[Bioinformatics analysis of Alu components at the level of genome 3D structure].

The interphase chromatin is folded in the nucleus in a hierarchical manner, including the nucleosome, the "beads on a string" structure composed of nucleosomes, the solenoid fiber structure, the chromatin/DNA loop structure (chromatin/DNA loop), and the topologically associated domain (TAD). Among them, TAD is considered to be the basic unit of the 3D structure of chromatin because it is relatively stable and conserved in different cell types. Alu elements occupy a large proportion in the mammalian genomes. There are a wide variety of Alu elements, but their functional characterizations are limited to date. This study investigates the role of Alu elements in the assembly of 3D chromatin conformation. The evolutionary process of the Alu subfamily was explored by the distance relationship of the 3D structure of chromatin. We found that the proportion of Alu elements in high-density chromatin interaction increased with higher similarity, indicating that Alu plays an important role in the construction of chromatin 3D structure. There is a certain positive correlation between the strength of the upper interaction and the evolutionary relationship. In sum, the Alu elements with relatively close distances in the 1D sequence will also be close to each other in the 3D structure of chromatin.

Efficacy and safety of tranexamic acid in reducing blood loss in scoliosis surgery: a systematic review and meta-analysis.

OBJECTIVE: The purpose of this systematic review and meta-analysis of randomized controlled trials (RCTs) and non-RCTs was to gather data to evaluate the efficacy and safety of tranexamic acid (TXA) versus placebo after a scoliosis surgery. METHODS: The electronic databases including Embase, PubMed, CENTRAL (Cochrane Controlled Trials Register), Web of Science, and Google database were searched to identify relevant studies published from the time of the establishment of these databases up to May 2016. This systematic review and meta-analysis was performed according to the PRISMA statement criteria. The primary outcomes were total blood loss, intraoperative blood loss, and hemoglobin after surgery. The second outcome is need for transfusion. Stata 12.0 software was used for the meta-analysis. After testing for publication bias and heterogeneity across studies, data were aggregated for random-effects modeling when necessary. RESULTS: A total of 685 patients (347 patients in the TXA group and 338 in the control group) were finally included for this meta-analysis. The pooled results revealed that administration of TXA can decrease the total blood loss after scoliosis surgery [mean difference (MD) = 682.30, 95% confidence interval (CI) -930.60 to -434.00; P = 0.000] and intraoperative blood loss [(MD) = -535.28; 95% CI -683.74 to -368.82; P = 0.000]. For the hemoglobin (Hb) value after scoliosis surgery, TXA can decrease the Hb value for 0.51 dL [(MD) = 0.51; 95% CI 0.25-0.78; P = 0.000]. There is no statistically significant difference between the TXA versus placebo in terms of the need for transfusion (relative risk = 0.55, 95% CI 0.25-1.20, P = 0.132). CONCLUSION: Based on the current meta-analysis, TXA can decrease the total blood loss and intraoperative blood loss during scoliosis surgery. It is recommended that it be routinely used in scoliosis surgery. High-dose TXA (>20 mg/kg) is more effective than low-dose TXA (<20 mg/kg) in controlling blood loss. However, for the need for transfusion, more high-quality RCTs need to be identified.

Characterization of the conbercept gene localization in DHFR- amplified CHO cells using fluorescence in situ hybridization.

Chinese-hamster ovary (CHO) cells are most widely used for mammalian protein expression. After integration into the CHO genome, the exogenous gene may be lost in the process of large-scale protein production due to the removal of related selection pressures. Therefore, it is necessary to test its stability in the genome. Conbercept is a fusion protein that specifically binds to the various isoforms of vascular endothelial growth factor (VEGF)-A, VEGF-B, and placental growth factor (PlGF), thereby exerting anti-angiogenic activities. It has been approved for Phase Ⅲ clinical trials in the United States. In this study, fluorescence in situ hybridization (FISH) was used to localize the conbercept gene in dihydrofolatereductase (DHFR)-amplified CHO cell lines. Metaphase FISH showed that genomic integration of the conbercept gene was stable after 4 and 19 passages, and manifested three characteristics: first, the gene locates on one chromosome, rather than a number of chromosomes; second, the gene locates on the longer chromosomes; third, there are many copies located on the same chromosome. At the same time, the copy number of the conbercept gene in the CHO genome and the conbercept protein expression levels are also stable, as verified by qPCR and ELISA assays, respectively. These experiments demonstrated that the conbercept gene remained stable in the genome after 19 passages, and could be actively expressed, which strongly support the mass production and the quality control of conbercept.

