Transcriptome profiling of indole-3-butyric acid-induced adventitious root formation in softwood cuttings of the Catalpa bungei variety ‘YU-1’ at different developmental stages

Peng Wang,Ya Li,Lingling Ma,Shu’an Wang,Linfang Li,Rutong Yang,Yuzhu Ma,Qing Wang 한국유전학회 2016 Genes & Genomics Vol.38 No.2

Catalpa bungei is a deciduous tree native to China. It is characterized as fast growing, being highly adaptable, and having excellent wood qualities. To better understand potential mechanisms involved in adventitious root (AR) formation, we performed transcriptome analysis of softwood cuttings of C. bungei ‘Yu-1’ at three stages of AR formation using the Illumina sequencing method. Following de novo assembly, 62,955 unigenes were obtained, 31,646 (50.26 %) of which were annotated. A total of 11,100 differentially expressed genes (DEGs), including 10,200 unique and 900 common, were identified in four comparisons. Based on the all GO enrichment networks, 46 common and 7 unique GO categories were identified. Cytoskeleton was only significantly enriched in the activation period, while DNA metabolic process was only significantly enriched in the callus formation. Functional annotation analysis revealed that many of these genes were involved in phenylpropanoid biosynthesis, glycolysis, and plant hormone metabolism, suggesting potential contributions to AR formation. Interestingly, the number of DEGs involved in glycolysis decreased while the number of DEGs involved in phenylpropanoid biosynthesis increased following the AR formative process. Overall, our comprehensive transcriptional overview will prove useful, not only in the understanding of molecular networks that regulate AR formation in C. bungei, but also for exploring genes that may improve rooting rates of other trees.

Potential Roles of Protease Inhibitors in Cancer Progression

Yang, Peng,Li, Zhuo-Yu,Li, Han-Qing Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.18

Proteases are important molecules that are involved in many key physiological processes. Protease signaling pathways are strictly controlled, and disorders in protease activity can result in pathological changes such as cardiovascular and inflammatory diseases, cancer and neurological disorders. Many proteases have been associated with increasing tumor metastasis in various human cancers, suggesting important functional roles in the metastatic process because of their ability to degrade the extracellular matrix barrier. Proteases are also capable of cleaving non-extracellular matrix molecules. Inhibitors of proteases to some extent can reduce invasion and metastasis of cancer cells, and slow down cancer progression. In this review, we focus on the role of a few proteases and their inhibitors in tumors as a basis for cancer prognostication and therapy.

AIDS-Related Non-Hodgkin Lymphoma: Imaging Feature Analysis of 27 Cases and Correlation with Pathologic Findings

Yang, Jun,Wang, Peng,Lv, Zhi-Bin,Wei, Lian-Gui,Xu, Yun-Liang,Zhou, An,Xu, Dong-Hai,Ma, Da-Qing Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.18

Background: Some tumor types are related to HIV, including non-Hodgkin lymphoma (NHL). The morbidity and mortality of NHL has remained high, even after highly active antiretroviral therapy (HAART) was introduced. We collected cases of AIDS with NHL, and evaluated the imaging features and strategies for diagnosis. Materials and Methods: There were 27 patients with AIDS and tumors confirmed by pathology. There were 9 patients with Burkitt lymphoma, 16 with diffuse large B cell lymphomas (DLBCLs), and 2 with primary central nervous system (PCNS) lymphomas. All of the patients underwent a series of imaging studies. Three radiologists analyzed the images, and any disagreement was discussed until consensus was reached. Results: The radiologic manifestations of AIDS with NHL were mainly masses and lymphadenopathy, 3 patients having one mass and 12 two or more masses. 7 patients had lymphadenopathy in one site and 3patients had lymphadenopathy in two or more sites. Coarse mucosal folds, thickening of the gastrointestinal wall, and lumen narrowing were typical manifestations of NHL within the gastrointestinal tract. There were 4 patients with masses and 5 with lymphadenopathy inthe 9 with Burkitt lymphoma, and 11 patients with masses 5 with lymphadenopathy in the 16 with DLBCLs. Conclusion: NHL is a malignancy that usually occurs in patients with AIDS. Imaging is an important method by which to evaluate lesions, masses, and lymphadenopathy. Fine needle aspiration biopsy and stereotaxis biopsy are useful methods by which to diagnose NHL.

