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Observation of a single protein by ultrafast X-ray diffraction

Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova johan Bielecki Rebecca Boll Benedikt J.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn Janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko Jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr Jannik Lübke Adrian P.Mancuso Tommaso Mazza carl Nettelblad Yevheniy Ovcharenko Daniel E.Rivas Max Rose Amit K.Samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko Daniel Westphal Tamme Wollweber Lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.chapman Jonas A.Sellberg carolin Seuring Ivan A.Vartanyants Jochen Küpper Michael Meyer Filipe R.N.c.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS cR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User cryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

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A positive feedback loop involving Gcm1 and Fzd5 directs chorionic branching morphogenesis in the placenta

A positive feedback loop involving Gcm1 and Fzd5 directs cho...

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2012全国发育生物学大会

作者： Haruo Nakano David G.Simmons johan H.van Es Hans clevers Gustavo Leone James c.cross State key laboratory of Reproductive Biology Institute of ZoologyChinese Academy of Sciences

chorioallantoic branching morphogenesis is a key milestone during placental development,creating the large surface area for nutrient and gas exchange and is therefore critical for the success of term *** Wnt pathway molecules have been shown to regulate placental ***,it remains largely unknown how Wnt-Frizzled (Fzd) signaling spatiotemporally interacts with other essential regulators,ensuring chorionic branching morphogenesis and angiogenesis during placental *** systemic and trophoblast-specific Fzd5 null and Gcm1 deficient mouse models,combining trophoblast stem cell lines and tetraploid aggregation assay,we demonstrate here that an amplifying signaling loop between Gcm1 and Fzd5 is essential for normal initiation of branching in the chorionic plate. While Gcm1 upregulates Fzd5 specifically at sites where branching initiates in the basal chorion,this elevated Fzd5 expression via nuclearβ-catenin signaling in turn maintains expression of ***,we show that Fzd5-mediated signaling induces the disassociation of cell junctions for branching initiation via downregulating ZO-1 expression in trophoblast cells at the base of the *** addition,Fzd5-mediated signaling is also important for upregulation of Vegf expression in chorion trophoblast ***,we demonstrate that Fzd5-Gcm1 signaling cascade is operative during human trophoblast differentiation. conclusions:These data indicate that Gcm1 and Fzd5 function in an evolutionary conserved positive feedback loop that regulates trophoblast differentiation and sites of chorionic branching morphogenesis.

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Where is Logic Going?

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逻辑学研究 2014年第1期7卷 84-99页

作者： johan van Benthem Fenrong Liu Institute for Logic Language&Computation University of Amsterdam Department of Philosophy Stanford University Department of Philosophy Tsinghua University

On October 14–16,2013,a large group of chinese and foreign logicians gatheredatTsinghuaUniversitytopresentabroadandlivelypictureofthefieldoflogicin its various ramifications *** can be seen in the scientific program ... 详细信息

关键词： Where is

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cancer risk and mortality in patients with solitary Peutz–Jeghers polyps

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Gastroenterology Report 2023年第1期11卷 576-578页

作者： Anne Marie Jelsig Laus Wullum Lilian Bomme Ousager johan Burish Tine Plato Kuhlmann John Gasdal Karstensen Department of clinical Genetics University Hospital of CopenhagenRigshospitaletCopenhagenDenmark Omicron Aps CopenhagenDenmark Department of clinical Genetics Odense University HospitalOdenseDenmark Human Genetics Institute of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark Gastrounit Medical DivisionCopenhagen University Hospital—Amager and HvidovreHvidovreDenmark Department of Pathology Copenhagen University HospitalHerlevDenmark Department of clinical Medicine University of CopenhagenCopenhagenDenmark Danish Polyposis Registry GastrounitCopenhagen University Hospital—Amager and HvidovreHvidovreDenmark

Introduction Solitary Peutz–Jeghers polyps are hamartomatous lesions in the gastrointestinal(GI)*** are rare and can be diagnosed in both children and adults(Figure 1A).Microscopically,Peutz–Jeghers polyps can have ... 详细信息

关键词： Jeghers Peutz polyps

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Transfer learning in demand response: A review of algorithms for data-efficient modelling and control

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能源与人工智能(英文) 2022年第1期7卷 183-196页

作者： Thijs Peirelinck Hussain Kazmi Brida V.Mbuwir chris Hermans Fred Spiessens johan Suykens Geert Deconinck ESAT KU LeuvenKasteelpark Arenberg 10 bus 24453001 LeuvenBelgium AMO Flemish Institute for Technological Research(VITO)Boeretang 2002400 MolBelgium AMO EnergyVilleThor Park 83103600 GenkBelgium

