In the context of muscle loss, bone repair is impaired, suggesting that muscle derived signals contribute to bone regeneration. However, how muscle surrounding the injury site communicates with the bone repair niche remains unclear. Here we found that CX3CL1 expression was induced in endothelial cells in muscle surrounding a femoral bone injury site. Deletion of Cx3cl1 impaired bone healing, demonstrating a functional role for CX3CL1 in bone repair. A CX3CL1 receptor, CX3CR1, was expressed by PDGFRα⁺ stromal progenitors and lineage tracing showed that CX3CR1 expressing osteoprogenitor lineage cells accumulated at the injury site during repair. PDGFRα⁺ stromal progenitors showed enhanced osteoblastogenesis in response to recombinant CX3CL1. In older mice, local CX3CL1 delivery increased PDGFRα⁺CX3CR1⁺ osteoprogenitor accumulation and improved bone repair. These findings identify a muscle bone signaling pathway in which endothelial CX3CL1 promotes bone repair through CX3CR1 expressing osteoprogenitors.

Fibrosis commonly occurs during adult skin wound healing, characterized by excessive extracellular matrix (ECM), leading to scarring. Mesenchymal cells, the primary ECM-producing population, are heterogeneous with varying fibrotic propensity during healing. While pro-fibrotic embryonically derived mesenchymal lineages have been identified, adult mesenchymal cells responsible for fibrosis are not yet fully characterized. In adult mice with conditional macrophage depletion during the early phase of wound healing, wounds exhibit attenuated fibrosis and a reduction in mesenchymal cell numbers. Here we show that early phase macrophage induces a distinct PDGFRα⁺ mesenchymal population expressing Fcer1g. This cell population expands rapidly after injury, shows high proliferative activity, and is largely absent when macrophages are depleted. Targeted ablation of this cell population does not delay wound closure but results in diminished scarring. Human wound datasets identified a transcriptionally conserved FCER1G-expressing mesenchymal subset, suggesting that this pro-fibrotic mesenchymal state is preserved in human wound healing.

Fibrosis commonly occurs during adult skin wound healing, characterized by excessive extracellular matrix (ECM), leading to scarring. Mesenchymal cells, the primary ECM-producing population, are heterogeneous with varying fibrotic propensity during wound healing. While pro-fibrotic embryonically derived mesenchymal lineages have been identified, adult mesenchymal cells responsible for fibrosis are not yet fully characterized. In adult mice with conditional macrophage depletion during the early phase of wound healing, wounds exhibited attenuated fibrosis and a reduction in mesenchymal cell numbers. Single-cell RNA sequencing revealed a Fcer1g-expressing mesenchymal subpopulation that was significantly decreased following macrophage depletion. Targeted ablation of this cell population did not delay wound closure but resulted in diminished cutaneous scarring. During wound healing, these Fcer1g-expressing mesenchymal cells localized at the wound bed and exhibited a high proliferation rate. Fibronectin is secreted by macrophages and known to modulate fibrosis during wound healing. Wounds from EDA fibronectin-deficient mice contained significantly fewer Fcer1g-expressing mesenchymal cells. Our findings reveal a macrophage-induced adult mesenchymal subpopulation responsible for fibrosis.

Enchondromas are a common tumor in bone that can occur as multiple lesions in enchondromatosis, which is associated with deformity of the effected bone. These lesions harbor mutations in IDH and driving expression of a mutant Idh1 in Col2 expressing cells in mice causes an enchondromatosis phenotype. In this study we compared growth plates from E18.5 mice expressing a mutant Idh1 with control littermates using single cell RNA sequencing. Data from Col2 expressing cells were analyzed using UMAP and RNA pseudo-time analyses. A unique cluster of cells was identified in the mutant growth plates that expressed genes known to be upregulated in enchondromas. There was also a cluster of cells that was underrepresented in the mutant growth plates that expressed genes known to be important in longitudinal bone growth. Immunofluorescence showed that the genes from the unique cluster identified in the mutant growth plates were expressed in multiple growth plate anatomic zones, and pseudo-time analysis also suggested these cells could arise from multiple growth plate chondrocyte subpopulations. This data identifies subpopulations of cells in control and mutant growth plates, and supports the notion that a mutant Idh1 alters the subpopulations of growth plate chondrocytes, resulting a subpopulation of cells that become enchondromas at the expense of other populations that contribute to longitudinal growth.

