The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

Xiao‑xia Ma,Yi‑ning Wang,Xiao‑an Cao,Xue‑rui Li,Yong‑sheng Liu,Jian‑hua Zhou,Xue‑peng Cai 한국유전학회 2018 Genes & Genomics Vol.40 No.9

The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (α-helix, β-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellular tRNA abundance variation might have potential effects on the formation of secondary structure of PPRV N protein.

Treatment of fever with traditional Chinese medicine according to Zheng on cancer patients (based on case reports)

Peng Cao,Lan-Ying Liu,Xue-Ting Cai,Xiao-Ning Wang,Jie-Ge Huo,Zhong-Ying Zhou 셀메드 세포교정의약학회 2012 셀메드 (CellMed) Vol.2 No.2

Fever in cancer patients is often due to the following causes: evil qi and toxity stagnancy, disorders of qi and blood, deficiencies of zang and fu organs, and the disorder of yin and yang. The treatments given to cancer patients with a fever are according to five: (a) Excessive inner heat and toxicants: remove heat and the toxicant, induce purgation. We use Cheng-Qi-Tang plus Qing-Wen-Bai-Du-Yin. (b) Tangle of damp and heat, and qi stagnancy: remove damp and heat, smooth the qi channel. We use Gan-Lu-Xiao-Du-Dan or San-Ren-Tang. (c) Obvious blood and heat stagnancy: remove heat and blood stasis. We use Xue-Fu-Zhu-Yu-Tang. (d) Deficiency of spleen qi, inner heat caused by a yin deficiency: nourish spleen qi and yin to remove the inner heat. We use Bu-Zhong-Yi-Qi-Tang or Xiao-Jian-Zhong-Tang. (e) Prominent yin deficiency and hectic fever: replenish yin and remove inner heat. We use Qing-Hao-Bie-Jia-Tang or Chai-Qian-Mei-Lian-San. The pathogenesis of fever in cancer patients is complicated. We can see both deficiency and excess in one differentiation. Therefore, we must make sure of it, then we can get the most effective treatment.

A Meta-Analysis of the Accuracy of Prostate Cancer Studies Which Use Magnetic Resonance Spectroscopy as a Diagnostic Tool

Peng Wang,You-min Guo,Min Liu,Yong-qian Qiang,Xiao-juan Guo,Yi-li Zhang,Xiao-Yi Duan,Qiu-Juan Zhang,Weifeng Liang 대한영상의학회 2008 Korean Journal of Radiology Vol.9 No.5

Objective: We aimed to do a meta-analysis of the existing literature to assess the accuracy of prostate cancer studies which use magnetic resonance spectroscopy (MRS) as a diagnostic tool. Materials and Methods: Prospectively, independent, blind studies were selected from the Cochrane library, Pubmed, and other network databases. The criteria for inclusion and exclusion in this study referenced the criteria of diagnostic research published by the Cochrane center. The statistical analysis was adopted by using Meta-Test version 6.0. Using the homogeneity test, a statistical effect model was chosen to calculate different pooled weighted values of sensitivity, specificity, and the corresponding 95% confidence intervals (95% CI). The summary receiver operating characteristic (SROC) curves method was used to assess the results. Results: We chose two cut-off values (0.75 and 0.86) as the diagnostic criteria for discriminating between benign and malignant. In the first diagnostic criterion, the pooled weighted sensitivity, specificity, and corresponding 95% CI (expressed as area under curve [AUC]) were 0.82 (0.73, 0.89), 0.68 (0.58, 0.76), and 83.4% (74.97, 91.83). In the second criterion, the pooled weighted sensitivity, specificity, and corresponding 95% CI were 0.64 (0.55, 0.72), 0.86 (0.79, 0.91) and 82.7% (68.73, 96.68). Conclusion: As a new method in the diagnostic of prostate cancer, MRS has a better applied value compared to other common modalities. Ultimately, large scale RCT randomized controlled trial studies are necessary to assess its clinical value. Objective: We aimed to do a meta-analysis of the existing literature to assess the accuracy of prostate cancer studies which use magnetic resonance spectroscopy (MRS) as a diagnostic tool. Materials and Methods: Prospectively, independent, blind studies were selected from the Cochrane library, Pubmed, and other network databases. The criteria for inclusion and exclusion in this study referenced the criteria of diagnostic research published by the Cochrane center. The statistical analysis was adopted by using Meta-Test version 6.0. Using the homogeneity test, a statistical effect model was chosen to calculate different pooled weighted values of sensitivity, specificity, and the corresponding 95% confidence intervals (95% CI). The summary receiver operating characteristic (SROC) curves method was used to assess the results. Results: We chose two cut-off values (0.75 and 0.86) as the diagnostic criteria for discriminating between benign and malignant. In the first diagnostic criterion, the pooled weighted sensitivity, specificity, and corresponding 95% CI (expressed as area under curve [AUC]) were 0.82 (0.73, 0.89), 0.68 (0.58, 0.76), and 83.4% (74.97, 91.83). In the second criterion, the pooled weighted sensitivity, specificity, and corresponding 95% CI were 0.64 (0.55, 0.72), 0.86 (0.79, 0.91) and 82.7% (68.73, 96.68). Conclusion: As a new method in the diagnostic of prostate cancer, MRS has a better applied value compared to other common modalities. Ultimately, large scale RCT randomized controlled trial studies are necessary to assess its clinical value.

