The subcommissural organ regulates brain development via secreted peptides.

The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. Here, to explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3 and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely, thymosin beta 4, thymosin beta 10 and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.

Bioinformatic Identification and Expression Analyses of the MAPK-MAP4K Gene Family Reveal a Putative Functional MAP4K10-MAP3K7/8-MAP2K1/11-MAPK3/6 Cascade in Wheat (Triticum aestivum L.).

The mitogen-activated protein kinase (MAPK) cascades act as crucial signaling modules that regulate plant growth and development, response to biotic/abiotic stresses, and plant immunity. MAP3Ks can be activated through MAP4K phosphorylation in non-plant systems, but this has not been reported in plants to date. Here, we identified a total of 234 putative TaMAPK family members in wheat (Triticum aestivum L.). They included 48 MAPKs, 17 MAP2Ks, 144 MAP3Ks, and 25 MAP4Ks. We conducted systematic analyses of the evolution, domain conservation, interaction networks, and expression profiles of these TaMAPK-TaMAP4K (representing TaMAPK, TaMAP2K, TaMAP3K, and TaMAP4K) kinase family members. The 234 TaMAPK-TaMAP4Ks are distributed on 21 chromosomes and one unknown linkage group (Un). Notably, 25 of these TaMAP4K family members possessed the conserved motifs of MAP4K genes, including glycine-rich motif, invariant lysine (K) motif, HRD motif, DFG motif, and signature motif. TaMAPK3 and 6, and TaMAP4K10/24 were shown to be strongly expressed not only throughout the growth and development stages but also in response to drought or heat stress. The bioinformatics analyses and qRT-PCR results suggested that wheat may activate the MAP4K10-MEKK7-MAP2K11-MAPK6 pathway to increase drought resistance in wheat, and the MAP4K10-MAP3K8-MAP2K1/11-MAPK3 pathway may be involved in plant growth. In general, our work identified members of the MAPK-MAP4K cascade in wheat and profiled their potential roles during their response to abiotic stresses and plant growth based on their expression pattern. The characterized cascades might be good candidates for future crop improvement and molecular breeding.

The subcommissural organ regulates brain development via secreted peptides.

The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. To explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3, and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely thymosin beta 4, thymosin beta 10, and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.

High-entropy engineering with regulated defect structure and electron interaction tuning active sites for trifunctional electrocatalysis.

High-entropy alloy nanoparticles (HEANs) possessing regulated defect structure and electron interaction exhibit a guideline for constructing multifunctional catalysts. However, the microstructure-activity relationship between active sites of HEANs for multifunctional electrocatalysts is rarely reported. In this work, HEANs distributed on multi-walled carbon nanotubes (HEAN/CNT) are prepared by Joule heating as an example to explain the mechanism of trifunctional electrocatalysis for oxygen reduction, oxygen evolution, and hydrogen evolution reaction. HEAN/CNT excels with unmatched stability, maintaining a 0.8V voltage window for 220 h in zinc-air batteries. Even after 20 h of water electrolysis, its performance remains undiminished, highlighting exceptional endurance and reliability. Moreover, the intrinsic characteristics of the defect structure and electron interaction for HEAN/CNT are investigated in detail. The electrocatalytic mechanism of trifunctional electrocatalysis of HEAN/CNT under different conditions is identified by in situ monitoring and theoretical calculation. Meanwhile, the electron interaction and adaptive regulation of active sites in the trifunctional electrocatalysis of HEANs were further verified by density functional theory. These findings could provide unique ideas for designing inexpensive multifunctional high-entropy electrocatalysts.

RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

Revealing the Orbital Interactions between Dissimilar Metal Sites during Oxygen Reduction Process.

A FeCo/DA@NC catalyst with the well-defined FeCoN6 moiety is customized through a novel and ultrafast Joule heating technique. This catalyst demonstrates superior oxygen reduction reaction activity and stability in an alkaline environment. The power density and charge-discharge cycling of znic-air batteries driven by FeCo/DA@NC also surpass those of Pt/C catalyst. The source of the excellent oxygen reduction reaction activity of FeCo/DA@NC originates from the significantly changed charge environment and 3d orbital spin state. These not only improve the bonding strength between active sites and oxygen-containing intermediates, but also provide spare reaction sites for oxygen-containing intermediates. Moreover, various in situ detection techniques reveal that the rate-determining step in the four-electron oxygen reduction reaction is *O2 protonation. This work provides strong support for the precise design and rapid preparation of bimetallic catalysts and opens up new ideas for understanding orbital interactions during oxygen reduction reactions.

