Unveiling Gene Expression Dynamics during Early Embryogenesis in Cynoglossus semilaevis: A Transcriptomic Perspective.

Commencing with sperm-egg fusion, the early stages of metazoan development include the cleavage and formation of blastula and gastrula. These early embryonic events play a crucial role in ontogeny and are accompanied by a dramatic remodeling of the gene network, particularly encompassing the maternal-to-zygotic transition. Nonetheless, the gene expression dynamics governing early embryogenesis remain unclear in most metazoan lineages. We conducted transcriptomic profiling on two types of gametes (oocytes and sperms) and early embryos (ranging from the four-cell to the gastrula stage) of an economically valuable flatfish-the Chinese tongue sole Cynoglossus semilaevis (Pleuronectiformes: Cynoglossidae). Comparative transcriptome analysis revealed that large-scale zygotic genome activation (ZGA) occurs in the blastula stage, aligning with previous findings in zebrafish. Through the comparison of the most abundant transcripts identified in each sample and the functional analysis of co-expression modules, we unveiled distinct functional enrichments across different gametes/developmental stages: actin- and immune-related functions in sperms; mitosis, transcription inhibition, and mitochondrial function in oocytes and in pre-ZGA embryos (four- to 1000-cell stage); and organ development in post-ZGA embryos (blastula and gastrula). These results provide insights into the intricate transcriptional regulation of early embryonic development in Cynoglossidae fish and expand our knowledge of developmental constraints in vertebrates.

Soil microbial community are more sensitive to ecological regions than cropping systems in alpine annual grassland of the Qinghai-Tibet Plateau.

Introduction: Modern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude. Methods: To fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone. Results: We found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m] < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase. Discussion: Our study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.

Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus).

Chinese sea bass (Lateolabrax maculatus) is a highly sought-after commercial seafood species in Asian regions due to its excellent nutritional value. With the rapid advancement of bioinformatics, higher standards for genome analysis compared to previously published reference genomes are now necessary. This study presents a gapless assembly of the Chinese sea bass genome, which has a length of 632.75 Mb. The sequences were assembled onto 24 chromosomes with a coverage of over 99% (626.61 Mb), and telomeres were detected on 34 chromosome ends. Analysis using Merqury indicated a high level of accuracy, with an average consensus quality value of 54.25. The ONT ultralong and PacBio HiFi data were aligned with the assembly using minimap2, resulting in a mapping rate of 99.9%. The study also identified repeating elements in 20.90% (132.25 Mb) of the genome and inferred 22,014 protein-coding genes. These results establish meaningful groundwork for exploring the evolution of the Chinese sea bass genome and advancing molecular breeding techniques.

Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) is becoming the most common chronic liver disease in the world. Immunity is the major contributing factor in NAFLD; however, the interaction of immune cells and hepatocytes in disease progression has not been fully elucidated. As a popular species for studying NAFLD, zebrafish, whose liver is a complex immune system mediated by immune cells and non-immune cells in maintaining immune tolerance and homeostasis. Understanding the cellular composition and immune environment of zebrafish liver is of great significance for its application in NAFLD. Here, we established a liver atlas that consists of 10 cell types using single-cell RNA sequencing (scRNA-seq). By examining the heterogeneity of hepatocytes and analyzing the expression of NAFLD-associated genes in the specific cluster, we provide a potential target cell model to study NAFLD. Additionally, our analysis identified two subtypes of distinct resident macrophages with inflammatory and non-inflammatory functions and characterized the successive stepwise development of T cell subclusters in the liver. Importantly, we uncovered the possible regulation of macrophages and T cells on target cells of fatty liver by analyzing the cellular interaction between hepatocytes and immune cells. Our data provide valuable information for an in-depth study of immune cells targeting hepatocytes to regulate the immune balance in NAFLD.

A Transcriptome Reveals the Mechanism of Nitrogen Regulation in Tillering.

