characterizes gastrulation in animal development. In amniote gastrulation, particularly in avian gastrula, a bilateral vortex-like counter-rotating cell flow, called 'polonaise movements', appears along the midline. Here, through experimental manipulations, we addressed relationships between the polonaise movements and morphogenesis of the primitive streak, the earliest midline structure in amniotes. Suppression of the Wnt/planar cell polarity (PCP) signaling pathway maintains the polonaise movements along a deformed primitive streak. Mitotic arrest leads to diminished extension and development of the primitive streak and maintains the early phase of the polonaise movements. Ectopically induced Vg1, an axis-inducing morphogen, generates the polonaise movements, aligned to the induced midline, but disturbs the stereotypical cell flow pattern at the authentic midline. Despite the altered cell flow, induction and extension of the primitive streak are preserved along both authentic and induced midlines. Finally, we show that ectopic axis-inducing morphogen, Vg1, is capable of initiating the polonaise movements without concomitant PS extension under mitotic arrest conditions. These results are consistent with a model wherein primitive streak morphogenesis is required for the maintenance of the polonaise movements, but the polonaise movements are not necessarily responsible for primitive streak morphogenesis. Our data describe a previously undefined relationship between the large-scale cell flow and midline morphogenesis in gastrulation.

Angiogenesis is a morphogenic process resulting in the formation of new blood vessels from pre-existing ones, usually in hypoxic micro-environments. The initial steps of angiogenesis depend on robust differentiation of oligopotent endothelial cells into the Tip and Stalk phenotypic cell fates, controlled by NOTCH-dependent cell-cell communication. The dynamics of spatial patterning of this cell fate specification are only partially understood. Here, by combining a controlled experimental angiogenesis model with mathematical and computational analyses, we find that the regular spatial Tip-Stalk cell patterning can undergo an order-disorder transition at a relatively high input level of a pro-angiogenic factor VEGF. The resulting differentiation is robust but temporally unstable for most cells, with only a subset of presumptive Tip cells leading sprout extensions. We further find that sprouts form in a manner maximizing their mutual distance, consistent with a Turing-like model that may depend on local enrichment and depletion of fibronectin. Together, our data suggest that NOTCH signaling mediates a robust way of cell differentiation enabling but not instructing subsequent steps in angiogenic morphogenesis, which may require additional cues and self-organization mechanisms. This analysis can assist in further understanding of cell plasticity underlying angiogenesis and other complex morphogenic processes.

As the most advanced non‐viral delivery system, lipid nanoparticles (LNPs) were approved by the FDA, propelling the advancements of gene therapy. However, their clinical applications are hampered by the potential immunogenicity of the lipid components that trigger immune‐related adverse events, like inflammation and allergy. Herein, we formulate various dLNPs with diminished immunogenicity by incorporating dexamethasone (Dex) into liver‐, spleen‐, and lung‐targeting LNPs formulations that exhibit excellent abilities to target specific organs and deliver various types of RNA, such as mRNA and siRNA. In vivo investigations demonstrate unparalleled advantages in safety as compared to conventional LNPs, showing promising potential in the development of RNA therapeutics. Intriguingly, the encapsulation of runt‐related transcription factor‐1 siRNA (siRUNX1) into lung‐targeting dLNPs (dLNPs@siRUNX1) demonstrates remarkable advantages in the treatment of pulmonary fibrosis through the synergy of gene therapy and drug therapy. This research establishes secure and universal platforms for the precise delivery of nucleic acid therapeutics, showcasing promising clinical applications in gene therapy. [ABSTRACT FROM AUTHOR]

Fungal pathogens must exhibit strong nutritional plasticity, effectively sensing and utilizing diverse nutrients to support virulence. How the signals generated by nutritional sensing are efficiently translated to the morphogenetic machinery for optimal growth and support of virulence remains incompletely understood. Here, we show that the conserved morphogenesis-related kinase, CotA, imparts isoform-specific control over Aspergillus fumigatus invasive growth in host-mimicking environments and during infection. CotA-mediated invasive growth is responsive to exogenous carbon source quality, with only preferred carbon sources supporting hyphal morphogenesis in a mutant lacking one of two identified protein isoforms. Strikingly, we find that the CotA protein does not regulate, nor is cotA gene expression regulated by, the carbon catabolite repression system. Instead, we show that CotA partially mediates invasive growth in specific carbon sources and virulence through the conserved downstream effector and translational repressor, SsdA. Therefore, A. fumigatus CotA accomplishes its conserved morphogenetic functions to drive pathogenic growth by translating host-relevant carbon source quality signals into morphogenetic outputs for efficient tissue invasive growth. Here, Martin-Vicente et al. show that the Aspergillus fumigatus protein kinase, CotA, controls invasive growth in an isoform dependent manner in response to carbon source diversity, partially mediated by the downstream effector, SsdA. [ABSTRACT FROM AUTHOR]

SUMMARY: De novo shoot apical meristem (SAM) organogenesis during regeneration in tissue culture has been investigated for several decades, but the precise mechanisms governing early‐stage cell fate specification remain elusive. In contrast to SAM establishment during embryogenesis, in vitro SAM formation occurs without positional cues and is characterized by autonomous initiation of cellular patterning. Here, we report on the initial stages of SAM organogenesis and on the molecular mechanisms that orchestrate gene patterning to establish SAM homeostasis. We found that SAM organogenesis in tobacco calli starts with protuberance formation followed by the formation of an intact L1 layer covering the nascent protuberance. We also exposed a complex interdependent relationship between L1 and WUS expression and revealed that any disruption in this interplay compromises shoot formation. Silencing WUS in nascent protuberances prevented L1 formation and caused the disorganization of the outer cell layers exhibiting both anticlinal and periclinal divisions, suggesting WUS plays a critical role in the proper establishment and organization of L1 during SAM organogenesis. We further discovered that silencing TONNEAU1 prevents the exclusive occurrence of anticlinal divisions in the outermost layer of the protuberances and suppresses the acquisition of L1 cellular identity and L1 formation, ultimately impeding SAM formation and regeneration. This study provides a novel molecular framework for the characterization of a WUS/L1 interplay that mediates SAM formation during regeneration. Significance Statement: This study highlights the importance of establishing an intact L1 cell layer to promote de novo shoot apical meristem (SAM) organogenesis in vitro. It identifies a complex interdependence between WUS and ML1 expression in directing anticlinal divisions for L1 formation, which in turn initiates gene expression patterning in the SAM and its formation. Disrupting this WUS/L1 interplay impairs SAM regeneration, underscoring its central role. [ABSTRACT FROM AUTHOR]

SUMMARY: Petal size is determined by cell division and cell expansion. Jasmonic acid (JA) has been reported to be associated with floral development, but its regulatory mechanism affecting petal size remains unclear. Here, we reveal the vital role of JA in regulating petal size and the duration of the cell division phase via the key JA signaling component RhMYC2. We show that RhMYC2 expression is induced by exogenous treatment with methyl jasmonate and decreases from stage 0 to stage 2 of flower organ development, corresponding to the cell division phase. Furthermore, silencing RhMYC2 shortened the duration of the cell division phase, ultimately accelerating flowering opening and resulting in smaller petals. In addition, we determined that RhMYC2 controls cytokinin homeostasis in rose petals by directly activating the expression of the cytokinin biosynthetic gene LONELY GUY3 (RhLOG3) and repressing that of the cytokinin catabolism gene CYTOKININ OXIDASE/DEHYDROGENASE6 (RhCKX6). Silencing RhLOG3 shortened the duration of the cell division period and produced smaller petals, similar to RhMYC2 silencing. Our results underscore the synergistic effects of JA and cytokinin in regulating floral development, especially for petal size in roses. [ABSTRACT FROM AUTHOR]

