Zygospore development of Spirogyra (Charophyta) investigated by serial block-face scanning electron microscopy and 3D reconstructions.

Sexual reproduction of Zygnematophyceae by conjugation is a less investigated topic due to the difficulties of the induction of this process and zygospore ripening under laboratory conditions. For this study, we collected field sampled zygospores of Spirogyra mirabilis and three additional Spirogyra strains in Austria and Greece. Serial block-face scanning electron microscopy was performed on high pressure frozen and freeze substituted zygospores and 3D reconstructions were generated, allowing a comprehensive insight into the process of zygospore maturation, involving storage compound and organelle rearrangements. Chloroplasts are drastically changed, while young stages contain both parental chloroplasts, the male chloroplasts are aborted and reorganised as 'secondary vacuoles' which initially contain plastoglobules and remnants of thylakoid membranes. The originally large pyrenoids and the volume of starch granules is significantly reduced during maturation (young: 8 ± 5 µm³, mature: 0.2 ± 0.2 µm³). In contrast, lipid droplets (LDs) increase significantly in number upon zygospore maturation, while simultaneously getting smaller (young: 21 ± 18 µm³, mature: 0.1 ± 0.2 and 0.5 ± 0.9 µm³). Only in S. mirabilis the LD volume increases (34 ± 29 µm³), occupying ~50% of the zygospore volume. Mature zygospores contain barite crystals as confirmed by Raman spectroscopy with a size of 0.02 - 0.05 µm³. The initially thin zygospore cell wall (~0.5 µm endospore, ~0.8 µm exospore) increases in thickness and develops a distinct, electron dense mesospore, which has a reticulate appearance (~1.4 µm) in Spirogyra sp. from Greece. The exo- and endospore show cellulose microfibrils in a helicoidal pattern. In the denser endospore, pitch angles of the microfibril layers were calculated: ~18 ± 3° in S. mirabilis, ~20 ± 3° in Spirogyra sp. from Austria and ~38 ± 8° in Spirogyra sp. from Greece. Overall this study gives new insights into Spirogyra sp. zygospore development, crucial for survival during dry periods and dispersal of this genus.

In vitro efficacy of Er:YAG laser-activated irrigation versus passive ultrasonic irrigation and sonic-powered irrigation for treating multispecies biofilms in artificial grooves and dentinal tubules: an SEM and CLSM study.

BACKGROUND: Multispecies biofilms located in the anatomical intricacies of the root canal system remain the greatest challenge in root canal disinfection. The efficacy of Er:YAG laser-activated irrigation techniques for treating multispecies biofilms in these hard-to-reach areas has not been proved. The objective of this laboratory study was to evaluate the effectiveness of two Er:YAG laser-activated irrigation techniques, namely, photon-induced photoacoustic streaming (PIPS) and shock wave-enhanced emission photoacoustic streaming (SWEEPS), in treating multispecies biofilms within apical artificial grooves and dentinal tubules, in comparison with conventional needle irrigation (CNI), passive ultrasonic irrigation (PUI), and sonic-powered irrigation (EDDY). Two types of multispecies root canal biofilm models were established in combination with two assessment methods using scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) with the aim to obtain more meaningful results. METHODS: Ninety extracted human single-rooted premolars were chosen for two multispecies biofilm models. Each tooth was longitudinally split into two halves. In the first model, a deep narrow groove was created in the apical segment of the canal wall. After cultivating a mixed bacterial biofilm for 4 weeks, the split halves were reassembled and subjected to five irrigation techniques: CNI, PUI, EDD, PIPS, and SWEEPS. The residual biofilms inside and outside the groove in Model 1 were analyzed using SEM. For Model 2, the specimens were split longitudinally once more to evaluate the percentage of killed bacteria in the dentinal tubules across different canal sections (apical, middle, and coronal thirds) using CLSM. One-way analysis of variance and post hoc multiple comparisons were used to assess the antibiofilm efficacy of the 5 irrigation techniques. RESULTS: Robust biofilm growth was observed in all negative controls after 4 weeks. In Model 1, within each group, significantly fewer bacteria remained outside the groove than inside the groove (P < 0.05). SWEEPS, PIPS and EDDY had significantly greater biofilm removal efficacy than CNI and PUI, both from the outside and inside the groove (P < 0.05). Although SWEEPS was more effective than both PIPS and EDDY at removing biofilms inside the groove (P < 0.05), there were no significant differences among these methods outside the groove (P > 0.05). In Model 2, SWEEPS and EDDY exhibited superior bacterial killing efficacy within the dentinal tubules, followed by PIPS, PUI, and CNI (P < 0.05). CONCLUSION: Er:YAG laser-activated irrigation techniques, along with EDDY, demonstrated significant antibiofilm efficacy in apical artificial grooves and dentinal tubules, areas that are typically challenging to access.