Nitrogen (N) application significantly increases tiller numbers and is accompanied by changes in endogenous hormone content. We treated seedlings of Festuca kirilowii-a perennial forage grass-with nitrogen, determined the endogenous hormone content in the tiller buds, and performed a transcriptome analysis. The application of N reduced GA3, ABA, and 5-DS content and increased ZT and IAA content. By screening DEGs in the transcriptome results, we obtained DEGs annotated to 25 GO entries and 8 KEGG pathways associated with endogenous hormones. Most of these GO entries and KEGG pathways were associated with IAA, GAS, and ABA. We conducted a validation analysis of hormone-related DEGs using qRT-PCR to demonstrate that nitrogen controls the content of endogenous hormones by regulating the expression of these DEGs, which further affects tillering in F. kirilowii.

Nitrogen addition enhances seed yield by improving soil enzyme activity and nutrients.

Nitrogen (N) addition is a simple and effective field management approach to enhancing plant productivity. Nonetheless, the regulatory mechanisms governing nitrogen concentrations and their effect on soil enzyme activity, nutrient levels, and seed yield in the Festuca kirilowii seed field have yet to be elucidated. Therefore, this study sought to investigate the effect of N fertilizer application on soil enzyme activities, soil nutrients, and seed yield of F. kirilowii Steud cv. Huanhu, the only domesticated variety in the Festuca genus of the Poaceae family, was investigated based on two-year field experiments in the Qinghai-Tibet Plateau (QTP). Results showed that N input significantly affected soil nutrients (potential of hydrogen, total nitrogen, organic matter, and total phosphorus). In addition, soil enzyme activities (urease, catalase, sucrase, and nitrate reductase) significantly increased in response to varying N concentrations, inducing changes in soil nutrient contents. Introducing N improved both seed yield and yield components (number of tillers and number of fertile tillers). These findings suggest that the introduction of different concentrations of N fertilizers can stimulate soil enzyme activity, thus hastening nutrient conversion and increasing seed yield. The exhaustive evaluation of the membership function showed that the optimal N fertilizer treatment was N4 (75 kg·hm-2) for both 2022 and 2023. This finding provides a practical recommendation for improving the seed production of F. kirilowii in QTP.

Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments.

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous ( Ka) to synonymous ( Ks) substitution ratio ( Ka/ Ks) suggested that the 14 protein-coding genes (PCGs) were under purifying selection, likely due to specific deep-sea environmental pressures. Correlation analysis of the median Ka/ Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b (cyt b) and DNA mismatch repair protein ( mutS) may be influenced by environmental factors in the context of deep-sea species formation. This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

Fully Reversible and Super-Fast Photo-Induced Morphological Transformation of Nanofilms for High-Performance UV Detection and Light-Driven Actuators.

Flexible and highly ultraviolet (UV) sensitive materials garner considerable attention in wearable devices, adaptive sensors, and light-driven actuators. Herein, a type of nanofilms with unprecedented fully reversible UV responsiveness are successfully constructed. Building upon this discovery, a new system for ultra-fast, sensitive, and reliable UV detection is developed. The system operates by monitoring the displacement of photoinduced macroscopic motions of the nanofilms based composite membranes. The system exhibits exceptional responsiveness to UV light at 375 nm, achieving remarkable response and recovery times of < 0.3 s. Furthermore, it boasts a wide detection range from 2.85 µW cm-2 to 8.30 mW cm-2, along with robust durability. Qualitative UV sensing is accomplished by observing the shape changes of the composite membranes. Moreover, the composite membrane can serve as sunlight-responsive actuators for artificial flowers and smart switches in practical scenarios. The photo-induced motion is ascribed to the cis-trans isomerization of the acylhydrazone bonds, and the rapid and fully reversible shape transformation is supposed to be a synergistic result of the instability of the cis-isomers acylhydrazone bonds and the rebounding property of the networked nanofilms. These findings present a novel strategy for both quantitative and qualitative UV detection.

Heat-Set Supramolecular Hydrogelation by Regulating the Hydrophilic-Lipophilic Balance for a Tunable Circularly Polarized Luminescent Switch.

