Search

Abstract The tumor microenvironment (TME) comprises immune-infiltrating cells that are closely linked to tumor development. By screening and analyzing genes associated with tumor-infiltrating M0 cells, we developed a risk model to provide therapeutic and prognostic guidance in clear cell renal cell carcinoma (ccRCC). First, the infiltration abundance of each immune cell type and its correlation with patient prognosis were analyzed. After assessing the potential link between the depth of immune cell infiltration and prognosis, we screened the infiltrating M0 cells to establish a risk model centered on three key genes (TMEN174, LRRC19, and SAA1). The correlation analysis indicated a positive correlation between the risk score and various stages of the tumor immune cycle, including B-cell recruitment. Furthermore, the risk score was positively correlated with CD8 expression and several popular immune checkpoints (ICs) (TIGIT, CTLA4, CD274, LAG3, and PDCD1). Additionally, the high-risk group (HRG) had higher scores for tumor immune dysfunction and exclusion (TIDE) and exclusion than the low-risk group (LRG). Importantly, the risk score was negatively correlated with the immunotherapy-related pathway enrichment scores, and the LRG showed a greater therapeutic benefit than the HRG. Differences in sensitivity to targeted drugs between the HRG and LRG were analyzed. For commonly used targeted drugs in RCC, including axitinib, pazopanib, temsirolimus, and sunitinib, LRG had lower IC50 values, indicating increased sensitivity. Finally, immunohistochemistry results of 66 paraffin-embedded specimens indicated that SAA1 was strongly expressed in the tumor samples and was associated with tumor metastasis, stage, and grade. SAA1 was found to have a significant pro-tumorigenic effect by experimental validation. In summary, these data confirmed that tumor-infiltrating M0 cells play a key role in the prognosis and treatment of patients with ccRCC. This discovery offers new insights and directions for the prognostic prediction and treatment of ccRCC.

Abstract Due to trauma and disease, bone defects endanger the healthy life of human beings. At present, the gold standard for bone defect repair is still autologous bone transplantation and allogeneic bone transplantation. However, its insufficient source, potential disease transmission and immune rejection limit its clinical application. Therefore, the development of bone repair materials plays an important role in promoting bone repair. As the interface between material and tissue, the surface of the material plays an important role in the reaction after implantation, which determines the effectiveness of defect repair treatment. With the development of surface engineering and technology, bone repair materials have developed from biological inertia to biological activity by endowing various biological functions by controlling the composition, topological morphology and structure of the material surface etc. The inspired biofunctionalisation of material surface includes the capacities of inducing osteogenesis, promoting angiogenesis, antibacterial, immune regulation etc., as well as integration of postoperative repair and treatment. The authors review the biofunctionalisation of biomaterial surface and the inspired biological effects for bone repair, mainly including physical and chemical properties of material surface to regulate osteogenesis, and functional strategy of bone repair material surface.

Disulfidptosis, a newly discovered mode of cell death caused by excessive accumulation of intracellular disulfide compounds, is closely associated with tumor development. This study focused on the relationship between disulfidptosis and clear cell renal cell carcinoma (ccRCC). Firstly, the characterizations of disulfidptosis-related genes (DRGs) in ccRCC were showed, which included number variation (CNV), single nucleotide variation (SNV), DNA methylation, mRNA expression and gene mutation. Then, the ccRCC samples were classified into three clusters through unsupervised clustering based on DRGs. Survival and pathway enrichment differences were evaluated among the three clusters. Subsequently, the differentially expressed genes (DEGs) among the three clusters were screened by univariate Cox, LASSO, and multivariate Cox analysis, and five key DEGs were obtained. Based on the five key DEGs, the ccRCC samples were reclassified into two geneclusters and the survival differences and immune cell infiltration between two geneclusters was investigated. In next step, ccRCC samples were divided into two groups according to PCA scores of five key DEGs, namely high PCA score group (HPSG) and low PCA score group (LPSG). On this basis, differences in survival prognosis, immune cell infiltration and correlation with immune checkpoint, as well as differences in sensitivity to targeted drugs were compared between HPSG and LPSG. The expression levels of four immune checkpoints were higher in HPSG than in LPSG, whereas the LPSG was more sensitive to targeted drug therapy than the HPSG. Finally, validation experiments on HDAC4 indicated that HDAC4 could increase the proliferation and colony formation ability of ccRCC cells.

Abstract Periodontitis is a chronic inflammatory disease caused by the local microbiome and the host immune response, resulting in periodontal structure damage and even tooth loss. Scaling and root planning combined with antibiotics are the conventional means of nonsurgical treatment of periodontitis, but they are insufficient to fully heal periodontitis due to intractable bacterial attachment and drug resistance. Novel and effective therapeutic options in clinical drug therapy remain scarce. Nanotherapeutics achieve stable cell targeting, oral retention and smart release by great flexibility in changing the chemical composition or physical characteristics of nanoparticles. Meanwhile, the protectiveness and high surface area to volume ratio of nanoparticles enable high drug loading, ensuring a remarkable therapeutic efficacy. Currently, the combination of advanced nanoparticles and novel therapeutic strategies is the most active research area in periodontitis treatment. In this review, we first introduce the pathogenesis of periodontitis, and then summarize the state-of-the-art nanotherapeutic strategies based on the triple concerto of antibacterial activity, immunomodulation and periodontium regeneration, particularly focusing on the therapeutic mechanism and ingenious design of nanomedicines. Finally, the challenges and prospects of nano therapy for periodontitis are discussed from the perspective of current treatment problems and future development trends. Graphical Abstract