Background: Cryptolaemus montrouzieri (Coccinellidae) is widely utilized as biological control agents in modern agriculture. A comprehensive understanding of its food preference can help guide mass rearing and safety management during field application of pest control. Although some studies have paid attentions to the impacts of prey shift on C. montrouzieri, little is known regarding the role of post-transcriptional regulations in its acclimation to unnatural preys. Results: We performed a genome-wide investigation on alternative splicing dynamics in C. montrouzieri in response to the predation transition from natural prey to unnatural ones. When feeding on undesired diets, 402–764 genes were differentially alternative spliced in C. montrouzieri. It is noteworthy that the majority of these genes (> 87%) were not differentially expressed, and these differentially spliced genes regulated distinct biological processes from differentially expressed genes, such as organ development and morphogenesis, locomotory behavior, and homeostasis processes. These suggested the functionally nonredendant role of alternative splicing in modulating physiological and metabolic responses of C. montrouzieri to the shift to undesired preys. In addition, the individuals feeding on aphids were subject to a lower level of changes in splicing than other alternative diets, which might be because of the similar chemical and microbial compositions. Our study further suggested a putative coupling of alternative splicing and nonsense-mediated decay (AS-NMD), which may play an important role in fine-tuning the protein repertoire of C. montrouzieri, and promoting its acclimation to predation changes. Conclusion: These findings highlight the key role of alternative splicing in modulating the acclimation of ladybirds to prey shift and provide new genetic clues for the future application of ladybirds in biocontrol. [ABSTRACT FROM AUTHOR]

A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues. Author summary: As organs grow during development, molecules called morphogens instruct cells to adopt specific fates at the right place and time. Morphogens are produced in specialized source regions and spread through organs, forming gradients of concentration. How morphogen source regions form in growing organs and contribute to the establishment of morphogen gradients is poorly understood. In this study, we combine theory and experiments to investigate the formation of a key morphogen source in the developing mouse spinal cord called floor plate. Uncommitted spinal cord cells adopt floor plate identity in response to the morphogen Sonic hedgehog (Shh), which is produced by the adjacent notochord and by the floor plate cells themselves. Over time, the floor plate expands, producing more Shh. We found that in theory, the floor plate could expand by distinct mechanisms. In one scenario, Shh produced by the floor plate itself is used to convert more cells into floor plate. Alternatively, once a few cells are initially specified, the floor plate expands passively by tissue growth. Our experimental and theoretical analysis indicate that the latter scenario is the one that is relevant to the biological system. Similar temporal decoupling of specification and growth might occur in other growing organs. [ABSTRACT FROM AUTHOR]

The terminal cells of the Drosophila larval tracheal system are perhaps the simplest delivery networks, providing an analogue for mammalian vascular growth and function in a system with many fewer components. These cells are a prime example of single-cell morphogenesis, branching significantly over time to adapt to the needs of the growing tissue they supply. While the genetic mechanisms governing local branching decisions have been studied extensively, an understanding of the emergence of a global network architecture is still lacking. Mapping out the full network architecture of populations of terminal cells at different developmental times of Drosophila larvae, we find that cell growth follows scaling laws relating the total edge length, supply area, and branch density. Using time-lapse imaging of individual terminal cells, we identify that the cells grow in three ways: by extending branches, by the side budding of new branches, and by internally growing existing branches. A generative model based on these modes of growth recapitulates statistical properties of the terminal cell network data. These results suggest that the scaling laws arise from the coupled contributions of branching and internal growth. This study establishes the terminal cell as a uniquely tractable model system for further studies of transportation and distribution networks. [ABSTRACT FROM AUTHOR]

Perionyx excavatus, an indigenous earthworm possesses exceptional regeneration capacity. Their anterior regeneration features wound closure, regeneration induction and morphogenesis of damaged organs. This study involved a complete analysis of their transcriptomic dataset, with an emphasis on identifying the genes expressed during regeneration and predicting their implications in the process of regeneration and morphogenesis. Control (first ten segments) and test (5th day blastema) RNA samples of biological replicates were isolated and sequenced on NovaSeq. 6000 using PE150 read length. An average of 98.64% of high-quality data was retained with assembly showing better continuity with the average transcript length with 823 bp and N50 value of 1,858 bp. This is the first report on the comparative transcriptome of P. excavatus during anterior regeneration and this study will shed light on the complexity of annelid regeneration. [ABSTRACT FROM AUTHOR]

The cortical cytoskeleton of subpellicular microtubules (SPMTs) supports the Plasmodium ookinete morphogenesis during mosquito transmission of malaria. SPMTs are hypothesized to function as the cytoskeletal tracks in motor-driven cargo transport for apical organelle and structure assembly in ookinetes. However, the SPMT-based transport motor has not been identified in the Plasmodium. The cytoplasmic dynein is the motor moving towards the minus end of microtubules (MTs) and likely be responsible for cargo transport to the apical part in ookinetes. Here we screen 7 putative dynein heavy chain (DHC) proteins in the P. yoelii and identify DHC3 showing peripheral localization in ookinetes. DHC3 is localized at SPMTs throughout ookinete morphogenesis. We also identify five other dynein subunits localizing at SPMTs. DHC3 disruption impairs ookinete development, shape, and gliding, leading to failure in mosquito infection of Plasmodium. The DHC3-deficient ookinetes display defective formation or localization of apical organelles and structures. Rab11A and Rab11B interact with DHC3 at SPMTs in a DHC3-dependent manner, likely functioning as the receptors for the cargoes driven by SPMT-dynein. Disturbing Rab11A or Rab11B phenocopies DHC3 deficiency in ookinete morphogenesis. Our study reveals an SPMT-based dynein motor driving the transport of Rab11A- and Rab11B-labeled cargoes in the ookinete morphogenesis of Plasmodium. Liu et al. identify a subpellicular microtubule-based dynein motor in ookinetes of Plasmodium. This motor transports the cargos for apical organelle and structure assembly in ookinetes. Dynein-deficient parasites fail ookinete morphogenesis and mosquito transmission of Plasmodium. [ABSTRACT FROM AUTHOR]

Talaromyces marneffei is a thermally dimorphic fungus that can cause life-threatening systemic mycoses, particularly in immunocompromised individuals. Fungal homeobox transcription factors control various developmental processes, including the regulation of sexual reproduction, morphology, metabolism, and virulence. However, the function of homeobox proteins in T. marneffei has not been fully explored. Here, we searched the T. marneffei genome for the total homeobox transcription factors and predicted their biological relevance by performing gene expression analysis in different cell types, including conidia, mycelia, yeasts, and during phase transition. RfeB is selected for further computational analysis since (i) its transcripts were differentially expressed in different phases of T. marneffei, and (ii) this protein contains the highly conserved protein-protein interaction region (IR), which could be important for pathobiology and have therapeutic application. To assess the structure-function of the IR region, in silico alanine substitutions were performed at three-conserved IR residues (Asp276, Glu279, and Gln282) of RfeB, generating a triple RfeB mutated protein. Using 3D modeling and molecular dynamics simulations, we compared the protein complex formation of wild-type and mutated RfeB proteins with the putative partner candidate TmSwi5. Our results demonstrated that the mutated RfeB protein exhibited increased free binding energy, elevated protein compactness, and a reduced number of atomic contacts, suggesting disrupted protein stability and interaction. Notably, our model revealed that the IR residues primarily stabilized the RfeB binding sites located in the central region (CR). This computational approach for protein mutagenesis could provide a foundation for future experimental studies on the functional characterization of RfeB and other homeodomain-containing proteins in T. marneffei. [ABSTRACT FROM AUTHOR]

