Genome-wide identification, evolution and expression analysis of the FtsH gene during fruit development in pear (Pyrus bretschneideri)

Guo Zhihua,Gao Xin,Cai Huaqing,Yu Lu,Gu Chao,Zhang Shao Ling 한국식물생명공학회 2021 Plant biotechnology reports Vol.15 No.4

Filtration temperature-sensitive H (FtsH) is an ATP-dependent protease family that plays important roles in many aspects of cellular processes and environmental adaption. However, little information is available about the FtsH genes in pear (Pyrus bretschneideri). In this study, 19 PbrFtsH genes were identified and classified into eight groups with several subgroups. The FtsH genes in pear show high sequence and structural conservation in the coding regions, and the majority of the FtsH members were located on the chromosome 3 (three members), chromosome 9 (four members), and chromosome 15 (three members). The WGD/segmenta, dispersed duplication played a major driving force in pear FtsH evolution. A Synteny analy- sis provided deep insight into the evolutionary relationships of PbrFtsH genes. The subcellular localization of the PbrFtsH genes showed them in the mitochondrion or chloroplast. Expression profiles derived from transcriptome data and RT-qPCR analysis revealed distinct expression patterns of PbrFtsH genes in different fruit developmental stages. These results provided valuable information that extends our understanding of the function, evolution and expression profile of the FtsH family during fruit development in pear, and a foundation for the further functional characterization of PbrFtsH genes, which can be applied to pear crop improvement.

Exploring the Creeping Landslide Characteristics Based on the Time Series InSAR in the Xianshuihe Fault Zone, Southwest China

( Zhihua Yang ),( Xiaoyi Liu ),( Changbao Guo ) 대한지질공학회 2019 대한지질공학회 학술발표회논문집 Vol.2019 No.2

The Xianshuihe Fault in the southwest China presents strong activities Since the Holocene. Under the joint action of strong earthquakes, fault activities and heavy rainfall, the landslides have shown high development intensity in the Xianshuihe fault zone and bring a serious threat to the safety of human life and property. In this study, the SBAS-InSAR method and ALOS PALSAR data (15 scenes) are used to calculate and analyze the deformation characteristics of the creeping landslide between 2007 and 2011. The results show that the active effect of the Xianshuihe Fault has an important influence on the landslide development and occurrence. The closer distance to the Xianshuihe Fault is, the more stable coherent points is, the greater landslide cumulative displacement is. A total of 98 creeping landslides in the Xianshuihe Fault zone are identified, which develop as a linear distribution on both sides of the Xianshuihe Fault. And, the surface deformation and development characteristics of several typical creeping landslides are analyzed in-depth. So, the InSAR method can be used to effectively analyze the slow surface deformation, change laws and development characteristics of creeping landslide in the active fault zone. The study results have a certain guiding role on the landslide prevention and mitigation along the Xianshuihe Fault zone and the similar tectonic activity area.

A Bi-objective Game-based Task Scheduling Method in Cloud Computing Environment

Wanwan Guo,Mengkai Zhao,Zhihua Cui,Liping Xie 한국인터넷정보학회 2022 KSII Transactions on Internet and Information Syst Vol.16 No.11

The task scheduling problem has received a lot of attention in recent years as a crucial area for research in the cloud environment. However, due to the difference in objectives considered by service providers and users, it has become a major challenge to resolve the conflicting interests of service providers and users while both can still take into account their respective objectives. Therefore, the task scheduling problem as a bi-objective game problem is formulated first, and then a task scheduling model based on the bi-objective game (TSBOG) is constructed. In this model, energy consumption and resource utilization, which are of concern to the service provider, and cost and task completion rate, which are of concern to the user, are calculated simultaneously. Furthermore, a many-objective evolutionary algorithm based on a partitioned collaborative selection strategy (MaOEA-PCS) has been developed to solve the TSBOG. The MaOEA-PCS can find a balance between population convergence and diversity by partitioning the objective space and selecting the best converging individuals from each region into the next generation. To balance the players' multiple objectives, a crossover and mutation operator based on dynamic games is proposed and applied to MaPEA-PCS as a player's strategy update mechanism. Finally, through a series of experiments, not only the effectiveness of the model compared to a normal many-objective model is demonstrated, but also the performance of MaOEA-PCS and the validity of DGame.