Transcriptome analysis reveals critical genes and key pathways involved in early phyllotaxy development in maize

Yang Zhao,Xiaojian Peng,Wenbo Chai,Yingquan Tan,Qing Dong,Haiyang Jiang,Beijiu Cheng 한국유전학회 2017 Genes & Genomics Vol.39 No.1

Integrated networks of gene expression, hormonal signaling and metabolite sensing regulate phyllotaxy pattern development. In this study, we characterized differentially expressed genes (DEGs) between maize plants with alternate and opposite phyllotaxies. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that 2432 DEGs were involved in biological processes, molecular functions, cellular components and many pathways. Importantly, we identified 19 DEGs related to plant hormone signal transduction. Additionally, we identified four main alternative splicing types: skipped exons, retained introns, alternative 50-splice sites, and alternative 30-splice sites, which exhibited different characteristics in the alternate and opposite phyllotaxy libraries. The reliability of the sequencing data was verified through using quantitative real-time reverse transcription PCR analysis of the 19 genes: 15 were validated to play a role in phytohormone signal transduction pathways. Taken together, our data provide new insight into the mechanisms of phyllotaxy pattern development, and will increase our understanding of how relative changes in gene expression determine alternate/opposite phyllotaxy in maize.

Association of preoperative body mass index with surgical textbook outcomes following hepatectomy for hepatocellular carcinoma: A multicenter study of 1,206 patients

Zhi-Peng LIU,Lan-Qing YAO,Yong-Kang DIAO,Zi-Xiang CHEN,Zi-Han FENG,Timothy M. PAWLIK,Wan Yee LAU,Feng SHEN,Zhi-Yu CHEN,Tian YANG 한국간담췌외과학회 2022 Annals of hepato-biliary-pancreatic surgery Vol.26 No.-

Magnetic Resonance Image Manifestations of the Atypical Meningioma

Wu, Qing-Wu,Yan, Rui-Fang,Li, Qiang,Hu, Ying,Zhou, Feng-Mei,Ren, Ji-Peng,Yang, Rui-Min,Zhang, Yan Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Through retrospective analysis of 13 cases of magnetic resonance image (MRI) manifestations of atypical meningiomas confirmed by operation and pathology in the First Affiliated Hospital of Xinxiang Medical University, the objective of this study was to evaluate the diagnostic value of MRI in order to improve the accuracy rate of preoperative diagnosis. In this retrospective analysis of MRI findings for atypical meningiomas in First Affiliated Hospital of Xinxiang Medical University from January to July in 2012, the location, morphology and tumor signals and other tumor imaging characteristics were covered. In 13 cases of atypical meningioma patients of this group, most tumors were located at typical sites (10/13), mainly the falx cerebri, parasagittal, convexity, saddle area. Only two cases were at atypical locations, 1 in the cerebellar hemisphere and 1 in a lateral ventricle. Most of the tumors showed T1 and T2 isointensity signals, and necrosis, calcification, and peritumoral edema were always featured. DWI showed isointensity in 11 cases (11/13), and hyperintensity in 2. Some 9 cases had dural tail signs, 12 had accurate positioning (12/13), and 2 were postoperative recurrences. MRI has high value in the diagnosis of atypical meningiomas, with important roles in early clinical diagnosis, treatment and prognosis evaluation.

The thermal stability of atomic layer deposited HfLaOx: Material and electrical characterization

Wen Yang,Qing-Qing Sun,Run-Chen Fang,Lin Chen,Peng Zhou,Shi-Jin Ding,David Wei Zhang 한국물리학회 2012 Current Applied Physics Vol.12 No.6

HfLaOx based Metaleoxideesemiconductor capacitors were fabricated by atomic layer deposition in this work. The material and electrical properties of the films along with the high temperature thermal treatment were investigated. It was found that samples undergoing annealing at 900 ℃ exhibited the best performance. The film was found to be crystallized to a cubic structure at 900 ℃, and the roughness of the films was estimated to be 0.332 nm. For electrical characterization, the C-V curve of the film is in good agreement with the corresponding simulated curve, and the capacitor does not show any hysteresis. Moreover, the Dit near the center of silicon band gap exhibits lowest value, and it was calculated to be 2.28 × 1011 eV-1 cm-2. HfLaOx based Metaleoxideesemiconductor capacitors were fabricated by atomic layer deposition in this work. The material and electrical properties of the films along with the high temperature thermal treatment were investigated. It was found that samples undergoing annealing at 900 ℃ exhibited the best performance. The film was found to be crystallized to a cubic structure at 900 ℃, and the roughness of the films was estimated to be 0.332 nm. For electrical characterization, the C-V curve of the film is in good agreement with the corresponding simulated curve, and the capacitor does not show any hysteresis. Moreover, the Dit near the center of silicon band gap exhibits lowest value, and it was calculated to be 2.28 × 1011 eV-1 cm-2.