A number of decarbonization scenarios for the energy sector are built on simultaneous electrification of energy demand,and decarbonization of electricity generation through renewable energy ***,increased electricity demand due to heat and transport electrification and the variability associated with renewables have the potential to disrupt stable electric grid *** address these issues using demand response,researchers and practitioners have increasingly turned towards automated decision support tools which utilize machine learning and optimization ***,when applied naively,these algorithms suffer from high sample complexity,which means that it is often impractical to fit sufficiently complex models because of a lack of observed *** advances have shown that techniques such as transfer learning can address this problem and improve their performance considerably—both in supervised and reinforcement learning *** formulations allow models to leverage existing domain knowledge and human expertise in addition to sparse observational *** formally,transfer learning embodies all techniques where one aims to increase(learning)performance in a target domain or task,by using knowledge gained in a source domain or *** paper provides a detailed overview of state-of-the-art techniques on applying transfer learning in demand response,showing improvements that can exceed 30%in a variety of *** observe that most research to date has focused on transfer learning in the context of electricity demand prediction,although reinforcement learning based controllers have also seen increasing ***,a number of limitations remain in these studies,including a lack of benchmarks,systematic performance improvement tracking,and consensus on techniques that can help avoid negative transfer.

关键词： Demand response Transfer learning Reinforcement learning Review Smart grid

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Nutritive Value of Four Lucerne cultivars Planted in Two Soil Types at Bathurst Research Station, Eastern cape Province, South Africa

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Agricultural Sciences 2022年第10期13卷 1048-1056页

作者： Mhlangabezi Solontsi Mfundo Phakama Maqubela johan Adam van Niekerk Jan Willem Swanepoel Gideon Jordaan Unathi Gulwa Sive Tokozwayo Department of Rural Development and Agrarian Reform Dohne ADI Stutterheim South Africa centre for Sustainable Agriculture University of Free State Bloemfontein South Africa Department of Rural Development and Agrarian Reform Cradock Experimental Farm Cradock South Africa

Medicago sativa (lucerne) is a widely used perennial fodder crop and ranked amongst the highly nutritive fodders globally. This study assessed the nutritive value (i.e. cP % and TDN %) of four lucerne cultivars under two soil types at Bathurst Research Station. A random grid (quadrant) sampling method was used for sampling and samples were submitted to the laboratory for analysis to determine forage quality. Data collection was carried out by separating harvested biomass for each cultivar using clean packs, weighed and dried at 70˚c for 48 hours then crude protein (cP %) and Total Digestible Nutrients (TDN %) were determined. The results of the study showed that soil type (site) had a significant (P ct on the overall quality of dry matter produced. In soil 1 (S1) the overall cP % content was 11.48% while it was 19.03% in soil 2 (S2). cultivar 3 (KKS 9911) was the least nutritive cultivar in site 1, while the same cultivar was the most nutritive cultivar in site 2 pertaining cP content. Soil type also significantly affected (P content of different lucerne cultivars. In S1, c4 (WL 525) had the highest (P content in comparison to the rest of the cultivars while in the same soil type c1 (SA Std.) had the least TDN content. The four tested lucerne cultivars generally produced highly nutritive lucerne in S2 while they produced less nutritive lucerne in relation to both cP and TDN content in S1.

关键词： Forage Quality Nutritive Value Fodder

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Aptamer-Based Extraction of Ergot Alkaloids from Ergot contaminated Rye Feed

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Advances in Bioscience and Biotechnology 2014年第8期5卷 692-698页

作者： Elsa Rouah Walid Maho Jaytry Mehta Sarah De Saeger Adrian covaci Bieke van Dorst Ronny Blust johan Robbens Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium Institute of Agricultural and Fisheries Research (ILVO) Oostende Belgium Laboratory of Systemic Physiological and Toxicological Research Department of Biology University of Antwerp Antwerp Belgium Laboratory of Systemic Physiological and Toxicological Research Department of BiologyUniversity of Antwerp Antwerp Belgium Toxicological center University of Antwerp Antwerp Belgium

Ergot alkaloids are mycotoxins which can be found in food based on cereal-crops, due to a contamination of plants by fungi of the genus claviceps. The ingestion of ergot contaminated cereal crops can lead to a severe poisoning known as ergotism. For food and feed safety purposes, the extraction of ergot alkaloids from ergot contaminated flour was investigated. For the specific recognition of ergot alkaloids, DNA aptamer ligands specially selected for ergot alkaloids were grafted onto silica gel in order to construct a specific solid phase extraction system. The aptamer-functionalized silica gels were used to extract ergot alkaloids from a contaminated rye feed sample. The presence of ergot alkaloids eluted from the aptamer-functionalized silica gels was analyzed using Lc-QTOF-MS. By using this simple system, it was possible to specifically extract ergosine, ergokryptine and ergocornine from an ergot contaminated rye feed sample. This aptamer-based extraction tool shows the applicability of aptamers for the specific extraction of toxins or natural compounds from turbid matrices in a one-step procedure.