Enchondromas are a common tumor in bone that can occur as multiple lesions in enchondromatosis, which is associated with deformity of the affected bone. These lesions harbor somatic mutations in IDH and driving expression of a mutant Idh1 in Col2 expressing cells in mice causes an enchondromatosis phenotype. Here we compared growth plates from E18.5 mice expressing a mutant Idh1 with control littermates using single cell RNA sequencing. Data from Col2 expressing cells were analysed using UMAP and RNA pseudo-time analyses. A unique cluster of cells was identified in the mutant growth plates that expressed genes known to be upregulated in enchondromas. There was also a cluster of cells that was underrepresented in the mutant growth plates that expressed genes known to be important in longitudinal bone growth. Immunofluorescence showed that the genes from the unique cluster identified in the mutant growth plates were expressed in multiple growth plate anatomic zones, and pseudo-time analysis also suggested these cells could arise from multiple growth plate chondrocyte subpopulations. This data supports the notion that a subpopulation of chondrocytes become enchondromas at the expense of contributing to longitudinal growth.

Summary: Postoperative evaluation of free flaps remains a challenging task. The current accepted standard for diagnosis of vascular compromise remains clinical observation. In recent years, near-infrared spectroscopy (NIRS) has been widely used as a noninvasive objective monitoring tool for postoperative evaluation of soft-tissue flaps. However, methods for monitoring bone flaps remain inadequate. In this study, NIRS was applied for the first time to monitor free buried bone flaps that were used for mandibular reconstruction. The penetrating property of NIRS was used to measure the tissue oxygenation index (TOI) of deep tissues, which reflected the microcirculatory status of the tissues. Changes in TOI values were monitored continuously in 59 cases of free bone flaps up to 72 hours after surgery. Five cases of vascular compromise were noted by clinical observation. Two fibula flaps were total failures, one of which showed a sharp decrease in TOI value to 45% in a short period of time; the other showed a continual gradual decrease to 55%. The observed sudden (<50%) and continuous (>10%) decreases in TOI values suggest that more attention should be paid to revision surgical procedures. The authors conclude that NIRS holds promise as an objective and valid method for clinical evaluation of buried bone flaps.

It has long been debated whether tree leaves from shady environments exhibit higher photosynthetic induction efficiency (IE) than those from sunny environments and how the shade tolerance of tree species and the light environment of leaves contribute to the dynamics of photosynthesis. To address these questions, we investigated leaf photosynthetic responses to simulated changes of light intensity in seedlings of six tree species with differential shade tolerance. The seedlings were growing under different light environments in a lowland tropical forest. We proposed an index of relative shade tolerance (RST) to assess species-specific capacity to tolerate shade, and we quantified the light environment of individual leaves by the index of daily light integral (DLI), the averaged daily total light intensity. We obtained the following results. Photosynthetic IE, which is the ratio of the achieved carbon gain to the expected carbon gain, was significantly higher for species with a higher RST than for that with a lower RST. The impacts of light environment on the IE of individual leaves within the same species varied largely among different species. In the three species with relatively low RST, the IE of individual leaves decreased at higher DLIs when DLI < 10 mol m-2 d-1. Seedlings with high initial stomatal conductance before induction (gs50) possessed a higher IE than those with low gs50 from the same species. A trade-off existed between IE and steady-state photosynthetic rates. These results suggest a complex interaction between the shade tolerance of species and the light environments of individual leaves for photosynthetic induction and provide new insights into the adaptation strategy for understory seedlings under sunfleck environments.

Morphological, genic and epigenetic differences often exist in separate sexes of dioecious and trioecious plants. However, the connections and relationships among them in different breeding systems are still unclear. Papaya has three sex types, which is genetically determined and epigenetically regulated, and was chosen as a model to study sex differentiation. Bisulfite sequencing of genomic DNA extracted from early-stage flowers revealed sex-specific genomic methylation landscapes and seasonally methylome reprogramming processes in dioecious and gynodioecious papaya grown in spring and summer. Extensive methylation of sex-determining region (SDR) was the distinguishing epigenetic characteristics of nascent XY sex chromosomes in papaya. Seasonal methylome reprogramming of early-stage flowers in both dioecy and gynodioecy systems were detected, resulting from transcriptional expression pattern alterations of methylation-modification-related and chromatin-remodeling-related genes, particularly from those genes involved in active demethylation. Genes involved in phytohormone signal transduction pathway in male flowers have played an important role in the formation of male-specific characteristics. These findings enhanced the understanding of the genetic and epigenetic contributions to sex differentiation and the complexity of sex chromosome evolution in trioecious plants.