Inhibition of RIPK1-dependent regulated acinar cell necrosis provides protection against acute pancreatitis via the RIPK1/NF- κB/AQP8 pathway

Gang Wang,Peng-yu Duan,Yuan Ma,Xi-na Li,Feng-zhi Qu,Liang Ji,Xiao-yu Guo,Wang-jun Zhang,Fan Xiao,Le Li,Ji-sheng Hu,Bei Sun 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

Currently, preliminary results have confirmed the existence of receptor-interacting protein kinase 3 (RIPK3) and mixed lineage kinase domain-like protein (MLKL)-dependent necroptosis of pancreatic acinar cells during early acute pancreatitis (AP), which might be a potential target for the effective regulation of necroinflammatory injury. However, the exact effect of receptor-interacting protein kinase 1 (RIPK1)-dependent regulated acinar cell necrosis on AP is still uncertain. In our study, we first explored the changes in the degree of local and systemic inflammation in AP rats when the activation of acinar cell RIPK1 was inhibited. The RIPK1 inhibitor Nec-1 was used to treat rats, and the levels of related inflammatory markers, necrosis indicators and apoptotic indicators were measured. Changes in pancreatic nuclear factor κB (NF-κB) and aquaporin 8 (AQP8) expression were noted. Next, the expression of AQP8 in AR42J cells was inhibited, and the degree of cell necrosis and inflammatory damage was found to be significantly reduced. Most importantly, we demonstrated that the RIPK1/NF-ĸB/AQP8 axis might be a potential regulatory pathway mediating RIPK1-dependent regulated acinar cell necrosis in early AP. Finally, we used the NF-κB inhibitor PDTC and Nec-1 to treat rats in different groups and measured the degree of pathological pancreatic injury, the activation of RIPK1, and the expression of NF-κB and AQP8. In summary, we hypothesized that there might be a RIPK1/NF-ĸB/AQP8 pathway controlling RIPK1-dependent regulated necrosis of acinar cells in AP, which might be a promising therapeutic target against AP-related injury.

Long-term Survivals, Toxicities and the Role of Chemotherapy in Early-Stage Nasopharyngeal Carcinoma Patients Treated with Intensity-modulated Radiation Therapy: A Retrospective Study with 15-year Follow-up

Lin Wang,Jingjing Miao,Huageng Huang,Boyu Chen,Xiao Xiao,Manyi Zhu,Yingshan Liang,Weiwei Xiao,Shaomin Huang,Yinglin Peng,Xiaowu Deng,Xing Lv,Weixiong Xia,Yanqun Xiang,Xiang Guo,Fei Han,Chong Zhao 대한암학회 2022 Cancer Research and Treatment Vol.54 No.1

