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Observation of a single protein by ultrafast X-ray diffraction

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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

Machine-learning driven global optimization of surface adsorbate geometries

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npj Computational Materials 2023年第1期9卷 1196-1203页

作者： Hyunwook Jung lena Sauerland Sina Stocker Karsten Reuter Johannes T.Margraf Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6D-14195 BerlinGermany

The adsorption energies of molecular adsorbates on catalyst surfaces are key descriptors in computational catalysis *** the relatively large reaction intermediates frequently encountered,e.g.,in syngas conversion,a multitude of possible binding motifs leads to complex potential energy surfaces(PeS),*** implies that finding the optimal structure is a difficult global optimization problem,which leads to significant uncertainty about the stability of many *** tackle this issue,we present a global optimization protocol for surface adsorbate geometries which trains a surrogate machine learning potential *** approach is applicable to arbitrary surface models and adsorbates and minimizes both human intervention and the number of required DFT calculations by iteratively updating the training set with configurations explored by the *** demonstrate the efficiency of this approach for a diverse set of adsorbates on the Rh(111)and(211)surfaces.

关键词： optimization global implies

Polarity,intramolecular charge transfer,and hydrogen bond comediated solvent effects on the optical properties of graphene quantum dots

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Nano Research 2023年第1期16卷 45-52页

作者： Yalei Hu Christof Neumann lena Scholtz Andrey Turchanin Ute Resch-Genger Siegfried eigler Institute of Chemistry and Biochemistry Freie Universität BerlinTakustraße 314195 BerlinGermany Institute of Physical Chemistry and Abbe Center of Photonics Friedrich Schiller University JenaLessingstraße 1007743 JenaGermany Federal Institute for Materials Research and Testing(BAM) Division BiophotonicsRichard Willstätter Straße 1112489 BerlinGermany

Graphene quantum dots(GQDs)have attracted increasing attention due to their favorable optical properties and have been widely used,e.g.,in the biomedical ***,the properties related to the chemical structure of GQDs,resulting in solventdependent optical properties,still remain ***,we present the synthesis of long-wavelength emitting GQDs with a size of about 3.6 nm via a solvothermal method using oxo-functionalized graphene(oxo-G)and p-phenylenediamine as precursors and their structural and surface chemical analysis by transmission electron and atomic force microscopy(TeM;AFM)as well as Fourier-transform infrared,Raman,and X-ray photoelectron spectroscopy(FTIR;Raman;XPS).Subsequently,the influence of solvent polarity and proticity on the optical properties of the as-prepared GQDs bearing–OH,–NH_(2),–COOH and pyridine surface groups was *** on the results of the absorption and fluorescence(FL)studies,a possible luminescence mechanism is *** observed solvent-induced changes in the spectral position of the FL maximum,FL quantum yield,and FL decay kinetics in protic and aprotic solvents of low and high polarity are ascribed to a combination of polarity effects,intramolecular charge transfer(ICT)processes,and hydrogen ***,the potential of GQDs for the optical sensing of trace amount of water was *** results of our systematic spectroscopic study will promote the rational design of GQDs and shed more light on the FL mechanism of carbon-based fluorescent nanomaterials.

关键词： graphene quantum dots(GQDs) polarity intramolecular charge transfer(ICT) hydrogen bond optical properties

Single-cell trajectories of melanoma cell resistance to targeted treatment

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Cancer Biology & Medicine 2022年第1期19卷 56-73页

作者： Maria Schmidt lena Sünke Mortensen Henry Loeffler-Wirth Corinna Kosnopfel Knut Krohn Hans Binder Manfred Kunz Interdisciplinary Centre for Bioinformatics University of LeipzigLeipzig 04107Germany Department of Dermatology Venereology and AllergologyUniversity of WürzburgWürzburg 97074Germany Core Unit DNA Technologies Medical FacultyUniversity of LeipzigLeipzig 04103Germany Department of Dermatology Venereology and AllergologyUniversity of Leipzig Medical CenterLeipzig 04103Germany

Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant *** developments in single-cell sequencing technology have provided deeper insights into these ***:Here,we analyzed a BRAFV600 e-mutant melanoma cell line by single-cell RNA-seq under various conditions:cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MeK1/2 inhibitors cobimetinib or *** reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state ***:Trajectories associated with resistance to single-agent treatment involved cell cycle,extracellular matrix,and de-differentiation *** contrast,shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation,with a small subpopulation showing markers of *** findings were validated in pseudotime analyses and RNA velocity ***:The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single-and double-agent *** study deepens our understanding of treatmentinduced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.