High expression of HOXC6 predicts a poor prognosis and induces proliferation and inflammation in multiple myeloma cells

Li Zhihua,Wang Yaru,Hou Xiaoxu,Guo Luyao,Li Yanling,Ma Yanping,Ma Yanping 한국유전학회 2023 Genes & Genomics Vol.45 No.7

Background Multiple myeloma (MM) is a common blood system malignance accompanied by monoclonal plasma cell hyperplasia. Homeobox C6 (HOXC6) acts as an oncogene in various cancers, but its function on MM is elusive. Objective The role of HOXC6 on MM development was clarified in this study. Methods HOXC6 expression and its clinical significance were determined in the peripheral blood samples collected from forty MM patients and thirty healthy adult volunteers. The overall survival was evaluated by Kaplan-Meier analysis with the log-rank test. Cell viability, proliferation and apoptosis were measured by CCK-8, EdU assay and Flow cytometry in U266 and MM.1R cells. Tumor growth was estimated by a xenograft assay. The apoptosis of tumor tissues was evaluated using TUNEL staining. The protein level in tissues was tested by immunohistochemistry. Results The HOXC6 expression was elevated in MM and high HOXC6 level was associated with the poor overall survival of MM. Besides, the HOXC6 expression was associated with hemoglobin level and ISS stage. Furthermore, silencing HOXC6 suppressed cell proliferation, induced cell apoptosis, and restrained the secretion of inflammatory factors (TNF-α, IL-6, and IL-8) in MM cells through inactivating the NF-κB pathway. Moreover, silencing HOXC6 suppressed the tumor growth of MM, the inflammatory factors levels, and the activation of NF-κB pathway but enhanced apoptosis in vivo. Conclusion HOXC6 was elevated in MM and associated with poor survival. Knockdown of HOXC6 suppressed proliferation, inflammation and tumorigenicity of MM cells via inactivating the NF-κB pathway. HOXC6 may be a meaningful target for MM therapy.

Model diagnostics of parametric Tobit model based on cumulative residuals

Sun Zhihua,Guo Yuanyuan,Xie Tianfa,Wang Miaomiao 한국통계학회 2021 Journal of the Korean Statistical Society Vol.50 No.1

In this paper, we investigate the adequate check of the parametric Tobit model. A Cramér–Von Mises type test statistic is constructed, and its asymptotic properties under the null and alternative hypotheses are rigorously studied. The method is efective for the adequacy check of parametric regression models with a scalar or multivariate covariate. Furthermore, it avoids the nonparametric smoothing of the regression function and the choice of the smoothing parameter. Simulation studies are conducted to compare the performance of the proposed test procedure and the existing methods in the literature. A real data set of income is analyzed by applying the proposed method.

Cloning and Functional Analysis of a cDNA Encoding Ginkgo biloba Farnesyl Diphosphate Synthase

Kexuan Tang,Peng Wang,Zhihua Liao,Liang Guo,Wenchao Li,Min Chen,Yan Pi,Yifu Gong,Xiaofen Sun 한국분자세포생물학회 2004 Molecules and cells Vol.18 No.2

Farnesyl diphosphate synthase (FPS; EC2.5.1.1/EC2. 5.1.10) catalyzes the synthesis of farnesyl diphosphate, and provides precursor for biosynthesis of sesquiterpene and isoprenoids containing more than 15 isoprene units in Ginkgo biloba. Here we report the cloning, characterization and functional analysis of a new cDNA encoding FPS from G. biloba. The full-length cDNA (designated GbFPS) had 1731 bp with an open reading frame of 1170 bp encoding a polypeptide of 390 amino acids. The deduced GbFPS was similar to other known FPSs and contained all the conserved regions of trans-prenyl chain-elongating enzymes. Structural modeling showed that GbFPS had the typical structure of FPS, the most prominent feature of which is the arrangement of 13 core helices around a large central cavity. Southern blot analysis revealed a small FPS gene family in G. biloba. Expression analysis indicated that GbFPS expression was high in roots and leaves, and low in stems. Functional complementation of GbFPS in an FPS-deficient strain confirmed that GbFPS mediates farnesyl diphosphate biosynthesis.