For bottom-up bone tissue engineering, microcarriers play crucial roles in serving as scaffolds that provide structural support and environmental cues for cell growth. Studies have demonstrated that the physicochemical properties of microcarriers, such as surface structure and chemistry, have significant effects on cell phenotype. However, current research on microcarriers has primarily focused on hydrogels or polymers, neglecting the exploration of hard materials that mimic the bone tissue environment. In this study, a new facile method to fabricate magnetic calcium phosphate (CaP)-based microcarriers were presented. By this method, magnetic calcium phosphate was obtained without changing the surface nanostructure of CaP microspheres. These magnetic CaP microspheres were utilized as cell-adhesive microcarriers, allowing for cell-guided assembly into spherical microtissue under a relatively low number of cells. However, when using CaP microspheres as microcarriers, only loose aggregates were observed. To enhance the biofunctionality of the magnetic CaP microcarriers, bisphosphonate-modified growth differentiation factor-5 (PGDF-5) were synthesized and selectively deposited onto the magnetic CaP surfaces. Coculture with preosteoblastic cells demonstrated that PGDF-5 modified microcarriers effectively improved cell osteogenic differentiation and angiogenesis, thereby facilitating the formation of highly stable cell spheroids. Collectively, all findings suggest that PGDF-5 modified magnetic CaP microcarriers hold great potential as tools for fabricating bottom-up tissue engineered bone-mimicking tissue.

Abstract Background Most displaced femoral neck fractures can achieve satisfactory anatomical reduction by closed reduction, but there are still some that cannot reset satisfactorily after closed reduction, and open reduction are required. Such fractures that cannot be repositioned successfully by closed reduction are called irreducible displaced femoral neck fractures in this study. The objective of our study was to evaluate the efficacy of direct anterior incision with the Femoral Neck System in the treatment of irreducible displaced femoral fractures. Methods A total of 16 young and middle-aged patients with irreducible displaced femoral neck fractures involving Garden type III and IV were treated using Femoral Neck System fixation by open reduction through Direct Anterior Approach between January 2020 to September 2021. Functional outcomes and postoperative complications were assessed during follow-up. Clinical outcomes were evaluated by the Hip Harris score. The postoperative reduction was evaluated by the Garden Index. Observe postoperative complications. Results All patients were followed up with a mean follow-up time of 21.1(12–30) months, and according to radiological results, all patients achieved fracture healing, with a mean healing time of 4.25 months. All 16 patients received grade Garden I and II reductions, and there was no significant difference in the anteroposterior Garden reduction index between the first day after surgery (166.13 ± 5.61) and the 12th month after surgery(164.94 ± 4.49) (P>0.05) and no significant difference in lateral Garden index between the first day after surgery(171.06 ± 4.46) and the 12th month after surgery(169.38 ± 3.98) (P

Abstract Due to the tolerance of mismatches between gRNA and targeting sequence, base editors frequently induce unwanted Cas9-dependent off-target mutations. Here, to develop models to predict such off-targets, we design gRNA-off- target pairs for adenine base editors (ABEs) and cytosine base editors (CBEs) and stably integrate them into the human cells. After five days of editing, we obtain valid efficiency datasets of 54,663 and 55,727 off-targets for ABEs and CBEs, respectively. We use the datasets to train deep learning models, resulting in ABEdeepoff and CBEdeepoff, which can predict off-target sites. We use these tools to predict off-targets for a panel of endogenous loci and achieve Spearman correlation values varying from 0.710 to 0.859. Finally, we develop an integrated tool that is freely accessible via an online web server http://www.deephf.com/#/bedeep/bedeepoff . These tools could facilitate minimizing the off-target effects of base editing.

Abstract Skin is the largest organ of the human body. It plays a vital role as the body’s first barrier: stopping chemical, radiological damage and microbial invasion. The importance of skin to the human body can never be overstated. Delayed wound healing after a skin injury has become a huge challenge in healthcare. In some situations, this can have very serious and even life-threatening effects on people’s health. Various wound dressings have been developed to promote quicker wound healing, including hydrogels, gelatin sponges, films, and bandages, all work to prevent the invasion of microbial pathogens. Some of them are also packed with bioactive agents, such as antibiotics, nanoparticles, and growth factors, that help to improve the performance of the dressing it is added to. Recently, bioactive nanoparticles as the bioactive agent have become widely used in wound dressings. Among these, functional inorganic nanoparticles are favored due to their ability to effectively improve the tissue-repairing properties of biomaterials. MXene nanoparticles have attracted the interest of scholars due to their unique properties of electrical conductivity, hydrophilicity, antibacterial properties, and biocompatibility. The potential for its application is very promising as an effective functional component of wound dressings. In this paper, we will review MXene nanoparticles in skin injury repair, particularly its synthesis method, functional properties, biocompatibility, and application.