Optimization and quality control of genome-wide Hi-C library preparation.

Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells. After preliminary quality control by Sanger sequencing, the two replicates were high-throughput sequenced. The bioinformatics analysis of the raw sequencing data revealed the mapping-ability and pair-mate rate of the raw data were around 90% and 72%, respectively. Additionally, after removal of self-circular ligations and dangling-end products, more than 96% of the valid pairs were reached. Genome-wide interactome profiling shows clear topological associated domains (TADs), which is consistent with previous reports. Further correlation analysis showed that the two biological replicates strongly correlate with each other in terms of both bin coverage and all bin pairs. All these results indicated that the optimized Hi-C procedure is robust and stable, which will be very helpful for the wide applications of the Hi-C assay.

Involvement of aberrant miR-139/Jun feedback loop in human gastric cancer.

Accumulating evidence indicates that some miRNAs could form feedback loops with their targets to fine-tune tissue homeostasis, while disruption of these loops constitutes an essential step towards human tumorigenesis. In this study, we report the identification of a novel negative feedback loop formed between miR-139 and its oncogenic target Jun. In this loop, miR-139 could inhibit Jun expression by targeting a conserved site on its 3'-UTR, whereas Jun could induce miR-139 expression in a dose dependent manner through a distant upstream regulatory element. Interestingly, aberration in this loop was found in human gastric cancer, where miR-139 was down-regulated and inversely correlated with Jun expression. Further functional analysis showed that restored expression of miR-139 in gastric cancer cells significantly induces apoptosis, and inhibits cell migration and proliferation as well as tumour growth through targeting Jun. Thus, our data strongly suggests a role of aberrant miR-139/Jun negative feedback loop in the development of human gastric cancer and miR-139 as a potential therapeutic target for gastric cancer. Given that miR-139 and Jun are deregulated in many cancers, our findings here might have broader implication in other types of human cancers.

Construction of CTCF degradation cell line by CRISPR/Cas9 mediated genome editing.

The CCCTC-binding factor (CTCF) is the main insulator protein described in vertebrates. It plays fundamental roles during diverse cellular processes. CTCF gene knockout mice led to death during embryonic development. To further explore the functions of CTCF, we employed a CRISPR/Cas9-based genome engineering strategy to in-frame insert the mitosis-special degradation domain (MD) of cyclin B into the upstream open reading frame of CTCF gene. Fusion protein is designed to degrade during mitosis leaded by MD. As a control group, mutation of a single arginine (R42A) within the destruction box inactivates the MD leading to constitutive expression of MD*-CTCF. The homozygous clones were obtained via the screening by puromycin when coexpressed with puromycin resistence gene. The protein level of CTCF in MD-CTCF cell line was about 10% of wild-type cells throughout cell cycles by the analyses of Western blotting and immunofluorescence. There was no significant difference between MD*-CTCF cell line and wild type. Flow cytometry results showed prolonged G1 phase in MD-CTCF cell line. Taken together, we demonstrated the feasibility of efficiently inserting MD domain into genome with the CRISPR/Cas9 technology and reported the first CTCF-specific degradation human cell line.

Functional screening for miRNAs targeting Smad4 identified miR-199a as a negative regulator of TGF-ß signalling pathway.