Organogenesis, the phase of embryonic development that starts at the end of gastrulation and continues until birth is the critical process for understanding cellular differentiation and maturation during organ development. The rapid development of single‐cell transcriptomics technology has led to many novel discoveries in understanding organogenesis while also accumulating a large quantity of data. To fill this gap, OrganogenesisDB (http://organogenesisdb.com/), which is a comprehensive database dedicated to exploring cell‐type identification and gene expression dynamics during organogenesis, is developed. OrganogenesisDB contains single‐cell RNA sequencing data for more than 1.4 million cells from 49 published datasets spanning various developmental stages. Additionally, 3324 cell markers are manually curated for 1120 cell types across 9 human organs and 4 mouse organs. OrganogenesisDB leverages various analysis tools to assist users in annotating and understanding cell types at different developmental stages and helps in mining and presenting genes that exhibit specific patterns and play key regulatory roles during cell maturation and differentiation. This work provides a critical resource and useful tool for deciphering cell lineage determination and uncovering the mechanisms underlying organogenesis. [ABSTRACT FROM AUTHOR]

Themorphology of cells in vivo can arise from a variety of mechanisms. In the Caenorhabditis elegans hermaphrodite gonad, the distal tip cell (DTC) elaborates into a complex plexus over a relatively short developmental time period, but the mechanisms underlying this change in cell morphology are not well defined. We correlated the time of DTC elaboration with the L4-to-adult molt, but ruled out a relevant heterochronic pathway as a cue for DTCelaboration. Instead, we found that the timing of gonad elongation and aspects of underlying germline flux influence DTC elaboration. We propose a 'hitch and tow' aspect of organ-level dynamics that contributes to cellular morphogenesis, whereby germline flux drags the flexible DTC cell cortex away from its stationary cell body. More broadly, we speculate that this mechanism may contribute to cell shape changes in other contexts with implications for development and disease. [ABSTRACT FROM AUTHOR]

Organ sizes and shapes are highly reproducible, or robust, within a species and individuals. Arabidopsis thaliana sepals, which are the leaf-like organs that enclose flower buds, have consistent size and shape, indicating robust development. Cell growth is locally heterogeneous due to intrinsic and extrinsic noise. To achieve robust organ shape, fluctuations in cell growth must average to an even growth rate, which requires that fluctuations are uncorrelated or anticorrelated in time and space. Here, we live image and quantify the development of sepals with an increased or decreased number of cell divisions (lgo mutant and LGO overexpression, respectively), a mutant with altered cell growth variability (ftsh4), and double mutants combining these. Changes in the number of cell divisions do not change the overall growth pattern. By contrast, in ftsh4 mutants, cell growth accumulates in patches of over- and undergrowth owing to correlations that impair averaging, resulting in increased organ shape variability. Thus, we demonstrate in vivo that the number of cell divisions does not affect averaging of cell growth, preserving robust organ morphogenesis, whereas correlated growth fluctuations impair averaging. [ABSTRACT FROM AUTHOR]

Pharyngeal endoderm cells undergo convergence and extension (C&E), which is essential for endoderm pouch formation and craniofacial development. Our previous work implicates Gα13/RhoAmediated signaling in regulating this process, but the underlying mechanisms remain unclear. Here, we have used endoderm-specific transgenic and Gα13mutant zebrafish to demonstrate that Gα13 plays a crucial role in pharyngeal endodermC&E by regulating RhoA activation and E-cadherin expression. We showed that during C&E, endodermal cells gradually establish stable cell-cell contacts, acquire apical-basal polarity and undergo actomyosin-driven apical constriction, which are processes that require Gα13. Additionally, we found that Gα13-deficient embryos exhibit reduced E-cadherin expression, partially contributing to endoderm C&E defects. Notably, interfering with RhoA function disrupts spatial actomyosin activation without affecting E-cadherin expression. Collectively, our findings identify crucial cellular processes for pharyngeal endoderm C&E and reveal that Gα13 controls this through two independent pathways - modulating RhoA activation and regulating E-cadherin expression - thus unveiling intricate mechanisms governing pharyngeal endoderm morphogenesis. [ABSTRACT FROM AUTHOR]

Carotenoid cleavage oxygenases (CCOs) cleave carotenoid molecules to produce bioactive products that influence the synthesis of hormones such as abscisic acid (ABA) and strigolactones (SL), which regulate plant growth, development, and stress adaptation. Here, to explore the molecular characteristics of all members of the OsCCO family in rice, fourteen OsCCO family genes were identified in the genome-wide study. The results revealed that the OsCCO family included one OsNCED and four OsCCD subfamilies. The OsCCO family was phylogenetically close to members of the maize ZmCCO family and the Sorghum SbCCO family. A collinearity relationship was observed between OsNCED3 and OsNCED5 in rice, as well as OsCCD7 and OsNCED5 between rice and Arabidopsis, Sorghum, and maize. OsCCD4a and OsCCD7 were the key members in the protein interaction network of the OsCCO family, which was involved in the catabolic processes of carotenoids and terpenoid compounds. miRNAs targeting OsCCO family members were mostly involved in the abiotic stress response, and RNA-seq data further confirmed the molecular properties of OsCCO family genes in response to abiotic stress and hormone induction. qRT-PCR analysis showed the differential expression patterns of OsCCO members across various rice organs. Notably, OsCCD1 showed relatively high expression levels in all organs except for ripening seeds and endosperm. OsNCED2a, OsNCED3, OsCCD1, OsCCD4a, OsCCD7, OsCCD8a, and OsCCD8e were potentially involved in plant growth and differentiation. Meanwhile, OsNCED2a, OsNCED2b, OsNCED5, OsCCD8b, and OsCCD8d were associated with reproductive organ development, flowering, and seed formation. OsNCED3, OsCCD4b, OsCCD4c, OsCCD8b, and OsCCD8c were related to assimilate transport and seed maturation. These findings provide a theoretical basis for further functional analysis of the OsCCO family. [ABSTRACT FROM AUTHOR]

The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso- ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3398 and 3433 were differentially regulated, respectively. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail, and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo. [ABSTRACT FROM AUTHOR]

Elucidating the molecular dependencies behind the cancer-type specificity of driver mutations may reveal new therapeutic opportunities. We hypothesized that developmental programs would impact the transduction of oncogenic signaling activated by a driver mutation and shape its cancer-type specificity. Therefore, we designed a computational analysis framework by combining single-cell gene expression profiles during fetal organ development, latent factor discovery, and information theory-based differential network analysis to systematically identify transcription factors that selectively respond to driver mutations under the influence of organ-specific developmental programs. After applying this approach to VHL mutations, which are highly specific to clear cell renal cell carcinoma (ccRCC), we revealed important regulators downstream of VHL mutations in ccRCC and used their activities to cluster patients with ccRCC into three subtypes. This classification revealed a more significant difference in prognosis than the previous mRNA profile-based method and was validated in an independent cohort. Moreover, we found that EP300, a key epigenetic factor maintaining the regulatory network of the subtype with the worst prognosis, can be targeted by a small inhibitor, suggesting a potential treatment option for a subset of patients with ccRCC. This work demonstrated an intimate relationship between organ development and oncogenesis from the perspective of systems biology, and the method can be generalized to study the influence of other biological processes on cancer driver mutations. [ABSTRACT FROM AUTHOR]