Heat-set supramolecular gels exhibited totally opposite phase behaviors of dissolution upon cooling and gelation on heating. They are commonly discovered by chance and their rational design remains a great challenge. Herein, a rational design strategy is proposed to realize heat-set supramolecular hydrogelation through regulation of the hydrophilic-lipophilic balance of the system. A newly synthesized amphiphile hydrogelator with pyrene embedded in its lipophilic terminal can self-assemble into a hydrogel through a heating and cooling cycle. However, the host-guest complex of the gelator and hydrophilic γ-cyclodextrin (γ-CyD) results in a sol at room temperature. Thus, heat-set hydrogelation is realized from the sol state in a controllable manner. Heat-set gelation mechanism is revealed by exploring critical heat-set supramolecular gelation and the related findings provide a general strategy for developing new functional molecular gels with tunable hydrophilic-lipophilic balance.

Legume-grass mixtures increase forage yield by improving soil quality in different ecological regions of the Qinghai-Tibet Plateau.

Introduction: Information on the relationship between soil quality and forage yield of legume-grass mixtures in different ecological regions can guide decision-making to achieve eco-friendly and sustainable pasture production. This study's objective was to assess the effects of different cropping systems on soil physical properties, nitrogen fractions, enzyme activities, and forage yield and determine suitable legume-grass mixtures for different ecoregions. Methods: Oats (Avena sativa L.), forage peas (Pisum sativum L.), common vetch (Vicia sativa L.), and fava beans (Vicia faba L.) were grown in monocultures and mixtures (YS: oats and forage peas; YJ: oats and common vetch; YC: oats and fava beans) in three ecological regions (HZ: Huangshui Valley; GN: Sanjiangyuan District; MY: Qilian Mountains Basin) in a split-plot design. Results: The results showed that the forage yield decreased with increasing altitude, with an order of GN (3203 m a.s.l.; YH 8.89 t·ha-1) < HZ (2661 m; YH 9.38 t·ha-1) < MY (2513m; YH 9.78 t·ha-1). Meanwhile, the forage yield was higher for mixed crops than for single crops in all ecological regions. In the 0-10 cm soil layer, the contents of total nitrogen (TN), microbial biomass nitrogen (MBN), soil organic matter (SOM), soluble organic nitrogen (SON), urease (UE), nitrate reductase (NR), sucrase (SC), and bacterial community alpha diversity, as well as relative abundance of dominant bacteria, were higher for mixed crops than for oats unicast. In addition, soil physical properties, nitrogen fractions, and enzyme activities varied in a wider range in the 0-10 cm soil layer than in the 10-20 cm layer, with larger values in the surface layer than in the subsurface layer. MBN, SON, UE, SC and catalase (CAT) were significantly and positively correlated with forage yield (P < 0.05). Ammonium nitrogen (ANN), nitrate nitrogen (NN), SOM and cropping systems (R) were significantly and positively correlated with Shannon and bacterial community (P < 0.05). The highest yields in the three ecological regions were 13.00 t·ha-1 for YS in MY, 10.59 t·ha-1 for YC in GN, and 10.63 t·ha-1 for YS in HZ. Discussion: We recommend planting oats and forage peas in the Qilian Mountains Basin, oats and fava beans in the Sanjiangyuan District, and oats and forage peas in Huangshui valley. Our results provide new insights into eco-friendly, sustainable, and cost-effective forage production in the Qinghai Alpine Region in China.

Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat.

Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in "Avena sativa, a genus Avena in the grass family Poaceae," have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function.

Microbial community structure and interactions between Aspergillus oryzae and bacteria in traditional solid-state fermentation of Jiangqu.