HSF4/COIL complex-dependent R-loop mediates ultraviolet-induced inflammatory skin injury.

Intense ultraviolet (UV) exposure can cause phototoxic reactions, such as skin inflammation, resulting in injury. UV is a direct cause of DNA damage, but the mechanisms underlying transcriptional regulation within cells after DNA damage are unclear. The bioinformatics analysis of transcriptome sequencing data from UV-irradiated and non-UV-irradiated skin showed that transcription-related proteins, such as HSF4 and COIL, mediate cellular response to UV irradiation. HSF4 and COIL can form a complex under UV irradiation, and the preference for binding target genes changed because of the presence of a large number of R-loops in cells under UV irradiation and the ability of COIL to recognize R-loops. The regulation of target genes was altered by the HSF4-COIL complex, and the expression of inflammation and ageing-related genes, such as Atg7, Tfpi, and Lims1, was enhanced. A drug screen was performed for the recognition sites of COIL and R-loop. N6-(2-hydroxyethyl)-adenosine can competitively bind COIL and inhibit the binding of COIL to the R-loop. Thus, the activation of downstream inflammation-related genes and inflammatory skin injury was inhibited.

Frozen mountain pine needles: The endodermis discriminates between the ice-containing central tissue and the ice-free fully functional mesophyll.

Conifer (Pinaceae) needles are the most frost-hardy leaves. During needle freezing, the exceptional leaf anatomy, where an endodermis separates the mesophyll from the vascular tissue, could have consequences for ice management and photosynthesis. The eco-physiological importance of needle freezing behaviour was evaluated based on the measured natural freezing strain at the alpine treeline. Ice localisation and cellular responses to ice were investigated in mountain pine needles by cryo-microscopic techniques. Their consequences for photosynthetic activity were assessed by gas exchange measurements. The freezing response was related to the microchemistry of cell walls investigated by Raman microscopy. In frozen needles, ice was confined to the central vascular cylinder bordered by the endodermis. The endodermal cell walls were lignified. In the ice-free mesophyll, cells showed no freeze-dehydration and were found photosynthetically active. Mesophyll cells had lignified tangential cell walls, which adds rigidity. Ice barriers in mountain pine needles seem to be realised by a specific lignification patterning of cell walls. This, additionally, impedes freeze-dehydration of mesophyll cells and enables gas exchange of frozen needles. At the treeline, where freezing is a dominant environmental factor, the elaborate needle freezing pattern appears of ecological importance.

3D (x-y-t) Raman imaging of tomato fruit cuticle: Microchemistry during development.

The cuticle is a protective extracellular matrix that covers the above-ground epidermis of land plants. Here, we studied the cuticle of tomato (Solanum lycopersicum L.) fruits in situ using confocal Raman microscopy. Microsections from cuticles isolated at different developmental stages were scanned to visualize cuticle components with a spatial resolution of 342 nm by univariate and multivariate data analysis. Three main components, cutin, polysaccharides, and aromatics, were identified, with the latter exhibiting the strongest Raman scattering intensity. Phenolic acids and flavonoids were differentiated within the cuticle, and three schematic cuticle models were identified during development. Phenolic acids were found across the entire cuticle at the earliest stage of development, i.e. during the formation of the procuticle layer. Based on a mixture analysis with reference component spectra, the phenolic acids were identified as mainly esterified p-coumaric acid together with free p-hydroxybenzoic acid. During the cell expansion period of growth, phenolic acids accumulated in an outermost layer of the cuticle and in the middle region of the pegs. In these stages of development, cellulose and pectin were detected next to the inner cuticle region, close to the epidermal cell where flavonoid impregnation started during ripening. In the first ripening stage, chalconaringenin was observed, while methoxylated chalcones were chosen by the algorithm to fit the mature cuticle spectra. The colocation of carbohydrates, esterified p-coumaric acid, and methoxylated chalconaringenin suggests that the latter two link polysaccharide and cutin domains. Elucidating the different distribution of aromatics within the cuticle, suggests important functions: (1) overall impregnation conferring mechanical and thermal functions (2) the outermost phenolic acid layer displaying UV-B protection of the plant tissue.