Introduction: Wound healing is a delicate and complex process influenced by many factors. The treatment of skin wounds commonly involves the use of wound dressings, which remain a routine approach. An ideal dressing can provide protection and a suitable environment for wound surfaces by maintaining moisture and exhibiting good biocompatibility, mechanical strength, and antibacterial properties to promote healing and prevent infection.Methods: We encapsulated tick-derived antibacterial polypeptides (Os) as a model drug within a methylacrylyl gelatin (GelMA) hydrogel containing MXene nanoparticles. The prepared composite hydrogels were evaluated for their wound dressing potential by analyzing surface morphology, mechanical properties, swelling behavior, degradation properties, antibacterial activity, and cytocompatibility.Results: The results demonstrated excellent mechanical strength, swelling performance, degradation behavior, and antibacterial activity of the prepared composite hydrogels, effectively promoting cell growth, adhesion, and expression of antibacterial peptide activity. A full-thickness rat wound model then observed the wound healing process and surface interactions between the composite hydrogels and wounds. The composite hydrogel significantly accelerated wound closure, reduced inflammation, and sped epithelial formation and maturation.Discussion: Incorporating antibacterial peptides into GelMA provides a feasible strategy for developing excellent antibacterial wound dressings capable of tissue repair. In conclusion, this study presents a GelMA-based approach for designing antibacterial dressings with strong tissue regenerative ability.

Summary: Bacterial memory refers to the phenomenon in which past experiences influence current behaviors in response to changing environments. It serves as a crucial process that enables adaptation and evolution. We first summarize the state-of-art approaches regarding history-dependent behaviors that impact growth dynamics and underlying mechanisms. Then, the phenotypic and genotypic origins of memory and how encoded memory modulates drug tolerance/resistance are reviewed. We also provide a summary of possible memory effects induced by antimicrobial nanoparticles. The regulatory networks and genetic underpinnings responsible for memory building partially overlap with nanoparticle and drug exposures, which may raise concerns about the impact of nanotechnology on adaptation. Finally, we provide a perspective on the use of nanotechnology to harness bacterial memory based on its unique mode of actions on information processing and transmission in bacteria. Exploring bacterial memory mechanisms provides valuable insights into acclimation, evolution, and the potential applications of nanotechnology in harnessing memory.

Abstract Background The surgical treatment of complex acetabular fractures is one of the most challenging procedures for orthopedic surgeons. The Pararectus approach, as a reasonable alternative to the existing surgical procedures, was performed for the treatment of acetabular fractures involving the anterior column. This study aimed to evaluate outcome using the Pararectus approach for acetabular fractures involving anterior columns. Methods Thirty-seven with displaced acetabular fractures involving anterior columns were treated between July 2016 and October 2019 using the Pararectus approach. The functional outcomes (using the Merle d Aubigné and Postel scoring system, WOMAC and modified Harris scoring), the quality of surgical reduction (using the Matta criteria), and postoperative complications were assessed during approximately 26 months follow-up period. Results Thirty-seven patients (mean age 53 years, range: 30–71; 28 male) underwent surgery. Mean intraoperative blood loss was 840 ml (rang: 400–2000 ml) and mean operating time was 210 min (rang: 140–500 min). The modified Merle d Aubigné score was excellent and good in 27 cases (73%), fair in 6 cases (16%), and poor in 3 cases (11%). The mean score was 88.5 (range:77–96) for the modified Harris Hip scores, and 22 (range:7–35) for the WOMAC scores after operation. Postoperative functional outcomes were significantly improved compared with preoperative outcomes (P

Ischemic stroke (IS) is one of the major global causes of death and disability. Because blood clots block the neural arteries provoking ischemia and hypoxia in the brain tissue, IS results in irreversible neurological damage. Available IS treatments are currently limited. Curcumin has gained attention for many beneficial effects after IS, including neuroprotective and anti-inflammatory; however, its precise mechanism of action should be further explored. With network pharmacology, molecular docking, and molecular dynamics (MD), this study aimed to comprehensively and systematically investigate the potential targets and molecular mechanisms of curcumin on IS. We screened 1096 IS-related genes, 234 potential targets of curcumin, and 97 intersection targets. KEGG and GO enrichment analyses were performed on these intersecting targets. The findings showed that the treatment of IS using curcumin is via influencing 177 potential signaling pathways (AGE-RAGE signaling pathway, p53 signaling pathway, necroptosis, etc.) and numerous biological processes (the regulation of neuronal death, inflammatory response, etc.), and the AGE-RAGE signaling pathway had the largest degree of enrichment, indicating that it may be the core pathway. We also constructed a protein-protein interaction network and a component-target-pathway network using network pharmacology. From these, five key targets were screened: NFKB1, TP53, AKT1, STAT3, and TNF. To predict the binding conformation and intermolecular affinities of the key targets and compounds, molecular docking was used, whose results indicated that curcumin exhibited strong binding activity to the key targets. Moreover, 100 ns MD simulations further confirmed the docking findings and showed that the curcumin-protein complex could be in a stable state. In conclusion, curcumin affects multiple targets and pathways to inhibit various important pathogenic mechanisms of IS, including oxidative stress, neuronal death, and inflammatory responses. This study offers fresh perspectives on the transformation of curcumin to clinical settings and the development of IS therapeutic agents.