关键词： Melanoma single-cell transcriptome sequencing treatment response

effect of processing and accelerated storage on the volatile composition and sensory profile of a tomato soup

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Food Quality and Safety 2022年第2期6卷 341-352页

作者： lena C.Strohla Krishnachandra S.Hidangmayum Sandra S.Waehrens Vibeke Orlien Mikael A.Petersen Department of Food Science University of Copenhagen1958 Frederiksberg CDenmark

The volatile and sensory profile of pasteurized(95℃,18 min)and sterilized(120℃,14 min)tomato soup and its changes at accelerated storage conditions(37℃and 42℃)were identified,characterized,and correlated by predictive *** led to more profound changes over storage compared to pasteurisation,showing enhanced levels of‘dark'odour,‘burnt'flavour,and‘complexity',while pasteurized soup had more pronounced‘green'odour,‘vegetables'flavour,‘harmony',and‘freshness'.Over time,‘dark'and‘burnt'significantly increased for sterilized soups,whereas‘green'decreased significantly only for sterilized soup stored at 42℃.The changes of‘dark',‘green',‘off-flavour,‘burnt',‘har mony',and‘freshness'were associated with formation of furans(furfural and 2-acetyl-5-methylfuran),and decline of unsaturated aldehydes like e-2-octenal and e,e-2,*** compounds were identified to represent potential shelf-life markers,yet more studies on their odour activity in the tomato soup matrix are necessary to understand their contribution to the sensory *** construction of partial least squares models allowed the prediction of‘green',‘off-flavour',‘burnt',and‘freshness'based on selected *** models will be important tools in the process of predicting the end of shelf life,but need to be supplemented with consumer acceptability levels.

关键词： Volatile composition sensory profile accelerated storage tomato soup shelf life prediction partial least dquares regression

Apoplastic barriers of Populus×canescens roots in reaction to different cultivation conditions and abiotic stress treatments

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Stress Biology 2023年第1期3卷 269-282页

作者： Paul Grunhofer Ines Heimerich lena Herzig Svenja Pohl Lukas Schreiber Department of ecophysiology Institute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115 BonnGermany

Populus is an important tree genus frequently cultivated for economical ***,the high sensitivity of poplars towards water deficit,drought,and salt accumulation significantly affects plant productivity and limits biomass *** cultivation and abiotic stress conditions have been described to significantly induce the formation of apoplastic barriers(Casparian bands and suberin lamellae)in roots of different monocotyledonous crop ***,this study aimed to investigate to which degree the roots of the dicotyledonous gray poplar(Populus×canescens)react to a set of selected cultivation conditions(hydroponics,aeroponics,or soil)and abiotic stress treatments(abscisic acid,oxygen deficiency)because a differing stress response could potentially help in explaining the observed higher stress *** apoplastic barriers of poplar roots cultivated in different environments were analyzed by means of histochemistry and gas chromatography and compared to the available literature on monocotyledonous crop ***,dicotyledonous poplar roots showed only a remarkably low induction or enhancement of apoplastic barriers in response to the different cultivation conditions and abiotic stress *** genetic optimization(e.g.,overexpression of biosynthesis key genes)of the apoplastic barrier development in poplar roots might result in more stress-tolerant cultivars in the future.

关键词： Hydroponics Aeroponics Soil Abscisic acid(ABA) Oxygen deficiency Poplar root suberin

SUSTAINABLe NITROGeN MANAGeMeNT INDeX: DeFINITION, GLOBAL ASSeSSMeNT AND POTeNTIAL IMPROVeMeNTS

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Frontiers of Agricultural Science and engineering 2022年第3期9卷 356-365页

作者： Xin ZHANG Yanyu WANG lena SCHULTe-UeBBING Wim De VRIeS Tan ZOU eric ADAVIDSON University of Maryland Center for environmental Science FrostburgMD 21532USA environmental Systems Analysis Group Wageningen University&ResearchWageningen6708 PBthe Netherlands PBL Netherlands environmental Assessment Agency The Hague2594 AVthe Netherlands.