Microbial interactions play an important role in the formation, stabilization and functional performance of natural microbial communities. However, little is known about how the microbes present interactions to build a stable natural microbial community. Here, we developed Jiangqu, the solid-state fermented starters of thick broad-bean sauce formed naturally in factory, as model microbial communities by characterizing its diversity of microbial communities and batch stability. The dominant microbial strains and their fungi-bacteria interactions during solid-state fermentation of Jiangqu were characterized. In all batches of Jiangqu, Aspergillus oryzae, Bacillus, Staphylococcus and Weissella dominated in the communities and such a community structure could almost reduplicate between batches. Direct adsorption and competition were identified as the main interactions between A. oryzae and dominant bacteria during solid-state fermentation, which were quite different from liquid co-cultivation of A. oryzae and dominant bacteria. These results will help us better understand the intrinsic mechanism in the formation and stabilization of microbial communities from traditional solid-state qu-making and fermentation.

Promoter engineering for efficient production of sucrose phosphorylase in Bacillus subtilis and its application in enzymatic synthesis of 2-O-α-D-glucopyranosyl-L-ascorbic acid.

2-O-α-D-glucopyranosyl-L-ascorbic acid (AA-2G), a stable glucoside derivative of L-ascorbic acid (L-AA), can be one-step synthesized by sucrose phosphorylase (SPase). In this study, we attempted to produce extracellular SPase in Bacillus subtilis WB800 for the food-grade production of AA-2G. The results showed that the secretion of SPases did not require signal peptide. Promoter and its compatibility to target SPase gene were proved to be the key factors for high-level secretion. The strong promoter P43 and synthetic SPase gene derived from Bifidobacterium longum (BloSPase) were selected due to generate a relatively high extracellular activity (0.94 U/mL) for L-AA glycosylation. A highly active dual-promoter system PsigH-100-P43 was further constructed, which produced the highest extracellular and intracellular activity were 5.53 U/mL and 6.85 U/mL in fed-batch fermentation, respectively. Up to 113.58 g/L of AA-2G could be achieved by the supernatant of fermentation broth and a higher yield of 146.42 g/L was obtained by whole-cells biotransformation. Therefore, the optimal dual-promoter system in B. subtilis is suitable for the food-grade scale-up production of AA-2G.

Polarization-Sensitive Photodetector Based on High Crystallinity Quasi-1D BiSeI Nanowires Synthesized via Chemical Vapor Deposition.

Bismuth chalcohalides (BiSeI and BiSI), a class of superior light absorbers, have recently garnered great attention owing to their promise in constructing next-generation optoelectronic devices. However, to date, the photodetection application of bismuth chalcohalides is still limited due to the challenge in controllable preparation. Herein, the synthesis of large-scale quasi-1D BiSeI nanowires via chemical vapor deposition growth is reported. By precisely tuning the growth temperature and the Se supply, it can effectively control the growth thermodynamics and kinetics of BiSeI crystal, and thus achieve high purity quasi-1D BiSeI nanowires with high crystal quality, uniform diameter, and tunable domain length. Theory and optical characterizations of the quasi-1D BiSeI nanowires reveal an indirect bandgap of 1.57 eV with prominent optical linear dichroism. As a result, the quasi-1D BiSeI nanowire-based photodetector demonstrates a broadband photoresponse (400-800 nm) with high responsivity of 5880 mA W-1 , fast response speed of 0.11 ms and superior air stability. More importantly, the photodetector displays strong polarization sensitivity (anisotropic ratio = 1.77) under the 532 nm light irradiation. This work will provide important guides to the synthesis of other quais-1D metal chalcohalides and shed light on their potential in constructing novel multifunctional optoelectronic devices.

Evolutionary Shift of Insect Diapause Strategy in a Warming Climate: An Intra-Population Evidence from Asian Corn Borer.

Herbivorous insects having variable numbers of generations annually depending on climate and day length conditions are increasingly breeding additional generations driven by elevated temperature under the scenario of global warming, which will increase insect abundance and result in more frequent damage events. Theoretically, this relies on two premises, i.e., either an evolutionary shift to facultative diapause for an insect behaving an obligatory diapause or developmental plasticity to alter voltinism productively for an insect with facultative diapause before shortening photoperiods inducing diapause. Inter-population evidence supporting the premise (theory) comes primarily from a model system with voltinism linked to thermal gradients across latitude. We examined the intra-population evidence in the field (47°24' N, 123°68' E) with Ostrinia furnacalis, one of the most destructive pests, on corn in Asia and Pacific islands. The species was univoltine in high latitudinal areas (≤46° N). Divergence of the diapause feature (obligatory and facultative) was observed within the field populations from 2016 to 2021. Warmer climates would provoke more facultative diapause individuals to initiate a second generation, which will significantly drive the population to evolve toward facultative diapause (multi-voltinism). Both divergent diapause and temperature must be considered for accurate prediction of phenology and population dynamics in ACB.