Single-cell profiling of the pig cecum at various developmental stages.

The gastrointestinal tract is essential for food digestion, nutrient absorption, waste elimination, and microbial defense. Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity, functional heterogeneity, and their importance in intestinal tract development and disease. Although such profiling has been extensively conducted in humans and mice, the single-cell gene expression landscape of the pig cecum remains unexplored. Here, single-cell RNA sequencing was performed on 45 572 cells obtained from seven cecal samples in pigs at four different developmental stages (days (D) 30, 42, 150, and 730). Analysis revealed 12 major cell types and 38 subtypes, as well as their distinctive genes, transcription factors, and regulons, many of which were conserved in humans. An increase in the relative proportions of CD8 + T and Granzyme A (low expression) natural killer T cells (GZMA low NKT) cells and a decrease in the relative proportions of epithelial stem cells, Tregs, RHEX + T cells, and plasmacytoid dendritic cells (pDCs) were noted across the developmental stages. Moreover, the post-weaning period exhibited an up-regulation in mitochondrial genes, COX2 and ND2, as well as genes involved in immune activation in multiple cell types. Cell-cell crosstalk analysis indicated that IBP6 + fibroblasts were the main signal senders at D30, whereas IBP6 - fibroblasts assumed this role at the other stages. NKT cells established interactions with epithelial cells and IBP6 + fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs. This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus.

The hippocampus is a brain region associated with memory, learning and spatial navigation, its aging-related dysfunction is a common sign of Alzheimer's disease. Pig is a good model for human neurodegenerative disease, but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited. Here, we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages. We identified 510,908 accessible chromatin regions (ACRs) in 12 major cell types, among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages. We revealed significant enrichment of transposable elements in cell type-specific ACRs, particularly in neuroblasts. We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development. We identified ACRs and key transcription factors underlying the trajectory of neurogenesis (such as POU3F3 and EGR1) and oligodendrocyte differentiation (RXRA and FOXO6). We examined 27 Alzheimer's disease-related genes in our data and found that 15 showed cell type-specific activity (TREM2, RIN3 and CLU), and 15 genes displayed age-associated dynamic activity (BIN1, RABEP1 and APOE). We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types. The present study provides a single nucleus-accessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases.

Regulated High-Spin State and Constrained Charge Behavior of Active Cobalt Sites in Covalent Organic Frameworks for Promoting Electrocatalytic Oxygen Reduction.

A novel type of covalent organic frameworks has been developed by assembling definite cobalt-nitrogen-carbon configurations onto carbon nanotubes using linkers that have varying electronic effects. This innovative approach has resulted in an efficient electrocatalyst for oxygen reduction, which is understood by a combination of in situ spectroelectrochemistry and the bond order theorem. The strong interaction between the electron-donating carbon nanotubes and the electron-accepting linker mitigates the trend of charge loss at cobalt sites, while inducing the generation of high spin state. This enhances the adsorption strength and electron transfer between the cobalt center and reactants/intermediates, leading to an improved oxygen reduction capability. This work not only presents an effective strategy for developing efficient non-noble metal electrocatalysts through reticular chemistry, but also provides valuable insights into regulating the electronic configuration and charge behavior of active sites in designing high-performance electrocatalysts.

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array.

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the "giant panda" (very precious) in the world's pig species by Chinese animal husbandry. Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs. Results: We found that the average GP value of Erhualian was unusually low (68.09 µmol/g), but the variation was large (10.4-112.7 µmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16-0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p < 3.8 × 10-7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits. Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.

Milk Fat Globule Membrane Relieves Fatigue via Regulation of Oxidative Stress and Gut Microbiota in BALB/c Mice.

Milk fat globule membranes (MFGMs) are complex structures that incorporate bioactive proteins and lipids to assist in infant development. However, the antifatigue and antioxidant potentials of MFGM have not been investigated. In this study, repeated force swimming measured fatigue in male BALB/c mice fed MFGM and saline for 18 weeks. The MFGM supplementation increased the time to exhaustion by 42.7% at 6 weeks and 30.6% at 14 weeks (p < 0.05). Fatigue and injury-related biomarkers, including blood glucose, lactic acid, and lactate dehydrogenase, were ameliorated after free swimming (p < 0.05). The activity of antioxidant enzymes in blood serum increased at 18 weeks, while malondialdehyde (MDA) content decreased by 45.0% after the MFGM supplementation (p < 0.05). The Pearson correlation analysis showed a high correlation between fatigue-related indices and antioxidant levels. The increased protein expression of hepatic Nrf2 reduced the protein expression of Caspase-3 in the gastrocnemius muscle (p < 0.05). Moreover, the MFGM supplementation increased the relative abundance of Bacteroides, Butyricimonas, and Anaerostipes. Our results demonstrate that MFGM may maintain redox homeostasis to relieve fatigue, suggesting the potential application of MFGM as an antifatigue and antioxidant dietary supplement.