Effect of aberrantly methylated androgen receptor target gene PCDH7 on the development of androgen-independent prostate cancer cells

Siqi Xu,Xiaoyan Wu,Zhihua Tao,Hongsheng Li1,Chenliang Fan,Songjin Chen,Jianwei Guo,Yao Ning,Xuqi Hu 한국유전학회 2020 Genes & Genomics Vol.42 No.3

Background Androgen-independent prostate cancer (AIPC) is an extremely malignant tumor developed from the androgen dependent (ADPC). However, the mechanism of transition process from ADPC to AIPC remains unknown. Objective Here we aimed to identify the androgen receptor (AR) target gene and its roles in AIPC. Methods Target genes of AR were identified by ChIP-seq in AIPC cells. AR target gene PCDH7 was detected by real time PCR and western blot. Methylation of PCDH7 was measured by bisulfite sequencing and bisulfite amplicon sequencing. Cell growth, invasion and apoptosis were measured by CCK-8, transwell and flow cytometry, respectively. Results AR was significantly enriched in the upstream of PCDH7 gene. The expression of PCDH7 was significantly decreased, while the methylation of PCDH7 was increased in the AIPC cells compared to the ADPC cells. DNA methyltransferase inhibitor significantly suppressed the methylation and increased the mRNA and protein level of PCDH7. Moreover, overexpression of DNMT1 remarkably reduced the mRNA and protein level of PCDH7. DNA methyltransferase inhibitor decreased the cell growth and invasion while promote the cell apoptosis in the AIPC cells. AR significantly target PCDH7, whose hypermethylation may repress cell growth and invasion, and promote apoptosis in AIPC. Conclusions This study might provide a novel potential target for the treatment of AIPC.

Hypoxia Mediates Runt-Related Transcription Factor 2 Expression via Induction of Vascular Endothelial Growth Factor in Periodontal Ligament Stem Cells

Xu, Qian,Liu, Zhihua,Guo, Ling,Liu, Rui,Li, Rulei,Chu, Xiang,Yang, Jiajia,Luo, Jia,Chen, Faming,Deng, Manjing Korean Society for Molecular and Cellular Biology 2019 Molecules and cells Vol.42 No.11

Periodontitis is characterized by the loss of periodontal tissues, especially alveolar bone. Common therapies cannot satisfactorily recover lost alveolar bone. Periodontal ligament stem cells (PDLSCs) possess the capacity of self-renewal and multilineage differentiation and are likely to recover lost alveolar bone. In addition, periodontitis is accompanied by hypoxia, and hypoxia-inducible $factor-1{\alpha}$ ($HIF-1{\alpha}$) is a master transcription factor in the response to hypoxia. Thus, we aimed to ascertain how hypoxia affects runt-related transcription factor 2 (RUNX2), a key osteogenic marker, in the osteogenesis of PDLSCs. In this study, we found that hypoxia enhanced the protein expression of $HIF-1{\alpha}$, vascular endothelial growth factor (VEGF), and RUNX2 ex vivo and in situ. VEGF is a target gene of $HIF-1{\alpha}$, and the increased expression of VEGF and RUNX2 proteins was enhanced by cobalt chloride ($CoCl_2$, $100{\mu}mol/L$), an agonist of $HIF-1{\alpha}$, and suppressed by 3-(5'-hydroxymethyl-2'-furyl)-1-benzyl indazole (YC-1, $10{\mu}mol/L$), an antagonist of $HIF-1{\alpha}$. In addition, VEGF could regulate the expression of RUNX2, as RUNX2 expression was enhanced by human VEGF ($hVEGF_{165}$) and suppressed by VEGF siRNA. In addition, knocking down VEGF could decrease the expression of osteogenesis-related genes, i.e., RUNX2, alkaline phosphatase (ALP), and type I collagen (COL1), and hypoxia could enhance the expression of ALP, COL1, and osteocalcin (OCN) in the early stage of osteogenesis of PDLSCs. Taken together, our results showed that hypoxia could mediate the expression of RUNX2 in PDLSCs via $HIF-1{\alpha}$-induced VEGF and play a positive role in the early stage of osteogenesis of PDLSCs.

