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A multi-platform analysis of human gingival crevicular fluid reveals ferroptosis as a relevant regulated cell death mechanism during the clinical progression of periodontitis

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International Journal of Oral Science 2024年第2期16卷 265-279页

作者： Alfredo Torres M.Angélica Michea Ákos Végvári Marion Arce Valentina Pérez Marcela Alcota Alicia Morales Rolando Vernal Mauricio Budini roman a.zubarev Fermín E.González Laboratory of Experimental Immunology&Cancer Faculty of DentistryUniversity of ChileSantiagoChile Department of Conservative Dentistry Faculty of DentistryUniversity of ChileSantiagoChile Division of Chemistry I Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden Periodontal Biology Laboratory Faculty of DentistryUniversidad de ChileSantiagoChile Laboratory of Cellular and Molecular Pathology Institute for Research in Dental SciencesFaculty of DentistryUniversity of ChileSantiagoChile

Ferroptosis is implicated in the pathogenesis of numerous chronic-inflammatory diseases,yet its association with progressive periodontitis remains *** investigate the involvement and significance of ferroptosis in periodontitis progression,we assessed sixteen periodontitis-diagnosed *** progression was clinically monitored over twelve weeks via weekly clinical evaluations and gingival crevicular fluid(GCF)collection was performed for further *** metrics,proteomic data,in silico methods,and bioinformatics tools were combined to identify protein profiles linked to periodontitis progression and to explore their potential connection with *** western blot analyses validated key ***,a single-cell RNA sequencing(scRNA-seq)dataset(GSE164241)for gingival tissues was analyzed to elucidate cellular dynamics during periodontitis *** progression was identified as occurring at a faster rate than traditionally *** samples from progressing and non-progressing periodontal sites showed quantitative and qualitatively distinct proteomic *** addition,specific biological processes and molecular functions during progressive periodontitis were revealed and a set of hub proteins,including SNCA,CA1,HBB,SLC4A1,and ANK1 was strongly associated with the clinical progression status of ***,we found specific proteins-drivers or suppressors-associated with ferroptosis(SNCA,FTH1,HSPB1,CD44,and GCLC),revealing the co-occurrence of this specific type of regulated cell death during the clinical progression of ***,the integration of quantitative proteomic data with scRNA-seq analysis suggested the susceptibility of fibroblasts to *** analyses reveal proteins and processes linked to ferroptosis for the first time in periodontal patients,which offer new insights into the molecular mechanisms of progressive periodontal *** findings may le

关键词： finding progression faster

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Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis

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Journal of Pharmaceutical Analysis 2024年第1期14卷 100-114页

作者： Sze Wan Hung Massimiliano Gaetani Yiran Li Zhouyurong Tan Xu Zheng Ruizhe Zhang Yang Ding Gene Chi Wai Man Tao Zhang Yi Song Yao Wang Jacqueline Pui Wah Chung Tak Hang Chan roman a.zubarev Chi Chiu Wang Department of Obstetrics&Gynaecology The Chinese University of Hong KongHong KongChina Division of Physiological Chemistry I Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSE 17177Sweden Chemical Proteomics Core Facility Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSE 17177Sweden Unit of Chemical Proteomics Science for Life Laboratory(SciLifeLab)StockholmSE 17177Sweden Center for Reproductive Medicine Henan Key Laboratory of Reproduction and GeneticsThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450003China Department of Chemistry McGill UniversityMontrealH3A2K6Canada Department of Pharmacological&Technological Chemistry I.M.Sechenov First Moscow State Medical UniversityMoscow119146Russia Reproduction and Development Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong KongChina School of Biomedical Sciences The Chinese University of Hong KongHong KongChina Chinese University of Hong Kong-Sichuan University Joint Laboratory in Reproductive Medicine The Chinese University of Hong KongHong KongChina