An actin filament branching surveillance system regulates cell cycle progression, cytokinesis and primary ciliogenesis.

Dysfunction of cell cycle control and defects of primary ciliogenesis are two features of many cancers. Whether these events are interconnected and the driving mechanism coordinating them remains elusive. Here, we identify an actin filament branching surveillance system that alerts cells of actin branching insufficiency and regulates cell cycle progression, cytokinesis and primary ciliogenesis. We find that Oral-Facial-Digital syndrome 1 functions as a class II Nucleation promoting factor to promote Arp2/3 complex-mediated actin branching. Perturbation of actin branching promotes OFD1 degradation and inactivation via liquid-to-gel transition. Elimination of OFD1 or disruption of OFD1-Arp2/3 interaction drives proliferating, non-transformed cells into quiescence with ciliogenesis by an RB-dependent mechanism, while it leads oncogene-transformed/cancer cells to incomplete cytokinesis and irreversible mitotic catastrophe via actomyosin ring malformation. Inhibition of OFD1 leads to suppression of multiple cancer cell growth in mouse xenograft models. Thus, targeting OFD1-mediated actin filament branching surveillance system provides a direction for cancer therapy.

Improvement of Spatial Memory and Cognitive Function in Mice via the Intervention of Milk Fat Globule Membrane.

With the improvement of living standards, dietary interventions have become an appropriate approach to enhance memory and cognitive performance. The present study investigated the potential mechanisms of spatial memory and cognitive function improvement with the milk fat globule membrane (MFGM) intervention in mice. The Morris water maze experiment revealed that the trajectories of mice in group M were more disordered. Also, the immunohistochemical results demonstrated a significantly higher number of neurons in group M compared with group C, especially in the hippocampal dentate gyrus (DG) area. It is suggested that MFGM enhanced mice's spatial memory and cognition from macroscopic behavior and microscopic cytology, respectively. Meanwhile, 47 differentially expressed proteins (DEPs) were identified, including 20 upregulated and 27 downregulated proteins. Upregulated (Sorbs 2, Rab 39, and Cacna 1e) and downregulated (Hp and Lrg 1) DEPs may improve spatial memory and cognition in mice by promoting synapse formation and increasing neurotransmitter receptors. KEGG enrichment analysis of the DEPs identified seven signaling pathways that were significantly enriched (p < 0.05). One of these pathways was neuroactive ligand-receptor interactions, which are strongly associated with improved spatial memory and cognitive performance. These findings give some new insights and references to the potential mechanisms of spatial memory and cognitive enhancement by MFGM.

Using phenotypic and genotypic big data to investigate the effect of muscle fiber characteristics on meat quality and eating quality traits in pigs.

Determining genetic correlations (GCs) between phenotypes that can be replicated across breeds or generations is important for animal breeding. A comprehensive and objective evaluation of this is dependent on enough variations in the studied phenotypes. To this end, we constructed a worldwide distributed eight-breeds crossbreed mosaic pig population and estimated the genetic and phenotypic correlations of muscle fiber characteristics (MFCs) with meat quality and eating quality traits using F6 and F7 generations (∼590 samples/generation) of this population. The GCs of the density of type IIA fibers and type IIB fibers with the loin-eye area, a*, color score, firmness score, and those of the proportions of the two fiber types with pH24h and b* were moderate to high (|rg| ≥ 0.3) in both populations. We also obtained moderate to high GCs of mean fiber density with five sensory quality traits. Our results provide an important reference for improving meat quality through the genetic regulation of MFCs.

Silver carp (Hypophthalmichthys molitrix) by-product hydrolysates: A new nitrogen source for Bifidobacterium animalis ssp. lactis BB-12.

Appropriate utilization of silver carp by-products is critical for enhancing industry profit and sustainability of aquaculture. This study explored the effect of the silver carp by-product hydrolysates on the growth of Bifidobacterium animalis ssp. lactis BB-12. Results indicated that papain recovered more nitrogen and < 1 kDa components from silver carp by-products than neutrase and alcalase. Papain-2 h (by-products hydrolyzed by papain for 2 hrs) was more effective in promoting the growth of BB-12. The content of < 1 kDa components, sulfhydryl-containing amino acids, and peptides composed of all the hydrophobic amino acids in hydrolysates was positively correlated to the growth of BB-12. BB-12 cultured by papain-2 h substituted medium exhibited a thinner and shorter morphology at 4 hrs of cultivation. This study provided a new nitrogen source for Bifidobacterium animalis ssp. lactis BB-12 and possible strategy for converting by-products to reduce aquacultural waste.