The walnut shell network: 3D visualisation of symplastic and apoplastic transport routes in sclerenchyma tissue.

MAIN CONCLUSION: High symplastic connectivity via pits was linked to the lignification of the developing walnut shell. With maturation, this network lessened, whereas apoplastic intercellular space remained and became relevant for shell drying. The shell of the walnut (Juglans regia) sclerifies within several weeks. This fast secondary cell wall thickening and lignification of the shell tissue might need metabolites from the supporting husk tissue. To reveal the transport capacity of the walnut shell tissue and its connection to the husk, we visualised the symplastic and apoplastic transport routes during shell development by serial block face-SEM and 3D reconstruction. We found an extensive network of pit channels connecting the cells within the shell tissue, but even more towards the husk tissue. Each pit channel ended in a pit field, which was occupied by multiple plasmodesmata passing through the middle lamella. During shell development, secondary cell wall formation progressed towards the interior of the cell, leaving active pit channels open. In contrast, pit channels, which had no plasmodesmata connection to a neighbouring cell, got filled by cellulose layers from the inner cell wall lamellae. A comparison with other nut species showed that an extended network during sclerification seemed to be linked to high cell wall lignification and that the connectivity between cells got reduced with maturation. In contrast, intercellular spaces between cells remained unchanged during the entire sclerification process, allowing air and water to flow through the walnut shell tissue when mature. The connectivity between inner tissue and environment was essential during shell drying in the last month of nut development to avoid mould formation. The findings highlight how connectivity and transport work in developing walnut shell tissue and how finally in the mature state these structures influence shell mechanics, permeability, conservation and germination.

Endocytic trafficking promotes vacuolar enlargements for fast cell expansion rates in plants.

The vacuole has a space-filling function, allowing a particularly rapid plant cell expansion with very little increase in cytosolic content (Löfke et al., 2015; Scheuring et al., 2016; Dünser et al., 2019). Despite its importance for cell size determination in plants, very little is known about the mechanisms that define vacuolar size. Here, we show that the cellular and vacuolar size expansions are coordinated. By developing a pharmacological tool, we enabled the investigation of membrane delivery to the vacuole during cellular expansion. Our data reveal that endocytic membrane sorting from the plasma membrane to the vacuole is enhanced in the course of rapid root cell expansion. While this 'compromise' mechanism may theoretically at first decelerate cell surface enlargements, it fuels vacuolar expansion and, thereby, ensures the coordinated augmentation of vacuolar occupancy in dynamically expanding plant cells.

Biomimetic Immunosuppressive Exosomes that Inhibit Cytokine Storms Contribute to the Alleviation of Sepsis.

Sepsis is a disease characterized by multiple organ failure caused by immune hyperactivation and cytokine storms. Studies have shown that the incidence of sepsis in melanoma patients is substantially lower compared to the general population. It is also observed that experimental tumor-bearing animals have high survival rates after sepsis induction, suggesting that tumors may suppress sepsis-associated immune overactivation, thereby alleviating sepsis. Based on the above-described findings, this work assesses whether tumor cells play an antisepsis role in mice through the secretion of exosomes. Analysis of exosome activity reveals that the induced exosomes (iExo) secreted by tumor cells following lipopolysaccharide (LPS) treatment improve sepsis to a greater extent than normal secretory exosomes. Further analysis reveals that iExo exert their protective effects mainly through seven key miRNAs. In vitro bionic simulation of exosomes is carried out using exosome mimics generated by loading the aforementioned microRNAs into hyaluronic acid-polyethylenimine nanoparticles. Exosome mimics at specific miRNA ratios alleviate sepsis in mice and cynomolgus monkeys, indicating that biomimetic simulation of tumor-suppressive exosomes may represent a promising therapeutic method for the treatment of sepsis and cytokine-storm-related conditions.

