Biodegradable polyvinyl alcohol/nano-hydroxyapatite composite membrane enhanced by MXene nanosheets for guided bone regeneration.

MXene, as a new category of two-dimensional nanomaterials, exhibits a promising prospect in biomedical applications due to its ultrathin structure and morphology, as well as a range of remarkable properties such as biological, chemical, electronic, and optical properties. In this work, different concentrations of MXene (M) were added to polyvinyl alcohol (PVA, P)/nano-hydroxyapatite (n-HA, H) mixed solution, and series of PVA/n-HA/MXene (PHM) composite membranes were obtained by combining sol-gel and freeze-drying processes. Morphology, chemical composition, surface, and mechanical properties of the prepared PHM membranes were characterized by various techniques. Subsequently, the swelling and degradation performances of the composite membranes were tested by swelling and degradation tests. In addition, in vitro studies like cell adhesion, cytotoxicity, proliferation, osteogenic differentiation, and antibacterial properties of MC3T3-E1 were also evaluated. The results showed that the addition of MXene could apparently improve the composite membranes' physicochemical properties, bioactivity, and osteogenic differentiation. Specially, PHM membrane had the best comprehensive properties when the concentration of MXene was set as 2.0% w/v. In a word, the addition of MXene has a positive effect on improving the mechanical properties, osteogenic induction, and antibacterial properties of PH composite membranes, and the prepared PHM composite membranes possess potential applications for guided bone regeneration.

A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.

Green synthetic sodium alginate-glycerol-MXene nanocomposite membrane with excellent flexibility and mineralization ability for guided bone regeneration.

Developing a novel bioactive material as a barrier membrane for guided bone regeneration (GBR) surgery remains challenging. As a new member of two-dimensional (2D) material family, MXene is a promising candidate component for barrier membranes due to its high specific surface area and osteogenic differentiation ability. In this work, a green and simple SA/glycerol/MXene (SgM) composite membrane was prepared via solvent casting method by using sodium alginate (SA) and MXene (M) as raw materials while employing glycerol (g) as a plasticizer. The addition of glycerol significantly increased the elongation at the break of SA from 10%-20% to 240%-360%, while the introduction of MXene promoted the deposition of calcium and phosphorus to form hydroxyapatite. At the same time, the roughness of the SgM composite membrane is apparently improved, which is conducive to cell adhesion and proliferation. This work provides a basis for further research on SgM composite membrane as GBR membrane for the treatment of bone defects.

Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research.

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and ß) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis between C. neglecta and C. sativa, we successfully used the method of calculating Ks to distinguish the three subgenomes of C. sativa and determined that C. neglecta was closest to the first subgenome (SG1) of C. sativa. Further, transcriptomic analysis revealed the key genes associated with seed oil biosynthesis and its transcriptional regulation, including SAD, FAD2, FAD3, FAE1, ABI3, WRI1 and FUS3 displaying high expression levels in C. neglecta seeds. The high representability of C. neglecta as a model species for Camelina-based biotechnology research has been demonstrated for the first time. In particular, floral Agrobacterium tumefaciens infiltration-based transformation of C. neglecta, leading to overexpression of CvLPAT2, CpDGAT1 and CvFatB1 transgenes, was demonstrated for medium-chain fatty acid accumulation in C. neglecta seed oil. This study provides an important genomic resource and establishes C. neglecta as a new model for oilseed biotechnology research.

A concave four-arc honeycomb with enhanced stiffness and desirable negative Poisson's effect.

The conventional star-shaped honeycomb (CSSH) structure is inherently rich in mechanical properties. Based on the CSSH structure, the Poisson's ratio and Young's modulus can be improved by adding the tip re-entrant angle (ISSH). In this paper, a new concave four-arc honeycomb (CFAH) structure is proposed by designing the straight rod as a curved rod and retaining the tip re-entrant angle from the ISSH structure. The Young's modulus, specific stiffness and Poisson's ratio of CFAH structures are derived from Castigliano's second theorem and Moore's theorem. The theoretical results show good agreement with the numerical and experimental results. The results show that the normalized effective specific stiffness and normalized effective Young's modulus of the CFAH structure are further improved by about 12.95% and 16.86%, respectively, compared with the ISSH structure, and more significant auxiliary effects are obtained. CFAH structures show good promise in aerospace, construction and other applications due to their enhanced mechanical property. Meanwhile, the present work provides guidance for the study of concave four-arc honeycomb structures.

Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks.

Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.

Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice.

One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two-step pathway remains to be identified. Here, we show that quantitative trait locus GY3 may boost grain yield by more than 20% through manipulating a two-step pathway. Locus GY3 encodes a LOG protein that acts as a 5'-ribonucleotide phosphohydrolase by excessively consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP to produce iPR. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds, which demonstrates the great value of GY302428 in indica rice production.

