Ultrafast relaxation of photoexcited superfluid He nanodroplets

Mudrich, M.; LaForge, Aaron; Ciavardini, Alessandra; O’Keeffe, Patrick; Callegari, Carlo; Coreno, Marcello; Demidovich, Alexander; Devetta, M.; Fraia, Michele Di; Drabbels, Marcel; Finetti, P.; Geßner, Oliver; Grazioli, Cesare; Hernando, Alberto; Neumark, Daniel M.; Ovcharenko, Yevheniy; Piseri, P.; Plekan, Oksana; Prince, Kevin C.; Richter, Robert; Ziemkiewicz, Michael; Möller, Thomas; Eloranta, Jussi; Pí, M.; Barranco, M.; Stienkemeier, F.

doi:10.1038/s41467-019-13681-6

Cited by 39 publications

(60 citation statements)

References 55 publications

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“…The Pal (Dshi_1112) (6.8%) and TolB (Dshi_1111) (4.4%) proteins belong to the Tol-Pal complex that spans the cell envelopes of Gram-negative bacteria and coordinates outer membrane constriction with septation during cell division ( 51 – 54 ). The Tol-Pal complex consists of the three inner membrane (IM) proteins TolA, TolR, and TolQ, the periplasmic protein TolB, and the outer membrane lipoprotein Pal ( 55 ).…”

Section: Resultsmentioning

confidence: 99%

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif

et al. 2021

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Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions. IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.

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Section: Resultsmentioning

confidence: 99%

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif

et al. 2021

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“…With the advent of ultrafast X-ray free-electron lasers (XFELs), time-resolved single-particle-imaging experiments are more and more addressing ultrafast phenomena in physical or chemical processes within nanoparticles, such as melting, driven fluctuations, etc. (Clark et al, 2013;Gomez et al, 2014;Rupp et al, 2017;Rose et al, 2018;Ihm et al, 2019;Wen et al, 2019;Sobolev et al, 2020;Mudrich et al, 2020). These experiments would benefit enormously from the development of a fast and reliable phase-retrieval method to reconstruct live images of particles in real time during the execution of these time-resolved experiments.…”

Section: Introductionmentioning

confidence: 99%

Complex imaging of phase domains by deep neural networks

Juhás

Yoo

et al. 2021

Int Union Crystallogr J

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The reconstruction of a single-particle image from the modulus of its Fourier transform, by phase-retrieval methods, has been extensively applied in X-ray structural science. Particularly for strong-phase objects, such as the phase domains found inside crystals by Bragg coherent diffraction imaging (BCDI), conventional iteration methods are time consuming and sensitive to their initial guess because of their iterative nature. Here, a deep-neural-network model is presented which gives a fast and accurate estimate of the complex single-particle image in the form of a universal approximator learned from synthetic data. A way to combine the deep-neural-network model with conventional iterative methods is then presented to refine the accuracy of the reconstructed results from the proposed deep-neural-network model. Improved convergence is also demonstrated with experimental BCDI data.

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“…The formation of Cor n ions at hν = 26 eV is due to charge transfer ionization through the ionized He nanodroplet [32], whereas at hν = 21.6 eV, Cor is ionized by Penning ionization as previously reported for other atomic and molecular dopants [23][24][25][26][27]. At hν = 21.6 eV, He nanodroplets are resonantly excited to their 1s2p 1 P state, and Penning ionization occurs after relaxation to the 1s2s 1,3 S state [23,26,33]. In the low-mass range (1-130 amu) of the mass spectrum recorded at hν = 26 eV, a series of He + k complexes is present with intensities reaching up to that of Cor + .…”

Section: Experimental Methodsmentioning

confidence: 55%

Photoelectron spectroscopy of coronene molecules embedded in helium nanodroplets

Ltaief,

Shcherbinin,

Mandal

et al. 2020

Preprint

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Ultrafast relaxation of photoexcited superfluid He nanodroplets

Cited by 39 publications

References 55 publications

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif

Complex imaging of phase domains by deep neural networks

Photoelectron spectroscopy of coronene molecules embedded in helium nanodroplets

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