Hypoxia Mediates Runt-Related Transcription Factor 2 Expression via Induction of Vascular Endothelial Growth Factor in Periodontal Ligament Stem Cells

Manjing Deng,Qian Xu,Zhihua Liu1,Ling Guo,Rui Liu,Rulei Li,Xiang Chu,Jiajia Yang,Jia Luo,Faming Chen 한국분자세포생물학회 2019 Molecules and cells Vol.42 No.11

Periodontitis is characterized by the loss of periodontal tissues, especially alveolar bone. Common therapies cannot satisfactorily recover lost alveolar bone. Periodontal ligament stem cells (PDLSCs) possess the capacity of self-renewal and multilineage differentiation and are likely to recover lost alveolar bone. In addition, periodontitis is accompanied by hypoxia, and hypoxia-inducible factor-1α (HIF-1α) is a master transcription factor in the response to hypoxia. Thus, we aimed to ascertain how hypoxia affects runt-related transcription factor 2 (RUNX2), a key osteogenic marker, in the osteogenesis of PDLSCs. In this study, we found that hypoxia enhanced the protein expression of HIF-1α, vascular endothelial growth factor (VEGF), and RUNX2 ex vivo and in situ. VEGF is a target gene of HIF-1α, and the increased expression of VEGF and RUNX2 proteins was enhanced by cobalt chloride (CoCl2, 100 μmol/L), an agonist of HIF-1α, and suppressed by 3-(5′-hydroxymethyl-2′-furyl)-1-benzyl indazole (YC-1, 10 μmol/L), an antagonist of HIF-1α. In addition, VEGF could regulate the expression of RUNX2, as RUNX2 expression was enhanced by human VEGF (hVEGF165) and suppressed by VEGF siRNA. In addition, knocking down VEGF could decrease the expression of osteogenesis-related genes, i.e., RUNX2, alkaline phosphatase (ALP), and type I collagen (COL1), and hypoxia could enhance the expression of ALP, COL1, and osteocalcin (OCN) in the early stage of osteogenesis of PDLSCs. Taken together, our results showed that hypoxia could mediate the expression of RUNX2 in PDLSCs via HIF-1α-induced VEGF and play a positive role in the early stage of osteogenesis of PDLSCs

MiR-466d Targeting MMP13 Promotes the Differentiation of Osteoblasts Exposed to a Static Magnetic Field

Fei Tong,Hongmeng Cheng,Jun Guo,Jianyong Wu,Hongshan Ge,Zhihua Li 한국생물공학회 2023 Biotechnology and Bioprocess Engineering Vol.28 No.1

The static magnetic field (SMF) and miRNAs are involved in the regulation of bone remodeling. Hence, this study was designed to investigate the effects of SMF on the proliferation and differentiation of osteoblasts, as well as identify related miRNAs. SMF promoted osteoblast proliferation and differentiation and inhibited osteoblast apoptosis. High-throughput sequencing identified that 41 miRNAs were upregulated and 25 miRNAs down-regulated when osteoblasts were exposed to SMF. The enrichment analysis and validation results indicated differentially expressed miR-466d and its target gene MMP13. In osteoblasts, miR-466d could directly target MMP13, and miR-466d overexpression combined with the exposure to SMF promoted differentiation, suppressing MMP13 expression. SMF increased miR-466 expression in osteoblasts, thereby inhibiting MMP13 expression and increasing osteoblast differentiation ability.