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arXiv 2023年

作者： Zariquiey, Francesc Sabanés Pérez, Adrià Majewski, Maciej Gallicchio, Emilio De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York United States Acellera Devonshire House 582 Honeypot Lane Stanmore Middlesex HA7 1JS United Kingdom Passeig Lluis Companys 23 Barcelona08010 Spain

The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary depending on the methodology. In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function. Copyright © 2023, The Authors. All rights reserved.

关键词： Ligands

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Nanomaterials in agricultural production: Benefits and possible threats?

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ACS Symposium Series 2013年 1124卷 73-90页

作者： Hong, Jie Peralta-Videa, Jose R. Gardea-Torresdey, Jorge L. Environmental Science and Engineering PhD Program University of Texas at El Paso 500 West University Ave. El Paso TX 79968 United States Chemistry Department University of Texas at El Paso 500 West University Ave. El Paso TX 79968 United States

ISBN: (纸本)9780841227842

Food and agricultural production are among the most sensitive fields of application of nanotechnology. It is predicted that nanotechnology will revolutionize agriculture through new tools for disease treatment and detection, smart delivery systems, sensors, and better management devices. However, the rapid development of nanotechnology could release a huge amount of engineered nanoparticles, which may cause adverse effects on edible plants. In this review article the authors analyzed the most recent literature on the application of nanotechnology in agriculture, including nanofertilizers, nanosensors, crop protection, pollution control, waste management, and pesticide detection. The negative effects caused by nanoparticles on edible plants are also discussed. © 2013 American Chemical Society.

关键词： Nanoparticles

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随机扩增多态性DNA技术研究发现二氧化钛纳米颗粒对西葫芦具有基因毒性(英文)

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2014年第8期15卷 618-623页

作者： Fabiola MORENO-OLIVAS Vincent U.GANT Jr. Kyle L.JOHNSON Jose R.PERALTA-VIDEA Jorge L.GARDEA-TORRESDEY Depertment of Chemistry The University of Texas at El Paso El Paso TX 79968 USA University of California Center for Environmental Implications of Nanotechnology (UC CEIN) The University of Texas at El Paso El Paso TX 79968 USA Department of Biological Sciences and Border Biomedical Research Center The University of Texas at El Paso El Paso TX 79968 USA Environmental Science and Engineering PhD Program The University of Texas at El Paso El Paso TX 79968 USA

研究目的:二氧化钛(TiO2)纳米颗粒已经广泛应用于化妆品、防晒霜、涂料和牙膏等。这些纳米颗粒性质非常稳定,能在废水和生物固体中转移和分散。现有研究表明,TiO2纳米颗粒对动物正常生理活动具有毒性等负面作用。但是,它们对植物是否具... 详细信息

研究目的:二氧化钛(TiO2)纳米颗粒已经广泛应用于化妆品、防晒霜、涂料和牙膏等。这些纳米颗粒性质非常稳定,能在废水和生物固体中转移和分散。现有研究表明,TiO2纳米颗粒对动物正常生理活动具有毒性等负面作用。但是,它们对植物是否具有毒性特别是是否会产生植物基因毒性至今尚不清楚。因此,本文使用随机扩增多态性DNA技术研究TiO2纳米颗粒是否对西葫芦具有基因毒性,为TiO2纳米颗粒排放进入环境后的潜在植物毒性风险评价提供依据。创新要点:首次发现了TiO2纳米颗粒对西葫芦具有基因毒性。重要结论:采用随机扩增多态性DNA技术,发现TiO2纳米颗粒污染处理的西葫芦样品与未处理样品的基因组DNA图谱相比,不仅在谱带强度有明显差异,而且存在谱带消失和新谱带产生现象,表明TiO2纳米颗粒对西葫芦具有基因毒性。

关键词：随机扩增多态性DNA技术 TiO2 纳米颗粒基因组DNA 西葫芦毒性

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TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells (vol 50, pg 83, 2017)

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NATURE GENETICS 2018年第5期50卷 764-764页