The transforming growth factor-ß (TGF-ß) signalling pathway participates in various biological processes. Dysregulation of Smad4, a central cellular transducer of TGF-ß signalling, is implicated in a wide range of human diseases and developmental disorders. However, the mechanisms underlying Smad4 dysregulation are not fully understood. Using a functional screening approach based on luciferase reporter assays, we identified 39 microRNAs (miRNAs) as potential regulators of Smad4 from an expression library of 388 human miRNAs. The screening was supported by bioinformatic analysis, as 24 of 39 identified miRNAs were also predicted to target Smad4. MiR-199a, one of the identified miRNAs, was inversely correlated with Smad4 expression in various human cancer cell lines and gastric cancer tissues, and repressed Smad4 expression and blocked canonical TGF-ß transcriptional responses in cell lines. These effects were dependent on the presence of a conserved, but not perfect seed paired, miR-199a-binding site in the Smad4 3'-untranslated region (UTR). Overexpression of miR-199a significantly inhibited the ability of TGF-ß to induce gastric cancer cell growth arrest and apoptosis in vitro, and promoted anchorage-independent growth in soft agar, suggesting that miR-199a plays an oncogenic role in human gastric tumourigenesis. In conclusion, our functional screening uncovers multiple miRNAs that regulate the cellular responsiveness to TGF-ß signalling and reveals important roles of miR-199a in gastric cancer by directly targeting Smad4.

Sustained release of naringin from silk-fibroin-nanohydroxyapatite scaffold for the enhancement of bone regeneration.

Bone defects are a common challenge in the clinical setting. Bone tissue engineering (BTE) is an effective treatment for the clinical problem of large bone defects. In this study, we fabricated silk fibroin (SF)/hydroxyapatite (HAp) scaffolds inlaid with naringin poly lactic-co-glycolic acid (PLGA) microspheres, investigating the feasibility of their application in BTE. Naringin PLGA microspheres were manufactured and adhered to the SF/HAp scaffold. Bone mesenchymal stem cells (BMSCs) were inoculated onto the SF/HAp scaffold containing naringin PLGA microsphere to examine the biocompatibility of the SF/HAp scaffolds. A rabbit femoral distal bone defect model was used to evaluate the in vivo function of the SF/HAp scaffolds containing naringin-loaded PLGA microspheres. The current study demonstrated that SF/HAp scaffolds containing naringin-loaded PLGA microspheres show promise as osteo-modulatory biomaterials for bone regeneration.

[The quality control of 4C-clone screening assay].

Circular chromosome conformation capture (4C) can be used to analyze the high-resolution interaction map of cis-regulatory elements in genome-wide studies. In this study, we optimized the condition of PCR with the mimical 4C sample in order to establish a specific and efficient assay, which was validated practically. This 4C-clone screening assay can be used as the quality control in the application of 4C assay.

Naringin-inlaid silk fibroin/hydroxyapatite scaffold enhances human umbilical cord-derived mesenchymal stem cell-based bone regeneration.

OBJECTIVES: Large bone defects are a common, debilitating clinical condition that have substantial global health and economic burden. Bone tissue engineering technology has become one of the most promising approaches for regenerating defective bones. In this study, we fabricated a naringin-inlaid composite silk fibroin/hydroxyapatite (NG/SF/HAp) scaffold to repair bone defects. MATERIALS AND METHODS: The salt-leaching technology was used to fabricate the NG/SF/HAp scaffold. The cytocompatibility of the NG/SF/HAp scaffold was assessed using scanning electron microscopy, live/dead cell staining and phalloidin staining. The osteogenic and angiogenic properties were assessed in vitro and in vivo. RESULTS: The porous NG/SF/HAp scaffold had a well-designed biomimetic porous structure with osteoinductive and angiogenic activities. A gene microarray identified 854 differentially expressed genes between human umbilical cord-derived mesenchymal stem cells (hUCMSCs) cultured on SF-nHAp scaffolds and cells cultured on NG/SF/HAp scaffolds. The underlying osteoblastic mechanism was investigated using hUCMSCs in vitro. Naringin facilitated hUCMSC ingrowth into the SF/HAp scaffold and promoted osteogenic differentiation. The osteogenic and angiogenic capabilities of cells cultured in the NG/SF/HAp scaffold were superior to those of cells cultured in the SF/HAp scaffold. CONCLUSIONS: The data indicate the potential of the SF/HAp composite scaffold incorporating naringin for bone regeneration.

[Conserved non-coding elements in human genome].