Modulation of exposed crystal facets enhances transferrin binding to chalcogenide nanocrystals and their subsequent delivery into cancer cells. Facet-dependent protein binding occurs through inner-sphere thiol complexation and is affected by the structure of the first solvation shell.

Abstract Clustered regularly interspaced short palindromic repeat (CRISPR)/SaCas9 is the most popular tool for in vivo genome editing due to its high efficiency and small genome. The authors previously developed four SaCas9 orthologs as genome‐editing tools. Here, to expand the targeting scope, they investigate the diversity of protospacer adjacent motifs (PAMs) by screening a list of 16 SaCas9 orthologs, twelve of which display editing activity in mammalian cells. They recognize five types of PAMs: NNGRRT, NNGRRR, NNGRC, NNGA, and NNGR. Importantly, SchCas9 recognizes the simple NNGR PAM, representing the most relaxed PAM preference of compact Cas9s to date. It is further demonstrated that SchCas9 enables efficient genome editing in multiple human cell lines. Altogether, these compact Cas9 tools offer a new option for both basic research and clinical applications.

Along with the growth of graph neural networks (GNNs), many researchers have adopted metapath-based GNNs to handle complex heterogeneous graph embedding. The conventional definition of a metapath only distinguishes whether there is a connection between nodes in the network schema, where the type of edge is ignored. This leads to inaccurate node representation and subsequently results in suboptimal prediction performance. In heterogeneous graphs, a node can be connected by multiple types of edges. In fact, each type of edge represents one kind of scene. The intuition is that if the embedding of nodes is trained under different scenes, the complete representation of nodes can be obtained by organically combining them. In this paper, we propose a novel definition of a metapath whereby the edge type, i.e., the relation between nodes, is integrated into it. A heterogeneous graph can be considered as the compound of multiple relation subgraphs from the view of a novel metapath. In different subgraphs, the embeddings of a node are separately trained by encoding and aggregating the neighbors of the intrapaths, which are the instance levels of a novel metapath. Then, the final embedding of the node is obtained by the use of the attention mechanism which aggregates nodes from the interpaths, which is the semantic level of the novel metapaths. Link prediction is a downstream task by which to evaluate the effectiveness of the learned embeddings. We conduct extensive experiments on three real-world heterogeneous graph datasets for link prediction. The empirical results show that the proposed model outperforms the state-of-the-art baselines; in particular, when comparing it to the best baseline, the F1 metric is increased by 10.35% over an Alibaba dataset.

The Chinese government is attempting to readjust the relationship of farmland rights by farmland rights system reform to optimize the allocation of farmland by market means. Therefore, this study is aimed at exploring the effectiveness of the farmland rights system reform from decentralization to centralization and its impacts on agricultural modernization. In this study, the shift theory of land rights is introduced to analyze the approach of the reform promoting agricultural modernization, and the practice of Yuyang District as evidence illustrates that the reform is a further extension of the land marketization reform, which clears the obstacles of market allocation of farmlands and promotes agricultural modernization by achieving three objectives of agricultural production. The results of this study show the reform is beneficial to a high level of yield, efficient production, and environment friendly in agricultural production, so the reform indirectly promotes agricultural modernization. Meanwhile, Yuyang District’s experiences show that the farmland issue is a complex one, which should be considered from the perspectives of public benefits and private benefits, and appropriate farmland rights system reform is a policy accelerator for facilitating agricultural modernization. Generally, this study not only innovatively links the farmland rights system reform with the three objectives of agricultural production to analysis impact mechanism of the reform on agricultural modernization, but it also confirms the effectiveness of the reform design of the central government and provides some advanced experiences for other regions.

CRISPR/Cas9 nucleases hold great potential for gene therapy, but they frequently induce unwanted off-target cleavage. We previously developed a GFP activation assay for detection of DNA cleavage in cells. Here, we demonstrate two novel applications of this assay. First, we use this assay to confirm off-target cleavage that cannot be detected by targeted deep sequencing in cells before. Second, we use this approach to detect multiple alternative PAMs recognized by SpCas9. These noncanonical PAMs are associated with low cleavage activity, but targets associated with these PAMs must be considered as potential off-target sites. Taken together, the GFP activation assay is a powerful platform for DNA cleavage detection in cells.

Abstract Restriction site‐associated DNA sequencing (RAD‐seq) is one of the most effective high‐throughput sequencing technologies for SNP development and utilization and has been applied to studying the origin and evolution of various species. The domestic Bactrian camels play an important role in economic trade and cultural construction. They are precious species resources and indispensable animals in China's agricultural production. Recently, the rapid development of modern transportation and agriculture, and the deterioration of the environment have led to a sharp decline in the number of camels. Although there have been some reports on the evolution history of the domestic Bactrian camel in China, the origin, evolutionary relationship, and genetic diversity of the camels are unclear due to the limitations of sample size and sequencing technology. Therefore, 47 samples of seven domestic Bactrian camel species from four regions (Inner Mongolia, Gansu, Qinghai, and Xinjiang) were prepared for RAD‐seq analysis to study the evolutionary relationship and genetic diversity. In addition, seven domestic Bactrian camel species are located in different ecological zones, forming different characteristics and having potential development value. A total of 6,487,849 SNPs were genotyped. On the one hand, the filtered SNP information was used to conduct polymorphism mapping construction, LD attenuation analysis, and nucleotide diversity analysis. The results showed that the number of SNPs in Dongjiang camel was the highest, the LD coefficient decayed the fastest, and the nucleotide diversity was the highest. It indicates that Dongjiang camel has the highest genetic diversity. On the other hand, the filtered SNPs information was used to construct the phylogenetic tree, and FST analysis, inbreeding coefficient analysis, principal component analysis, and population structure analysis were carried out. The results showed that Nanjiang camel and Beijiang camels grouped together, and the other five Bactrian camel populations gathered into another branch. It may be because the mountains in the northern part of Xinjiang and the desert in the middle isolate the two groups from the other five groups.