To further study the characteristics of peach codon usage, this study analyzed codon usage biases and codon usage patterns of peach genome, based on the statistical calculations of related GC content, effective number of codons (ENC) and relative synonymous codons (RSCU) from 26 873 coding sequences. The results showed that there were obvious biases in codon usage of peach, and 4 out of 61 codons (UCA, ACA, GCA and GAA) were defined as the optimal codons, all of which end with Adenine at the third codon position. Further analyses of codon usage frequency among peach and other 9 relative species in Rosaceae found that the codon usage patterns in the relative genus were similar. These results also suggested that there was a positive correlation between the copy number of tRNA genes and the occurrence frequency of corresponding amino acids (and specific codons) in the peach genome. These results revealed codon usage patterns in Peach and provide an important reference for the relevant studies on codon usage mechanism and the genetic engineering.

Background Bougainvillea is a popular ornamental plant with brilliant color and long flowering periods. It is widely distributed in the tropics and subtropics. The primary ornamental part of the plant is its colorful and unusual bracts, rich in the stable pigment betalain. The developmental mechanism of the bracts is not clear, and the pathway of betalain biosynthesis is well characterized in Bougainvillea. Results At the whole-genome level, we found 23,469 protein-coding genes by assembling the RNA-Seq and Iso-Seq data of floral and leaf tissues. Genome evolution analysis revealed that Bougainvillea is related to spinach; the two diverged approximately 52.7 million years ago (MYA). Transcriptome analysis of floral organs revealed that flower development of Bougainvillea was regulated by the ABCE flower development genes; A-class, B-class, and E-class genes exhibited high expression levels in bracts. Eight key genes of the betalain biosynthetic pathway were identified by homologous alignment, all of which were upregulated concurrently with bract development and betalain accumulation during the bract initiation stage of development. We found 47 genes specifically expressed in stamens, including seven highly expressed genes belonging to the pentose and glucuronate interconversion pathways. BgSEP2b, BgSWEET11, and BgRD22 are hub genes and interacted with many transcription factors and genes in the carpel co-expression network. Conclusions We assembled protein-coding genes of Bougainvilea, identified the floral development genes, and constructed the gene co-expression network of petal, stamens, and carpel. Our results provide fundamental information about the mechanism of flower development and pigment accumulation in Bougainvillea, and will facilitate breeding of cultivars with high ornamental value.

Fatty acid-binding proteins (FABPs) function as fatty acid chaperones, and they play a key role in lipid meta-bolism. The diversity of fabp gene family members is important for different fatty acid absorption and transport. In the present study, we identified 13 fabp genes from Chinese perch (Siniperca chuatsi). The spatiotemporal expression profiles of these 13 Sc-fabp genes, their circadian rhythm expression characteristics in intestine, and transcriptional regulation under cadmium exposure were investigated. Phylogenetic analysis indicated that the teleost-specific genome duplication event made a contribution to the expansion of Sc-fabp genes. The protein coding regions of all the 13 Sc-fabp genes were composed of 4 exons. These 13 genes exhibited similar protein length, but a low identity in protein sequences. The tissue expression profiles of most fabp genes in Chinese perch (Sc-fabp2a, Sc-fabp2b, Sc-fabp3, Sc-fabp6a, Sc-fabp7a, and Sc-fabp7b) were consistent with those of their orthol-ogous genes in mammalian, but the Sc-fabp1, Sc-fabp6ba, and Sc-fabp6bb showed distinct tissue expression patterns from their orthologous genes in mammalian. The total expression level of Sc-fabps was increased with embryonic development, but it was decreased significantly after hatching. Sc-fabp1, Sc-fabp3, Sc-fabp11a, and Sc-fabp11b were the mainly expressed subtypes in embryonic development stages. Under natural conditions, the expression of these 4 subtypes Sc-fabp1, Sc-fabp2a, Sc-fabp2b, and Sc-fabp6a exhibited significant circadian rhythm in intestine, and their peak expression levels were observed from ZT 8.83 h to ZT 13.54 h. Cadmium exposure resulted in the up-regulation of fabp gene expression and the loss of circadian rhythm in Chinese perch intestine. Our results provide reference for further investigation of the biological functions of fabp gene subtypes in fish.