Based on recent single-cell transcriptomics and lineage tracing, sst1.1 + cell transdifferentiation and krt4 + cell differentiation have recently been recognized as the major sources of regeneration of insulin-producing cells in zebrafish. Large-scale in vivo small molecule screening has been successfully applied in zebrafish for the unbiased identification of chemicals promoting β-cell regeneration and glucose control. Multiple compounds have been validated to also promote β-cell proliferation, differentiation, or function in mammalian systems. Live imaging in zebrafish enables visualization of complex biological processes at the single-cell resolution in vivo (e.g., calcium flux in β-cells) as well as innervation and immune cell behaviors in the islet. Role of genes identified in human genetic data [e.g. genome-wide association studies (GWAS) and single-cell sequencing data] can be efficiently elucidated in zebrafish. The zebrafish has become an outstanding model for studying organ development and tissue regeneration, which is prominently leveraged for studies of pancreatic development, insulin-producing β-cells, and diabetes. Although studied for more than two decades, many aspects remain elusive and it has only recently been possible to investigate these due to technical advances in transcriptomics, chemical-genetics, genome editing, drug screening, and in vivo imaging. Here, we review recent findings on zebrafish pancreas development, β-cell regeneration, and how zebrafish can be used to provide novel insights into gene functions, disease mechanisms, and therapeutic targets in diabetes, inspiring further use of zebrafish for the development of novel therapies for diabetes. [ABSTRACT FROM AUTHOR]

Purpose: In patients with acute necrotizing pancreatitis (ANP), the site, size, and the number of acute necrotic collections (ANC) may determine the outcome of patients. The current study aimed to correlate the nature of ANC with the adverse outcomes in ANP patients. Methods: This was a single-center, prospective study (August 2019-August 2022) recruiting patients with ANP, correlating the site, size, and number of ANC with the length of hospital stay, intensive care unit (ICU) stays, development of organ failure and infection, need for intervention, and mortality. Results: A total of 114 patients (mean age: 37.3 ± 13.4 years, 85.1% males) with ANP were included in the study. The number and maximum diameter of collections significantly correlated with the length of the hospital and ICU stay and the need for intervention. Taking a cut-off size of 8 cm, the sensitivity and specificity for predicting the need for intervention were 82.7% and 74.2%, respectively. ANCs located in the perinephric, paracolic, subhepatic, and epigastric regions had a significant correlation with two or more adverse outcomes. Additional points were added to the modified CT severity index (mCTSI) based on the present study's findings. The new score had significantly higher AUROC than mCTSI for predicting infection, need for intervention, ICU stay > 1 week, and mortality. Conclusion: The site, size, and number of EPNs have a significant correlation with adverse clinical outcomes in patients with ANP. The inclusion of these parameters, along with present scoring systems, will help further improve the prognostication of patients. [ABSTRACT FROM AUTHOR]

Recent years have seen a surge of interest in the potential use of 3D bioprinting technologies for the development of tissues and organs with the aim of restoring, maintaining, or improving tissue function. Bioprinting studies frequently claim to be close to clinical translation, yet only report research at very early stages of the translational pipeline. Technology readiness levels (TRLs) are a systematic metric used to objectively assess the maturity of a technology, allowing researchers and stakeholders to understand how far a particular project has progressed from the conceptual stage towards clinical application. Bioprinting is an annex of additive manufacturing, as defined by the American Society for Testing and Materials (ASTM) and International Organization for Standardization (ISO) standards, characterized by the automated deposition of living cells and biomaterials. The tissue engineering and regenerative medicine (TE&RM) community has eagerly adopted bioprinting, while review articles regularly herald its imminent translation to the clinic as functional tissues and organs. Here we argue that such proclamations are premature and counterproductive; they place emphasis on technological progress while typically ignoring the critical stage-gates that must be passed through to bring a technology to market. We suggest the technology readiness level (TRL) scale as a valuable metric for gauging the relative maturity of a bioprinting technology in relation to how it has passed a series of key milestones. We suggest guidelines for a bioprinting-oriented scale and use this to discuss the state-of-the-art of bioprinting in regenerative medicine (BRM) today. Finally, we make corresponding recommendations for improvements to BRM research that would support its progression to clinical translation. [ABSTRACT FROM AUTHOR]

The success with which minority teachers cope with socio-cultural integration indicates their transformative agency. However, teachers' ideational projects, which are converted into a set of established practices, are tightly connected with their ideologies. In this case what they transform is not a matter of integration for them but is irrevocably intertwined with protecting their own culture. Applying a symbolic interactionist methodological lens and Archer's 'social morphogenesis' explanatory framework, in this qualitative research I aim to examine the unique educational context of Estonia. Schools with Russian as the language of instruction co-exist with schools where instruction is in the national language. The paper explores the mechanisms that stand behind the social agency of minority teachers and why their practices are considered 'morphostatic' for the whole education system. The paper concludes that these teachers' agency is culturally mediated and their strategies are reflexive and morphogenetic in nature, even though they don't lead to integration. [ABSTRACT FROM AUTHOR]

Background: The ductus arteriosus (DA) is critical in maintaining postnatal circulation in neonates with obstructed systemic circulation (OSC) and pulmonary circulation (OPC). We hypothesized that the size of the DA and aortic isthmus (AoI) undergoes adaptive growth in utero to counteract the hemodynamic challenges in these congenital heart diseases (CHD). Methods: Postnatal echocardiograms of neonates diagnosed prenatally with ductal-dependent CHD who were started on prostaglandins within 24 h of birth were reviewed. We assessed the cross-sectional area of the aortic valve opening, pulmonary valve opening, AoI, and DA by calculating (diameter)2/body surface area. Neonates were classified into OSC or OPC then subgrouped depending upon the patency of semilunar valves: OSC with and without aortic atresia (OSC-AA and OSC-nAA, respectively) and OPC with and without pulmonary atresia (OPC-PA and OPC-nPA, respectively). Results: Ninety-four cases were studied. The DA in OSC was significantly larger than OPC, and the DA in OSC-AA was significantly larger than OSC-nAA. The size of the AoI was significantly larger in OPC than OSC and larger in OSC-AA than OSC-nAA. Within the OSC-nAA group, there was no significant difference in the size of the DA, AoI, or pulmonary valve opening between those with retrograde flow (RF) at the AoI and without (nRF) except the aortic valve opening was significantly larger in nRF. All groups had comparable cross-sectional areas of systemic output. Conclusions: Our findings suggest that DA and AoI show compensatory growth to maintain critical blood flow to vital organs against primary anatomical abnormalities in ductus-dependent CHD. (249 words) [ABSTRACT FROM AUTHOR]

The content of endogenous hormones (auxin IAA, cytokinines, ABA) in explants of various types (segments of the leaf, bud, and stem), primary calluses induced from them, and morphogenic and nonmorphogenic calluses at the initial stages of in vitro culture by the immunoassay method was studied for the first time for Lavandula angustifolia Mill. The maximum value of the hormone levels in explants such as segments of a bud was shown. An increase in the content of hormones in primary calluses was revealed in comparison with similar characteristics in all types of explants. The higher level of the active form of cytokinin (trans-zeatin) and ABA, as well as the lower level of the inactive form of cytokinin (zeatin-nucleotide) and auxin IAA, were identified in the morphogenic callus compared with the nonmorphogenic one. It is suggested that the content of endogenous hormones in explants and calluses of L. angustifolia is due to their histological status. A conclusion is made about the unified histophysiological mechanisms of callusogenesis and morphogenesis in vitro in the studied plant. [ABSTRACT FROM AUTHOR]