Application of highly specific Cas9 variants can be restricted by the design of the guide RNA. Here the authors present DeepHF, a gRNA activity prediction tool built from genome-scale screens of 50,000 guides covering 20,000 genes.

Abstract Background For coronal shear fractures of humeral capitellum, the lateral approach is the most commonly used surgical approach. However, exposure range of the anterior aspect of the distal humerus is inadequate. The anterolateral approach has also been adopted to overcome this disadvantage. However, this approach seems anatomically complex due to the risk of iatrogenic injury to the radial nerve. So far, the optimal approach for the treatment of capitellar shear fractures remains inconclusive. The purpose of this study is to prospectively review and compare the early clinical and radiographic outcomes of treated with open reduction and Herbert screw internal fixation through the lateral approach or the anterolateral approach. Methods Twenty-six patients with isolated capitellar shear fractures were enrolled from January 2013 to December 2017, and randomly assigned to lateral approach group or anterolateral approach group. All the fractures were treated with open reduction and Herbert screw internal fixation through lateral approach or anterolateral approach. Operation time, wound healing complication, elbow joint function, and radiographic evidence were evaluated and compared between two groups. Results The operation via the anterolateral approach took significantly shorter time than via lateral approach (p 0.05). There is no significant difference with respect to MEPI score of elbow joint between two groups (p > 0.05). Conclusion Based on our findings, both lateral approach and anterolateral approach with Herbert screw internal fixation are suitable for coronal shear fractures of capitellum with satisfactory early outcomes. Compared with the lateral approach, the anterolateral approach made the surgical procedure easier and time saving in current series. When the medial aspect of the trochlea is involved for capitellar coronal fractures, the anterolateral lateral approach should be preferred.

Metallic ions have been widely investigated and incorporated into bone substitutes for bone regeneration owing to their superior capacity to induce angiogenesis and osteogenesis. Exosomes are key paracrine mediators that play a crucial role in cell-to-cell communication. However, the role of exosomes in metallic ion-induced bone formation and their underlying mechanisms remain unclear. Thus, this review systematically analyzes the effects of metallic ions and metallic ion-incorporated biomaterials on exosome secretion from mesenchymal stem cells (MSCs) and macrophages, as well as the effects of secreted exosomes on inflammation, angiogenesis, and osteogenesis. In addition, possible signaling pathways involved in metallic ion-mediated exosomes, followed by bone regeneration, are discussed. Despite limited investigation, metallic ions have been confirmed to regulate exosome production and function, affecting immune response, angiogenesis, and osteogenesis. Although the underlying mechanism is not yet clear, these insights enrich our understanding of the mechanisms of the metallic ion-induced microenvironment for bone regeneration, benefiting the design of metallic ion-incorporated implants.

Implant-related infection (IRI) is a major problem in orthopedics. Copper (Cu) is an essential trace element with strong bactericidal activity and, thus, presents potential for reducing IRI. The present study explored a straightforward strategy for releasing Cu2+ from titanium (Ti) implants, and we conducted a preliminary study to assess the feasibility of this approach in clinical translation. Polylactic acid (PLA) coatings containing different concentrations of copper ions were prepared on Ti discs. The antibacterial activity and biocompatibility of the copper ion-incorporated Ti implants were evaluated using Staphylococcus aureus (S. aureus), bone marrow mesenchymal stem cells (BMSCs) and animal models. In vitro, the coatings produced burst release of Cu2+ in 12 h, and inhibited S. aureus growth in a dose-dependent manner. The coatings prepared from PLA solutions containing 0.5 or 1.0 mg/mL reduced the viability and osteogenic differentiation of BMSCs, but these effects were negated after the coatings were immersed in culture medium for 6 h. Four weeks after implantation, the Cu-free K-wires challenged with S. aureus had persistent infection and inferior fracture healing to the other three groups, while Cu-coated wires had no evidence of infection. Furthermore, the Cu-coated wires placed in rabbits without S. aureus challenge showed superior fracture healing to the other three groups. These results suggest that PLA coatings containing Cu2+ may be an effective design for reducing IRI without adversely affecting adjacent bone healing.