Whole-genome sequence-based association analyses on an eight-breed crossed heterogeneous stock of pigs reveal the genetic basis of skeletal muscle fiber characteristics.

Skeletal muscle fiber characteristics (MFCs) have been extensively studied due to their importance to human health and athletic ability, as well as to the quantity and quality of livestock meat production. Hence, we performed a genome-wide association study (GWAS) on nine muscle fiber traits by using whole genome sequence data in an eight-breed crossed heterogeneous stock pig population. This GWAS revealed 67 quantitative trait loci (QTLs) for these traits. The most significant GWAS signal was detected in the region of Sus scrofa chromosome 12 (SSC12) containing the MYH gene family. Notably, we identified a significant SNP rs322008693 (P = 7.52E-09) as the most likely causal mutation for the total number of muscle fibers (TNMF) QTL on SSC1. The results of EMSA and luciferase assays indicated that the rs322008693 SNP resided in a functional element. These findings provide valuable molecular markers for pig meat production selection as well as for deciphering the genetic mechanisms of the muscle fiber physiology.

Genome Analysis of a Novel Polysaccharide-Degrading Bacterium Paenibacillus algicola and Determination of Alginate Lyases.

Carbohydrate-active enzymes (CAZymes) are an important characteristic of bacteria in marine systems. We herein describe the CAZymes of Paenibacillus algicola HB172198T, a novel type species isolated from brown algae in Qishui Bay, Hainan, China. The genome of strain HB172198T is a 4,475,055 bp circular chromosome with an average GC content of 51.2%. Analysis of the nucleotide sequences of the predicted genes shows that strain HB172198T encodes 191 CAZymes. Abundant putative enzymes involved in the degradation of polysaccharides were identified, such as alginate lyase, agarase, carrageenase, xanthanase, xylanase, amylases, cellulase, chitinase, fucosidase and glucanase. Four of the putative polysaccharide lyases from families 7, 15 and 38 were involved in alginate degradation. The alginate lyases of strain HB172198T exhibited the maximum activity 152 U/mL at 50 °C and pH 8.0, and were relatively stable at pH 7.0 and temperatures lower than 40 °C. The average degree of polymerization (DP) of the sodium alginate oligosaccharide (AOS) degraded by the partially purified alginate lyases remained around 14.2, and the thin layer chromatography (TCL) analysis indicated that it contained DP2-DP8 oligosaccharides. The complete genome sequence of P. algicola HB172198T will enrich our knowledge of the mechanism of polysaccharide lyase production and provide insights into its potential applications in the degradation of polysaccharides such as alginate.

Comprehensive Genome-Wide Identification, Characterization, and Expression Analysis of CCHC-Type Zinc Finger Gene Family in Wheat (Triticum aestivum L.).

The CCHC-type zinc finger proteins (CCHC-ZFPs) play versatile roles in plant growth, development and adaptation to the environment. However, little is known about functions of CCHC-ZFP gene family memebers in Triticum aestivum. In the present study, we identified a total of 50 TaCCHC-ZFP genes from the 21 wheat chromosomes, which were phylogenetically classified into eight groups based on their specific motifs and gene structures. The 43 segmentally duplicated TaCCHC-ZFP genes were retrieved, which formed 36 segmental duplication gene pairs. The collinearity analyses among wheat and other eight mono/dicots revealed that no gene pairs were found between wheat and the three dicots. The promoter analyses of the TaCCHC-ZFP genes showed that 636 environmental stress-responsive and phytohormone-responsive cis-elements. The gene ontology enrichment analysis indicated that all the TaCCHC-ZFP genes were annotated under nucleic acid binding and metal ion binding. A total of 91 MicroRNA (miRNA) binding sites were identified in 34 TaCCHC-ZFP genes according to the miRNA target analysis. Based on the public transcriptome data, the 38 TaCCHC-ZFP genes were identified as differentially expressed gene. The expression profiles of 15 TaCCHC-ZFP genes were verified by the quantitative real-time PCR assays, and the results showed that these genes were responsive to drought or heat treatments. Our work systematically investigated the gene structures, evolutionary features, and potential functions of TaCCHC-ZFP genes. It lays a foundation for further research and application of TaCCHC-ZFP genes in genetic improvement of T. aestivum.