Purpose This study was aimed to investigate long-term survivals and toxicities of early-stage nasopharyngeal carcinoma (NPC) in endemic area, evaluating the role of chemotherapy in stage II patients. Materials and Methods Totally 187 patients with newly diagnosed NPC and restaged American Joint Committee on Cancer/ International Union Against Cancer 8th T1-2N0-1M0 were retrospectively recruited. All received intensity-modulated radiotherapy (IMRT)±chemotherapy (CT) from 2001 to 2010. Results With 15.7-year median follow-up, 10-year locoregional recurrence-free survival, distant metastasis-free survival (DMFS), disease-specific survival (DSS), and overall survival (OS) were 93.3%, 93.5%, 92.9% and 88.2%, respectively. Multivariable analyses showed cervical lymph nodes positive and pre-treatment prognostic nutritional index ≥ 52.0 could independently predict DMFS (p=0.036 and p=0.011), DSS (p=0.014 and p=0.026), and OS (p=0.002 and p < 0.001); Charlson comorbidity index < 3 points could predict DSS (p=0.011); age > 45 years (p=0.002) and pre-treatment lactate dehydrogenase ≥ 240 U/L (p < 0.001) predicted OS. No grade 4 late toxicity happened; grade 3 late toxicities included subcutaneous fibrosis (4.3%), deafness or otitis (4.8%), skin dystrophy (2.1%), and xerostomia (1.1%). No differences on survivals were shown between IMRT+CT vs. IMRT alone in stage II patients, even in T2N1M0 (p > 0.05). Unsurprising, patients in IMRT+CT had more acute gastrointestinal reaction, myelosuppression, mucositis, late ear toxicity, and cranial nerve injury (all p < 0.05) than IMRT alone group. Conclusion Superior tumor control and satisfying long-term outcomes could be achieved with IMRT in early-stage NPC with mild late toxicities. As CT would bring more toxicities, it should be carefully performed to stage II patients.

Breastfeeding and Ovarian Cancer Risk: a Systematic Review and Meta-analysis of 40 Epidemiological Studies

Li, Da-Peng,Du, Chen,Zhang, Zuo-Ming,Li, Guang-Xiao,Yu, Zhi-Fu,Wang, Xin,Li, Peng-Fei,Cheng, Cheng,Liu, Yu-Peng,Zhao, Ya-Shuang Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.12

The present systematic review and meta-analysis was conducted to assess any association between breastfeeding and the risk of ovarian cancer. A systematic search of published studies was performed in PUBMED and EMBASE and by reviewing reference lists from retrieved articles through March 2013. Data extraction was conducted independently by two authors. Pooled relative risk ratios were calculated using random-effect models. Totals of 5 cohort studies and 35 case-control studies including 17,139 women with ovarian cancer showed a 30% reduced risk of ovarian cancer when comparing the women who had breastfed with those who had never breastfed (pooled RR = 0.70, 95% CI: 0.64-0.76; p = 0.00), with significant heterogeneity in the studies (p = 0.00; I2 = 76.29%). A significant decreasd in risk of epithelial ovarian cancer was also observed (pooled RR = 0.68, 95% CI: 0.61-0.76). When the participants were restricted to only parous women, there was a slightly attenuated but still significant risk reduction of ovarian cancer (pooled RR = 0.76, 95% CI: 0.69-0.83). For total breastfeeding duration, the pooled RRs in the < 6 months, 6-12 months and > 12 months of breastfeeding subgroups were 0.85 (95% CI: 0.77-0.93), 0.73 (95% CI: 0.65-0.82) and 0.64 (95%CI: 0.56-0.73), respectively. Meta-regression of total breastfeeding duration indicated an increasing linear trend of risk reduction of ovarian cancer with the increasing total breastfeeding duration (p = 0.00). Breastfeeding was inversely associated with the risk of ovarian cancer, especially long-term breastfeeding duration that demonstrated a stronger protective effect.

Evolution of ALPPS: The Simpler, Safer and Effective One---TELPP

( Shu You Peng ),( Xu An Wang ),( Cong Yun Huang ),( You Yong Zhang ),( Jiang Tao Li ),( De Fei Hong ),( Xiu Jun Cai ),( Yi Fang Wang ),( Xiao Liang ),( Jian Wei Wang ) 대한간학회 2017 춘·추계 학술대회 (KASL) Vol.2017 No.1