The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has changed constantly during worldwide community transmission of this virus. However, the reasons for the changes in mutation patterns are still unclear. Accordingly, in this study, we present a comprehensive analysis of over 300 million peptides derived from 13,432 SARS-CoV-2 strains harboring 4,420 amino acid mutations to analyze the potential selective pressure of the host immune system and reveal the driver of mutations in circulating SARS-CoV-2 isolates. The results showed that the nonstructural protein ORF1ab and the structural protein Spike were most susceptible to mutations. Furthermore, mutations in cross-reactive T-cell epitopes between SARS-CoV-2 and seasonal human coronavirus may help SARS-CoV-2 to escape cellular immunity under long-term and large-scale community transmission. Additionally, through homology modeling and protein docking, mutations in Spike protein may enhance the ability of SARS-CoV-2 to invade host cells and escape antibody-mediated B-cell immunity. Our research provided insights into the potential mutation patterns of SARS-CoV-2 under natural selection, improved our understanding of the evolution of the virus, and established important guidance for potential vaccine design.

The domestic Bactrian camel is a valuable livestock resource in arid desert areas. Therefore, it is essential to understand the roles of important genes responsible for its characteristics. We used restriction site-associated DNA sequencing (RAD-seq) to detect single nucleotide polymorphism (SNP) markers in seven domestic Bactrian camel populations. In total, 482,786 SNPs were genotyped. The pool of all remaining others were selected as the reference population, and the Nanjiang, Sunite, Alashan, Dongjiang, Beijiang, Qinghai, and Hexi camels were the target populations for selection signature analysis. We obtained 603, 494, 622, 624, 444, 588, and 762 selected genes, respectively, from members of the seven target populations. Gene Ontology classifications and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and the functions of these genes were further studied using Genecards to identify genes potentially related to the unique characteristics of the camel population, such as heat resistance and stress resistance. Across all populations, cellular process, single-organism process, and metabolic process were the most abundant biological process subcategories, whereas cell, cell part, and organelle were the most abundant cellular component subcategories. Binding and catalytic activity represented the main molecular functions. The selected genes in Alashan camels were mainly enriched in ubiquitin mediated proteolysis pathways, the selected genes in Beijiang camels were mainly enriched in MAPK signaling pathways, the selected genes in Dongjiang camels were mainly enriched in RNA transport pathways, the selected genes in Hexi camels were mainly enriched in endocytosis pathways, the selected genes in Nanjiang camels were mainly enriched in insulin signaling pathways, while the selected genes in Qinghai camels were mainly enriched in focal adhesion pathways; these selected genes in Sunite camels were mainly enriched in ribosome pathways. We also found that Nanjiang (HSPA4L and INTU), and Alashan camels (INO80E) harbored genes related to the environment and characteristics. These findings provide useful insights into the genes related to the unique characteristics of domestic Bactrian camels in China, and a basis for genomic resource development in this species.

Compact CRISPR/Cas9 systems that can be delivered by AAV for in vivo genome editing hold great promise for clinical applications. Brevibacillus laterosporus Cas9 (BlatCas9) is a compact Cas9 nuclease that has been identified for plant genome editing. Here, we characterize BlatCas9 as an alternative tool for mammalian genome editing. We demonstrate that BlatCas9 prefers a N4CNAA protospacer adjacent motif (PAM), but N4C PAM is also editable in mammalian cells. We next demonstrate that BlatCas9 enables genome editing in a variety of cell types. Furthermore, BlatCas9 can be packaged into AAV for genome editing. Finally, we characterize the specificity of BlatCas9. In summary, BlatCas9 offers an alternative tool for both basic research and clinical applications.

The pandemic of coronavirus disease 2019 (COVID-19), a disease which causes severe lung injury and multiple organ damage, presents an urgent need for new drugs. The case severity and fatality of COVID-19 are associated with excessive inflammation, namely, a cytokine storm. Metformin, a widely used drug to treat type 2 diabetes (T2D) mellitus and metabolic syndrome, has immunomodulatory activity that reduces the production of proinflammatory cytokines using macrophages and causes the formation of neutrophil extracellular traps (NETs). Metformin also inhibits the cytokine production of pathogenic Th1 and Th17 cells. Importantly, treatment with metformin alleviates various lung injuries in preclinical animal models. In addition, a recent proteomic study revealed that metformin has the potential to directly inhibit SARS-CoV-2 infection. Furthermore, retrospective clinical studies have revealed that metformin treatment reduces the mortality of T2D with COVID-19. Therefore, metformin has the potential to be repurposed to treat patients with COVID-19 at risk of developing severe illness. This review summarizes the immune pathogenesis of SARS-CoV-2 and addresses the effects of metformin on inhibiting cytokine storms and preventing SARS-CoV-2 infection, as well as its side effects.

The domestic Bactrian camel is indispensable to agricultural production in the desertification area of China owning to its endurance to hunger and thirst, cold resistance, drought resistance, and good long-distance transportation. Therefore, it is necessary to investigate the genetic diversity, genetic structure, and genes with important roles in the evolution of this species. In this study, 1,568,087 SNPs were identified in 47 domestic Bactrian camels inhabiting four regions of China, namely Inner Mongolia, Gansu, Qinghai, and Xinjiang, by restriction site associated DNA sequencing (RAD-seq). The SNP data were used for nucleotide diversity analysis (π) and linkage disequilibrium (LD) attenuation analysis to elucidate the genetic diversity of the domestic Bactrian camel in the four regions studied. Results showed that Xinjiang camels had the highest nucleotide diversity and the fastest decay rate of the LD coefficient; therefore, Xinjiang camels had the highest genetic diversity. Structure analysis, principal component analysis (PCA), and phylogenetic tree construction by the neighbor-joining (NJ) method showed that Qinghai camels clustered separately, at a larger phylogenetic distance from camels in the other regions. Through analyses of selection signals, it was found that the number of selected genes shared by Inner Mongolia camels, Qinghai camels, Xinjiang camels, and Gansu camels was 7, 24, 25, and 113, respectively. The shared selected genes of the domestic Bactrian camel in the four regions were further analyzed, and three shared genes (GRIA3, XIAP, and THOC2) of the domestic Bactrian camel in China were identified. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the shared selected genes of the domestic Bactrian camel in all four regions studied. Across all regions, genes involved in the cellular process were the most abundant subcategory under biological process. Cell and cell part represented the main proportion of genes under cellular component. Binding represented the main molecular function. In addition, the shared selected genes of the domestic Bactrian camel in the four regions of China were significantly enriched in the long-term depression pathway. The research should enable further study of the genetic resources of the domestic Bactrian camel, as well as the conservation of these resources.