Study of comparative genomics has revealed that about 5% of the human genome are under purifying selection, 3.5% of which are conserved non-coding elements (CNEs). While the coding regions comprise of only a small part. In human, the CNEs are functionally important, which may be associated with the process of the establishment and maintain of chromatin architecture, transcription regulation, and pre-mRNA processing. They are also related to ontogeny of mammals and human diseases. This review outlined the identification, functional significance, evolutionary origin, and effects on human genetic defects of the CNEs.

[In vivo delivery of siRNA].

RNA interference (RNAi) is a mechanism of posttranscriptional gene silencing mediated by small interfering RNA (siRNA). The ability of synthetic siRNA to silence genes in vivo has made it well suited as therapeutic drug, but the instability and polarity of siRNA and the complexity of in vivo circumstances retarded rapid development of RNAi-based therapies. In this review, a summary of the advances on in vivo siRNA delivery is presented and discussed.

Relationship between hospital or surgeon volume and outcomes in joint arthroplasty: protocol for a suite of systematic reviews and dose-response meta-analyses.

INTRODUCTION: Joint arthroplasty is a particularly complex orthopaedic surgical procedure performed on joints, including the hip, knee, shoulder, ankle, elbow, wrist and even digit joints. Increasing evidence from volume-outcomes research supports the finding that patients undergoing joint arthroplasty in high-volume hospitals or by high-volume surgeons achieve better outcomes, and minimum case load requirements have been established in some areas. However, the relationships between hospital/surgeon volume and outcomes in patients undergoing arthroplasty are not fully understood. Furthermore, whether elective arthroplasty should be restricted to high-volume hospitals or surgeons remains in dispute, and little is known regarding where the thresholds should be set for different types of joint arthroplasties. METHODS AND ANALYSES: This is a protocol for a suite of systematic reviews and dose-response meta-analyses, which will be amended and updated in conjunction with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols. Electronic databases, including PubMed and Embase, will be searched for observational studies examining the relationship between the hospital or surgeon volume and clinical outcomes in adult patients undergoing primary or revision of joint arthroplasty. We will use records management software for study selection and a predefined standardised file for data extraction and management. Quality will be assessed using the Newcastle-Ottawa Scale, and the meta-analysis, subgroup analysis and sensitivity analysis will be performed using Stata statistical software. Once the volume-outcome relationships are established, we will examine the potential non-linear relationships between hospital/surgeon volume and outcomes and detect whether thresholds or turning points exist. ETHICS AND DISSEMINATION: Ethical approval is not required, because these studies are based on aggregated published data. The results of this suite of systematic reviews and meta-analyses will be submitted to peer-reviewed journals for publication. PROSPERO REGISTRATION NUMBER: CRD42017056639.

Impact of inhalational anesthetics on postoperative cognitive function: Study protocol of a systematic review and meta-analysis.

BACKGROUND: Conflict findings of the impact of inhalational anesthetics on postoperative cognitive function are reported. No systematic review has been performed to solve the problem. The aim of the study was to assess the effect of different inhalational anesthetics on postoperative cognitive function in a network meta-analysis. METHODS: We will search MEDLINE, EMBASE, the Central Register of Controlled Trials in the Cochrane library, and CINAHL for randomized controlled trials or cohort studies assessing the short-term or long-term cognitive function of elderly patients (over 60 years) receiving major surgeries and inhalational anesthetics (desflurane, isoflurane, sevoflurane, halothane, and nitrous oxide) during surgery. Two reviewers will independently screen study eligibility, extract information from eligible studies, and appraise study quality. The impact of inhalational anesthetics will be assessed through: incidence of postoperative cognitive dysfunction at 1 week, 3 months, 1 year, and over 1 year after surgery; incidence of post-operative delirium; test of postoperative cognitive function. RESULTS: The results of this systematic review and meta-analysis will be published in a peer-reviewed journal. CONCLUSION: To our knowledge, this systematic review will be the first to evaluate existing research on the incidence of postoperative cognitive function after inhalational anesthetics. Our study will assess the effect of different inhalational anesthetics on postoperative cognitive function. ETHICS AND DISSEMINATION: The review will be finished in December 2017, and the result will be published in a peer-reviewed journal or disseminated through conference posters or abstracts. REVIEW REGISTRATION NUMBER: CRD42017056675 (www.crd.york.ac.uk/PROSPERO).

Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions.

Interferon-induced transmembrane protein (IFITM) 1, 2 and 3 genes encode a family of interferon (IFN)-induced transmembrane proteins that block entry of a broad spectrum of pathogens. However, the transcriptional regulation of these genes, especially whether there exist any enhancers and their roles during the IFN induction process remain elusive. Here, through public data mining, episomal luciferase reporter assay and in vivo CRISPR-Cas9 genome editing, we identified an IFN-responsive enhancer located 35kb upstream of IFITM3 gene promoter upregulating the IFN-induced expression of IFITM1, 2 and 3 genes. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA) and luciferase reporter assay demonstrated that signal transducers and activators of transcription (STAT) 1 bound to the enhancer with the treatment of IFN and was indispensable for the enhancer activity. Furthermore, using chromosome conformation capture technique, we revealed that the IFITM1, 2 and 3 genes physically clustered together and constitutively looped to the distal enhancer through long-range interactions in both HEK293 and A549 cells, providing structural basis for coordinated regulation of IFITM1, 2 and 3 by the enhancer. Finally, we showed that in vivo truncation of the enhancer impaired IFN-induced resistance to influenza A virus (IAV) infection. These findings expand our understanding of the mechanisms underlying the transcriptional regulation of IFITM1, 2 and 3 expression and its ability to mediate IFN signaling.

Continuous Local Infiltration Analgesia for Pain Control After Total Knee Arthroplasty: A Meta-analysis of Randomized Controlled Trials.

A total knee arthroplasty (TKA) has always been associated with moderate to severe pain. As more research is conducted on the use of continuous local infiltration analgesia (CLIA) to manage pain after a TKA, it is necessary to reassess the efficacy and safety of the TKA method. The purpose of this systematic review and meta-analysis of randomized controlled trials was to evaluate the efficacy and safety of pain control of CLIA versus placebo after a TKA. In January 2015, a systematic computer-based search was conducted in the Medline, Embase, PubMed, CENTRAL (Cochrane Controlled Trials Register), Web of Science, Google database, and Chinese Wanfang databases. This systematic review and meta-analysis were performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses statement criteria. The primary endpoint was the visual analog scale score after a TKA with rest or mobilization at 24, 48, and 72 hours, which represents the effect of pain control after TKA. The complications of infection, nausea, and whether it prolonged wound drainage were also compiled to assess the safety of CLIA. RevMan 5.30 software was used for the meta-analysis. After testing for publication bias and heterogeneity across studies, data were aggregated for random-effects modeling when necessary. Ten studies involving 735 patients met the inclusion criteria. The meta-analysis revealed that continuous infusion analgesia provided better pain control with rest at 24 hours (mean difference [MD] -12.54, 95% confidence interval [CI] -16.63 to 8.45), and with mobilization at 24 hours (MD -18.27, 95% CI -27.52 to 9.02) and 48 hours (MD -14.19, 95% CI -21.46 to 6.93). There was no significant difference with respect to the visual analog scale score at 48 hours (MD -6.15, 95% CI -13.51 to 1.22, P = 0.10) and 72 hours (MD -3.63, 95% CI -10.43 to 3.16, P = 0.29) with rest and at 72 hours with mobilization (MD -4.25, 95% CI -16.27 to 7.77, P = 0.49). However, CLIA increased the rate of infection (relative risk [RR] 3.16, 95% CI 1.18-8.50, P = 0.02) and the rate of nausea or vomiting (RR 0.60, 95% CI 0.37-0.96, P = 0.03). There were no significant differences in the length of hospital stay (MD -0.34, 95% CI -1.09 to 0.42, P = 0.38), deep venous thrombosis (RR 1.02, 95% CI 0.30 to 1.41, P = 0.99), or duration of surgery (MD 1.20, 95% CI -4.59 to 6.98, P = 0.69). On the basis of the current meta-analysis, CLIA was more efficacious for reducing postoperative pain than the placebo at 24 hours with rest and at 24 and 48 hours with mobilization, but it increased the risk of infection. However, CLIA did not prolong the length of hospital stay or the duration of surgery. There was also a higher heterogeneity of different analgesic drugs mixed and a high risk of selection bias in this analysis; therefore, more high-quality randomized controlled trials with standardized CLIA are necessary for proper comparisons of this technique with other methods.