The second heart field (SHF) plays a pivotal role in heart development, particularly in outflow tract (OFT) morphogenesis and septation, as well as in the expansion of the right ventricle (RV). Two mouse Cre lines, the Mef2c - AHF - Cre (Mef2c - Cre) and Isl1 - Cre , have been widely used to study the SHF development. However, Cre activity is triggered not only in the SHF but also in the RV in the Mef2c - Cre mice, and in the Isl1 - Cre mice, Cre activation is not SHF-specific. Therefore, a more suitable SHF-Cre line is desirable for better understanding SHF development. Here, we generated and characterized the Prdm1 -Cre knock-in mice. In comparison with Mef2c - Cre mice, the Cre activity is similar in the pharyngeal and splanchnic mesoderm, and in the OFT of the Prdm1 - Cre mice. Nonetheless, it was noticed that Cre expression is largely reduced in the RV of Prdm1 - Cre mice compared to the Mef2c - Cre mice. Furthermore, we deleted Hand2 , Nkx2-5 , Pdk1 and Tbx20 using both Mef2c - Cre and Prdm1 - Cre mice to study OFT morphogenesis and septation, making a comparison between these two Cre lines. New insights were obtained in understanding SHF development including differentiation into cardiomyocytes in the OFT using Prdm1 - Cre mice. In conclusion, we found that Prdm1 - Cre mouse line is a more appropriate tool to monitor SHF development, while the Mef2c-Cre mice are excellent in studying the role and function of the SHF in OFT morphogenesis and septation. [Display omitted] • Lineage tracing using Prdm1 - Cre mice reveals Cre expression in the second heart field progenitors and derivatives. • Comparison of Prdm1 - Cre and Mef2c - Cre mediated gene deletion distinguishes difference in second heart field development. • Prdm1 - Cre is suitable for studying second heart development. • Mef2c - Cre is an excellent tool to investigate cardiac outflow tract morphogenesis and septation. [ABSTRACT FROM AUTHOR]

To bring about sexual dimorphism in form, information from the sex determination pathway must trigger sex-specific modifications in developmental programs. DM-domain encoding genes have been found to be involved in sex determination in a multitude of animals, often at the level of male somatic gonad formation. Here we report our findings that the DM-domain transcription factors MAB-3 and DMD-3 function together in multiple steps during the late stages of C. elegans male somatic gonad development. Both mab-3 and dmd-3 are expressed in the linker cell and hindgut of L4 males and dmd-3 is also expressed in presumptive vas deferens cells. Furthermore, dmd-3 , but not mab-3 , expression in the linker cell is downstream of nhr-67, a nuclear hormone receptor that was previously shown to control late stages of linker cell migration. In mab-3 ; dmd-3 double mutant males, the last stage of linker cell migration is partially defective, resulting in aberrant linker cell shapes and often a failure of the linker cell to complete its migration to the hindgut. When mab-3; dmd-3 double mutant linker cells do complete their migration, they fail to be engulfed by the hindgut, indicating that dmd-3 and mab-3 activity are essential for this process. Furthermore, linker cell death and clearance are delayed in mab-3; dmd-3 double mutants, resulting in the linker cell persisting into adulthood. Finally, DMD-3 and MAB-3 function to activate expression of the bZIP transcription factor encoding gene zip-5 and downregulate the expression of the zinc metalloprotease ZMP-1 in the linker cell. Taken together, these results demonstrate a requirement for DM-domain transcription factors in controlling C. elegans male gonad formation, supporting the notion that the earliest DM-domain genes were involved in male somatic gonad development in the last common ancestor of the bilaterians. [Display omitted] • Two C. elegans DM domain transcription factor encoding genes, mab-3 and dmd-3 , are expressed in multiple tissues involved in male somatic gonad development. • m ab-3; dmd-3 double mutants display defects in linker cell migration, resulting in aberrant linker cell morphology and premature arrest in many double mutant males. • m ab-3; dmd-3 double mutants also display defects in linker cell engulfment by the hindgut and subsequent linker cell death and clearance. • MAB-3 and DMD-3 partially inhibit expression of the zinc matrix metalloproteinase encoding gene zmp-1 and activate expression of a basic leucine zipper containing transcription factor encoding gene zip-5 in the linker cell. • These results support the hypothesis that ancestral DM-domain genes were involved in male somatic gonad development. [ABSTRACT FROM AUTHOR]

Despite a massive investment in subsidized housing, informal settlement remains a significant aspect of urban development in Chilean cities. This paper first surveys the urban morphology of contemporary settlements in four Chilean cities to maps the extent and location of neighbourhoods that have developed informally or semi-formally. The broad pattern is that the more informal of settlements have been practically eliminated from the capital of Santiago, yet mixed informality flourishes and is expanding on the peripheries of regional cities. Four cases are then mapped and analysed to show the morphogenesis—the ways buildings and street networks are incrementally designed and produced. A range of morphogenic patterns are identified including highly irregular morphologies on escarpment conditions, semi-regular street grids, and informal encrustations within formal housing projects. It is argued that informal production will remain significant and that a better understanding of informal settlement morphology is crucial to the design and planning for the future of Chilean cities. [ABSTRACT FROM AUTHOR]

We present data on the ability for organogenesis in 22 genotypes of grapevine and developed a direct organogenesis protocol for the cultivar Podarok Magaracha and the rootstock Kober 5BB. The protocol does not require replacement of culture media and growth regulators, and the duration is 11 weeks. The cultivation of explants occurs on modified MS medium with the addition of 2.0 mg L−1 benzyladenine and indole-3-butyric acid (0.15 mg L−1 for the rootstock Kober 5BB or 0.05 mg L−1 for the cultivar Podarok Magaracha). The direct organogenesis protocol consists of three time periods: (1) culturing explants for 2 weeks in dark conditions for meristematic bulk tissue, (2) followed by 4 weeks of cultivation in light conditions for regeneration, and (3) 5 weeks of cultivation in dark conditions for shoot elongation. Based on this protocol, conditions for the Agrobacterium-mediated transformation of the Podarok Magaracha cultivar were developed with an efficiency of 2.0% transgenic plants per 100 explants. Two stably transformed lines with integration into the genome of the pBin35SGFP plasmid construction, confirmed by Southern blotting, were obtained. [ABSTRACT FROM AUTHOR]

Inner ear organoids play a crucial role in hearing research. In comparison to other animal models and 2D cell culture systems, inner ear organoids offer significant advantages for studying the mechanisms of inner ear development and exploring novel approaches to disease treatment. Inner ear organoids derived from human cells are more closely resemble normal human organs in development and function. The 3D culture system of the inner ear organoid enhances cell–cell interactions and mimics the internal environment. In this review, the progress and limitations of organoid culture methods derived from tissue‐specific progenitors and pluripotent stem cells (PSCs) are summarized, which may offer new insights into generating organoids that closely resemble the inner ear in terms of morphology and function. [ABSTRACT FROM AUTHOR]