Compact CRISPR/Cas9 systems that can be packaged into an adeno-associated virus (AAV) hold great promise for gene therapy. Unfortunately, currently available small Cas9 nucleases either display low activity or require a long protospacer adjacent motif (PAM) sequence, limiting their extensive applications. Here, we screened a panel of Cas9 nucleases and identified a small Cas9 ortholog from Staphylococcus auricularis (SauriCas9), which recognizes a simple NNGG PAM, displays high activity for genome editing, and is compact enough to be packaged into an AAV for genome editing. Moreover, the conversion of adenine and cytosine bases can be achieved by fusing SauriCas9 to the cytidine and adenine deaminase. Therefore, SauriCas9 holds great potential for both basic research and clinical applications.

Abstract Background Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear. The transcriptome database created by RNA-Seq is used to identify critical genes related to defoliation traits. Results In this study, we sequenced the transcriptomes of the Zhungeer variety (with easy leaf abscission) and WL319HQ variety (without easy leaf abscission). Among the identified 66,734 unigenes, 706 differentially expressed genes (DEGs) upregulated, and 392 unigenes downregulated in the Zhungeer vs WL319HQ leaf. KEGG pathway annotations showed that 8,414 unigenes were annotated to 87 pathways and contained 281 DEGs. Six DEGs belonging to the “Carotenoid biosynthesis”, “Plant hormone signal transduction” and “Circadian rhythm-plant” pathways involved in defoliation traits were identified and validated by RT-qPCR analyses. Conclusions This study used RNA-Seq to discover genes associated with defoliation traits between two alfalfa varieties. Our transcriptome data dramatically enriches alfalfa functional genomic studies. In addition, these data provide theoretical guidance for field production practice and genetic breeding, as well as references for future study of defoliation traits in alfalfa.

Abstract Background Due to the intraarticular and complex nature of the coronal shear fracture of the humeral capitellum and its rarity, it has been difficult to formulate a universally accepted method of surgical management. The purpose of this study is to retrospectively evaluate the clinical outcomes of 15 patients with isolated coronal shear fractures of the capitellum treated by Herbert screw fixation through anterolateral approach, and to address the safety and tips for this surgical procedure. Methods This retrospective study included 15 isolated coronal shear fractures of the capitellum without posterior involvement, which were classified according to the Dubberley classification as 11 type 1A fractures and 4 type 3A fractures. All fractures were treated with Herbert screws fixation via the anterolateral approach. Clinical and radiographic evaluation was performed regularly, with a mean follow-up of 29 months. Results The mean operative time was 81 min. There were no wound healing problems or infection. One incomplete posterior interosseous nerve injury occurred, which recovered soon without residual compromise. All fractures healed well. At the final follow-up, the average range of motion was 134°in flexion-extension and 172°in supination-pronation. There was no significant difference between the affected and the unaffected elbows with regard to motion in flexion-extension or flexion-extension. The average Mayo Elbow Performance Index Score was 93 with 11 excellent and 4 good. No evidence of avascular necrosis, posttraumatic osteoarthritis, or heterotrophic ossification was found. Conclusion Open reduction and internal fixation using Herbert screws through a anterolateral approach is a reliable and effective treatment for coronal shear fractures of capitellum, and able to achieve stable fixation and restoration of a functional range of motion.

Abstract Background The purpose of the study is to investigate whether autologous platelet-rich plasma (PRP) can serve as bone-inducing factors to provide osteoinduction and improve bone regeneration for tissue-engineered bones fabricated with bone marrow mesenchymal stem cells (MSCs) and beta-tricalcium phosphate (β-TCP) ceramics. The current study will give more insight into the contradictory osteogenic capacity of PRP. Methods The concentration of platelets, platelet-derived growth factor-AB (PDGF-AB), and transforming growth factor-β1 (TGF-β1) were measured in PRP and whole blood. Tissue-engineered bones using MSCs on β-TCP scaffolds in combination with autologous PRP were fabricated (PRP group). Controls were established without the use of autologous PRP (non-PRP group). In vitro, the proliferation and osteogenic differentiation of MSCs on fabricated constructs from six rabbits were evaluated with MTT assay, alkaline phosphatase (ALP) activity, and osteocalcin (OC) content measurement after 1, 7, and 14 days of culture. For in vivo study, the segmental defects of radial diaphyses of 12 rabbits from each group were repaired by fabricated constructs. Bone-forming capacity of the implanted constructs was determined by radiographic and histological analysis at 4 and 8 weeks postoperatively. Results PRP produced significantly higher concentration of platelets, PDGF-AB, and TGF-β1 than whole blood. In vitro study, MTT assay demonstrated that the MSCs in the presence of autologous PRP exhibited excellent proliferation at each time point. The results of osteogenic capacity detection showed significantly higher levels of synthesis of ALP and OC by the MSCs in combination with autologous PRP after 7 and 14 days of culture. In vivo study, radiographic observation showed that the PRP group produced significantly higher score than the non-PRP group at each time point. For histological evaluation, significantly higher volume of regenerated bone was found in the PRP group when compared with the non-PRP group at each time point. Conclusions Our study findings support the osteogenic capacity of autologous PRP. The results indicate that the use of autologous PRP is a simple and effective way to provide osteoinduction and improve bone regeneration for tissue-engineered bone reconstruction.