The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-h head regeneration and 72-h budding time courses. In order to understand the regulatory elements controlling Hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of the organism body or regenerating tissue. We used histone modification ChIP-seq to identify 9,998 candidate proximal promoter and 3,018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.

The majority of Alzheimer's disease (AD) cases are late-onset and occur sporadically, however most mouse models of the disease harbor pathogenic mutations, rendering them better representations of familial autosomal-dominant forms of the disease. Here, we generated knock-in mice that express wildtype human Aβ under control of the mouse App locus. Remarkably, changing 3 amino acids in the mouse Aβ sequence to its wild-type human counterpart leads to age-dependent impairments in cognition and synaptic plasticity, brain volumetric changes, inflammatory alterations, the appearance of Periodic Acid-Schiff (PAS) granules and changes in gene expression. In addition, when exon 14 encoding the Aβ sequence was flanked by loxP sites we show that Cre-mediated excision of exon 14 ablates hAβ expression, rescues cognition and reduces the formation of PAS granules.

桃(Prunus persica)是我国重要的经济果树,对农业经济的发展具有重要作用.低温影响桃树生长发育,是桃早春生产的威胁之一.为探究亚热带地区桃树的低温适应及冷驯化机制,本研究对比分析了 4℃48 h低温处理后桃树低需冷量种质'MX14-1'叶片转录表达谱的变化,差异表达基因的GO功能注释和KEGG通路功能富集分析显示,低温胁迫下桃树叶片差异表达基因主要与胁迫应答相关,富集于次生代谢物合成途径,涉及类黄酮、芪类、二苯基庚酮、姜酚和苯丙烷合成、亚油酸代谢等途径.利用qRT-PCR技术对类黄酮代谢相关基因进行分析,结果显示4℃48 h处理后,苯丙氨酸解氨酶(phenylalanine ammonialyase,PAL)、肉桂酸4-羟酶(cinnamic acid 4-hydroxylase,C4H)、4-香豆酸辅酶 A 连接酶(4-coumarate:CoA ligase,4CL)、查尔酮合酶(chalcone synthase,CHS)、查尔酮异构酶(chalcone isomerase,CHI)、类黄酮-3-羟化酶(flavanone 3-hydroxylase,F3H)基因表达显著上调,和转录组测序结果一致.叶片代谢物含量测定表明,低温胁迫桃树叶片中类黄酮代谢相关的黄酮醇及衍生物含量显著增加.4℃48 h处理组和对照同时进行-2℃冷冻处理,结果表明经4℃低温处理桃树叶片中类黄酮物质总量和抗氧化能力显著提高,-2℃冷冻处理时损伤降低.本研究可为进一步探究桃树低温响应与抗寒的分子机制提供参考.

We set out to uncover transcriptome and chromatin landscape changes that occur in HER2 + breast cancer (BC) cells upon acquiring resistance to trastuzumab. RNA-seq analysis was applied to two independently-derived BC cell lines with acquired resistance to trastuzumab (SKBr3.HerR and BT-474HerR) and their parental drug-sensitive cell lines (SKBr3 and BT-474). Chromatin landscape analysis indicated that the most significant increase in accessibility in resistant cells occurs in PPP1R1B within a segment spanning introns 1b through intron 3. Footprint analysis of this segment revealed that FoxJ3 (within intron 2) and Pou5A1/Sox2 (within inton 3) transcription factor motifs are protected in resistant cells. Overall, 344 shared genes were upregulated in both resistant cell lines relative to their parental counterparts and 453 shared genes were downregulated in both resistant cell lines relative to their parental counterparts. In resistant cells, genes associated with autophagy and mitochondria organization are upregulated and genes associated with ribosome assembly and cell cycle are downregulated relative to parental cells. The five top upregulated genes in drug-resistant breast cancer cells are APOD, AZGP1, ETV5, ALPP, and PPP1R1B. This is the first report of increased chromatin accessibility within PPP1R1B associated with its t-Darpp transcript increase, and points to a possible mechanism for its activation in trastuzumab-resistant cells.

