Supplementary Material for: Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica)

<p>The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.</p

Supplementary Material for: The skeletal muscle transcriptome profile of elderly men with metabolic syndrome based on weighted gene co-expression network analysis

Introduction: This study aims to understand the transcriptome characteristics of the skeletal muscle of old man with metabolic syndrome (MS), to find the hub genes and insight into the molecular mechanisms of skeletal muscle in the occurrence and development of MS. Methods: In this study, the Limma package of R software was used to analyze the differentially expressed genes in the skeletal muscle of healthy young adult (YO) men, healthy elderly (EL) men, and elderly men diagnosed with metabolic syndrome (SX) for at least 10 years. Bioinformatics methods, such as GO enrichment analysis, KEGG enrichment analysis and gene interaction network analysis, were used to explore the biological functions of differentially expressed genes, and WGCNA was used to cluster differentially expressed genes into modules. Results: Among the YO group, EL group, and SX group, 65 co-differentially expressed genes were found may be regulated by age factor and metabolic syndrome factor. Those co-differentially expressed genes were enriched into 25 biological process terms and 3 KEGG pathways. Based on the WGCNA results, a total of five modules were identified. Fifteen hub genes may play an essential role in regulating the function of skeletal muscle of old men with metabolic syndrome. Conclusions: 65 differentially expressed genes and 5 modules may regulate the function of skeletal muscle of old men with MS, among which fifteen hub genes may play an essential role in the occurrence and development of MS

Supplementary Material for: The skeletal muscle transcriptome profile of elderly men with metabolic syndrome based on weighted gene co-expression network analysis

Introduction: This study aims to understand the transcriptome characteristics of the skeletal muscle of old man with metabolic syndrome (MS), to find the hub genes and insight into the molecular mechanisms of skeletal muscle in the occurrence and development of MS. Methods: In this study, the Limma package of R software was used to analyze the differentially expressed genes in the skeletal muscle of healthy young adult (YO) men, healthy elderly (EL) men, and elderly men diagnosed with metabolic syndrome (SX) for at least 10 years. Bioinformatics methods, such as GO enrichment analysis, KEGG enrichment analysis and gene interaction network analysis, were used to explore the biological functions of differentially expressed genes, and WGCNA was used to cluster differentially expressed genes into modules. Results: Among the YO group, EL group, and SX group, 65 co-differentially expressed genes were found may be regulated by age factor and metabolic syndrome factor. Those co-differentially expressed genes were enriched into 25 biological process terms and 3 KEGG pathways. Based on the WGCNA results, a total of five modules were identified. Fifteen hub genes may play an essential role in regulating the function of skeletal muscle of old men with metabolic syndrome. Conclusions: 65 differentially expressed genes and 5 modules may regulate the function of skeletal muscle of old men with MS, among which fifteen hub genes may play an essential role in the occurrence and development of MS

Supplementary Material for: Rapid initiation of peritoneal dialysis by automated peritoneal dialysis or hemodialysis: a randomized clinical trial

Introduction: It is still controversial whether automated peritoneal dialysis (APD) or hemodialysis (HD) is a more favorable choice for the rapid initiation of peritoneal dialysis. Methods: A pilot randomized prospective controlled trial was carried out in Shanghai Ruijin Hospital. Sixty-seven patients who chose long-term peritoneal dialysis treatment and needed unplanned dialysis were enrolled and randomized into HD-CAPD group (33 cases) or APD-CAPD group (34 cases) based on the dialysis modality during the transition period (within 14 days from the day PD catheter was implanted). Continuous ambulatory peritoneal dialysis started after the transition period. The primary outcome was the decline rates of residual glomerular filtration rate (GFR). Secondary outcomes included the rates of mechanical complications, the rates of infectious complications and complications of ESRD. Results: We found residual GFR decline were faster in HD-CAPD group than in APD-CAPD group (0.06 ml/min/w vs 0.03ml/min/w, P<0.01). The incidences of mechanical complications were similar in APD-CAPD group comparing with HD-CAPD group, including hernia (2.9% vs 3.0%, P=1.00), catheter malposition (0.02 episodes/patient-months vs 0.02 episodes/patient-months, P=0.70), leakage (5.9% vs 6.1%, P=1.00) and omental wrap (0 episode vs 3 episodes, P=0.368). Though the one-year overall infection rates were similar (0.03 episodes/patient-months vs 0.05 episodes/patient-months, P=0.10), APD-CAPD group had lower rate of bacteremia compared to HD-CAPD group (0 episodes/patient-months vs 0.02 episodes/patient-months, P<0.01). Conclusions: Both APD and HD could be used for patients who need to start dialysis in an unplanned manner. APD may have the advantage in protecting residual renal functions among these patients

Supplementary Material for: Rapid initiation of peritoneal dialysis by automated peritoneal dialysis or hemodialysis: a randomized clinical trial