Aims: The characteristic of associating liver partition and portal vein ligation for staged hepatectomy(ALPPS) carries high mortality and morbidity. There is room for improvement. We suggest Terminal Branches Portal Vein Embolization (TBPVE) as a way to compart the liver. As a result, only a single surgical operation is required.This method is termed Terminal branches portal vein Embolization Liver Partition Planned hepatectomy (TELPP). Methods: Patients with unresectable primary or metastatic liver tumor were performed with TELPP. The procedure of TELPP was that in addition to PVE, embolization agent was infused to the terminal branches of portal vein of S5,S8 or S4. CT scan was taken one or two weeks later, and standard liver volume(SLV), FLR and FLR/SLV are calculated. Two weeks later when the FLR and liver function is appropriate, open or laparoscopic hepatectomy is performed. Results: The study included 11patients including hepatocellular carcinoma: n =8, intrahepatic cholangiocarcinoma: n = 1, hilarcholangiocarcinoma: n =1, colorectal liver metastasis: n =1. After a waiting period of 14 days, the volume of theFLR had increased from 382mlto 578ml, representing a median volume increase of 51% (range =32.5%-86.7%). Of the 11patients with hepatectomy, right hemihepatectomy (n=2), extended right hemihepatectomy (n=5), right trisecmentectomy(2), extended left hemihepatectomy (n=1) and left trisecmentectomy(1). No patient died, and no serve perioperative morbidity occurred. Conclusions: ALPPS and all modifications need two-stage operations with a high morbidity and mortality rate. It seems that TELPP is very promising. It has the merit of ALPPS as extraordinarily rapid increasement of FLRvolume, yet the morbidity and mortality is much lower, owing to the fact that unlike ALPPS, there is no two liver raw surfaces left behind in the abdominal cavity to produce bile leak, as only single surgical operation is required

No Association Between the USP7 Gene Polymorphisms and Colorectal Cancer in the Chinese Han Population

Li, Xin,Wang, Yang,Li, Xing-Wang,Liu, Bao-Cheng,Zhao, Qing-Zhu,Li, Wei-Dong,Chen, Shi-Qing,Huang, Xiao-Ye,Yang, Feng-Ping,Wang, Quan,Wang, Jin-Fen,Xiao, Yan-Zeng,Xu, Yi-Feng,Feng, Guo-Yin,Peng, Zhi-Ha Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.5

Colorectal cancer (CRC), now the third most common cancer across the world, is known to aggregate in families. USP7 is a very important protein with an important role in regulating the p53 pathway, which is critical for genomic stability and tumor suppression. We here genotyped eight SNPs within the USP7 gene and conducted a case-control study in 312 CRC patients and 270 healthy subjects in the Chinese Han population. No significant associations were found for any single SNP and CRC risk. Our data eliminate USP7 as a potential candidate gene towards for CRC in the Han Chinese population.

Synthesis of Tailed Metalloporphyrins Modified with 2-Chloronicotinic Acid and Interactions with Human Serum Albumin

Shu-Jun Wang,Yu-Ling Peng,Cheng-Gen Zhang,Qi Peng Ma,Xiao Xia Peng,Li Lei Ren 대한화학회 2017 Bulletin of the Korean Chemical Society Vol.38 No.7

Two kinds of free-base tailed porphyrins modified with 2-chloronicotinic acid and the corresponding Zn porphyrins have been synthesized. They have been characterized by elemental analysis and NMR, UV/Vis, fluorescence spectra, and infrared spectroscopies. Their configurations have been optimized through theoretical calculations. The fluorescence quantum yields were determined by a comparative method. The interactions between the Zn porphyrins and human serum albumin have been studied by means of fluorescence spectra. The experimental results showed that the interaction mechanism involved a combined fluorescence quenching process (static and dynamic quenching) and that the main driving force was hydrophobic in nature. Quenching constants, binding constants, thermodynamic parameters, and binding distances have been determined.

Shortest Path Analyses in the Protein-Protein Interaction Network of NGAL (Neutrophil Gelatinase-associated Lipocalin) Overexpression in Esophageal Squamous Cell Carcinoma

Du, Ze-Peng,Wu, Bing-Li,Wang, Shao-Hong,Shen, Jin-Hui,Lin, Xuan-Hao,Zheng, Chun-Peng,Wu, Zhi-Yong,Qiu, Xiao-Yang,Zhan, Xiao-Fen,Xu, Li-Yan,Li, En-Min Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.16

NGAL (neutrophil gelatinase-associated lipocalin) is a novel cancer-related protein involves multiple functions in many cancers and other diseases. We previously overexpressed NGAL to analyze its role in esophageal squamous cell carcinoma (ESCC). In this study, a protein-protein interaction (PPI) was constructed and the shortest paths from NGAL to transcription factors in the network were analyzed. We found 28 shortest paths from NGAL to RELA, most of them obeying the principle of extracellular to cytoplasm, then nucleus. These shortest paths were also prioritized according to their normalized intensity from the microarray by the order of interaction cascades. A systems approach was developed in this study by linking differentially expressed genes with publicly available PPI data, Gene Ontology and subcellular localizaton for the integrated analyses. These shortest paths from NGAL to DEG transcription factors or other transcription factors in the PPI network provide important clues for future experimental identification of new pathways.