[Effects of heterogeneous habitats on the coexistence of aquatic ecotype Alternanthera philoxeroides and Paspalum paspaloides]. / 异质生境对水生型空心莲子草-åŒç©—é›€ç¨—å ±å­˜çš„å½±å“.

Species coexistence depends on the comprehensive effects of biological properties and habitat heterogeneity. Based on a large-scale field survey (21°-35° N), we compared the differences on morphological and stoichiometric characteristics between the invasive aquatic species Alternanthera philoxeroides and the native co-occurring species Paspalum paspaloides, and examined the effects of environmental factors on such differences. The results showed that the coverage and importance value (IV) of A. philoxeroides were all significantly greater than P. paspa-loides (34.3% and 104.0%, respectively), whereas the height of P. paspaloides was significantly greater than A. philoxeroides (13.8%). Moreover, the total nitrogen concentration (TN) and N:P of A. philoxeroides were significantly greater than those of P. paspaloides (55.1% and 55.8%, respectively), whereas the total carbon concentration (TC) and C:N of P. paspaloides were significantly greater than those of A. philoxeroides (4.1% and 83.8%, respectively). A. philoxeroides coverage increased with the increases of longitude, and its abundance increased with the increases of water nitrate concentration and longitude, while its IV increased with the increases of water ammonium concentration. However, the coverage, abundance, and IV of P. paspaloides decreased with the increases of ammonium concentration. C:N of A. philoxeroides decreased with the increase of ammonium concentration. Increased mean annual temperature and mean annual precipitation increased C:N but decreased N:P of P. paspa-loides. The C:P of both species decreased with the increases of ammonium concentration and electrical conductivity. N:P of A. philoxeroides was little affected by environment. These results indicated that A. philoxeroides had greater coverage and N absorption capacity than P. paspaloides, and that enriched water nitrogen would aggravate the invasion of A. philoxeroides. Meanwhile, P. paspaloides improved its C-assimilate reserves and chose the growth competition strategy for resisting A. philoxeroides invasion under the superior hydrothermal conditions. Different responses to environmental changes contributed to their coexistence in aquatic ecosystem.

DriverMP enables improved identification of cancer driver genes.

BACKGROUND: Cancer is widely regarded as a complex disease primarily driven by genetic mutations. A critical concern and significant obstacle lies in discerning driver genes amid an extensive array of passenger genes. FINDINGS: We present a new method termed DriverMP for effectively prioritizing altered genes on a cancer-type level by considering mutated gene pairs. It is designed to first apply nonsilent somatic mutation data, protein‒protein interaction network data, and differential gene expression data to prioritize mutated gene pairs, and then individual mutated genes are prioritized based on prioritized mutated gene pairs. Application of this method in 10 cancer datasets from The Cancer Genome Atlas demonstrated its great improvements over all the compared state-of-the-art methods in identifying known driver genes. Then, a comprehensive analysis demonstrated the reliability of the novel driver genes that are strongly supported by clinical experiments, disease enrichment, or biological pathway analysis. CONCLUSIONS: The new method, DriverMP, which is able to identify driver genes by effectively integrating the advantages of multiple kinds of cancer data, is available at https://github.com/LiuYangyangSDU/DriverMP. In addition, we have developed a novel driver gene database for 10 cancer types and an online service that can be freely accessed without registration for users. The DriverMP method, the database of novel drivers, and the user-friendly online server are expected to contribute to new diagnostic and therapeutic opportunities for cancers.

Oak wood drying: precipitation of crystalline ellagic acid leads to discoloration.

Oak heartwood usually darkens during and after drying. This darkening can be heterogeneous, leaving noncolored areas in the wood board. These light discolorations have been linked to heterogeneous distribution of tannins, but compelling evidence on the microscale is lacking. In this study Raman and fluorescence microscopy revealed precipitations of crystalline ellagic acid, especially in the ray cells but also in lumina, cell corners and cell walls in the non-colored areas (NCA), which also had higher density. In these denser areas free water is longer present during drying and leads to accumulation of hydrolyzed tannins. When eventually falling dry, these tannins precipitate irreversible as non-colored ellagic acid and are not available for chemical reactions leading to darkening of the wood. Therefore, pronounced density fluctuations in wood boards require adjusting the drying and processing parameters so that water domains and ellagic acid precipitations are avoided during drying.