Introduction: It is still controversial whether automated peritoneal dialysis (APD) or hemodialysis (HD) is a more favorable choice for the rapid initiation of peritoneal dialysis. Methods: A pilot randomized prospective controlled trial was carried out in Shanghai Ruijin Hospital. Sixty-seven patients who chose long-term peritoneal dialysis treatment and needed unplanned dialysis were enrolled and randomized into HD-CAPD group (33 cases) or APD-CAPD group (34 cases) based on the dialysis modality during the transition period (within 14 days from the day PD catheter was implanted). Continuous ambulatory peritoneal dialysis started after the transition period. The primary outcome was the decline rates of residual glomerular filtration rate (GFR). Secondary outcomes included the rates of mechanical complications, the rates of infectious complications and complications of ESRD. Results: We found residual GFR decline were faster in HD-CAPD group than in APD-CAPD group (0.06 ml/min/w vs 0.03ml/min/w, P<0.01). The incidences of mechanical complications were similar in APD-CAPD group comparing with HD-CAPD group, including hernia (2.9% vs 3.0%, P=1.00), catheter malposition (0.02 episodes/patient-months vs 0.02 episodes/patient-months, P=0.70), leakage (5.9% vs 6.1%, P=1.00) and omental wrap (0 episode vs 3 episodes, P=0.368). Though the one-year overall infection rates were similar (0.03 episodes/patient-months vs 0.05 episodes/patient-months, P=0.10), APD-CAPD group had lower rate of bacteremia compared to HD-CAPD group (0 episodes/patient-months vs 0.02 episodes/patient-months, P<0.01). Conclusions: Both APD and HD could be used for patients who need to start dialysis in an unplanned manner. APD may have the advantage in protecting residual renal functions among these patients

Supplementary Material for: Secreted Expression of a Hyperthermophilic α-Amylase Gene from <b><i>Thermococcus</i></b> sp. HJ21 in <b><i>Bacillus subtilis</i></b>

The hyperthermophilic α-amylase from <i>Thermococcus</i> sp. HJ21 possesses unique traits (Ca²⁺-independent thermostability and optimal temperature of 95°C) that make it a great potential candidate for use in the food industry. However, this Archaea isolated from a deep-sea thermal vent requires strict control of culture conditions and produces only small amounts of α-amylase. To solve these problems, the α-amylase gene was cloned and expressed in <i>Bacillus subtilis</i>, which is an ideal food-grade host for heterologous protein expression. To express high levels of this α-amylase in <i>B. subtilis</i>, the promoters P_<i>grac</i>, P_<i>xylA</i>, P43, and P_<i>hag</i> were used to construct four different expression vectors for testing. The vector containing the P_<i>xylA</i> promoter was found to have the highest transcriptional activity and produce the highest amylase activity (19.6 U/ml). To test the secretion efficiency of signal peptides in <i>B. subtilis</i>, three signal peptides were cloned and fused to the α-amylase gene (lacking its native signal peptide). The optimal signal peptide was S_<i>amyQ</i>, with a secretion efficiency of approximately 90%. These results indicate that the promoter P_<i>xylA</i> and signal peptide S_<i>amyQ</i> tested in this study may be useful for the expression and secretion of archaeal proteins in <i>B. subtilis</i>

Supplementary Material for: Demineralized Dentin Matrix Induces Odontoblastic Differentiation of Dental Pulp Stem Cells

<br>The aim of this study was to investigate the effect of demineralized dentin matrix (DDM) on dental pulp stem cells (DPSCs) and the potential of complexes with DPSCs and DDM for mineralized tissue formation. Stem cells derived from the dental pulp of healthy pigs aged 18 months were isolated and cultured. DPSCs were incubated with alpha-minimum essential medium treated with DDM extract at 1 mg/ml (DDM1) or 10 mg/ml (DDM10). The concentrations of 3 growth factors in DDM extract was measured by enzyme-linked immunosorbent assay. Adhesion of DPSCs on DDM and hydroxyapatite-tricalcium phosphate (HA-TCP) surfaces was observed using scanning electron microscopy. Cell proliferation was evaluated with cell counting kit-8 and migration by Transwell migration assays. Odontoblastic differentiation was assessed by alkaline phosphatase (ALP) and alizarin red staining, ALP activity and real-time polymerase chain reaction analysis of markers of ALP, runt-related transcription factor 2, type I collagen, dentin matrix acidic phosphoprotein-1, osteonectin and dentin sialophosphoprotein (DSPP). Finally, DPSCs were combined with DDM and placed subcutaneously in nude mice for 12 weeks; DPSCs combined with HA-TCP and DDM alone served as controls. DDM could promote DPSC adhesion, migration and odontoblastic differentiation. Mineralized tissue formation was observed with the DPSC and DDM combination and the DPSC and HA-TCP combination. The mineralized tissue of the DPSC + DDM combination stained positive for DSPP, similar to the dentin tissue. These results indicate that DDM induces DPSC odontoblastic differentiation, suggesting applications for dentin regeneration