Endometriosis is a common chronic gynecological disease with endometrial cell implantation outside the *** is a major pathophysiology in *** previous studies have demonstrated that the prodrug of epigallocatechin gallate(ProEGCG)exhibits superior anti-endometriotic and anti-angiogenic effects compared to epigallocatechin gallate(EGCG).However,their direct binding targets and underlying mechanisms for the differential effects remain *** this study,we demonstrated that oral ProEGCG can be effective in preventing and treating ***,1D and 2D Proteome Integral Solubility Alteration assay-based chemical proteomics identified metadherin(MTDH)and PX domain containing serine/threonine kinase-like(PXK)as novel binding targets of EGCG and ProEGCG,*** simulation and BioLayer interferometry were used to confirm their binding *** results showed that MTDH-EGCG inhibited protein kinase B(Akt)-mediated angiogenesis,while PXK-ProEGCG inhibited epidermal growth factor(EGF)-mediated angiogenesis via the EGF/hypoxia-inducible factor(HIF-1a)/vascular endothelial growth factor(VEGF)*** vitro and in vivo knockdown assays and microvascular network imaging further confirmed the involvement of these signaling ***,our study demonstrated that ProEGCG has superior therapeutic effects than EGCG by targeting distinct signal transduction pathways and may act as a novel antiangiogenic therapy for endometriosis.

关键词： Molecular targets ProEGCG EGCG Angiogenesis Treatment Endometriosis

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Role of Stable Isotopes in Life——Testing Isotopic Resonance Hypothesis

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Genomics, Proteomics & Bioinformatics 2011年第1期9卷 15-20页

作者： roman A. zubarev Division of Physiological Chemistry I Department of Medical Biochemistry and Biophysics Karolinska Institute SE-17 177 Stockholm Sweden

Stable isotopes of most important biological elements, such as C, H, N and O, affect living organisms. In rapidly growing species, deuterium and to a lesser extent other heavy isotopes reduce the growth rate. At least for deuterium it is known that its depletion also negatively impacts the speed of biological processes. As a rule, living organisms ＂resist＂ changes in their isotopic environment, preferring natural isotopic abundances. This preference could be due to evolutionary optimization; an additional effect could be due to the presence of the ＂isotopic resonance＂. The isotopic resonance phenomenon has been linked to the choice of earliest amino acids, and thus af- fected the evolution of genetic code. To test the isotopic resonance hypothesis, literature data were analyzed against quantitative and qualitative predictions of the hypothesis. Four studies provided five independent datasets, each in very good quantitative agreement with the predictions. Thus, the isotopic resonance hypothesis is no longer simply plausible; it can now be deemed likely. Additional testing is needed, however, before full acceptance of this hypothesis.

关键词： origin of life stable isotope isotopic resonance

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Rapid Purification and Identification of Osteopontin from Human Milk by HPLC Coupled to FT-ICR-MS

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Chemical Research in Chinese Universities 2010年第1期26卷 17-22页

作者： SHI Lei YANG Tie-zheng zubarev A. roman College of Public Health Jilin University Changchun 130021 P. R. China Affiliated Hospital of Changchun University of Chinese Medicine Changchun 130021 P. R. China Laboratory for Biological and Medical Mass Spectrometry BMC Uppsala University Box 583 75123 Uppsala Sweden

Milk as a key element for infant nutrition represents the only source of feeding for newborns and infants, breast-feeding milk normally contains several bioactive proteins or peptides useful for the development of the immune system that protects infants from diseases. Osteopontin（OPN） plays a distinct role during the processes of lactation, Some studies on OPN isolated and purified from the human milk via HPLC on SCX and Ca columns adopted biological mass spectrometry. After digesting the purified OPN sample with trypsin, the typical correlative polypeptide fragments GDSVVYGLR and QNLLAPQTLPSK are identified by FT-ICR-MS. The rapid identification of OPN is assumed to be reasonably well behaving in a standard bottom-up experiment. It shows that nano-spray HPLC combined with FT-ICR-MS and Mascot search can be used as a high efficient method for the identification of purified OPN and its polypeptide fragments. Further study will provide more academic theories of their different modifications and the bioactivity as well.