Available potassium in most agricultural soils is not sufficient for requirement of crop growth and development, and K deficiency has become a bottleneck of crop production worldwide. Development of low-K tolerant crop cultivars is an effective approach for relieving K deficiency. In the previous studies we identified some Tibetan annual wild barley accessions with higher low-K tolerance than cultivated barley. In this study, Illumina RNA-Sequencing was performed on the four-leaves seedlings of a Tibetan wild barley accession (XZ153, low-K tolerance) and a barley cultivar (ZD9, low-K sensitivity) to compare their transcriptome profiles in response to low-K stress. A total of 7263 differentially expressed genes (DEGs) were detected in the topmost 2 and 3 leaves (YL2, YL3) of the two genotypes under low-K stress, with XZ153 and YL2 having larger change than ZD9 and YL3, respectively, in terms of DEGs number and expression level. Meanwhile, 1395 low-K tolerance associated DEGs were mapped to metabolic process, translation, RNA methylation and responses to abscisic acid and other gene ontology (GO). The responses of XZ153 and ZD9 to low-K stress differed dramatically at the transcriptional level. The higher low-K tolerance in XZ153 is attributed to its more K uptake and accumulation in the topmost 2 leaf (YL2). The S-Adenosyl-L-methionine (SAM) cycle and methionine pathway involving in ethylene biosynthesis may account for the genotypic difference in low-K tolerance.

A third of the population sustains a bone fracture, and the pace of fracture healing slows with age. The slower pace of repair is responsible for the increased morbidity in older individuals who sustain a fracture. Bone healing progresses through overlapping phases, initiated by cells of the monocyte/macrophage lineage. The repair process ends with remodeling. This last phase is controlled by osteoclasts, which are bone-specific multinucleated cells also of the monocyte/macrophage lineage. The slower rate of healing in aging can be rejuvenated by macrophages from young animals, and secreted proteins from macrophage regulate undifferentiated mesenchymal cells to become bone-forming osteoblasts. Macrophages can derive from fetal erythromyeloid progenitors or from adult hematopoietic progenitors. Recent studies show that fetal erythromyeloid progenitors are responsible for the osteoclasts that form the space in bone for hematopoiesis and the fetal osteoclast precursors reside in the spleen postnatally, traveling through the blood to participate in fracture repair. Differences in secreted proteins between macrophages from old and young animals regulate the efficiency of osteoblast differentiation from undifferentiated mesenchymal precursor cells. Interestingly, during the remodeling phase osteoclasts can form from the fusion between monocyte/macrophage lineage cells from the fetal and postnatal precursor populations. Data from single cell RNA sequencing identifies specific markers for populations derived from the different precursor populations, a finding that can be used in future studies. Here, we review the diversity of macrophages and osteoclasts, and discuss recent finding about their developmental origin and functions, which provides novel insights into their roles in bone homeostasis and repair.

Separate sexes in dioecious plants display different morphology and physiological characteristics. The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype, which is genetically determined and epigenetically modified. In dioecious papaya (Carica papaya L.), global comparisons of epigenetic DNA methylation and gene expressions were still limited. We conducted bisulfite sequencing of early-stage flowers grown in three seasons (spring, summer and winter) and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in papaya. Methylation variances between female and male papaya were conserved among three different seasons. However, combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes, and the differentially expressed genes were most overrepresented in phytohormone signal transduction pathways. Further analyses showed diverse stress-responsive methylation alteration in male and female flowers. Male flower methylation was more responsive to stress whereas female flower methylation varied less under stress. Early flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific hypomethylation. These findings provide insights into the sex-specific DNA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.

The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Corticotropes exhibit an early intermediate state prior to full differentiation. Three cell types of the PIT-1 lineage (somatotropes, lactotropes and thyrotropes) segregate from a common progenitor coexpressing lineage-specific transcription factors of different sublineages. Gonadotropes experience two multistep developmental trajectories. Furthermore, we identify a fetal gonadotrope cell subtype expressing the primate-specific hormone chorionic gonadotropin. We also characterize the cellular heterogeneity of pituitary stem cells and identify a hybrid epithelial/mesenchymal state and an early-to-late state transition. Here, our results provide insights into the transcriptional landscape of human pituitary development, defining distinct cell substates and subtypes and illustrating transcription factor dynamics during cell fate commitment.