Porous biochar derived from walnut shell as an efficient adsorbent for tetracycline removal.

In this study, a high-performance porous adsorbent was prepared from biochar through a simple one-step alkali-activated pyrolysis treatment of walnut shells, and it was effective in removing tetracycline (TC). The specific surface area (SSA) of potassium hydroxide-pretreated walnut shell-derived biochar pyrolyzed at 900 °C (KWS900) increased remarkably compared to that of the pristine walnut shell and reached 1713.87 ± 37.05 m2·g-1. The maximum adsorption capacity of KWS900 toward TC was 607.00 ± 31.87 mg·g-1. The pseudo-second-order kinetic and Langmuir isotherm models were well suited to describe the TC adsorption process onto KWS900. The KWS900 exhibited high stability and reusability for TC adsorption in the presence of co-existing anions or cations over a wide pH range of 1.0-11.0. Further investigations demonstrated that the proposed adsorption mechanism involved pore filling, hydrogen bonding, π-π stacking, and electrostatic interaction. These findings provide a valuable reference for developing biochar-based adsorbents for pollutant removal.

Towards a scalable and controllable preparation of highly-uniform surface-enhanced Raman scattering substrates: Defect-free nanofilms as templates.

The uniformity and reproducibility of substrates highly determine the applicability of surface-enhanced Raman scattering (SERS). Production of them, however, remains a challenge. Herein, we report a template-based strategy for the strictly controllable and handily scalable preparation of a very uniform SERS substrate, Ag nanoparticles (AgNPs)/nanofilm, where the template used is a flexible, transparent, self-standing, defect-free and robust nanofilm. Importantly, the obtained AgNPs/nanofilm is self-adhesive to surfaces of different properties and morphologies, ensuring in-situ and at real-time SERS detection. The enhancement factor (EF) of the substrate for rhodamine 6G (R6G) could reach 5.8 × 1010 with a detection limit (DL) of 1.0 × 10-15 mol L-1. Moreover, 500 bending tests and one-month storage showed no observable performance degradation, and up to 50.0 cm2 scaled-up preparation depicted negligible effect upon the structure and the sensing performance. The real-life applicability of AgNPs/nanofilm was demonstrated by the sensitive detection of tetramethylthiuram disulfide on cherry tomato and fentanyl in methanol with a routine handheld Raman spectrometer. This work thus provides a reliable strategy for large area wet-chemical preparation of high-quality SERS substrates.

Supramolecular Adhesives with Extended Tolerance to Extreme Conditions via Water-Modulated Noncovalent Interactions.

Development of supramolecular adhesives with strong tolerance to extreme conditions has emerged as an important research area. In this study, by balancing supramolecular interactions such as hydrogen bonding interactions, electrostatic interactions, π-π stacking interactions, and cation-π interactions, we designed and prepared a series of two-component supramolecular adhesives derived from small organic molecules. Highly efficient interfacial adhesion with maximum adhesion strength of ≈10.0 MPa was realized on various surfaces in air, organic solvents, or liquid nitrogen. Owing to balanced supramolecular interactions, water participation prolonged and increased the tolerance of the adhesives in extreme environments. We demonstrate that the combination of imidazole-based ionic liquids and phenols can be applied for various interfacial adhesions, thereby aiding the development of next-generation adhesives capable of adapting to various extreme conditions in a controlled manner.

Correction to "Granular Calcium Carbonate Reinforced the Cement Paste Cured by Elevated Temperatures".

[This corrects the article DOI: 10.1021/acsomega.2c07090.].

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.