Babassu is an oleaginous palm tree native to Brazil and holds significant socioeconomic importance. Since it does not produce tillers, somatic embryogenesis is the only way to propagate this species vegetatively. In this study, a protocol for babassu somatic embryogenesis from mature zygotic embryos was developed. This included testing two auxins for primary callus induction: 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-amino-3,5,6-trichloropicolinic acid (Picloram) at high concentrations (0, 225, 450, and 675 µM) and low concentrations (2,4-D − 0.0, 11.3, and 22.6 µM, and Picloram − 0.0, 10.4, and 20.7 µM), with and without the use of activated charcoal (2.5 g L− 1), respectively. The Murashige and Skoog medium was used as the basic medium, with the addition of L-glutamine (0.5 g L− 1), L-cysteine (0.1 g L− 1), and sucrose (30 g L− 1). The best results led to a final experiment using MS medium with 11.3 µM 2,4-D and Picloram. After six months, the embryogenic calluses were transferred to a medium containing pantothenic acid (0.25 mg L− 1) and biotin (0.25 mg L− 1) for the differentiation and maturation of somatic embryos and their conversion into plantlets. Morphoanatomical analyses were also performed to confirm the embryogenic events. The best results were obtained with a concentration of 11.3 µM of 2,4-D, enabling normal somatic embryo formation in 80% of the embryogenic calluses, comprising 50% of the total number of explants. This treatment was more appropriate for babassu’s somatic embryogenesis induction. The somatic embryos were morphoanatomically similar to zygotic embryos, particularly those from compact calluses that arose from mucilaginous primary calluses in the basal region of the explant. In conclusion, a protocol for babassu somatic embryogenesis from zygotic embryos was established, with an estimated time from the induction of embryogenic callus to the conversion into plantlets taking up to 22 months, depending on the treatment used. The protocol of embryogenic somatic induction of babassu with a low concentration of auxin is preferred due to reducing costs with compounds of the culture medium and avoiding the possible occurrence of somaclonal variations in the materials under cultivation. This is the first report of somatic embryogenesis for the genus Attalea and serves as an essential starting point for obtaining clonal plants of babassu.Key message: This work presents a pioneering protocol for somatic embryogenesis from zygotic embryos of Attalea speciosa, a palm tree native to Brazil of substantial socioeconomic importance. [ABSTRACT FROM AUTHOR]

Glucocorticoids (GCs) are steroid hormones fundamental to the body's normal physiological functions and are pivotal in fetal growth and development. During gestation, the mother's cortisol concentration (active GCs) escalates to accommodate the requirements of fetal organ development and maturation. A natural placental GCs barrier, primarily facilitated by 11b hydroxysteroid dehydrogenase 2, exists between the mother and fetus. This enzyme transforms biologically active cortisol into biologically inactive corticosterone, thereby mitigating fetal GCs exposure. However, during pregnancy, the mother may be vulnerable to adverse factor exposures such as stress, hypoxia, caffeine, and synthetic GCs use. In these instances, maternal serum GCs levels may surge beyond the protective capacity of the placental GCs barrier. Moreover, these adverse factors could directly compromise the placental GCs barrier, resulting in excessive fetal exposure to GCs. It is well-documented that prenatal GCs exposure can detrimentally impact the offspring's cardiovascular system, particularly in relation to blood pressure, vascular function, and heart function. In this review, we succinctly delineate the alterations in GCs levels during pregnancy and the potential mechanisms driving these changes, and also analyze the possible causes of prenatal GCs exposure. Furthermore, we summarize the current advancements in understanding the adverse effects and mechanisms of prenatal GCs exposure on the offspring's cardiovascular system. [ABSTRACT FROM AUTHOR]

Extracorporeal membrane oxygenation (ECMO), as an extracorporeal life support technique, can save the lives of reversible critically ill patients when conventional treatments fail. However, ECMO-related acute organ injury is a common complication that increases the risk of death in critically ill patients, including acute kidney injury, acute brain injury, acute lung injury, and so on. In ECMO supported patients, an increasing number of studies have shown that activation of the inflammatory response plays an important role in the development of acute organ injury. Cross-cascade activation of the complement system, the contact system, and the coagulation system, as well as the mechanical forces of the circuitry are very important pathophysiological mechanisms, likely leading to neutrophil activation and the production of neutrophil extracellular traps (NETs). NETs may have the potential to cause organ damage, generating interest in their study as potential therapeutic targets for ECMO-related acute organ injury. Therefore, this article comprehensively summarized the mechanism of neutrophils activation and NETs formation following ECMO treatment and their actions on acute organ injury. [ABSTRACT FROM AUTHOR]

Background: Spiders evolved different types of eyes, a pair of primary eyes that are usually forward pointing, and three pairs of secondary eyes that are typically situated more posterior and lateral on the spider's head. The best understanding of arthropod eye development comes from the vinegar fly Drosophila melanogaster, the main arthropod model organism, that also evolved different types of eyes, the larval eyes and the ocelli and compound eyes of the imago. The gene regulatory networks that underlie eye development in this species are well investigated revealing a conserved core network, but also show several differences between the different types of eyes. Recent candidate gene approaches identified a number of conserved genes in arthropod eye development, but also revealed crucial differences including the apparent lack of some key factors in some groups of arthropods, including spiders. Results: Here, we re-analysed our published scRNA sequencing data and found potential key regulators of spider eye development that were previously overlooked. Unlike earlier research on this topic, our new data suggest that Hedgehog (Hh)-signalling is involved in eye development in the spider Parasteatoda tepidariorum. By investigating embryonic gene expression in representatives of all main groups of spiders, we demonstrate that this involvement is conserved in spiders. Additionally, we identified genes that are expressed in the developing eyes of spiders, but that have not been studied in this context before. Conclusion: Our data show that single-cell sequencing represents a powerful method to gain deeper insight into gene regulatory networks that underlie the development of lineage-specific organs such as the derived set of eyes in spiders. Overall, we gained deeper insight into spider eye development, as well as the evolution of arthropod visual system formation. [ABSTRACT FROM AUTHOR]

The β-catenin-dependent canonical Wnt signaling is pivotal in organ development, tissue homeostasis, and cancer. Here, we identified an upstream enhancer of Ctnnb1 - the coding gene for β-catenin, named ieCtnnb1 (intestinal enhancer of Ctnnb1), which is crucial for intestinal homeostasis. ieCtnnb1 is predominantly active in the base of small intestinal crypts and throughout the epithelia of large intestine. Knockout of ieCtnnb1 led to a reduction in Ctnnb1 transcription, compromising the canonical Wnt signaling in intestinal crypts. Single-cell sequencing revealed that ieCtnnb1 knockout altered epithelial compositions and potentially compromised functions of small intestinal crypts. While deletion of ieCtnnb1 hampered epithelial turnovers in physiologic conditions, it prevented occurrence and progression of Wnt/β-catenin-driven colorectal cancers. Human ieCTNNB1 drove reporter gene expression in a pattern highly similar to mouse ieCtnnb1. ieCTNNB1 contains a single-nucleotide polymorphism associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues was stronger than that in adjacent normal tissues. HNF4α and phosphorylated CREB1 were identified as key trans-factors binding to ieCTNNB1 and regulating CTNNB1 transcription. Together, these findings unveil an enhancer-dependent mechanism controlling the dosage of Wnt signaling and homeostasis in intestinal epithelia. [ABSTRACT FROM AUTHOR]