关键词： Single-Stranded Nucleic Acid Aptamer Aptamer-Functionalized Silica Gel Ergosine Ergokryptine Ergocornine

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编者导言(英文)

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逻辑学研究 2011年第3期4卷 1-2页

作者： Jeremy Seligman johan van Benthem 不详

This special issue of the journal‘Studies in Logic’ results from an international workshopon‘TheHistory of Logic in china’held in Amsterdam,The Netherlands,on November 24-26, 2010 (http://***/history-logic-china).... 详细信息

关键词：英文摘要内容介绍编辑工作期刊

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Leukocyte ABc-transporter A1 and LDL Receptor Play Independent Roles in Atherosclerosis： the Potential contribution of T cells

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中国动脉硬化杂志 2013年第9期21卷 I0075-I0075页

作者： Ying Zhao Jun Wang Laura calpe-Berdiel Amanda c. Foks Bart Lammers johan Kuiper Theo J.c. van Berkel Miranda van Eck Department of Pathology and Pathophysiology Soochow University Suzhou Jiangsu 215123 China Division of Biopharmaeeutics leiden~Amsterdam Center for Drug Research leiden University leiden 2333 CCThe Netherlands Institute of Biology and Medical Sciences Soochow University Suzhou Jiangsu 215123 China

Objective The present study aims to investigate whether LDL receptor (LDLR) deficiency influences the atheroprotective effects of leukocyte ABc-transporter A1 (ABcA1) in vivo. Methods and Results LDLR -/- mice were transplanted with bone marrow from LDLR -/-/ABcA1 -/- mice, LDLR + / +/ABcA1 -/- mice, and their respective controls. Although leukocyte ABcA1defi- ciency reduced plasma cholesterol levels, after 8 weeks of Western-type diet feeding, animals transplanted with LDLR / /ABcA1 /- and LDLR + / +/ABcA1 -/- bone marrow developed 1.6-fold ( P compared to their respective controls. This clearly indicates that the atheroprotection of leukocyte ABcA1 is not affected by LDLR. Two-way ANOVA analysis also demonstrated that deletion of the leukocyte LDLR reduced lesion development ( P cially in the absence of leukocyte ABcA1. However, leukocyte LDLR deficiency does not affect monocytosis, recruitment of moncocytes and macrophage foam cell formation. Interestingly, the deletion of leukocyte ABcA1did reduce lymphocytosis and recruitment of T cells into the ad- ventitia of lesions. These effects are associated with smaller lesion size in LDLR -/-/ABcA1 -/- transplanted mice, indicating the potential contribution of lymphocytosis and recruitment of T cells to atherogenesis. conclusions Leukocyte LDLR deficiency does not affect the atheroprotective effects of leukocyte ABcA1, and vice versa. Furthermore, suppression of lymphocytosis and T cell re- cruitment into the adventitia could contribute to the atheroprotection of leukocyte LDLR deficiency and ABcA1.

关键词：低密度脂蛋白受体动脉粥样硬化 ABcA1 白细胞减少 T细胞转运子单核细胞增多淋巴细胞

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cancer diagnosis is one quarter lower than the expected cancer incidence in the first year of cOVID-19 pandemic in Germany:A retrospective register-based cohort study

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cancer communications 2022年第7期42卷 673-676页

作者： johannes Diers Laura Acar johanna c.Wagner Philip Baum Mohammed Hankir Sven Flemming carolin Kastner christoph-Thomas Germer Helmut L’hoest Ursula Marschall johan Friso Lock Armin Wiegering Department of General VisceralTransplantationVascular and Pediatric SurgeryUniversity HospitalUniversity of WuerzburgWuerzburg 97080Germany Department Medizin und Versorgungsforschung Institut fuer GesundheitssystemforschungBarmerWuppertal 42275Germany Department of Biochemistry and Molecular Biology University ofWuerzburgWuerzburg 97074Germany comprehensive cancer centre Mainfranken University of Wuerzburg Medical CentreWuerzburg 97080Germany

Dear Editor,The coronavirus disease of 2019(cOVID-19)pandemic has necessitated that semi-urgent and elective medical cases,including cancer screenings,are postponed in hospitals worldwide to accommodate the increasing number of patients with severe cOVID-19 symptoms[1-4].consequently,several reports from the first cOVID-19 wave in spring 2020 showed a significant decrease in new cancer diagnoses as well as cancer therapy and screenings[5,6].

关键词： diagnosis cancer cancer

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