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Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats Article

Yifan Liu, Jing Chen, Zhonglin Liu, Zhaowei Hou, Bo Liang, Liying Wang, Lei Zhou, Libin Shou, Dandan Lin, Shizhong Yang, Jinfeng Liu, Xiaolin Wu, Jidong Gu, Bozhong Mu

Engineering 2023, Volume 24, Issue 5,   Pages 265-276 doi: 10.1016/j.eng.2021.08.027

Abstract:

The microbial conversion of alkanes to methane in hydrocarbon contaminated environments is an intrinsic bioremediation strategy under anoxic conditions. However, the mechanism of microbial methanogenic alkane degradation is currently unclear. Under ten-years of continuous efforts, we obtained a methanogenic n-alkane-degrading (C15–C20) enrichment culture that exhibited sustained improvements in the kinetic properties of methane production. The integrated metagenomic and metatranscriptomic analyses revealed that n-alkanes were mainly attacked by members of Desulfosarcinaceae, Firmicutes, and Synergistetes using the fumarate addition strategy, and were then further degraded in a common effort by Tepidiphilus members. Meanwhile, the abundant members of Anaerolineaceae were mainly responsible for cell debris recycling. However, according to the metatranscriptomic analyses, methane was predicted to be produced mainly via H2-dependent methylotrophic methanogenesis, primarily from necromass-derived trimethylamine mediated by Methanomethyliaceae within the candidate phylum Verstraetearchaeota. These findings reveal that H2-dependent methylotrophic methanogens, as well as methylotrophic methanogens, may play important ecological roles in the carbon cycle of hydrocarbon enriched subsurface ecosystems.

Keywords： Methanogenic hydrocarbon degradation     Oily sludge     Bioremediation     Alkanes    

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Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Frontiers of Medicine doi: 10.1007/s11684-023-1020-z

Abstract: Retroperitoneal liposarcoma (RLPS) is the main subtype of retroperitoneal soft sarcoma (RSTS) and has a poor prognosis and few treatment options, except for surgery. The proteomic and metabolic profiles of RLPS have remained unclear. The aim of our study was to reveal the metabolic profile of RLPS. Here, we performed proteomic analysis (n = 10), metabolomic analysis (n = 51), and lipidomic analysis (n = 50) of retroperitoneal dedifferentiated liposarcoma (RDDLPS) and retroperitoneal well-differentiated liposarcoma (RWDLPS) tissue and paired adjacent adipose tissue obtained during surgery. Data analysis mainly revealed that glycolysis, purine metabolism, pyrimidine metabolism and phospholipid formation were upregulated in both RDDLPS and RWDLPS tissue compared with the adjacent adipose tissue, whereas the tricarboxylic acid (TCA) cycle, lipid absorption and synthesis, fatty acid degradation and biosynthesis, as well as glycine, serine, and threonine metabolism were downregulated. Of particular importance, the glycolytic inhibitor 2-deoxy-D-glucose and pentose phosphate pathway (PPP) inhibitor RRX-001 significantly promoted the antitumor effects of the MDM2 inhibitor RG7112 and CDK4 inhibitor abemaciclib. Our study not only describes the metabolic profiles of RDDLPS and RWDLPS, but also offers potential therapeutic targets and strategies for RLPS.

Keywords： RLPS     proteomics     metabolomics     lipidomics     metabolism    

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Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Frontiers of Medicine 2014, Volume 8, Issue 1,   Pages 58-67 doi: 10.1007/s11684-014-0318-2

Abstract: Omics technologies allow high-throughput screening of sepsis biomarkers.This review paper serves as a reference for future studies that employ an integrated, multi-omics approach

Keywords： sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

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Efficacy and safety of benralizumab in patients with eosinophilic asthma: a meta-analysis of randomized

Ting Liu, Faping Wang, Geng Wang, Hui Mao

Frontiers of Medicine 2018, Volume 12, Issue 3,   Pages 340-349 doi: 10.1007/s11684-017-0565-0