Twist and lock: nutshell structures for high strength and energy absorption.

Nutshells achieve remarkable properties by optimizing structure and chemistry at different hierarchical levels. Probing nutshells from the cellular down to the nano- and molecular level by microchemical and nanomechanical imaging techniques reveals insights into nature's packing concepts. In walnut and pistachio shells, carbohydrate and lignin polymers assemble to form thick-walled puzzle cells, which interlock three-dimensionally and show high tissue strength. Pistachio additionally achieves high-energy absorption by numerous lobes interconnected via ball-joint-like structures. By contrast, the three times more lignified walnut shells show brittle LEGO-brick failure, often along the numerous pit channels. In both species, cell walls (CWs) show distinct lamellar structures. These lamellae involve a helicoidal arrangement of cellulose macrofibrils as a recurring motif. Between the two nutshell species, these lamellae show differences in thickness and pitch angle, which can explain the different mechanical properties on the nanolevel. Our in-depth study of the two nutshell tissues highlights the role of cell form and their interlocking as well as plant CW composition and structure for mechanical protection. Understanding these plant shell concepts might inspire biomimetic material developments as well as using walnut and pistachio shell waste as sustainable raw material in future applications.

A belt for the cell: cellulosic wall thickenings and their role in morphogenesis of the 3D puzzle cells in walnut shells.

Walnut (Juglans regia) kernels are protected by a tough shell consisting of polylobate sclereids that interlock into a 3D puzzle. The shape transformations from isodiametric to lobed cells is well documented for 2D pavement cells, but not for 3D puzzle sclereids. Here, we study the morphogenesis of these cells by using a combination of different imaging techniques. Serial face-microtomy enabled us to reconstruct tissue growth of whole walnut fruits in 3D, and serial block face-scanning electron microscopy exposed cell shapes and their transformation in 3D during shell tissue development. In combination with Raman and fluorescence microscopy, we revealed multiple loops of cellulosic thickenings in cell walls, acting as stiff restrictions during cell growth and leading to the lobed cell shape. Our findings contribute to a better understanding of the 3D shape transformation of polylobate sclereids and the role of pectin and cellulose within this process.

Topological Interlocking and Geometric Stiffening as Complementary Strategies for Strong Plant Shells.

Many organisms encapsulate their embryos in hard, protective shells. While birds and reptiles largely rely on mineralized shells, plants often develop highly robust lignocellulosic shells. Despite the abundance of hard plant shells, particularly nutshells, it remains unclear which fundamental properties drive their mechanical stability. This multiscale analysis of six prominent (nut)shells (pine, pistachio, walnut, pecan, hazelnut, and macadamia) reveals geometric and structural strengthening mechanisms on the cellular and macroscopic length scales. The strongest tissues, found in walnut and pistachio, exploit the topological interlocking of 3D-puzzle cells and thereby outperform the fiber-reinforced structure of macadamia under tensile and compressive loading. On the macroscopic scale, strengthening occurs via an increased shell thickness, spherical shape, small size, and a lack of extended sutures. These functional interrelations suggest that simple geometric modifications are a powerful and resource-efficient strategy for plants to enhance the fracture resistance of entire shells and their tissues. Understanding the interplay between structure, geometry, and mechanics in hard plant shells provides new perspectives on the evolutionary diversification of hard seed coats, as well as insights for nutshell-based material applications.

Winter Nights during Summer Time: Stress Physiological Response to Ice and the Facilitation of Freezing Cytorrhysis by Elastic Cell Wall Components in the Leaves of a Nival Species.