关键词： Osteopontin(OPN) FT-ICR-MS Purification Identification

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电子捕获解离技术在生物质谱中的作用

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化学进展 2011年第8期23卷 1710-1718页

作者：石磊刘淑莹 zubarev roman A 吉林大学公共卫生学院长春130021 中科院长春应用化学研究所长春130022 Division of Molecular Biometry Department of Medical Biochemistry&BiophysicsKarolinska Institute

电子捕获解离(ECD)是一种非各态历经的(non-ergodic)解离方式,可导致多肽中N—Cα键断裂,也能更优先断裂S—S键,在较高电子能量条件下还可以区分亮氨酸和异亮氨酸,并且在断裂过程中能完整保留蛋白质分子的修饰位点。因此,它与碰撞活化解... 详细信息

电子捕获解离(ECD)是一种非各态历经的(non-ergodic)解离方式,可导致多肽中N—Cα键断裂,也能更优先断裂S—S键,在较高电子能量条件下还可以区分亮氨酸和异亮氨酸,并且在断裂过程中能完整保留蛋白质分子的修饰位点。因此,它与碰撞活化解离(CAD)等传统解离方式形成了较为理想的互补。ECD与CAD的联合使用可提供更广泛的多肽覆盖率序列信息,提高蛋白测序的效率与准确度。本文在介绍ECD基本原理、解离机理的基础上,简要地总结了ECD技术在生物质谱中的作用。

关键词：电子捕获解离解离机理生物质谱

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In silico Proteome-wide Amino aCid and Elemental Composition (PACE) Analysis of Expression Proteomics Data Provides A Fingerprint of Dominant Metabolic Processes

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Genomics, Proteomics & Bioinformatics 2013年第4期11卷 219-229页

作者： David M. Good Anwer Mamdoh Harshavardhan Budamgunta roman A. zubarev Division of Physiological Chemistry I Department of Medical Biochemistry and Biophysics Karolinska InstituteSE17177 Stockholm Sweden Science for Life Laboratory SE17121 Solna Sweden

Proteome-wide Amino aCid and Elemental composition （PACE） analysis is a novel and informative way of interrogating the proteome. The PACE approach consists of in silico decompo- sition of proteins detected and quantified in a proteomics experiment into 20 amino acids and five elements （C, H, N, O and S）, with protein abundances converted to relative abundances of amino acids and elements. The method is robust and very sensitive; it provides statistically reliable differ- entiation between very similar proteomes. In addition, PACE provides novel insights into prote- ome-wide metabolic processes, occurring, e.g., during cell starvation. For instance, both Escherichia coli and Synechocystis down-regulate sulfur-rich proteins upon sulfur deprivation, but E. coli preferentially down-regulates cysteine-rich proteins while Synechocystis mainly down- regulates methionine-rich proteins. Due to its relative simplicity, flexibility, generality and wide applicability, PACE analysis has the potential of becoming a standard analytical tool in proteomics.

关键词： Shotgun proteomics Mass spectrometry LC-MS/MS Data reduction Cyanobacterium Arginine deprivation

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On the Homology of the Dual de Rham Complex

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Acta Mathematica Sinica,English Series 2022年第10期38卷 1666-1676页

作者： roman MIKHAILOV Laboratory of Modern Algebra and Applications St.Petersburg State University14th Line29bSaint Petersburg199178Russia St.Petersburg Department of Steklou Mathematical Institute Fontanka 27SaintPetersburg191023Russia

We study the homology of the dual de Rham complex as functors on the category of abelian *** give a description of homology of the dual de Rham complex up to degree 7 for free abelian groups and present a corrected ve... 详细信息

关键词： Dual de Rham complex polynomial functor divided powers derived functors

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Dynamic Modelling of the DEP Controlled Boiling in a Microchannel

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Journal of Thermal Science 2018年第2期27卷 167-174页

作者： Marcin Lackowski roman Kwidzinski Institute of Fluid Flow Machinery Polish Academy of Sciences