Optimizing Processing Parameters and Surface Quality of TC18 via Ultrasonic-Assisted Milling (UAM): An Experimental Study.

This study conducted longitudinal ultrasonic-assisted milling (UAM) tests and optimized a combination of milling technological parameters to achieve high-quality machining of TC18 titanium alloy. The motion paths of the cutter under the coupled superposition states of longitudinal ultrasonic vibration and end milling were analyzed. Based on the orthogonal test, the cutting forces, cutting temperatures, residual stresses, and surface topographical patterns of TC18 specimens under different UAM conditions (cutting speeds, feeds per tooth, cutting depths, and ultrasonic vibration amplitudes) were examined. The differences between ordinary milling and UAM in terms of machining performance were compared. Using UAM, numerous characteristics (including variable cutting thickness in the cutting area, variable cutting front angles of the tool, and the lifting of the cuttings by the tool) were optimized, reducing the average cutting force in all directions, lowering the cutting temperature, increasing the surface residual compressive stress, and significantly improving the surface morphology. Finally, fish scale bionic microtextures with clear, uniform, and regular patterns were formed on the machined surface. High-frequency vibration can improve material removal convenience, thus reducing surface roughness. The introduction of longitudinal ultrasonic vibration to the end milling process can overcome the limitations of traditional processing. The optimal combination of UAM parameters for titanium alloy machining was determined through the end milling orthogonal test with compound ultrasonic vibration, which significantly improved the surface quality of TC18 workpieces. This study provides insightful reference data for subsequent machining process optimization.

Biodegradable and biocompatible alginate/gelatin/MXene composite membrane with efficient osteogenic activity and its application in guided bone regeneration.

Guided bone regeneration (GBR) utilizes a barrier membrane to maintain the osteogenic space and promote osseointegration of the implants. Developing a novel biomaterial to meet the mechanical and biological performance requirements of GBR membrane (GBRM) remains a huge challenge. Here, the sodium alginate (SA, S)/gelatin (G)/MXene (M) composite membrane (SGM) was prepared by combining sol-gel and freeze-drying processes. The incorporation of MXene improved the mechanical properties and hydrophilicity of the SA/G (SG) membrane, and also enhanced its cell proliferation and osteogenic differentiation. More importantly, when the concentration of MXene is 0.25%W/V, the SGM composite membrane exhibited the best tensile strength (40 MPa), high swelling rate (1012%), and appropriate degradation rate (40%). Meanwhile, the biological improvements were more significant. Therefore, the appropriate amount addition of MXene has a positive and obvious effect on the improvements of the mechanical properties, biocompatibility, and osteogenic induction of the SG composite membranes. This work provides a more extendable development idea for the application of SGM composite membrane as GBRM.

Clinical-radiomics nomogram for predicting esophagogastric variceal bleeding risk noninvasively in patients with cirrhosis.

BACKGROUND: Esophagogastric variceal bleeding (EGVB) is a serious complication of patients with decompensated cirrhosis and is associated with high mortality and morbidity. Early diagnosis and screening of cirrhotic patients at risk for EGVB is crucial. Currently, there is a lack of noninvasive predictive models widely available in clinical practice. AIM: To develop a nomogram based on clinical variables and radiomics to facilitate the noninvasive prediction of EGVB in cirrhotic patients. METHODS: A total of 211 cirrhotic patients hospitalized between September 2017 and December 2021 were included in this retrospective study. Patients were divided into training (n = 149) and validation (n = 62) groups at a 7:3 ratio. Participants underwent three-phase computed tomography (CT) scans before endoscopy, and radiomic features were extracted from portal venous phase CT images. The independent sample t-test and least absolute shrinkage and selection operator logistic regression were used to screen out the best features and establish a radiomics signature (RadScore). Univariate and multivariate analyses were performed to determine the independent predictors of EGVB in clinical settings. A noninvasive predictive nomogram for the risk of EGVB was built using independent clinical predictors and RadScore. Receiver operating characteristic, calibration, clinical decision, and clinical impact curves were applied to evaluate the model's performance. RESULTS: Albumin (P = 0.001), fibrinogen (P = 0.001), portal vein thrombosis (P = 0.002), aspartate aminotransferase (P = 0.001), and spleen thickness (P = 0.025) were selected as independent clinical predictors of EGVB. RadScore, constructed with five CT features of the liver region and three of the spleen regions, performed well in training (area under the receiver operating characteristic curve (AUC) = 0.817) as well as in validation (AUC = 0.741) cohorts. There was excellent predictive performance in both the training and validation cohorts for the clinical-radiomics model (AUC = 0.925 and 0.912, respectively). Compared with the existing noninvasive models such as ratio of aspartate aminotransferase to platelets and Fibrosis-4 scores, our combined model had better predictive accuracy with the Delong's test less than 0.05. The Nomogram had a good fit in the calibration curve (P > 0.05), and the clinical decision curve further supported its clinical utility. CONCLUSION: We designed and validated a clinical-radiomics nomogram able to noninvasively predict whether cirrhotic patients will develop EGVB, thus facilitating early diagnosis and treatment.

Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.

Non-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. However, cistrome dynamics in plants remain largely underexplored. Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. Although the function of GLKs is conserved, most of their binding sites are species-specific. Conserved binding sites are often found near photosynthetic genes dependent on GLK for expression, but sites near non-differentially expressed genes in the glk mutant are nevertheless under purifying selection. The binding sites' regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. Our study show that genome cis-variation caused wide-spread TF binding divergence, and most of the TF binding sites are genetically redundant. This poses a major challenge for interpreting the effect of individual sites and highlights the importance of quantitatively measuring TF occupancy.

Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.

BACKGROUND: Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an important trait of B. napus. RESULTS: We perform a comprehensive analysis of the transcriptional variability in the seeds of B. napus at two developmental stages, 20 and 40 days after flowering (DAF). We detect 53,759 and 53,550 independent expression quantitative trait loci (eQTLs) for 79,605 and 76,713 expressed genes at 20 and 40 DAF, respectively. Among them, the local eQTLs are mapped to the adjacent genes more frequently. The adjacent gene pairs are regulated by local eQTLs with the same open chromatin state and show a stronger mode of expression piggybacking. Inter-subgenomic analysis indicates that there is a feedback regulation for the homoeologous gene pairs to maintain partial expression dosage. We also identify 141 eQTL hotspots and find that hotspot87-88 co-localizes with a QTL for the seed oil content. To further resolve the regulatory network of this eQTL hotspot, we construct the XGBoost model using 856 RNA-seq datasets and the Basenji model using 59 ATAC-seq datasets. Using these two models, we predict the mechanisms affecting the seed oil content regulated by hotspot87-88 and experimentally validate that the transcription factors, NAC13 and SCL31, positively regulate the seed oil content. CONCLUSIONS: We comprehensively characterize the gene regulatory features in the seeds of B. napus and reveal the gene networks regulating the seed oil content of B. napus.

Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus.

BACKGROUND: Brassica napus is an important vegetable oil source worldwide. Seed coat content is a complex quantitative trait that negatively correlates with the seed oil content in B. napus. RESULTS: Here we provide insights into the genetic basis of natural variation of seed coat content by transcriptome-wide association studies (TWAS) and genome-wide association studies (GWAS) using 382 B. napus accessions. By population transcriptomic analysis, we identify more than 700 genes and four gene modules that are significantly associated with seed coat content. We also characterize three reliable quantitative trait loci (QTLs) controlling seed coat content by GWAS. Combining TWAS and correlation networks of seed coat content-related gene modules, we find that BnaC07.CCR-LIKE (CCRL) and BnaTT8s play key roles in the determination of the trait by modulating lignin biosynthesis. By expression GWAS analysis, we identify a regulatory hotspot on chromosome A09, which is involved in controlling seed coat content through BnaC07.CCRL and BnaTT8s. We then predict the downstream genes regulated by BnaTT8s using multi-omics datasets. We further experimentally validate that BnaCCRL and BnaTT8 positively regulate seed coat content and lignin content. BnaCCRL represents a novel identified gene involved in seed coat development. Furthermore, we also predict the key genes regulating carbon allocation between phenylpropane compounds and oil during seed development in B. napus. CONCLUSIONS: This study helps us to better understand the complex machinery of seed coat development and provides a genetic resource for genetic improvement of seed coat content in B. napus breeding.

Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice.

In rice, the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance, as shown by their extremely high yield. However, the mechanisms underlying the success of these rice hybrids are unclear. In this study, three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids. Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies, respectively, although introgression of 20% of the Xian ancestry and 14% of the Geng ancestry are observed. Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments, which harbors hybrid sterility genes such as Sd, Sc, f5, and qS12 and favorable alleles of key yield-related genes, including NAL1, Ghd7, and Ghd8. None of the parents carries the S5+ killer of the S5 killer-protector system. Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids. Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values. Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis. These factors result in an extremely high yield of the hybrids. These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.

The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains.