Abstract: We conducted a meta-analysis to evaluate the safety and efficacy of different doses of benralizumab inRandomized-effect models were used in the meta-analysis to calculate the pooled mean difference, relativeFurthermore, our meta-analysis showed that benralizumab with 30 mg (every eight weeks) dosage can improve

Keywords： benralizumab     anti-interleukin-5     monoclonal antibody     eosinophilic asthma     meta-analysis    

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Association between telomere length and survival in cancer patients: a meta-analysis and review of literature

Xinsen Xu,Kai Qu,Qing Pang,Zhixin Wang,Yanyan Zhou,Chang Liu

Frontiers of Medicine 2016, Volume 10, Issue 2,   Pages 191-203 doi: 10.1007/s11684-016-0450-2

Abstract:

The relationship between telomere length and cancer survival has been widely studied. To gain a deeper insight, we reviewed the published studies. A total of 29 studies evaluated telomere length in the peripheral blood; 22 studies evaluated telomere length in the tumor tissue. First, in the peripheral blood studies, for solid tumor patients with shortened telomere length, the combined hazard ratios (HRs) for mortality and tumor progression were 1.21 (95%CI, 1.10–1.32) and 1.71 (95%CI, 1.37–2.13), respectively. Meanwhile, in hematology malignancy, the combined HRs for mortality and tumor progression were 2.83 (95%CI, 2.14–3.74) and 2.65 (95%CI, 2.18–3.22), respectively. Second, in the studies that use tumor tissue, for patients with shortened telomeres, the combined HRs for mortality and tumor progression were 1.26 (95%CI, 0.95–1.66) and 1.65 (95%CI, 1.26–2.15), respectively. In the studies that calculate the telomere length ratios of tumor tissue to adjacent normal mucosa, for patients with lower telomere length ratios, the combined HRs were 0.66 (95%CI, 0.53–0.83) and 0.74 (95%CI, 0.41–1.32) for mortality and tumor progression, respectively. In conclusion, shortened telomere in peripheral blood and tumor tissue might indicate poor survival for cancer patients. However, by calculating the telomere length ratios of tumor tissue to adjacent normal mucosa, the lower ratio might indicate better survival.

Keywords： telomere     survival     cancer     meta-analysis    

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Deciphering the pharmacological mechanism of Guan-Jie-Kang in treating rat adjuvant-induced arthritis using omics

Hudan Pan, Yanfang Zheng, Zhongqiu Liu, Zhongwen Yuan, Rutong Ren, Hua Zhou, Ying Xie, Liang Liu

Frontiers of Medicine 2019, Volume 13, Issue 5,   Pages 564-574 doi: 10.1007/s11684-018-0676-2

Abstract: Thus, this study establishes a new omics analytical method integrated with bioinformatics analysis for

Keywords： arthritis     traditional Chinese medicine     pharmacological mechanism     metabolism     adjuvant-induced arthritis     omics    

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Treatment outcomes of pulmonary tuberculosis in the past decade in the mainland of China: a meta-analysis

Xiangwei Li, Yu Yang, Jianmin Liu, Feng Zhou, Wei Cui, Ling Guan, Fei Shen, Cong Gao, Mufei Li, Qi Jin, Lei Gao

Frontiers of Medicine 2013, Volume 7, Issue 3,   Pages 354-366 doi: 10.1007/s11684-013-0257-3

Abstract: treatment outcomes of smear-positive pulmonary TB in the mainland of China in the past decade using meta-analysis

Keywords： tuberculosis     treatment     outcome     China     meta-analysis    

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Innate immune checkpoint Siglec10 in cancers: mining of comprehensive omics data and validation in patient

Frontiers of Medicine 2022, Volume 16, Issue 4,   Pages 596-609 doi: 10.1007/s11684-021-0868-z

Abstract: Sialic acid binding Ig-like lectin 10 (Siglec10) is a member of innate immune checkpoints that inhibits the activation of immune cells through the interaction with its ligand CD24 on tumor cells. Here, by analyzing public databases containing 64 517 patients of 33 cancer types, we found that the expression of Siglec10 was altered in 18 types of cancers and was associated with the clinical outcomes of 11 cancer types. In particular, Siglec10 was upregulated in patients with kidney renal clear cell carcinoma (KIRC) and was inversely associated with the prognosis of the patients. In 131 KIRC patients of our settings, Siglec10 was elevated in the tumor tissues of 83 (63.4%) patients compared with that in their counterpart normal kidney tissues. Moreover, higher level of Siglec10 was associated with advanced disease (stages III and IV) and worse prognosis. Silencing of CD24 in KIRC cells significantly increased the number of Siglec10-expressing macrophages phagocytosing KIRC cells. In addition, luciferase activity assays suggested that Siglec10 was a potential target of the transcription factors c-FOS and GATA1, which were identified by data mining. These results demonstrate that Siglec10 may have important oncogenic functions in KIRC, and represents a novel target for the development of immunotherapies.

Keywords： innate immune checkpoint     Siglec10     kidney renal clear cell carcinoma    

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An update and cumulative meta-analysis

Jiangang Pan,Mo Liu,Xing Zhou

Frontiers of Medicine 2014, Volume 8, Issue 2,   Pages 241-249 doi: 10.1007/s11684-014-0328-0

Abstract: recurrence in patients with NMIBC, we analyzed this relationship by conducting an updated detailed meta-analysis

Keywords： non-muscle invasive bladder cancer     bacillus Calmette-Guérin (BCG)     meta-analysis    

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Machine perfusion versus cold storage of livers: a meta-analysis

Sushun Liu,Qing Pang,Jingyao Zhang,Mimi Zhai,Sinan Liu,Chang Liu

Frontiers of Medicine 2016, Volume 10, Issue 4,   Pages 451-464 doi: 10.1007/s11684-016-0474-7

Abstract: preserved through machine perfusion (MP) or static cold storage (CS) were compared by conducting a meta-analysisTwenty-four studies involving MP preservation were included in the meta-analysis.

Keywords： machine perfusion     cold storage     DCD     meta-analysis    

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Chinese medicine combined with Western therapy on primary hepatic carcinoma: a systematic review with meta-analysis

Li Ma, Bin Wang, Yuanxiong Long, Hanmin Li

Frontiers of Medicine 2017, Volume 11, Issue 2,   Pages 191-202 doi: 10.1007/s11684-017-0512-0

Abstract: This systematic review with meta-analysis aimed to assess the effect of TCM combined with Western therapyMeta-analysis results indicated that the overall effect of TCM and Western integrative treatment on PHC

Keywords： traditional Chinese medicine     primary hepatic carcinoma     meta-analysis    

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Research and Practice of Meta-synthesis Management for the Government-led Urban Complex Construction

Ru-gui Chen,Jia-meng Chen

Frontiers of Engineering Management 2014, Volume 1, Issue 1,   Pages 52-61 doi: 10.15302/J-FEM-2014008

Abstract: based on the perspective of sustainable urban development.In order to achieve benefit maximization, the meta-synthesisThese examples point to thefeasibility of government-led meta-synthesis management and demonstrate the

Keywords： government-led construction project     urban complex     meta-synthesis management     sustainable development     benefit    

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Scientific publications on systematic review and meta-analysis from Chinese authors: a 10-year survey

Zhiping Yang, Qiong Wu, Kaichun Wu, Daiming Fan

Frontiers of Medicine 2012, Volume 6, Issue 1,   Pages 94-99 doi: 10.1007/s11684-012-0181-y

Abstract:

Systematic reviews and meta-analyses are playing an increasingly important role in clinical researchThis study aimed to measure the scientific production of systematic review and meta-analysis from theEnglish articles on systematic review and meta-analysis from ML, HK, and TW from 2001 to 2010 were retrievedChinese authors have been very active to enhance the systematic review and meta-analysis research overthere is still considerable room for Chinese authors to improve their studies on systematic review and meta-analysis