作者： Verma, Nipun Pan, Heng Dore, Louis C. Shukla, Abhijit Li, Qing V. Pelham-Webb, Bobbie Teijeiro, Virginia Gonzalez, Federico Krivtsov, Andrei Chang, Chan-Jung Papapetrou, Eirini P. He, Chuan Elemento, Olivier Huangfu, Danwei Developmental Biology Program Sloan Kettering Institute New York NY USA Weill Graduate School of Medical Sciences at Cornell University/The Rockefeller University/Sloan Kettering Institute Tri-Institutional MD-PhD Program New York NY USA Department of Physiology and Biophysics Englander Institute for Precision Medicine Institute for Computational Biomedicine Weill Cornell Medical College New York NY USA Weill Cornell Graduate School of Medical Sciences Weill Cornell Medical College New York NY USA Department of Chemistry Department of Biochemistry and Molecular Biology Institute for Biophysical Dynamics Howard Hughes Medical Institute University of Chicago Chicago IL USA Louis V. Gerstner Jr. Graduate School of Biomedical Sciences Memorial Sloan Kettering Cancer Center New York NY USA Cancer Biology and Genetics Program Sloan Kettering Institute New York NY USA Department of Oncological Sciences and Black Family Stem Cell Institute Icahn School of Medicine at Mount Sinai New York NY USA

TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we show that TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding decrease in gene expression in the undifferentiated state. Focusing on the bivalent PAX6 locus, we find that increased DNMT3B binding is associated with promoter hypermethylation, which precipitates a neural differentiation defect and failure of PAX6 induction during differentiation. dCas9-mediated locus-specific demethylation and global inactivation of DNMT3B in TKO hESCs partially reverses the hypermethylation at the PAX6 promoter and improves differentiation to neuroectoderm. Taking these findings together with further genome-wide methylation and TET1 and DNMT3B ChIP-seq analyses, we conclude that TET proteins safeguard bivalent promoters from de novo methylation to ensure robust lineage-specific transcription upon differentiation.

关键词： Epigenetics Stem cells

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Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein

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IUCrJ 2024年第PT 3期11卷 384-394页

作者： Chang Yi Liu Han Pin Cheng Chan Pin Lin Yi Ting Liao Tzu Ping Ko Shin Jen Lin Shih Shun Lin Hao Ching Wang The PhD Program for Translational Medicine College of Medical Science and Technology Taipei Medical University and Academia Sinica Taipei Taiwan. Institute of Biotechnology National Taiwan University Taipei Taiwan. Institute of Biological Chemistry Academia Sinica Taipei Taiwan. International Center for the Scientific Development of Shrimp Aquaculture National Cheng Kung University Tainan Taiwan.

Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP-F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches' broom phytoplasma-infected Catharanthus roseus. The association between IMP and PHYL1 is substantiated through in vivo immunoprecipitation, an in vitro cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.

关键词： X-ray crystallography actin-binding proteins immunodominant membrane proteins phytoplasma protein structure α-helix bundles

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The Scalability of Third Generation Photovoltaics: Deposition Techniques and Modularity

The Scalability of Third Generation Photovoltaics: Depositio...

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2023 Sharjah International Conference on Physics of Advanced Materials, SICPAM 2023

作者： Ayoub, Mohamad Alashkar, Adnan Mdallal, Ayman Ibrahim, Taleb Khamis, Mustafa Alami, Abdul Hai Sustainable and Renewable Energy Engineering Department University of Sharjah Sharjah27272 United Arab Emirates PhD Program in Materials Science and Engineering American University of Sharjah Sharjah26666 United Arab Emirates Department of Chemical Engineering American University of Sharjah Sharjah26666 United Arab Emirates Department of Biology Chemistry and Environmental Sciences College of Arts and Sciences American University of Sharjah Sharjah26666 United Arab Emirates Center for Advanced Materials Research Research Institute of Science and Engineering University of Sharjah Sharjah27272 United Arab Emirates

The development of third-generation photovoltaic (TGPV) technologies promises to address some of the limitations of conventional silicon-based solar cells. However, the scalability of these technologies is a critical factor in their practical application. TGPV include Perovskite Solar Cells (PSC), Organic Solar Cells (OSC), and Dye-Sensitized Solar Cell (DSSC). This paper reviews and summarizes the recent trends and research on the deposition techniques and modularity of TGPV. Various deposition techniques such as slot-die coating, thermal evaporation, and spray pyrolysis are discussed, along with their advantages and limitations. Modularity, which allows for the integration of TGPV cells into different structures, is also examined as a critical factor in scalability. The paper concludes that the scalability of TGPV technologies depends on the development of efficient and cost-effective deposition techniques and modularity, which will facilitate the integration of the TGPV cells into various structures and enable the widespread use of these promising technologies. © Published under licence by IOP Publishing Ltd.