Ranunculus glacialis grows and reproduces successfully, although the snow-free time period is short (2-3 months) and night frosts are frequent. At a nival site (3185 m a.s.l.), we disentangled the interplay between the atmospheric temperature, leaf temperatures, and leaf freezing frequency to assess the actual strain. For a comprehensive understanding, the freezing behavior from the whole plant to the leaf and cellular level and its physiological after-effects as well as cell wall chemistry were studied. The atmospheric temperatures did not mirror the leaf temperatures, which could be 9.3 °C lower. Leaf freezing occurred even when the air temperature was above 0 °C. Ice nucleation at on average -2.6 °C started usually independently in each leaf, as the shoot is deep-seated in unfrozen soil. All the mesophyll cells were subjected to freezing cytorrhysis. Huge ice masses formed in the intercellular spaces of the spongy parenchyma. After thawing, photosynthesis was unaffected regardless of whether ice had formed. The cell walls were pectin-rich and triglycerides occurred, particularly in the spongy parenchyma. At high elevations, atmospheric temperatures fail to predict plant freezing. Shoot burial prevents ice spreading, specific tissue architecture enables ice management, and the flexibility of cell walls allows recurrent freezing cytorrhysis. The peculiar patterning of triglycerides close to ice rewards further investigation.

Construction of Organelle-Like Architecture by Dynamic DNA Assembly in Living Cells.

The design of controllable dynamic systems is vital for the construction of organelle-like architectures in living cells, but has proven difficult due to the lack of control over defined topological transformation of self-assembled structures. Herein, we report a DNA based dynamic assembly system that achieves lysosomal acidic microenvironment specifically inducing topological transformation from nanoparticles to organelle-like hydrogel architecture in living cells. Designer DNA nanoparticles are constructed from double-stranded DNA with cytosine-rich stick ends (C-monomer) and are internalized into cells through lysosomal pathway. The lysosomal acidic microenvironment can activate the assembly of DNA monomers, inducing transformation from nanoparticles to micro-sized organelle-like hydrogel which could further escape into cytoplasm. We show how the hydrogel regulates cellular behaviors: cytoskeleton is deformed, cell tentacles are significantly shortened, and cell migration is promoted.

Metal-Organic Framework Disintegrants: Enzyme Preparation Platforms with Boosted Activity.

An enzyme formulation using customized enzyme activators (metal ions) to directly construct metal-organic frameworks (MOFs) as enzyme protective carriers is presented. These MOF carriers can also serve as the disintegrating agents to simultaneously release enzymes and their activators during biocatalysis with boosted activities. This highly efficient enzyme preparation combines enzyme immobilization (enhanced stability, easy operation) and homogeneous biocatalysis (fast diffusion, high activity). The MOF serves as an ion pump that continuously provides metal ion activators that greatly promote the enzymatic activities (up to 251 %). This MOF-enzyme composite demonstrated an excellent protective effect against various perturbation environments. A mechanistic investigation revealed that the spontaneous activator/enzyme release and ion pumping enable enzymes to sufficiently interact with their activators owing to the proximity effects, leading to a boost in biocatalytic performance.

From the Soft to the Hard: Changes in Microchemistry During Cell Wall Maturation of Walnut Shells.

The walnut shell is a hard and protective layer that provides an essential barrier between the seed and its environment. The shell is based on only one unit cell type: the polylobate sclerenchyma cell. For a better understanding of the interlocked walnut shell tissue, we investigate the structural and compositional changes during the development of the shell from the soft to the hard state. Structural changes at the macro level are explored by X-ray tomography and on the cell and cell wall level various microscopic techniques are applied. Walnut shell development takes place beneath the outer green husk, which protects and delivers components during the development of the walnut. The cells toward this outer green husk have the thickest and most lignified cell walls. With maturation secondary cell wall thickening takes place and the amount of all cell wall components (cellulose, hemicelluloses and especially lignin) is increased as revealed by FTIR microscopy. Focusing on the cell wall level, Raman imaging showed that lignin is deposited first into the pectin network between the cells and cell corners, at the very beginning of secondary cell wall formation. Furthermore, Raman imaging of fluorescence visualized numerous pits as a network of channels, connecting all the interlocked polylobate walnut shells. In the final mature stage, fluorescence increased throughout the cell wall and a fluorescent layer was detected toward the lumen in the inner part. This accumulation of aromatic components is reminiscent of heartwood formation of trees and is suggested to improve protection properties of the mature walnut shell. Understanding the walnut shell and its development will inspire biomimetic material design and packaging concepts, but is also important for waste valorization, considering that walnuts are the most widespread tree nuts in the world.