Keywords： systematic review     meta-analysis     China     Chinese     impact factor    

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Applying TCM Constitution Theory to Infertility via Omics

Qi Wang

Engineering 2023, Volume 30, Issue 11,   Pages 30-31 doi: 10.1016/j.eng.2023.05.005

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The role of prophylactic transpapillary pancreatic stenting in distal pancreatectomy: a meta-analysis

Xiangsong Wu, Maolan Li, Wenguang Wu, Jiasheng Mu, Lin Zhang, Qichen Ding, Qian Ding, Hao Weng, Runfa Bao, Yijun Shu, Ping Dong, Jun Gu, Jianhua Lu, Yingbin Liu

Frontiers of Medicine 2013, Volume 7, Issue 4,   Pages 499-505 doi: 10.1007/s11684-013-0296-9

Abstract: In this meta-analysis, a comprehensive search was performed in the PubMed, Embase, and Cochrane LibraryStudies analyzing the results of PTPS in DP were considered eligible for this meta-analysis.

Keywords： pancreatic fistula     distal pancreatectomy     pancreatic stent     meta-analysis    

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Title Author Date Type Operation

Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats

Yifan Liu, Jing Chen, Zhonglin Liu, Zhaowei Hou, Bo Liang, Liying Wang, Lei Zhou, Libin Shou, Dandan Lin, Shizhong Yang, Jinfeng Liu, Xiaolin Wu, Jidong Gu, Bozhong Mu

Journal Article

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Journal Article

Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Journal Article

Efficacy and safety of benralizumab in patients with eosinophilic asthma: a meta-analysis of randomized

Ting Liu, Faping Wang, Geng Wang, Hui Mao

Journal Article

Association between telomere length and survival in cancer patients: a meta-analysis and review of literature

Xinsen Xu,Kai Qu,Qing Pang,Zhixin Wang,Yanyan Zhou,Chang Liu

Journal Article

Deciphering the pharmacological mechanism of Guan-Jie-Kang in treating rat adjuvant-induced arthritis using omics

Hudan Pan, Yanfang Zheng, Zhongqiu Liu, Zhongwen Yuan, Rutong Ren, Hua Zhou, Ying Xie, Liang Liu

Journal Article

Treatment outcomes of pulmonary tuberculosis in the past decade in the mainland of China: a meta-analysis

Xiangwei Li, Yu Yang, Jianmin Liu, Feng Zhou, Wei Cui, Ling Guan, Fei Shen, Cong Gao, Mufei Li, Qi Jin, Lei Gao

Journal Article

Innate immune checkpoint Siglec10 in cancers: mining of comprehensive omics data and validation in patient

Journal Article

An update and cumulative meta-analysis

Jiangang Pan,Mo Liu,Xing Zhou

Journal Article

Machine perfusion versus cold storage of livers: a meta-analysis

Sushun Liu,Qing Pang,Jingyao Zhang,Mimi Zhai,Sinan Liu,Chang Liu

Journal Article

Chinese medicine combined with Western therapy on primary hepatic carcinoma: a systematic review with meta-analysis

Li Ma, Bin Wang, Yuanxiong Long, Hanmin Li

Journal Article

Research and Practice of Meta-synthesis Management for the Government-led Urban Complex Construction

Ru-gui Chen,Jia-meng Chen

Journal Article

Scientific publications on systematic review and meta-analysis from Chinese authors: a 10-year survey

Zhiping Yang, Qiong Wu, Kaichun Wu, Daiming Fan

Journal Article

Applying TCM Constitution Theory to Infertility via Omics

Qi Wang

Journal Article

The role of prophylactic transpapillary pancreatic stenting in distal pancreatectomy: a meta-analysis

Xiangsong Wu, Maolan Li, Wenguang Wu, Jiasheng Mu, Lin Zhang, Qichen Ding, Qian Ding, Hao Weng, Runfa Bao, Yijun Shu, Ping Dong, Jun Gu, Jianhua Lu, Yingbin Liu

Journal Article