Erratum: A Retrospective Analysis of Stereoelectroencephalography and Subdural Electroencephalography for Preoperative Evaluation of Intractable Epilepsy

<b><i>Background:</i></b> Different methods for intracranial electrode recording have various advantages and disadvantages, and controversy exists regarding the complications of stereoelectroencephalography (SEEG) and subdural EEG. <b><i>Objective:</i></b> The purpose of this study was to determine the efficacy and safety of SEEG by comparing it with subdural EEG. <b><i>Methods:</i></b> Data from 100 patients who underwent SEEG (<i>n</i> = 48) and subdural EEG (<i>n</i> = 52) to evaluate the epileptogenic zone were collected from June 2011 to June 2015. The evaluation results, surgical outcomes, and complications were compared. <b><i>Results:</i></b> No significant differences were noted between the SEEG and subdural EEG groups in identifying the epileptogenic zone or undergoing epileptic surgery. Of the 88 patients who underwent epilepsy surgery after assessment, 59.5% in the SEEG group and 52.2% in the subdural EEG group became seizure free. No significant differences in postoperative seizure control or intelligence improvement were noted. The overall complication rate in SEEG patients (8/48; 16.7%) was lower than that in subdural EEG patients (13/52; 25%), particularly for hemorrhage and infection (4.2 vs. 17.3%, <i>p</i> < 0.05). <b><i>Conclusions:</i></b> This retrospective review indicates that SEEG has low associated complications, particularly regarding hemorrhage and infection. SEEG is a safe and effective method for intracranial monitoring

Supplementary Material for: Identification of Subpathway Signatures For Ovarian Cancer Prognosis by Integrated Analyses of High-Throughput miRNA and mRNA Expression

<b><i>Background/Aims:</i></b> Ovarian cancer (OC) causes more death and serious conditions than any other female reproductive cancers, and many expression signatures have been identified for OC prognoses. However, no significant overlap is found among signatures from different studies, indicating the necessity of signature identifications at the functional level. <b><i>Methods:</i></b> We performed an integrated analyses of miRNA and gene expressions to identify OC prognostic subpathways (pathway regions). Using The Cancer Genome Atlas data set, we identified core prognostic subpathways, and calculated subpathway risk scores using both miRNA and gene components. Finally, we performed global risk impact analyses to optimize core subpathways using the random walk algorithm. <b><i>Results:</i></b> Subpathway-level analyses displayed more robust results than the gene- and miRNA-level analyses. Moreover, we verified the advantage of core subpathways over the entire pathway-based results and their prognostic performance in two independent validation data sets. Based on the global impact score, 13 subpathway signatures were selected and a combined subpathway-based risk score was further calculated for OC patient prognoses. <b><i>Conclusions:</i></b> Overall, it was possible to systematically perform integrated analyses of the expression levels of miRNAs and genes to identify prognostic subpathways and infer subpathway risk scores for use in OC clinical applications

PowerPoint Slides for: Genetic Features of Chinese Patients with Gitelman Syndrome: Sixteen Novel SLC12A3 Mutations Identified in a New Cohort

<i>Background:</i> Gitelman syndrome (GS) is an autosomal recessive renal tubulopathy caused by inactivating mutations in the <i>SLC12A3</i> gene. Although hundreds of different mutations across the <i>SLC12A3</i> gene have been reported worldwide, data from mainland China are limited. We investigated the clinical manifestations and genetic features of Chinese patients with GS. <i>Methods:</i> Fifty-four unrelated Chinese patients with clinically diagnosed GS were included. Clinical manifestations and biochemical parameters were collected and analyzed. All exons and flanking regions of the <i>SLC12A3</i> and <i>CLCNKB</i> genes were screened by direct sequencing. <i>Results:</i>Weakness was the most commonly reported symptom in this cohort of patients with GS. In gender-based analyses, higher systolic blood pressure and urine protein excretion were observed in male patients. For genetic screening, 2 pathogenic<i>SLC12A3</i> mutations were identified in 38 patients (70.4%), 1 mutation in 11 patients (20.4%) and no mutation in 5 patients (9.3%). In total, 42 distinct pathogenic mutations throughout <i>SLC12A3</i> were identified; 16 were novel, including 9 missense, 1 deletion, 1 insertion, 3 splice site and 2 nonsense mutations. Eleven mutations were recurrently found in different patients. Among them, T60M and D486N were identified in 11 individuals. No <i>CLCNKB</i> mutations were found. <i>Conclusion:</i> Sixteen novel <i>SLC12A3</i> pathogenic mutations were identified in a cohort of Chinese patients with GS. T60M and D486N were most frequent and appear to be important candidate alleles in Chinese patients with GS