Prediction of regulatory factor X1 binding sites in promoters of RNA-binding proteins genes in mouse brain.

BACKGROUND: There is an increasing interest in the role of regulatory factor X1 (RFX1) and RNA-binding proteins (RBPs) during neural development. However, there are few reports about their interaction.   METHODS: We extracted RNA and performed reverse transcription polymerase chain reaction (RT-PCR) to identify RFX1 expression in imprinting control region (ICR) mouse tissues, analyzed RFX1 domains and motif consensus by comparing public databases on the Internet, tested the motif consensus with affinity-capture and western blotting experiments with mouse brain tissue, and predicted the binding sites of RFX1 in promoter regions of mouse RBPs genes. RESULTS: The expression of RFX1 was higher in embryonic brain compared to embryonic kidney, heart, and liver, and its expression level was relatively stable and higher in mouse embryonic brain than neonatal brain. RFX1 had several domains, including domain A as an activation domain, DBD as a DNA binding domain, domain B and C which played an important role in dimerization, and domain D as dimerization domain. RFX1 had three different profiles motif consensus RFX1M00281, RFX1M00280, and RFX1 (EF-C) M00626. There were 79 RFX1 binding sites at the promoters of 65 of 323 RBPs genes. CONCLUSION: RFX1 as regulatory factor will have putative important regulating role in the expression of RBPs genes during embryonic development of mouse brain.

Impact of sildenafil therapy on pulmonary arterial hypertension in adults with congenital heart disease.

BACKGROUND: It has been demonstrated that sildenafil is effective in patients with pulmonary arterial hypertension (PAH). However, the impact of sildenafil on PAH in adults with congenital heart disease (CHD) has been less investigated. OBJECTIVE: In this prospective, open-label, uncontrolled and multicenter study, 60 patients with PAH related to CHD received oral sildenafil (75 mg/day) for 12 weeks. The enrolled patients underwent six-minute walk test (SMWT) and cardiac catheterization at the beginning and the end of the 12 weeks. The primary end point was the changes in exercise capacity assessed by SMWT; the secondary end point included assessment of functional class, evaluation of cardiopulmonary hemodynamics, and clinical worsening (defined as death, transplantation, and rehospitalization for PAH). Drug safety and tolerability were also examined. RESULTS: Oral sidenafil significantly increased SMWT distances (422.94 ± 76.95 m vs. 371.99 ± 78.73 m, P < 0.0001). There was also remarkable improvement in Borg dyspnea score (2.1 ± 1.32 vs. 2.57 ± 1.42, P = 0.0307). Moreover, significant improvements in World Healthy Organization (WHO) functional class and cardiopulmonary hemodynamics were also discovered (mean pulmonary artery pressure, P = 0.0002; cardiac index, P < 0.0001; pulmonary vascular resistance, P < 0.0001). Side effects in this study were mild and consistent with reported studies. None of the enrolled patients experienced significant clinical worsening. CONCLUSIONS: This study confirmed and extended previous studies. It suggested that oral sildenafil was safe and effective for the treatment of adult patients with CHD-related PAH.

[Functional expression of DNA binding domain of Zif268 in Escherichia coli].

As the ubiquitous nucleic acids recognizing motif, Zinc finger protein play important role in regulation of gene expression. The study of recognization specific will greatly facilitate understanding the delicate interaction of Zinc finger protein and DNA. By the choice of expression vector, the induction and culture conditions, the DNA binding domain of Zif268 was expressed in Escherichia coli partly solubly. The gel mobility shift assay shows that purified DNA binding domain can bind its natural target sequence specifically, which indicates the DNA binding domain remains its DNA binding activity in Escherichia coli. The functional expression of DNA binding domain of Zif268 will greatly facilitate the development of in vivo genetic selection assay for the study of Zinc fingers-DNA interaction.