Knockdown of HMGN5 Expression by RNA Interference Induces Cell Cycle Arrest in Human Lung Cancer Cells

Chen, Peng,Wang, Xiu-Li,Ma, Zhong-Sen,Xu, Zhong,Jia, Bo,Ren, Jin,Hu, Yu-Xin,Zhang, Qing-Hua,Ma, Tian-Gang,Yan, Bing-Di,Yan, Qing-Zhu,Li, Yan-Lei,Li, Zhen,Yu, Jin-Yan,Gao, Rong,Fan, Na,Li, Bo,Yang, Jun Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.7

HMGN5 is a typical member of the HMGN (high mobility group nucleosome-binding protein) family which may function as a nucleosomal binding and transcriptional activating protein. Overexpression of HMGN5 has been observed in several human tumors but its role in tumorigenesis has not been fully clarified. To investigate its significance for human lung cancer progression, we successfully constructed a shRNA expression lentiviral vector in which sense and antisense sequences targeting the human HMGN5 were linked with a 9-nucleotide loop. Inhibitory effects of siRNA on endogenous HMGN5 gene expression and protein synthesis were demonstrated via real-time RT-PCR and western blotting. We found HMGN5 silencing to significantly inhibit A549 and H1299 cell proliferation assessed by MTT, BrdU incorporation and colony formation assays. Furthermore, flow cytometry analysis showed that specific knockdown of HMGN5 slowed down the cell cycle at the G0/G1 phase and decreased the populations of A549 and H1299 cells at the S and G2/M phases. Taken together, these results suggest that HMGN5 is directly involved in regulation cell proliferation in A549 and H1299 cells by influencing signaling pathways involved in cell cycle progression. Thus, our finding suggests that targeting HMGN5 may be an effective strategy for human lung cancer treatment.

Molecular and Cellular Microbiology / Biomedical Sciences : Surface-Displayed IL-10 by Recombinant Lactobacillus plantarum Reduces Th1 Responses of RAW264.7 Cells Stimulated with Poly(I:C) or LPS

( Ruo Peng Cai ),( Yan Long Jiang ),( Wei Yang ),( Wen Tao Yang ),( Shao Hua Shi ),( Chun Wei Shi ),( Jing Tao Hu ),( Wei Gu ),( Li Ping Ye ),( Fang Yu Zhou ),( Qing Long Gong ),( Wen Yu Han ),( Guil 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.2

Recently, poly-γ-glutamic acid synthetase A (pgsA) has been applied to display exogenous proteins on the surface of Lactobacillus casei or Lactococcus lactis, which results in a surfacedisplayed component of bacteria. However, the ability of carrying genes encoded by plasmids and the expression efficiency of recombinant bacteria can be somewhat affected by the longer gene length of pgsA (1,143 bp); therefore, a truncated gene, pgsA, was generated based on the characteristics of pgsA by computational analysis. Using murine IL-10 as an exogenous gene, recombinant Lactobacillus plantarum was constructed and the capacity of the surface-displayed protein and functional differences between exogenous proteins expressed by these strains were evaluated. Surface expression of IL-10 on both recombinant bacteria with anchorins and the higher expression levels in L. plantarum-pgsA’-IL-10 were confirmed by western blot assay. Most importantly, up-regulation of IL-1β, IL-6, TNF-α, IFN-γ, and the nuclear transcription factor NF-κB p65 in RAW264.7 cells after stimulation with Poly(I:C) or LPS was exacerbated after co-culture with L. plantarum-pgsA. By contrast, IL-10 expressed by these recombinant strains could reduce these factors, and the expression of these factors was associated with recombinant strains that expressed anchorin (especially in L. plantarum-pgsA’-IL-10) and was significantly lower compared with the anchorin-free strains. These findings indicated that exogenous proteins could be successfully displayed on the surface of L. plantarum by pgsA or pgsA’, and the expression of recombinant bacteria with pgsA’ was superior compared with bacteria with pgsA.

Investigation of Data Representation Issues in Computerizing Clinical Practice Guidelines in China

Danhong Liu,Qing Ye,Peng Yang,Yongyong Xu,Jingkuan Su 대한의료정보학회 2014 Healthcare Informatics Research Vol.20 No.3

Objectives: From the point of view of clinical data representation, this study attempted to identify obstacles in translating clinical narrative guidelines into computer interpretable format and integrating the guidelines with data in Electronic Health Records in China. Methods: Based on SAGE and K4CARE formulism, a Chinese clinical practice guideline for hypertension was modeled in Protégé by building an ontology that had three components: flowchart, node, and vMR. Meanwhile, data items imperative in Electronic Health Records for patients with hypertension were reviewed and compared with those from the ontology so as to identify conflicts and gaps between. Results: A set of flowcharts was built. A flowchart comprises three kinds of node: State, Decision, and Act, each has a set of attributes, including data input/output that exports data items, which then were specified following ClinicalStatement of HL7 vMR. A total of 140 data items were extracted from the ontology. In modeling the guideline, some narratives were found too inexplicit to formulate, and encoding data was quite difficult. Additionally, it was found in the healthcare records that there were 8 data items left out, and 10 data items defined differently compared to the extracted data items. Conclusions: The obstacles in modeling a clinical guideline and integrating with data in Electronic Health Records include narrative ambiguity of the guideline, gaps and inconsistencies in representing some data items between the guideline and the patient’ records, and unavailability of a unified medical coding system. Therefore, collaborations among various participants in developing guidelines and Electronic Health Record specifications is needed in China.