关键词： Perovskite solar cells

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Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

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Nano Energy 2024年 125卷

作者： Cheng, Yu-Ying Ganguly, Anindita Cheng, Yi-Yun Ortiz, Christopher Llynard D. Pal, Arnab Shah, Pramod Kaswan, Kuldeep Yang, Lee-Wei Lin, Zong-Hong Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Internet of Senses Research Center National Tsing Hua University Hsinchu30013 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300044 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu300044 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu300044 Taiwan Biomedical Artificial Intelligence PhD Program National Tsing Hua University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei Taiwan

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available. © 2024 Elsevier Ltd

关键词： Nanosensors

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Structural and magnetic properties of molecular beam epitaxy (MnSb2Te4)x(Sb2Te3)1-x topological materials with exceedingly high Curie temperature

arXiv

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arXiv 2023年

作者： Forrester, Candice R. Testelin, Christophe Wickramasinghe, Kaushini Levy, Ido Demaille, Dominique Hrabovski, David Ding, Xiaxin Krusin-Elbaum, Lia Lopez, Gustavo E. Tamargo, Maria C. Department of Chemistry The City College of New York New YorkNY10031 United States PhD Program in Chemistry CUNY Graduate Center New YorkNY10016 United States Department of Chemistry Lehman College BronxNY10468 United States Sorbonne Université CNRS Institut des NanoScience de Paris ParisF-75005 France Department of Physics New York University New YorkNY10003 United States Sorbonne Université MPBT Platform 4 Place Jussieu Paris75252 France Department of Physics The City College of New York New YorkNY10031 United States PhD Program in Physics CUNY Graduate Center New YorkNY10016 United States

Tuning magnetic properties of magnetic topological materials is of interest to realize elusive physical phenomena such as quantum anomalous hall effect (QAHE) at higher temperatures and design topological spintronic devices. However, current topological materials exhibit Curie temperature (TC) values far below room temperature. In recent years, significant progress has been made to control and optimize TC, particularly through defect engineering of these structures. Most recently we showed evidence of TC values up to 80K for (MnSb2Te4)x(Sb2Te3)1-x, where 0.7 ≤ x ≤ 0.85, by controlling the compositions and Mn content in these structures. Here we show further enhancement of the TC, as high as 100K, by maintaining high Mn content and reducing the growth rate from 0.9 nm/min to 0.5 nm/min. Derivative curves reveal the presence of two TC components contributing to the overall value and propose TC1 and TC2 have distinct origins: excess Mn in SLs and Mn in Sb2-yMnyTe3QLs alloys, respectively. In pursuit of elucidating the mechanisms promoting higher Curie temperature values in this system, we show evidence of structural disorder where Mn is occupying not only Sb sites but also Te sites, providing evidence of significant excess Mn and a new crystal structure:(Mn1+ySb2-yTe4)x(Sb2-yMnyTe3)1-x. Our work shows progress in understanding how to control magnetic defects to enhance desired magnetic properties and the mechanism promoting these high TC in magnetic topological materials such as (Mn1+ySb2-yTe4)x(Sb2-yMnyTe3)1-x Copyright © 2023, The Authors. All rights reserved.

