Graceffa, Rita

[["dc.bibliographiccitation.firstpage","10562"],["dc.bibliographiccitation.issue","29"],["dc.bibliographiccitation.journal","PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA"],["dc.bibliographiccitation.lastpage","10567"],["dc.bibliographiccitation.volume","111"],["dc.contributor.author","Nobrega, R. Paul"],["dc.contributor.author","Arora, Karunesh"],["dc.contributor.author","Kathuria, Sagar V."],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Barrea, Raul A."],["dc.contributor.author","Guo, Liang"],["dc.contributor.author","Chakravarthy, Srinivas"],["dc.contributor.author","Bilsel, Osman"],["dc.contributor.author","Irving, Thomas C."],["dc.contributor.author","Brooks, Charles L., III"],["dc.contributor.author","Matthews, C. Robert"],["dc.date.accessioned","2018-11-07T09:37:35Z"],["dc.date.available","2018-11-07T09:37:35Z"],["dc.date.issued","2014"],["dc.description.abstract","Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY."],["dc.identifier.doi","10.1073/pnas.1324230111"],["dc.identifier.isi","000339310700046"],["dc.identifier.pmid","25002512"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32871"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0027-8424"],["dc.title","Modulation of frustration in folding by sequence permutation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4281"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Journal of Mechanical Science and Technology"],["dc.bibliographiccitation.lastpage","4289"],["dc.bibliographiccitation.volume","33"],["dc.contributor.author","Inguva, Venkatesh"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Schulz-Schaeffer, Walter Joachim"],["dc.contributor.author","Bilsel, Osman"],["dc.contributor.author","Perot, Blair J."],["dc.date.accessioned","2020-03-03T08:11:21Z"],["dc.date.available","2020-03-03T08:11:21Z"],["dc.date.issued","2019"],["dc.description.abstract","A focused jet is an axisymmetric jet of liquid surrounded by an outer coaxial gas jet. The gas jet is typically used to compress the liquid jet in the radial direction thereby focusing it. At microscales, it is difficult to manufacture micro-scale delivery nozzles (needles) and to consistently align and axially position the liquid and the gas needles. However, it is very easy, using standard etching technologies to make precise and repeatable rectangular nozzle designs. This work will therefore explore the geometric and fluid dynamics constraints that allow one to design rectangular nozzles that produce round coaxial micro-jets of liquid and gas. Because of the small scales, the fluid dynamics of the focusing jet is unusual, and this work demonstrates that the liquid jet is best focused by shear stretching and not via gas compression. This paper shows that sheet jetting occurs when the Reynolds number of the gas is too high. Dripping occurs when the Weber number of the liquid is too low. The desired round jet occurs by balancing Weber number of the liquid jet and Reynolds number of the gas such that surface tension at the interface holds the water jet round while the acceleration of the water jet due to shear at the interface from fast-moving air causes the liquid jet cross-sectional area to decrease. The goal of this initial paper is to demonstrate that a parameter region exists where this flow behavior is possible."],["dc.identifier.doi","10.1007/s12206-019-0824-x"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63065"],["dc.language.iso","en"],["dc.relation.issn","1738-494X"],["dc.relation.issn","1976-3824"],["dc.title","Creating round focused micro-jets from rectangular nozzles"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1220"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","ChemPhysChem"],["dc.bibliographiccitation.lastpage","1223"],["dc.bibliographiccitation.volume","18"],["dc.contributor.author","Saldanha, Oliva"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Hémonnot, Clément Y. J."],["dc.contributor.author","Ranke, Christiane"],["dc.contributor.author","Brehm, Gerrit"],["dc.contributor.author","Liebi, Marianne"],["dc.contributor.author","Marmiroli, Benedetta"],["dc.contributor.author","Weihausen, Britta"],["dc.contributor.author","Burghammer, Manfred"],["dc.contributor.author","Köster, Sarah"],["dc.date.accessioned","2018-02-12T12:27:30Z"],["dc.date.available","2018-02-12T12:27:30Z"],["dc.date.issued","2017"],["dc.description.abstract","Encapsulating reacting biological or chemical samples in microfluidic droplets has the great advantage over single‐phase flows of providing separate reaction compartments. These compartments can be filled in a combinatoric way and prevent the sample from adsorbing to the channel walls. In recent years, small‐angle X‐ray scattering (SAXS) in combination with microfluidics has evolved as a nanoscale method of such systems. Here, we approach two major challenges associated with combining droplet microfluidics and SAXS. First, we present a simple, versatile, and reliable device, which is both suitable for stable droplet formation and compatible with in situ X‐ray measurements. Second, we solve the problem of “diluting” the sample signal by the signal from the oil separating the emulsion droplets by multiple fast acquisitions per droplet and data thresholding. We show that using our method, even the weakly scattering protein vimentin provides high signal‐to‐noise ratio