The paper presents theoretical analysis of flow dynamics in a heated microchannel in which flow rate may be controlled by dielectrophoretic(DEP) forces. Proposed model equations were derived in terms of lumped parameters characterising the system comprising of DEP controller and the microchannel. In result, an equation for liquid height of rise in the controller was obtained from momentum balances in the two elements of the considered system. In the model, the boiling process in the heated section of microchannel is taken into account through a pressure drop, which is a function of flow rate and uniform heat flux. Presented calculation results show that the DEP forces influence mainly the flow rate in the microchannel. In this way, by proper modulation of voltage applied to the DEP controller, it is possible to lower the frequency of Ledinegg instabilities.

关键词： dielectrophoresis boiling microchannel two-phase flow pressure drop

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Modeling static friction behavior of elastic–plastic spherical adhesive microcontact in full-stick condition

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Friction 2024年第11期12卷 2594-2610页

作者： Guo XIANG roman GOLTSBERG Izhak ETSION Department of Mechanical Engineering TechnionHaifa 32000Israel

The static friction behavior of an elastic–plastic spherical adhesive microcontact between a rigid flat and a deformable sphere under combined normal and tangential loading is studied by the finite element method(FEM).The contact between the sphere and the rigid flat is assumed to be full-stick,and the sliding inception is related to a loss of tangential *** intermolecular force between the rigid flat and the sphere is assessed by the Lennard–Jones(LJ)potential,which is applied to the sphere and the rigid flat by a user *** evolution of the adhesive force with tangential displacement in the full-stick condition is *** results indicate that the increasing effect of adhesive energy on the static friction coefficient gradually diminishes with an increase in the adhesive energy and the external normal ***,based on an extensive parametric study,an empirical dimensionless expression is obtained to predict the static friction coefficient of the spherical adhesive microcontact considering the intermolecular force.

关键词： adhesive spherical microcontact Lennard–Jones(LJ)potential elastic–plastic static friction

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An in vitro demonstration of a passive,acoustic metamaterial as a temperature sensor with mK resolution for implantable applications

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Microsystems & Nanoengineering 2024年第1期10卷 41-54页

作者： Lucrezia Maini Vicente Genovés roman Furrer Nikola Cesarovic Christofer Hierold Cosmin roman Micro-and Nanosystems Department of Mechanical and Process EngineeringETH ZurichTannenstrasse 38092 ZurichSwitzerland. Translational Cardiovascular Technology Department of Health Science and TechnologyETH ZurichLeopold-Ruzicka-Weg 48093 ZurichSwitzerland. Transport at Nanoscale Interfaces Swiss Federal Laboratories for Materials Science and TechnologyEMPAÜberlandstrasse 1298600 DübendorfSwitzerland Department of Cardiothoracic and Vascular Surgery Deutsches Herzzentrum der Charite(DHZC)13353 BerlinGermany

Wireless medical sensors typically utilize electromagnetic coupling or ultrasound for energy transfer and sensor *** transfer and management is a complex aspect that often limits the applicability of implantable sensor *** this work,we report a new passive temperature sensing scheme based on an acoustic metamaterial made of silicon embedded in a polydimethylsiloxane *** to other approaches,this concept is implemented without additional electrical components in situ or the need for a customized receiving unit.A standard ultrasonic transducer is used for this demonstration to directly excite and collect the reflected *** metamaterial resonates at a frequency close to a typical medical value(5 MHz)and exhibits a high-quality *** the design features of the metamaterial with the high-temperature sensitivity of the polydimethylsiloxane matrix,we achieve a temperature resolution of 30 *** value is below the current standard resolution required in infrared thermometry for monitoring postoperative complications(0.1 K).We fabricated,simulated,in vitro tested,and compared three acoustic sensor designs in the 29-43℃(~302-316 K)temperature *** this concept,we demonstrate how our passive metamaterial sensor can open the way toward new zero-power smart medical implant concepts based on acoustic interrogation.

关键词： passive resolution utilize

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