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Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation

《医学前沿（英文）》 2022年 第16卷 第3期   页码 429-441 doi: 10.1007/s11684-021-0842-9

摘要： The local microenvironment is essential to stem cell-based therapy for ischemic stroke, and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeutic mechanisms. However, relevant studies on microenvironmental changes were mainly confined in the acute phase of stroke, and long-term changes remain unclear. This study aimed to investigate the microenvironmental changes in the subacute and chronic phases of ischemic stroke after stem cell transplantation. Herein, induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) were transplanted into the ischemic brain established by middle cerebral artery occlusion surgery. Positron emission tomography imaging and neurological tests were applied to evaluate the metabolic and neurofunctional alterations of rats transplanted with stem cells. Quantitative proteomics was employed to investigate the protein expression profiles in iPSCs-transplanted brain in the subacute and chronic phases of stroke. Compared with NSCs-transplanted rats, significantly increased glucose metabolism and neurofunctional scores were observed in iPSCs-transplanted rats. Subsequent proteomic data of iPSCs-transplanted rats identified a total of 39 differentially expressed proteins in the subacute and chronic phases, which are involved in various ischemic stroke-related biological processes, including neuronal survival, axonal remodeling, antioxidative stress, and mitochondrial function restoration. Taken together, our study indicated that iPSCs have a positive therapeutic effect in ischemic stroke and emphasized the wide-ranging microenvironmental changes in the subacute and chronic phases.

关键词： ischemic stroke     microenvironment     induced pluripotent stem cells (iPSCs)     positron emission tomography (PET)     quantitative proteomics    

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Transcriptomics and proteomics in stem cell research

null

《医学前沿（英文）》 2014年 第8卷 第4期   页码 433-444 doi: 10.1007/s11684-014-0336-0

摘要：

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

关键词： embryonic stem cells     transcriptomics     proteomics    

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Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

《环境科学与工程前沿（英文）》 2009年 第3卷 第4期   页码 393-403 doi: 10.1007/s11783-009-0145-x

摘要： Proteomics involves the separation of proteins, identification of the amino acid sequence of the interested or target proteins, study of the function of the proteins, modification, structure and ultimate assignments to functional pathways in the cell. The proteomic investigations have contributed greatly to human diseases studies, new drugs discovery researches, and environmental science in recent years. This article provides a review on the development of the main proteomic technologies, including both the gel based and non-gel based technologies, and their applications in environmental science. Proteomic technologies have been utilized in the environmental stresses studies to analyze the induction or reduction of proteins at expression level and identify the target proteins to investigate their function in response to environmental stresses, such as high or low pH, oxidation stress, and toxic chemicals. Such protein responses are also helpful to understand the mechanisms of some cellular activities and the functions of some proteins.

关键词： proteomics     environmental stress     two dimensional (2D) gel electrophoresis     mass spectrometry    

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Sepsis biomarkers: an omics perspective

null

《医学前沿（英文）》 2014年 第8卷 第1期   页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

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

《医学前沿（英文）》 doi: 10.1007/s11684-023-1020-z

摘要： 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.

关键词： RLPS     proteomics     metabolomics     lipidomics     metabolism    

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Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

《医学前沿（英文）》 2022年 第16卷 第3期   页码 378-388 doi: 10.1007/s11684-021-0840-y

摘要： Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia     children     proteomics     Fc fragment of the IgG-binding protein     mechanistic target of rapamycin kinase inhibitor    

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A computational toolbox for molecular property prediction based on quantum mechanics and quantitative

《化学科学与工程前沿（英文）》 2022年 第16卷 第2期   页码 152-167 doi: 10.1007/s11705-021-2060-z

摘要： Chemical industry is always seeking opportunities to efficiently and economically convert raw materials to commodity chemicals and higher value-added chemical-based products. The life cycles of chemical products involve the procedures of conceptual product designs, experimental investigations, sustainable manufactures through appropriate chemical processes and waste disposals. During these periods, one of the most important keys is the molecular property prediction models associating molecular structures with product properties. In this paper, a framework combining quantum mechanics and quantitative structure-property relationship is established for fast molecular property predictions, such as activity coefficient, and so forth. The workflow of framework consists of three steps. In the first step, a database is created for collections of basic molecular information; in the second step, quantum mechanics-based calculations are performed to predict quantum mechanics-based/derived molecular properties (pseudo experimental data), which are stored in a database and further provided for the developments of quantitative structure-property relationship methods for fast predictions of properties in the third step. The whole framework has been carried out within a molecular property prediction toolbox. Two case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction and solid-liquid phase equilibriums are presented.

关键词： molecular property     quantum mechanics     quantitative structure-property relationship     heat of reaction     solid-liquid phase equilibrium    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 72-88 doi: 10.1007/s11705-016-1580-4

摘要： Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of overexpression in an industrial strain of WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that , and were upregulated in all conditions. Then the three genes were over-expressed in WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.

关键词： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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Erratum to: Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

《环境科学与工程前沿（英文）》 2011年 第5卷 第3期   页码 488-488 doi: 10.1007/s11783-011-0342-2

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Estimation of photolysis half-lives of dyes in a continuous-flow system with the aid of quantitative

Davoud BEIKNEJAD,Mohammad Javad CHAICHI

《环境科学与工程前沿（英文）》 2014年 第8卷 第5期   页码 683-692 doi: 10.1007/s11783-014-0680-y

摘要： In this paper the photolysis half-lives of the model dyes in water solutions and under ultraviolet (UV) radiation were determined by using a continuous-flow spectrophotometric method. A quantitative structure-property relationship (QSPR) study was carried out using 21 descriptors based on different chemometric tools including stepwise multiple linear regression (MLR) and partial least squares (PLS) for the prediction of the photolysis half-life ( ) of dyes. For the selection of test set compounds, a K-means clustering technique was used to classify the entire data set, so that all clusters were properly represented in both training and test sets. The QSPR results obtained with these models show that in MLR-derived model, photolysis half-lives of dyes depended strongly on energy of the highest occupied molecular orbital ( ), largest electron density of an atom in the molecule ( ) and lipophilicity (log ). While in the model derived from PLS, besides aforementioned and descriptors, the molecular surface area ( ), molecular weight ( ), electronegativity ( ), energy of the second highest occupied molecular orbital ( ) and dipole moment ( ) had dominant effects on logt values of dyes. These were applicable for all classes of studied dyes (including monoazo, disazo, oxazine, sulfonephthaleins and derivatives of fluorescein). The results were also assessed for their consistency with findings from other similar studies.

关键词： dye     photolysis half-life     quantitative structure-property relationship     continuous-flow     stepwise multiple linear regression     partial least squares    

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Application of quantum chemical descriptors into quantitative structure-property relationship models

Yueping BAO, Qiuying HUANG, Wenlong WANG, Jiangjie XU, Fan JIANG, Chenghong FENG

《环境科学与工程前沿（英文）》 2011年 第5卷 第4期   页码 505-511 doi: 10.1007/s11783-011-0318-2

摘要： Quantitative structure-property relationship (QSPR) models were developed for prediction of photolysis half-life ( ) of polychlorinated biphenyls (PCBs) in water under ultraviolet (UV) radiation. Quantum chemical descriptors computed by the PM3 Hamiltonian software were used as independent variables. The cross-validated value for the optimal QSPR model is 0.966, indicating good prediction capability for lg values of PCBs in water. The QSPR results show that the largest negative atomic charge on a carbon atom ( ) and the standard heat of formation (Δ ) have a dominant effect on values of PCBs. Higher values or lower Δ values of the PCBs leads to higher lg values. In addition, the lg values of PCBs increase with the increase in the energy of the highest occupied molecular orbital values. Increasing the largest positive atomic charge on a chlorine atom and the most positive net atomic charge on a hydrogen atom in PCBs leads to the decrease of lg values.

关键词： photolysis     polychlorinated biphenyls (PCBs)     quantitative structure-property relationships (QSPRs)     quantum chemical descriptors    

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Design and use of group-specific primers and probes for real-time quantitative PCR

Juntaek LIM, Seung Gu SHIN, Seungyong LEE, Seokhwan HWANG

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 28-39 doi: 10.1007/s11783-011-0302-x

摘要： Real-time quantitative polymerase chain reaction (qPCR) has gained popularity as a technique to detect and quantify a specific group of target microorganisms from various environmental samples including soil, water, sediments, and sludge. Although qPCR is a very useful technique for nucleic acid quantification, accurately quantifying the target microbial group strongly depends on the quality of the primer and probe used. Many aspects of conducting qPCR assays have become increasingly routine and automated; however, one of the most important aspects, designing and selecting primer and probe sets, is often a somewhat arcane process. In many cases, failed or non-specific amplification can be attributed to improperly designed primer-probe sets. This paper is intended to provide guidelines and general principles for designing group-specific primers and probes for qPCR assays. We demonstrate the effectiveness of these guidelines by reviewing the use of qPCR to study anaerobic processes and biologic nutrient removal processes. qPCR assays using group-specific primers and probes designed with this method, have been used to successfully quantify 16S ribosomal Ribonucleic Acid (16S rRNA) gene copy numbers from target methanogenic and ammonia- oxidizing bacteria in various laboratory- and full-scale biologic processes. Researchers with a good command of primer and probe design can use qPCR as a valuable tool to study biodiversity and to develop more efficient control strategies for biologic processes.

关键词： absolute quantification     design guideline     primer     probe     real-time quantitative polymerase chain reaction (qPCR)    

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Quantitative analysis of CO

Xianbing LIU, Can WANG

《环境科学与工程前沿（英文）》 2009年 第3卷 第1期   页码 12-19 doi: 10.1007/s11783-009-0011-x

摘要： The increasing volume of CO embodiment in international trade adds a layer of complexity to environmental policies and has raised arguments on the traditional production based responsibility for CO emissions. In order to help understand the quantity of CO embodiment in trade and its policy implications, this paper gives observations to recently emerging literatures that quantitatively discuss CO embodiment in trade. The analytical approaches share the principle of using input and output modeling but vary dramatically in study boundary and estimation accuracy. The calculations can be roughly categorized into three types: direct quantification of CO embodiments in multiregional trade, direct quantification of CO embodiment in bilateral trade, and indirect analysis by comparing the scenarios with or without trade. The practical estimations strongly rely on trade partner selection and data availability. An obvious imbalance of net CO embodiment in the commodity trade between major developed countries and developing economies as a whole was confirmed by these literatures. Carbon taxes and other possible limitations on CO emissions have been addressed. The consistency across the calculations could be enhanced by systematic analyses in more detail to convince the international community to take binding commitments for the reduction of global CO emissions.

关键词： CO2 embodiment     international trade     quantitative estimation     analytical approach    

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Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 21-27 doi: 10.1007/s11783-011-0303-9

摘要： New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time polymerase chain reaction (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems are discussed. The parallel sequencing of amplicon libraries and using barcodes to differentiate multiple samples in a pyrosequencing run are explained. The best procedures and chemistries for QPCR amplifications are also described and advantages of applying automation to increase accuracy are addressed. Three examples in which pyrosequencing and QPCR were used together to define and quantify members of microbial communities are provided: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. The key findings in these systems and how both methods were used in concert to achieve those findings are highlighted.

关键词： polymerase chain reaction (PCR)     microbial communities     pyrosequencing     gut     microbial fuel cell     sludge    

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Decoding and quantitative detection of antibiotics by a luminescent mixed-lanthanide-organic framework

《环境科学与工程前沿（英文）》 2022年 第16卷 第12期 doi: 10.1007/s11783-022-1589-5

摘要：

● A series of mixed-LOFs and portable LOF-fibers were synthesized.

关键词： Antibiotics     Sensor     Luminescence     Lanthanide-organic frameworks    

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标题 作者 时间 类型 操作

Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation

期刊论文

Transcriptomics and proteomics in stem cell research

null

期刊论文

Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

期刊论文

Sepsis biomarkers: an omics perspective

null

期刊论文

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

期刊论文

Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

期刊论文

A computational toolbox for molecular property prediction based on quantum mechanics and quantitative

期刊论文

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

期刊论文

Erratum to: Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

期刊论文

Estimation of photolysis half-lives of dyes in a continuous-flow system with the aid of quantitative

Davoud BEIKNEJAD,Mohammad Javad CHAICHI

期刊论文

Application of quantum chemical descriptors into quantitative structure-property relationship models

Yueping BAO, Qiuying HUANG, Wenlong WANG, Jiangjie XU, Fan JIANG, Chenghong FENG

期刊论文

Design and use of group-specific primers and probes for real-time quantitative PCR

Juntaek LIM, Seung Gu SHIN, Seungyong LEE, Seokhwan HWANG

期刊论文

Quantitative analysis of CO

Xianbing LIU, Can WANG

期刊论文

Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

期刊论文

Decoding and quantitative detection of antibiotics by a luminescent mixed-lanthanide-organic framework

期刊论文