Developmental biology-inspired strategies for tissue-building have extraordinary promise for regenerative medicine, spurring interest in the relationship between cell biophysical properties and morphological transitions. However, mapping gene or protein expression data to cell biophysical properties to physical morphogenesis remains challenging with current techniques. Here, we present multiplexed adhesion and traction of cells at high yield (MATCHY). MATCHY advances the multiplexing and throughput capabilities of existing traction force and cell-cell adhesion assays using microfabrication and a semiautomated computation scheme with machine learning-driven cell segmentation. Both biophysical assays are coupled with serial downstream immunofluorescence to extract cell type/signaling state information. MATCHY is especially suited to complex primary tissue-, organoid-, or biopsy-derived cell mixtures since it does not rely on a priori knowledge of cell surface markers, cell sorting, or use of lineage-specific reporter animals. We first validate MATCHY on canine kidney epithelial cells engineered for rearranged during transfection (RET) tyrosine kinase expression and quantify a relationship between downstream signaling and cell traction. We then use MATCHY to create a biophysical atlas of mouse embryonic kidney primary cells and identify distinct biophysical states along the nephron differentiation trajectory. Our data complement expression-level knowledge of adhesion molecule changes that accompany nephron differentiation with quantitative biophysical information. These data reveal an "energetic ratchet" that accounts for spatial trends in nephron progenitor cell condensation as they differentiate into early nephron structures, which we validate through agent-based computational simulation. MATCHY offers semiautomated cell biophysical characterization at >10,000-cell throughput, an advance benefiting fundamental studies and new synthetic tissue strategies for regenerative medicine. [ABSTRACT FROM AUTHOR]

Tartrazine, an azo dye prevalent in pharmaceuticals and food items, was investigated for its impact on fetal development, specifically examining visceral and skeletal abnormalities in rat offspring exposed to daily oral doses throughout pregnancy. Fourteen pregnant rats were randomly assigned to control and tartrazine groups (seven animals each), with tartrazine administered via oral gavage at 7.5 mg/kg throughout gestation. Offspring were categorized by gender for histopathological and genetic analysis of visceral structures. Bone quality and fracture resistance assessments involved micro‐CT, Raman spectroscopy, and biomechanical testing. Results highlighted distinct internal organ tissue differences in the tartrazine group, notably increased hemorrhagic and inflammatory cell infiltration, degeneration, and vacuolization compared to controls. Gender‐specific alterations in mRNA levels of IL‐6, IL‐1β, TNF‐α, and TRPM2 genes (p < .001) were also noted. Moreover, tartrazine‐exposed groups exhibited reduced trabecular thickness, bone volume, and significant alterations in bone matrix composition and quality alongside significant decreases in fracture resistance (p < 0.05). This study concludes that intrauterine exposure to tartrazine can result in adverse impacts on organ and bone development in rat offspring. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Distiller's grains are a by‐product of liquor production with a higher yield than liquor. Developing and utilizing distiller's grains well could alleviate the problem of scarce feed resources. Our present experiment was conducted with 6000 yellow‐feathered broilers to study the effects of adding distiller's grains yeast cultures (DGYC) to the diet on growth performance and immunity of broilers. The broilers were divided into five groups, receiving different DGYC concentrations during two stages. Growth performance, intestinal microorganisms and immune organ development were measured.The results showed that groups B and D, supplemented with medium and high concentrations of DGYC, respectively, had significantly improved growth performance compared to the control group (P < 0.05). Group D also showed higher immune organ index (P < 0.01), increased serum total protein, high‐density lipoprotein and immunoglobulin levels (P < 0.05) and lower levels of low‐density lipoprotein, triglycerides, interleukin 1β and tumor necrosis factor α (P < 0.05). Hematoxylin and eosin staining confirmed improved immune organ development in group D (P < 0.05). Furthermore, in high‐concentration group D, levels of short‐chain fatty acids (SCFA; acetic, propionic and butyric acids) in cecal chyme were significantly increased (P < 0.05). The richness (Chao1) and diversity (Faith‐pd) index of cecal microbiota were significantly higher in group D compared to the control group (P < 0.05). The microbial composition in group D differed from the control and medium‐concentration group B. Seven bacteria (Clostridia‐UCG‐014, UCG‐009, DTU089, UCG‐010, Campylobacter, Harryflintia, Shuttleworthia) showed significant differences (P < 0.05). After DGYC feeding, DTU089 decreased, while other SCFA‐producing bacteria increased (P < 0.05). Subsequently, KEGG function and corresponding signal pathway predictions were performed on bacteria with significant differences. Group D exhibited a higher enrichment of immune function pathways (P < 0.01) and showed significant changes in four immune signaling pathways according to the signal pathway heatmap.Our data suggest that high concentrations of DGYC can be applied as a feed additive for broilers that promotes growth, improves intestinal health and enhances certain immunity. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Simple Summary: Birds and poultry are seasonal breeding animals, and photoperiod is an important environmental factor affecting their broodiness. The Zhedong white goose has a strong broodiness, and extending the photoperiod can improve its egg-laying performance. Photoperiod can advance the sexual maturity of poultry and accelerate the development of reproductive organs and follicles. The growth and development of the ovary and follicles play a major role in the ability of a goose to produce eggs. Therefore, this paper investigates the effects of different photoperiods on the ovaries and small white follicles in the Zhedong white goose. Transcriptome sequencing identified differentially expressed genes and key gene modules, and revealed the effect of photoperiod on gene expression of ovaries and small white follicles. Functional enrichment analysis showed that photoperiod could affect smooth muscle cell proliferation in ovaries, as well as extracellular matrix-related function in small white follicles. In conclusion, the results provide a more comprehensive insight into the molecular mechanism through which photoperiod influences reproduction in geese. Photoperiod can regulate the broodiness of geese and thus increase their egg-laying rate. The laying performance of geese is mainly determined by ovary and follicle development. To understand the effect of photoperiod on the ovary and small white follicles, sixteen 220-day-old healthy female Zhedong white geese were randomly divided into two groups for long photoperiods (15L:9D) and short photoperiods (9L:15D). The geese were euthanized after two months of feeding, and their ovaries and follicles were collected for transcriptome sequencing. RNA-seq analysis identified 187 and 448 differentially expressed genes in ovaries and small white follicles of different photoperiod groups, respectively. A long photoperiod promotes high expression of SPP1, C6, MZB1, GP1BA, and FCGBP genes in the ovaries, and increases the expression of SPP1, ANGPTL5, ALPL, ZP1, and CHRNA4 genes in small white follicles. Functional enrichment analysis showed that photoperiod could affect respiratory system development, smooth muscle cell proliferation in ovaries, and extracellular matrix-related function in small white follicles. WGCNA revealed 31 gene modules, of which 2 were significantly associated with ovarian weight and 17 with the number of small white follicles. Our results provide a better understanding of the molecular regulation in the photoperiod affecting goose reproduction. [ABSTRACT FROM AUTHOR]

Background: Grains make up a large proportion of both human and animal diets. With threats to food production, such as climate change, growing sustainable and successful crops is essential to food security in the future. Germination is one of the most important stages in a plant's lifecycle and is key to the success of the resulting plant as the grain undergoes morphological changes and the development of specific organs. Micro-computed tomography is a non-destructive imaging technique based on the differing x-ray attenuations of materials which we have applied for the accurate analysis of grain morphology during the germination phase. Results: Micro Computed Tomography conditions and parameters were tested to establish an optimal protocol for the 3-dimensional analysis of barley grains. When comparing optimal scanning conditions, it was established that no filter, 0.4 degrees rotation step, 5 average frames, and 2016 × 1344 camera binning is optimal for imaging germinating grains. It was determined that the optimal protocol for scanning during the germination timeline was to scan individual grains at 0 h after imbibition (HAI) and then the same grain again at set time points (1, 3, 6, 24 HAI) to avoid any negative effects from X-ray radiation or disruption to growing conditions. Conclusion: Here we sought to develop a method for the accurate analysis of grain morphology without the negative effects of possible radiation exposure. Several factors have been considered, such as the scanning conditions, reconstruction, and possible effects of X-ray radiation on the growth rate of the grains. The parameters chosen in this study give effective and reliable results for the 3-dimensional analysis of macro structures within barley grains while causing minimal disruption to grain development. [ABSTRACT FROM AUTHOR]