To represent the sustainability of nitrogen management in the Sustainable Development Goals indicator framework,this paper proposes a sustainable nitrogen management index(SNMI).This index combines the performance in N crop yield and N use efficiency(NUe),thereby accounting for the need for both food production and environmental *** SNMI to countries around the world,the results showed improvement in the overall sustainability of crop N management over the past four decades,but this improvement has been mainly achieved by crop yield increase,while global NUe has improved only *** values vary largely among countries,and this variation has increased since the 1970s,implying different levels of success,even failure,in improving N management for countries around the *** the standard SNMI assessment,the reference NUe was defined as 1.0(considered an ideal NUe)and the reference yield was defined as 90 kg·ha^(−1)·yr^(−1) N(considering a globally averaged yield target for meeting food demand in 2050).A sensitivity test that replaced the reference NUe of 1.0 with more realistic NUe targets of 0.8 or 0.9 showed overall reduction in SNMI values(i.e.,improved performance),but little change in the ranking among *** another test that replaced the universal reference yield with region-specific attainable yield,SNMI values declined(i.e.,improved performance)for most countries in Africa and West Asia,whereas they increased for many countries in europe and South *** index can be improved by further investigation of approaches for setting region-specific yield targets and high-quality data on crop yield ***,SNMI offers promise for a simple and transparent approach to assess progress of countries toward sustainable N management with a single indicator.

关键词： global assessment indicator nitrogen management sustainable agriculture sustainable development goals

Saccharomyces cerevisiae prevents postoperative recurrence of Crohn's disease modeled by ileocecal resection in HLA-B27 transgenic rats

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World Journal of Gastroenterology 2023年第5期29卷 851-866页

作者： Caroline Valibouze Silvia Speca Caroline Dubuquoy Florian Mourey lena M'Ba Lucil Schneider Marie Titecat Benoît Foligné Michaël Genin Christel Neut Philippe Zerbib Pierre Desreumaux Department of Digestive Surgery and Transplantation Lille University HospitalLille 59037France U1286-INFINITe-Institute for Translational Research in Inflammation Univ.LilleInsermCHU LilleLille 59000France Intestinal Biotech Development Lille 59045France Department of Research and Applications Gnosis by LesaffreLesaffre GroupMarcq-en-Baroeul 59700France ULR 2694-MeTRICS:évaluation des Technologies de Santéet des Pratiques Médicales University of LilleLille University HospitalLille 59000France Department of Hepato-Gastroenterology Lille University HospitalLille 59037France

BACKGROUND Postoperative recurrence(POR)after ileocecal resection(ICR)affects most Crohn's disease patients within 3-5 years after ***-invasive escherichia coli(AIeC)typified by the LF82 strain are pathobionts that are frequently detected in POR of Crohn's disease and have a potential role in the early stages of the disease *** cerevisiae CNCM I-3856 is a probiotic yeast reported to inhibit AIeC adhesion to intestinal epithelial cells and to favor their elimination from the *** To evaluate the efficacy of CNCM I-3856 in preventing POR induced by LF82 in an HLA-B27 transgenic(TgB27)rat *** Sixty-four rats[strain F344,38 TgB27,26 control non-Tg(nTg)]underwent an ICR at the 12th wk(W12)of life and were sacrificed at the 18th wk(W18)of ***27 rats were challenged daily with oral administration of LF82(109 colony forming units(CFUs)/day(d),n=8),PBS(n=5),CNCM I-3856(109 CFUs/d,n=7)or a combination of LF82 and CNCM I-3856(n=18).nTg rats receiving LF82(n=5),PBS(n=5),CNCM I-3856(n=7)or CNCM I-3856 and LF82(n=9)under the same conditions were used as *** was analyzed using macroscopic(from 0 to 4)and histologic(from 0 to 6)*** LF82 quantifications were performed weekly for each *** LF82 and inflammatory/regulatory cytokines were quantified in biopsies at W12 and *** are expressed as the median with the interquartile *** nTg animals did not develop POR.A total of 7/8(87%)of the TgB27 rats receiving LF82 alone had POR(macroscopic score≥2),which was significantly prevented by CNCM I-3856 administration[6/18(33%)TgB27 rats,P=0.01].Macroscopic lesions were located 2 cm above the anastomosis in the TgB27 rats receiving LF82 alone and consisted of ulcerations with a score of 3.5(2-4).Seven out of 18 TgB27 rats(39%)receiving CNCM I-3856 and LF82 had no macroscopic *** to untreated TgB27 animals receiving LF82 alone,coadministration of CNCM I-3856 and LF82 significantly red

关键词： Crohn's disease Recurrence escherichia coli Probiotic Saccharomyces cerevisiae Colorectal surgery

Conformational Proteomics Of Macromolecular Architecture: Approaching The Structure Of Large Molecular Assemblies And Their Mechanisms Of Action (With Cd-rom)

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