The widely used rice variety Lijiangxintuanheigu (LTH) shows a universal susceptibility to thousands of Magnaporthe oryzae isolates, the causal agent of devastating rice blast, making LTH an ideal line in resistance (R) gene cloning. However, the underlying genetic mechanism of the universal susceptibility has not been fully revealed because of the lack of a high-quality genome. Here, we took a genomic approach together with experimental assays to investigate LTH's universal susceptibility to rice blast. Using Nanopore long reads, we assembled a chromosome-level genome. Millions of genomic variants were detected by comparing LTH with 10 other rice varieties, of which large-effect variants could affect plant immunity. Gene family analyses show that the number of R genes and leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding genes decrease significantly in LTH. Rice blast resistance genes called Pi genes are either absent or disrupted by genomic variations. Additionally, residual R genes of LTH are likely under weak pathogen selection pressure, and other plant defense-related genes are weakly induced by rice blast. In contrast, the pattern-triggered immunity (PTI) of LTH is normal, as demonstrated by experimental assays. Therefore, we conclude that weak effector-trigger immunity (ETI)-mediated primarily by Pi genes but not PTI results in the universal susceptibility of LTH to rice blast. The attenuated ETI of LTH may be also associated with reduced numbers of R genes and LRR-RLKs, and minimally functional residual defense-related genes. Finally, we demonstrate the use of the LTH genome by rapid cloning of the Pi gene Piak from a resistant variety.

Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants.

It is challenging to identify the smallest microexons (≤15-nt) due to their small size. Consequently, these microexons are often misannotated or missed entirely during genome annotation. Here, we develop a pipeline to accurately identify 2,398 small microexons in 10 diverse plant species using 990 RNA-seq datasets, and most of them have not been annotated in the reference genomes. Analysis reveals that microexons tend to have increased detained flanking introns that require post-transcriptional splicing after polyadenylation. Examination of 45 conserved microexon clusters demonstrates that microexons and associated gene structures can be traced back to the origin of land plants. Based on these clusters, we develop an algorithm to genome-wide model coding microexons in 132 plants and find that microexons provide a strong phylogenetic signal for plant organismal relationships. Microexon modeling reveals diverse evolutionary trajectories, involving microexon gain and loss and alternative splicing. Our work provides a comprehensive view of microexons in plants.

CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer.

MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10 554 samples from 33 TCGA projects and 28 633 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available at http://bioinfo.jialab-ucr.org/CancerMIRNome.

The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research.

Rapeseed is a globally cultivated commercial crop, primarily grown for its oil. High-density single nucleotide polymorphism (SNP) arrays are widely used as a standard genotyping tool for rapeseed research, including for gene mapping, genome-wide association studies, germplasm resource analysis, and cluster analysis. Although considerable rapeseed genome sequencing data have been released, DNA arrays are still an attractive choice for providing additional genetic data in an era of high-throughput whole-genome sequencing. Here, we integrated re-sequencing DNA array data (32,216, 304 SNPs) from 505 inbred rapeseed lines, allowing us to develop a sensitive and efficient genotyping DNA array, Bnapus50K, with a more consistent genetic and physical distribution of probes. A total of 42,090 high-quality probes were filtered and synthesized, with an average distance between adjacent SNPs of 8 kb. To improve the practical application potential of this array in rapeseed breeding, we also added 1,618 functional probes related to important agronomic traits such as oil content, disease resistance, male sterility, and flowering time. The additional probes also included those specifically for detecting genetically modified material. These probes show a good detection efficiency and are therefore useful for gene mapping, along with crop variety improvement and identification. The novel Bnapus50K DNA array developed in this study could prove to be a quick and versatile genotyping tool for B. napus genomic breeding and research.

Oxygen Plasma Technology-Assisted Preparation of Three-Dimensional Reduced Graphene Oxide/Polypyrrole/Strontium Composite Scaffold for Repair of Bone Defects Caused by Osteoporosis.

Repairs of bone defects caused by osteoporosis have always relied on bone tissue engineering. However, the preparation of composite tissue engineering scaffolds with a three-dimensional (3D) macroporous structure poses huge challenges in achieving osteoconduction and osteoinduction for repairing bone defects caused by osteoporosis. In the current study, a three-dimensional macroporous (150-300 µm) reduced graphene oxide/polypyrrole composite scaffold modified by strontium (Sr) (3D rGO/PPY/Sr) was successfully prepared using the oxygen plasma technology-assisted method, which is simple, safe, and inexpensive. The findings of the MTT assay and AO/EB fluorescence double staining showed that 3D rGO/PPY/Sr has a good biocompatibility and effectively promoted MC3T3-E1 cell proliferation. Furthermore, the ALP assay and alizarin red staining showed that 3D rGO/PPY/Sr increased the expression levels of ALP activity and the formation of calcified nodules. The desirable biocompatibility, osteoconduction, and osteoinduction abilities, assure that the 3D macroporous rGO/PPY/Sr composite scaffold offers promising potential for use in the repair of bone defects caused by osteoporosis in bone tissue engineering.