Tissue self‐assembly relies on the interplay between structural cues imparted by the extracellular matrix (ECM) and instructive chemical factors that guide cellular signaling pathways. Here, it is reported that endothelial cell‐laden gelatin‐based hydrogels with optimized mechanical and chemical properties facilitate de novo vasculogenesis and recruitment of endogenous blood vessels in vivo. It is demonstrated that these engineered matrices, with tailored viscoelastic features and stiffness, drive vascular self‐assembly in a yes‐associated protein (YAP) mechanosensing‐dependent manner through integrin alpha V beta 3 (αvβ3) and matrix metalloproteinase 2 activity (MMP2). This research highlights how the ECM, in the form of gelatin‐based hydrogels with adjustable stress relaxation rates, drives vascular morphogenesis in the absence of growth factor supplementation, lending to a minimalistic platform for discretizing features of the microenvironment niche. Collectively, these results demonstrate a testbed that enables mechanistic evaluation of morphogenetic processes. Specifically, the results show how mechanical cues impact signaling pathways that modulate vascular remodeling, a critical tissue engineering paradigm needed for the translational application of vascularized grafts for regenerative medicine applications. [ABSTRACT FROM AUTHOR]

ABSTRACT Reproductive development plays an essential role in the perpetuation of genetic material and environmental adaptation. In angiosperms, the Short Vegetative Phase (SVP) serves as a flowering repressor, influencing the development of floral organs. In this study, heterologous transformation of Arabidopsis thaliana with SVP‐like genes (PtSVL1 and PtSVL2) derived from Pinus tabuliformis significantly impacted stamen formation and pollen fertility, without altering flowering time. Gene co‐expression networks revealed that SVP‐like and SOC1‐like genes function as key coregulatory transcription factors during the initial stages of cone development in P. tabuliformis. Interestingly, the regulatory module of SOC1 regulated by SVP in angiosperms is absent in conifers and conifer SVP‐like exercises its function in a form that is physically bound to SOC1‐like. Furthermore, combining the yeast one‐hybrid scanning with co‐expression network analysis, revealed that SPLs and TPSs were the principal downstream target genes of PtSVL1. Notably, the PtSPL16 promoter is positively regulated by PtSVL1, and overexpression of PtSPL16 results in delayed flowering in Arabidopsis, suggesting that the PtSVL1‐PtSPL16 module plays a crucial role in regulating reproductive development in conifers. Collectively, these findings enhance our understanding of the roles of SVP‐like genes in conifers and the key regulatory networks centred on PtSVL1 during reproductive cone development. [ABSTRACT FROM AUTHOR]

Silica cell-wall formation in diatoms is a showcase for the ability of organisms to control inorganic mineralization. The process of silicification by these unicellular algae is tightly regulated within a membrane-bound organelle, the silica deposition vesicle (SDV). Two opposing scenarios were proposed to explain the tight regulation of this intracellular process: a template-mediated process that relies on preformed scaffolds, or a template-independent self-assembly process. The present work points to a third scenario, where the SDV membrane is a dynamic mold that shapes the forming silica. We use in-cell cryo-electron tomography to visualize the silicification process in situ, in its native-state, and with a nanometer-scale resolution. This reveals that the plasma membrane interacts with the SDV membrane via physical tethering at membrane contact sites, where the curvature of the tethered side of the SDV membrane mirrors the intricate silica topography. We propose that silica growth and morphogenesis result from the biophysical properties of the SDV and plasma membranes. The silica cell wall of unicellular algae has intricate architecture unattainable by current technology. In this work it is shown that membrane contact sites are the biological morphogenesis handles to shape such intracellular mineralization. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is a chronic joint disease characterized by the degeneration, destruction, and excessive ossification of articular cartilage. The prevalence of OA is rising annually, concomitant with the aging global population and increasing rates of obesity. This condition imposes a substantial and escalating burden on individual health, healthcare systems, and broader social and economic frameworks. The etiology of OA is multifaceted and not fully understood. Current research suggests that the death of chondrocytes, encompassing mechanisms such as cellular apoptosis, pyroptosis, autophagy, ferroptosis and cuproptosis, contributes to both the initiation and progression of the disease. These cell death pathways not only diminish the population of chondrocytes but also exacerbate joint damage through the induction of inflammation and other deleterious processes. This paper delineates the morphological characteristics associated with various modes of cell death and summarizes current research results on the molecular mechanisms of different cell death patterns in OA. The objective is to review the advancements in understanding chondrocyte cell death in OA, thereby offering novel insights for potential clinical interventions. [ABSTRACT FROM AUTHOR]

Prostate cancer (PC) is an age-related disease and represents, after lung cancer, the second cause of cancer death in males worldwide. Mortality is due to the metastatic disease, which mainly involves the bones, lungs, and liver. In the last 20 years, the incidence of metastatic PC has increased in Western Countries, and a further increase is expected in the near future, due to the population ageing. Current treatment options, including state of the art cancer immunotherapy, need to be more effective to achieve long-term disease control. The most significant anatomical barrier to overcome to improve the effectiveness of current and newly designed drug strategies consists of the prostatic stroma, in particular the fibroblasts and the extracellular matrix, which are the most abundant components of both the normal and tumor prostatic microenvironment. By weaving a complex communication network with the glandular epithelium, the immune cells, the microbiota, the endothelium, and the nerves, in the healthy prostatic microenvironment, the fibroblasts and the extracellular matrix support organ development and homeostasis. However, during inflammation, ageing and prostate tumorigenesis, they undergo dramatic phenotypic and genotypic changes, which impact on tumor growth and progression and on the development of therapy resistance. Here, we focus on the characteristics and functions of the prostate associated fibroblasts and of the extracellular matrix in health and cancer. We emphasize their roles in shaping tumor behavior and the feasibility of manipulating and/or targeting these stromal components to overcome the limitations of current treatments and to improve precision medicine's chances of success. [ABSTRACT FROM AUTHOR]

Three-dimensional Spatial Transcriptomics has revolutionized our understanding of tissue regionalization, organogenesis, and development. However, existing approaches overlook either spatial information or experiment-induced distortions, leading to significant discrepancies between reconstruction results and in vivo cell locations, causing unreliable downstream analysis. To address these challenges, we propose ST-GEARS (Spatial Transcriptomics GEospatial profile recovery system through AnchoRS). By employing innovative Distributive Constraints into the Optimization scheme, ST-GEARS retrieves anchors with exceeding precision that connect closest spots across sections in vivo. Guided by the anchors, it first rigidly aligns sections, next solves and denoises Elastic Fields to counteract distortions. Through mathematically proved Bi-sectional Fields Application, it eventually recovers the original spatial profile. Studying ST-GEARS across number of sections, sectional distances and sequencing platforms, we observed its outstanding performance on tissue, cell, and gene levels. ST-GEARS provides precise and well-explainable 'gears' between in vivo situations and in vitro analysis, powerfully fueling potential of biological discoveries. Existing 3D Spatial Transcriptomics reconstruction approaches often overlook spatial information or experiment-induced distortions. Here, authors propose ST-GEARS to bridge the gap between in vivo cell locations and in vitro analysis, accurately recovering spatial profiles. [ABSTRACT FROM AUTHOR]