data."],["dc.identifier.doi","10.1002/cphc.201700221"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12175"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.orgunit","Institut für Röntgenphysik"],["dc.relation.workinggroup","RG Köster (Cellular Biophysics)"],["dc.subject.gro","x-ray scattering"],["dc.subject.gro","cytoskeleton"],["dc.subject.gro","molecular biophysics"],["dc.subject.gro","microfluidics"],["dc.title","Rapid Acquisition of X-Ray Scattering Data from Droplet-Encapsulated Protein Systems"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3553"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","ACS Nano"],["dc.bibliographiccitation.lastpage","3561"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Hemonnot, Clement Y. J."],["dc.contributor.author","Reinhardt, Juliane"],["dc.contributor.author","Saldanha, Oliva"],["dc.contributor.author","Patommel, Jens"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Weinhausen, Britta"],["dc.contributor.author","Burghammer, Manfred"],["dc.contributor.author","Schroer, Christian G."],["dc.contributor.author","Köster, Sarah"],["dc.date.accessioned","2017-09-07T11:54:36Z"],["dc.date.available","2017-09-07T11:54:36Z"],["dc.date.issued","2016"],["dc.description.abstract","In recent years, X-ray imaging of biological cells has emerged as a complementary alternative to fluorescence and electron microscopy. Different techniques were established and successfully applied to macromolecular assemblies and structures in cells. However, while the resolution is reaching the nanometer scale, the dose is increasing. It is essential to develop strategies to overcome or reduce radiation damage. Here we approach this intrinsic problem by combing two different X-ray techniques, namely ptychography and nanodiffraction, in one experiment and on the same sample. We acquire low dose ptychography overview images of whole cells at a resolution of 65 nm. We subsequently record high-resolution nanodiffraction data from regions of interest. By comparing images from the two modalities, we can exclude strong effects of radiation damage on the specimen. From the diffraction data we retrieve quantitative structural information from intracellular bundles of keratin intermediate filaments such as a filament radius of 5 nm, hexagonal geometric arrangement with an interfilament distance of 14 nm and bundle diameters on the order of 70 nm. Thus, we present an appealing combined approach to answer a broad range of questions in soft matter physics, biophysics and biology."],["dc.identifier.doi","10.1021/acsnano.5b07871"],["dc.identifier.gro","3141720"],["dc.identifier.isi","000372855400058"],["dc.identifier.pmid","26905642"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/324"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1936-086X"],["dc.relation.issn","1936-0851"],["dc.relation.orgunit","Institut für Röntgenphysik"],["dc.relation.workinggroup","RG Köster (Cellular Biophysics)"],["dc.subject.gro","x-ray imaging"],["dc.subject.gro","x-ray scattering"],["dc.subject.gro","cytoskeleton"],["dc.subject.gro","cellular biophysics"],["dc.title","X-rays Reveal the Internal Structure of Keratin Bundles in Whole Cells"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","064702"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Structural Dynamics"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Yefanov, Oleksandr"],["dc.contributor.author","Oberthür, Dominik"],["dc.contributor.author","Bean, Richard"],["dc.contributor.author","Wiedorn, Max O."],["dc.contributor.author","Knoska, Juraj"],["dc.contributor.author","Pena, Gisel"],["dc.contributor.author","Awel, Salah"],["dc.contributor.author","Gumprecht, Lars"],["dc.contributor.author","Domaracky, Martin"],["dc.contributor.author","Sarrou, Iosifina"],["dc.contributor.author","Lourdu Xavier, P."],["dc.contributor.author","Metz, Markus"],["dc.contributor.author","Bajt, Saša"],["dc.contributor.author","Mariani, Valerio"],["dc.contributor.author","Gevorkov, Yaroslav"],["dc.contributor.author","White, Thomas A."],["dc.contributor.author","Tolstikova, Aleksandra"],["dc.contributor.author","Villanueva-Perez, Pablo"],["dc.contributor.author","Seuring, Carolin"],["dc.contributor.author","Aplin, Steve"],["dc.contributor.author","Estillore, Armando D."],["dc.contributor.author","Küpper, Jochen"],["dc.contributor.author","Klyuev, Alexander"],["dc.contributor.author","Kuhn, Manuela"],["dc.contributor.author","Laurus, Torsten"],["dc.contributor.author","Graafsma, Heinz"],["dc.contributor.author","Monteiro, Diana C. F."],["dc.contributor.author","Trebbin, Martin"],["dc.contributor.author","Maia, Filipe R. N. C."],["dc.contributor.author","Cruz-Mazo, Francisco"],["dc.contributor.author","Gañán-Calvo, Alfonso M."],["dc.contributor.author","Heymann, Michael"],["dc.contributor.author","Darmanin, Connie"],["dc.contributor.author","Abbey, Brian"],["dc.contributor.author","Schmidt, Marius"],["dc.contributor.author","Fromme, Petra"],["dc.contributor.author","Giewekemeyer, Klaus"],["dc.contributor.author","Sikorski, Marcin"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Vagovic, Patrik"],["dc.contributor.author","Kluyver, Thomas"],["dc.contributor.author","Bergemann, Martin"],["dc.contributor.author","Fangohr, Hans"],["dc.contributor.author","Sztuk-Dambietz, Jolanta"],["dc.contributor.author","Hauf, Steffen"],["dc.contributor.author","Raab, Natascha"],["dc.contributor.author","Bondar, Valerii"],["dc.contributor.author","Mancuso, Adrian P."],["dc.contributor.author","Chapman, Henry