关键词： Topology

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Exhaled volatile organic compounds for cholangiocarcinoma diagnosis

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Liver Research 2022年第3期6卷 191-197页

作者： Nanicha Siriwong Thanikan Sukaram Rossarin Tansawat Terapap Apiparakoon Thodsawit Tiyarattanachai Sanparith Marukatat Rungsun Rerknimitr Roongruedee Chaiteerakij Department of Medicine Faculty of MedicineChulalongkorn UniversityBangkokThailand Division of Gastroenterology Department of MedicineFaculty of MedicineChulalongkorn Universityand King Chulalongkorn Memorial HospitalThai Red Cross SocietyBangkokThailand Department of Food and Pharmaceutical Chemistry Faculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand Department of Computer Engineering Faculty of EngineeringChulalongkorn UniversityBangkokThailand Clinical Sciences PhD International Program Faculty of MedicineChulalongkorn UniversityThailand Image Processing and Understanding Team Artificial Intelligence Research GroupNational Electronics and Computer Technology Center(NECTEC)Thailand Center of Excellence for Innovation and Endoscopy in Gastrointestinal Oncology Chulalongkorn UniversityBangkokThailand

Objectives:The difficulties in the early detection consequent to the lack of sensitive biomarkers render patients with cholangiocarcinoma(CCA)to have poor ***,sensitive and specific volatile organic compounds(VOCs)were identified in several ***,the VOC profiles in CCA are not ***,we investigated the VOC profiles in exhaled breath of CCA patients and ***:We prospectively collected exhaled breath samples from 30 consecutive patients newly diagnosed with CCA and 30 controls who did not have CCA(seven had benign biliary strictures and 23 had other medical conditions).Exhaled VOCs were identified using gas chromatography mass spectrometry Triple Quadrupoles *** of the significant differences in VOCs between cases and controls was conducted using supervised multivariate regression *** validation was performed for these VOCs in another cohort of 18 CCA patients and 22 ***:Levels of six compounds were significantly different between CCA patients and controls,namely,acetone,isopropyl alcohol,dimethyl sulfide,1,4-pentadiene,allyl methyl sulfide,and N,*** and dimethyl sulfide were independently associated with CCA as demonstrated in the multivariate *** the cut-off value of 8.59107 arbitrary unit(AU),acetone had a sensitivity and specificity of 82.1%and 75.8%,respectively,with an area under the receiving operator curve(AUROC)of 0.85 for the CCA *** level was also significantly different between cases and controls in the validation *** the same cut-off value,the sensitivity,specificity,and AUROC was 59.1%,66.7%,and 0.85,***:Breath analysis may potentially be useful for CCA diagnosis.A cohort of patients with earlystage CCA in further studies is needed to confirm the ability of exhaled VOCs for the early detection of CCA.

关键词： Cholangiocarcinoma(CCA) Bile duct cancer Volatile organic compounds(VOCs) Biomarker Cancer screening Diagnostic model

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Cryo-EM structure of the plant 26S proteasome

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Plant Communications 2022年第3期3卷 116-126页

作者： Susanne Kandolf Irina Grishkovskaya Katarina Belacic Derek L.Bolhuis Sascha Amann Brent Foster Richard Imre Karl Mechtler Alexander Schleiffer Hemant D.Tagare Ellen D.Zhong Anton Meinhart Nicholas G.Brown David Haselbach Research Institute of Molecular Pathology(IMP) Vienna BioCenter(VBC)Campus-Vienna-BioCenter 11030 ViennaAustria Department of Radiology and Biomedical Imaging Yale UniversityNew HavenCT 06510USA Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina School of MedicineChapel HillNC 27599USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of TechnologyCambridgeMA 02139USA Vienna BioCenter PhD Program Doctoral School of the University at Vienna and Medical University of ViennaVienna BioCenter(VBC)ViennaAustria Institute of Physical Chemistry University of FreiburgAlbertstraße 21Freiburg 79104Germany CIBSS Centre for Integrative Biological Signalling Studies University of FreiburgFreiburgGermany

Targeted proteolysis is a hallmark of *** is especially important in long-lived cells that can be found in higher eukaryotes,like *** task is mainly fulfilled by the ubiquitin–proteasome ***,proteolysis by the 26S proteasome is vital to development,immunity,and cell *** the yeast and animal proteasomes are well characterized,there is only limited information on the plant *** determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 A°.We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and ***,we noticed a structural difference in the proteolytic active b1 ***,we uncovered an unseen compression state by characterizing the proteasome’s conformational *** suspect that this new conformation of the 20S core protease,in correlation with a partial opening of the unoccupied gate,may contribute to peptide release after *** data provide a structural basis for the plant proteasome,which is crucial for further studies.

关键词： 26S proteasome spinach UPS cryo-EM conformational landscape

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