Abstract Background Pulmonary arterial hypertension (PAH) is a devastating disease that lacks sufficient treatment. Studies have shown that the Nod-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome contributes to PAH pathogenesis, but the role of the upstream molecular P2X7 receptor (P2X7R) has remained unexplored. We investigated the role of P2X7R in the pathogenesis of PAH. Methods and results PH was induced by a single subcutaneous injection of monocrotaline (MCT) (60 mg/kg) on left pneumonectomised Sprague-Dawley rats, as validated by significant increases in pulmonary artery pressure and vessel wall thickness. Marked P2X7R was detected by predominant PA immunostaining in lungs from PH rats. Western blot revealed a significant increase in the protein levels of P2X7R as well as NLRP3 and caspase-1 in the diseased lung tissue compared with normal tissue. The rats received A-740003 (a selective P2X7 receptor antagonist, 30 mg/kg) daily starting from 1 week before or 2 weeks after MCT injection. Consequently, A-740003 reversed the NLRP3 inflammasome upregulation, significantly decreased the mean right ventricular (RV) pressure and RV hypertrophy, and reversed pulmonary arterial remodelling 4 weeks after MCT injection, as both a pretreatment and rescue intervention. Notably, A-740003 significantly reduced macrophage and pro-inflammatory cytokine levels, as measured via bronchoalveolar lavage. The recruitment of macrophages as well as collagen fibre deposition in the perivascular areas were also reduced, as confirmed by histological staining. Conclusions P2X7R contributes to the pathogenesis of PH, probably in association with activation of the NLRP3 inflammasome. Blockade of P2X7R might be applied as a novel therapeutic approach for the treatment of PAH.

After liver transplantation, the liver function of a patient is gradually restored over a period of time that can be divided into a convalescence period (CP) and a stabilizing period (SP). The plasma concentration of tacrolimus, an immunosuppressant commonly used to prevent organ rejection, varies as a result of variations in its metabolism. The effects of genetic and clinical factors on the plasma concentration of tacrolimus appear to differ in the CP and SP. To establish a model explaining the variation in tacrolimus trough concentration between individuals in the CP and SP, we conducted a retrospective, single-center, discovery study of 115 pairs of patients (115 donors and 115 matched recipients) who had undergone liver transplantation. Donors and recipients were genotyped by a genome-wide association study (GWAS) using an exome chip. Novel exons were identified that influenced tacrolimus trough concentrations and were verified with bootstrap analysis. In donors, two single-nucleotide polymorphisms showed an effect on the CP (rs1927321, rs1057192) and four showed an effect on the SP (rs776746, rs2667662, rs7980521, rs4903096); in recipients, two single-nucleotide polymorphisms showed an effect in the SP (rs7828796, rs776746). Genetic factors played a crucial role in tacrolimus metabolism, accounting for 44.8% in the SP, which was higher than previously reported. In addition, we found that CYP3A5, which is known to affect the metabolism of tacrolimus, only influenced tacrolimus pharmacokinetics in the SP.

PARP-1 (poly(ADP-ribose) polymerase-1) plays an important role in tumorigenesis. Since its effects on different populations are varied, this study investigated the impact of PARP-1 on primary hepatocellular carcinoma in a Southern Chinese Zhuang population. We assessed the global PARP-1 messenger RNA expression in patients with hepatocellular carcinoma using The Cancer Genome Atlas dataset. Increased PARP-1 expression, related to alpha-fetoprotein level, was observed. The area under the receiver operating characteristic curve value was 0.833. Kaplan–Meier survival curves indicated that higher PARP-1 expression was not correlated with poorer overall survival and recurrence-free survival. In a Zhuang population, PARP-1 messenger RNA and protein levels were increased in the hepatocellular carcinoma tissue and its adjacent liver tissues as assessed by quantitative polymerase chain reaction, immunohistochemistry, and western blotting. Higher PARP-1 level was associated with a higher tumor stage (p 0.05). Further analysis suggested that H2AX , a PARP-1 protein interaction partner, was coordinated with PARP-1 in hepatocellular carcinoma tumorigenesis. Overall, some new characteristics of PARP-1 expression were noted in the Zhuang population. PARP-1 is a novel promising diagnostic marker for hepatocellular carcinoma in the Southern Chinese Zhuang population.

The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification.