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S-Adenosyl-L-methionine towards hepatitis C virus expression: Need to consider S-Adenosyl-L-methionine's chemistry, physiology and pharmacokinetics

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World Journal of Gastroenterology 2017年第40期23卷 7343-7346页

作者： Dimitrios Tsikas Erik Hanff Alexander Bollenbach core Unit proteomics Hannover Medical School

S-Adenosyl-L-methionine(SAM) is a cofactor serving as a methyl donor in numerous enzymatic reactions. It has been reported that SAM has the potential to modify antioxidant-enzymes, glutathione-biosynthesis and methionine adenosyltransferases-1/2 in hepatitis C virus-expressing cells at millimolar concentrations. The efficacy of SAM at micromolar concentrations and the underlying mechanisms remain to be demonstrated.

关键词： S-Adenosyl-L-methionine Bioavailability Concentration Liver

Recovery of DDBla （DAMAGED DNA BINDING PROTEIN la） in a Screen to Identify Novel RUB-Modified Proteins in Arabidopsis thaliana

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Molecular Plant 2012年第5期5卷 1163-1166页

作者： Sara K. Hotton Meliza F. Castro Richard A. Eigenheer Judy Callis Molecular and Cellular Biology University of California Davis CA 95616 USA proteomics core facility University of California Davis CA 95616 USA

Dear Editor, RUB/Nedd8 （RELATED TO UBIQUITIN/neuronal precur- sor cell-expressed developmentally downregulated 8） is a 76-amino acid protein that modifies other proteins and has homology to UBIQUITIN （UBQ）. Like UBQ, RUB modifies pro- teins through an isopeptide linkage between its C-terminal carboxyl group and the e-amino group of a lysine in the accep- tor protein and attachment occurs via an E1-E2-E3 enzymatic cascade.

关键词： DNA结合蛋白 Arabidopsis 蛋白质拟南芥屏幕 LA 损坏修饰

Web Resources for Model Organism Studies

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Genomics, proteomics & Bioinformatics 2015年第1期13卷 64-68页

作者： Bixia Tang Yanqing Wang Junwei Zhu Wenming Zhao core Genomic facility Beijing Institute of Genomics Chinese Academy of Sciences University of Chinese Academy of Sciences

An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States（NIH; http：//***/science/models/）. We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition,we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s––such as the Mouse Genome Database（MGD）, Saccharomyces Genome Database（SGD）, and Fly Base––have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.

关键词： Model organism Database Genome Bioinformatics Biology

BAG6 restricts pancreatic cancer progression by suppressing the release of IL33-presenting extracellular vesicles and the activation of mast cells

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Cellular & Molecular Immunology 2024年第8期21卷 918-931页

作者： Bilal Alashkar Alhamwe Viviane Ponath Fahd Alhamdan Bastian Dörsam Clara Landwehr Manuel Linder Kim Pauck Sarah Miethe Holger Garn Florian Finkernagel Anna Brichkina Matthias Lauth Dinesh Kumar Tiwari Malte Buchholz Daniel Bachurski Sabrina Elmshäuser Andrea Nist Thorsten Stiewe Lisa Pogge von Strandmann Witold Szymański Vanessa Beutgen Johannes Graumann Julia Teply-Szymanski Corinna Keber Carsten Denkert Ralf Jacob Christian Preußer Elke Pogge von Strandmann Institute for Tumor Immunology Philipps-University35043MarburgGermany core facility Extracellular Vesicles Philipps-University35043MarburgGermany Department of Anesthesiology Critical Careand Pain MedicineCardiac Anesthesia DivisionBoston Children’s HospitalBostonUSA Department of Immunology and Anaesthesia Harvard Medical SchoolBostonMAUSA Translational Inflammation Research Division&core facility for Single Cell Multiomics Philipps-University35043MarburgGermany core facility Bioinformatics Philipps-University35043MarburgGermany Clinic for Gastroenterology Endocrinology and MetabolismCenter for Tumor and Immune BiologyPhilipps-University35043MarburgGermany Institute of Systems Immunology Philipps-University35043MarburgGermany Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases(CECAD) University of CologneCologneGermany Institute of Molecular Oncology and Genomics core facility Member of the German Center for Lung Research(DZL)Philipps-University35043MarburgGermany Institute of Lung Health Justus Liebig University35392GiessenGermany Institute of Translational proteomics&core facility Translational proteomics Biochemical/Pharmacological CentrePhilipps-University35043MarburgGermany Institute of Pathology Philipps-University Marburg and University Hospital Marburg(UKGM)MarburgGermany Department of Cell Biology and Cell Pathology Philipps-University35043MarburgGermany

Recent studies reveal a critical role of tumor cell-released extracellular vesicles(EVs)in pancreatic cancer(PC)***,driver genes that direct EV function,the EV-recipient cells,and their cellular response to EV uptake remain to be ***,we studied the role of Bcl-2-associated-anthanogene 6(BAG6),a regulator of EV biogenesis for cancer *** used a Cre recombinase/LoxP-based reporter system in combination with single-cell RNA sequencing to monitor in vivo EV uptake and tumor microenvironment(TME)changes in mouse models for pancreatic ductal adenocarcinoma(PDAC)in a Bag6 pro-or deficient *** vivo data were validated using mouse and human organoids and patient *** data demonstrated that Bag6-deficient subcutaneous and orthotopic PDAC tumors accelerated tumor growth dependent on EV ***,this was attributed to mast cell(MC)activation via EV-associated *** MCs promoted tumor cell proliferation and altered the composition of the TME affecting fibroblast polarization and immune cell *** cell proliferation and fibroblast polarization were mediated via the MC secretome containing high levels of PDGF and *** with high BAG6 gene expression and high protein plasma level have a longer overall survival indicating clinical *** current study revealed a so far unknown tumor-suppressing activity of BAG6 in ***6-deficiency allowed the release of EV-associated IL33 which modulate the TME via MC activation promoting aggressive tumor *** depletion using imatinib diminished tumor growth providing a scientific rationale to consider imatinib for patients stratified with low BAG6 expression and high MC infiltration.

关键词： Pancreatic cancer EVs BAG6 Mast cells

Bile proteomics for differentiation of malignant from benign biliary strictures:a pilot study

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Gastroenterology Report 2015年第2期3卷 136-143页

作者： Udayakumar Navaneethan Vennisvasanth Lourdusamy Preethi GK Venkatesh Belinda Willard Madhusudhan R Sanaka Mansour A Parsi Department of Gastroenterology and Hepatology Digestive Disease InstituteCleveland ClinicClevelandOHUSA proteomics core Laboratory Lerner Research InstituteCleveland ClinicClevelandOHUSA

Background:Determining the etiology of biliary strictures is challenging,and the sensitivities of the current tests to diagnose them are *** biomarkers in bile,in combination with other tests,may improve sensitivity in diagnosing biliary ***:To analyse the differential abundance of proteins in benign and malignant biliary strictures through proteomic analysis of ***:In this prospective,cross-sectional study,bile was aspirated in 24 patients undergoing endoscopic retrograde cholangiopancreatography(ERCP)including six patients with primary sclerosing cholangitis(PSC),three with cholangiocarcinoma(CCA),ten with pancreatic cancer,and five with benign biliary *** chromatography/mass spectrometry was used to examine the bile for differential abundance of protein *** relative abundance of various proteins was compared in the malignant *** groups and in CCA ***:The majority of the proteins identified in bile were similar to those of the plasma(plasma proteins)and certain proteins were differentially expressed among the different groups(CCA,pancreatic cancer,PSC or benign).A total of 18 proteins were identified as being more abundant in the malignant group(CCA and pancreatic cancer)than in the benign strictures group,including myeloperoxidase,complement C3,inter-alpha-trypsin inhibitor heavy chain H4,apolipoprotein B-100,and kininogen-1 isoform 2.A total of 30 proteins were identified to be less abundant in the malignant group than in the benign group,including trefoil factor 2,superoxide dismutase[Cu-Zn],kallikrein-1,carboxypeptidase B and trefoil factor ***:Protein biomarkers in bile may differentiate malignant from benign biliary *** studies are warranted to validate these observations.

关键词： pancreatic cancer proteomics bile cholangiocarcinoma

Genetic and Proteomic Analyses of a Xanthomonas campestris *** purC Mutant Deficient in Purine Biosynthesis and Virulence

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Journal of Genetics and Genomics 2013年第9期40卷 473-487页

作者： Zhihui Yuan Li Wang Shutao Sun Yao Wu Wei Qian State Key Laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences Center of core facility Institute of MicrobiologyChinese Academy of Sciences

Bacterial proliferation in hosts requires activation of a number of housekeeping pathways, including purine de novo biosynthesis. Although inactivation of purine biosynthesis genes can attenuate virulence, it is unclear which biochemical or virulence factors are associated with the purine biosynthesis pathway in vivo. We report that inactivation of purC, a gene encoding phosphoribosylaminoimidazole-succinocarboxamide synthase, caused complete loss of virulence in Xanthomonas campestris pv. cam- pestris, the causal agent of black rot disease of cruciferous plants. The purC mutant was a purine auxotroph; it could not grow on minimal medium, whereas addition of purine derivatives, such as hypoxanthine or adenine plus guanine, restored growth of the mutant. The purC mutation also significantly enhanced the production of an unknown purine synthesis associated pigment and extracellular polysaccharides by the bacterium. In addition, comparative proteomic analyses of bacteria grown on rich and minimal media revealed that the purC mutation affected the expression levels of diverse proteins involved in purine and pyrimidine synthesis, carbon and energy metabolisms, iron uptake, proteolysis, protein secretion, and signal transduction. These results provided clues to understanding the contributions of purine synthesis to bacterial virulence and interactions with host immune systems.