N."],["dc.contributor.author","Barty, Anton"],["dc.date.accessioned","2020-03-03T08:07:43Z"],["dc.date.available","2020-03-03T08:07:43Z"],["dc.date.issued","2019"],["dc.description.abstract","The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL."],["dc.identifier.doi","10.1063/1.5124387"],["dc.identifier.pmid","31832488"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63064"],["dc.language.iso","en"],["dc.relation.issn","2329-7778"],["dc.title","Evaluation of serial crystallographic structure determination within megahertz pulse trains"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","820"],["dc.bibliographiccitation.journal","Journal of Synchrotron Radiation"],["dc.bibliographiccitation.lastpage","825"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Nobrega, R. Paul"],["dc.contributor.author","Barrea, Raul A."],["dc.contributor.author","Kathuria, Sagar V."],["dc.contributor.author","Chakravarthy, Srinivas"],["dc.contributor.author","Bilsel, Osman"],["dc.contributor.author","Irving, Thomas C."],["dc.date.accessioned","2018-11-07T09:18:19Z"],["dc.date.available","2018-11-07T09:18:19Z"],["dc.date.issued","2013"],["dc.description.abstract","Small-angle X-ray scattering (SAXS) is a well established technique to probe the nanoscale structure and interactions in soft matter. It allows one to study the structure of native particles in near physiological environments and to analyze structural changes in response to variations in external conditions. The combination of microfluidics and SAXS provides a powerful tool to investigate dynamic processes on a molecular level with sub-millisecond time resolution. Reaction kinetics in the sub-millisecond time range has been achieved using continuous-flow mixers manufactured using micromachining techniques. The time resolution of these devices has previously been limited, in part, by the X-ray beam sizes delivered by typical SAXS beamlines. These limitations can be overcome using optics to focus X-rays to the micrometer size range providing that beam divergence and photon flux suitable for performing SAXS experiments can be maintained. Such micro-SAXS in combination with microfluidic devices would be an attractive probe for time-resolved studies. Here, the development of a high-duty-cycle scanning microsecond-time-resolution SAXS capability, built around the Kirkpatrick-Baez mirror-based microbeam system at the Biophysics Collaborative Access Team (BioCAT) beamline 18ID at the Advanced Photon Source, Argonne National Laboratory, is reported. A detailed description of the microbeam small-angle-scattering instrument, the turbulent flow mixer, as well as the data acquisition and control and analysis software is provided. Results are presented where this apparatus was used to study the folding of cytochrome c. Future prospects for this technique are discussed."],["dc.identifier.doi","10.1107/S0909049513021833"],["dc.identifier.isi","000325639200002"],["dc.identifier.pmid","24121320"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/28382"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1600-5775"],["dc.relation.issn","0909-0495"],["dc.title","Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10661"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","ACS Nano"],["dc.bibliographiccitation.lastpage","10670"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Hémonnot, Clément Y. J."],["dc.contributor.author","Ranke, Christiane"],["dc.contributor.author","Saldanha, Oliva"],["dc.contributor.author","Graceffa, Rita"],["dc.contributor.author","Hagemann, Johannes"],["dc.contributor.author","Köster, Sarah"],["dc.date.accessioned","2017-11-28T10:03:27Z"],["dc.date.available","2017-11-28T10:03:27Z"],["dc.date.issued","2016"],["dc.description.abstract","X-ray imaging of intact biological cells is emerging as a complementary method to visible light or electron microscopy. Owing to the high penetration depth and small wavelength of X-rays, it is possible to resolve subcellular structures at a resolution of a few nanometers. Here, we apply scanning X-ray nanodiffraction in combination with time-lapse bright-field microscopy to nuclei of 3T3 fibroblasts and thus relate the observed structures to specific phases in the cell division cycle. We scan the sample at a step size of 250 nm and analyze the individual diffraction patterns according to a generalized Porod’s law. Thus, we obtain information on the aggregation state of the nuclear DNA at a real space resolution on the order of the step size and in parallel structural information on the order of few nanometers. We are able to distinguish nucleoli, heterochromatin, and euchromatin in the nuclei and follow the compaction and decompaction during the cell division cycle."],["dc.identifier.doi","10.1021/acsnano.6b05034"],["dc.identifier.fs","623722"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/10593"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1936-086X"],["dc.relation.issn","1936-0851"],["dc.relation.orgunit","Institut für Röntgenphysik"],["dc.relation.workinggroup","RG Köster (Cellular Biophysics)"],["dc.subject","biological cells; cell division cycle; DNA compaction; nanostructure; X-ray nanodiffraction"],["dc.subject.gro","x-ray imaging"],["dc.subject.gro","x-ray scattering"],["dc.subject.gro","cellular biophysics"],["dc.title","Following DNA Compaction During the Cell Cycle by X-ray Nanodiffraction"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]