关键词： Purine biosynthesis Virulence Xanthomonas campestris pv. campestris proteomics

Implementation of Automated Sample Quality Control in Whole Exome Sequencing

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Journal of Life Sciences 2017年第6期11卷 261-268页

作者： Elisa Viering Jana Molitor Leslie Friedmann Jana Petersen Marie Beckhaus Stephan Wolf Agilent Technologies Inc. Waldbronn 76337 Germany DKFZ Genomics and proteomics core facility High Throughput Sequencing Unit Heidelberg 69120 Germany

Aims： High-quality DNA as input material for a NGS （next-generation sequencing） workflow is essential for the successful preparation of a DNA library. Additionally, DNA quality has a strong impact on sequencing results. Therefore, it is important to include QC （quality control） steps to assess size, concentration, molarity, and integrity of the DNA during the workflow. Material and Methods： The WES （Whole Exome Sequencing） workflow at the Genomics and proteomics core facility of DKFZ （the German Cancer Research Center） was performed with several QC steps： QC of the input material, QC of intermediate products during library preparation, and QC of final libraries. The Agilent 4200 TapeStation system, which offers automated sample processing, was used to evaluate quantity, size, molarity, and integrity of the samples. Key Findings： The Agilent Genomic DNA ScreenTape assay offers an unbiased genomic DNA integrity assessment, which enables protocol adaption for optimized library preparation, for example, selection of a suitable shearing protocol. Additionally, QC steps during library preparation such as evaluation of library size, concentration, and molarity ensure maximal sequencing output. Significance： The automated and fast high-throughput analysis of genomic DNA with the 4200 TapeStation system helps to save labor time and costs. Additionally, the easy-to-use system can be integrated as a QC tool into the NGS workflow to ensure successful library preparation. QC steps enable the confirmation of suitable library size and concentration for the workflow.

关键词： NGS FFPE (Formalin-fixed Paraffin-embedded) WES DIN (DNA Integrity Number) QC 4200 TapeStation system.

Old strategies against an old plague: new attenuated tuberculosis vaccines

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医学争鸣 2012年第2期3卷 30-31页

作者： YIN Wen core facility School of Preclinical MedicineFourth Military Medical UniversityXi'an 710032China

Tuberculosis(TB)is still a global health emergency according to WHO and one of the important global control efforts targeting TB is BCG(bacille Calmette-Guérin)***,BCG has been found

关键词：摘要编辑部编辑工作读者

Pulsed laser interference patterning of transition-metal carbides for stable alkaline water electrolysis kinetics

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Carbon Energy 2024年第5期6卷 65-80页

作者： Yewon Oh Jayaraman Theerthagiri Ahreum Min Cheol Joo Moon Yiseul Yu Myong Yong Choi Department of Chemistry(BK21 FOUR) Research Institute of Natural SciencesGyeongsang National UniversityJinjuRepublic of Korea core−facility Center for Photochemistry and Nanomaterials Gyeongsang National UniversityJinjuRepublic of Korea

We investigated the role of metal atomization and solvent decomposition into reductive species and carbon clusters in the phase formation of transition-metal carbides(TMCs;namely,Co_(3)C,Fe_(3)C,TiC,and MoC)by pulsed laser ablation of Co,Fe,Ti,and Mo metals in *** interaction between carbon s-p-orbitals and metal d-orbitals causes a redistribution of valence structure through charge transfer,leading to the formation of surface defects as observed by X-ray photoelectron *** defects influence the evolved TMCs,making them effective for hydrogen and oxygen evolution reactions(HER and OER)in an alkaline ***_(3)C with more oxygen affinity promoted CoO(OH)intermediates,and the electrochemical surface oxidation to Co_(3)O_(4)was captured via in situ/operando electrochemical Raman probes,increasing the number of active sites for OER *** with more d-vacancies exhibits strong hydrogen binding,promoting HER kinetics,whereas Fe_(3)C and TiC with more defect states to trap charge carriers may hinder both OER and HER *** results show that the assembled membrane-less electrolyzer with Co_(3)C∥Co_(3)C and MoC∥MoC electrodes requires~2.01 and 1.99 V,respectively,to deliver a 10 mA cm−2 with excellent electrochemical and structural *** addition,the ascertained pulsed laser synthesis mechanism and unit-cell packing relations will open up sustainable pathways for obtaining highly stable electrocatalysts for electrolyzers.

关键词： acetone H_(2)and O_(2)evolution reactions pulsed laser ablation surface defects transition-metal carbides water electrolyzer