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Open data set of live cyanobacterial cells imaged using an X-ray laser.

ABSTRACT: Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

SUBMITTER: van der Schot G

PROVIDER: S-EPMC4968219 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Open data set of live cyanobacterial cells imaged using an X-ray laser.

van der Schot Gijs G Svenda Martin M Maia Filipe R N C FR Hantke Max F MF DePonte Daniel P DP Seibert M Marvin MM Aquila Andrew A Schulz Joachim J Kirian Richard A RA Liang Mengning M Stellato Francesco F Bari Sadia S Iwan Bianca B Andreasson Jakob J Timneanu Nicusor N Bielecki Johan J Westphal Daniel D Nunes de Almeida Francisca F Odić Duško D Hasse Dirk D Carlsson Gunilla H GH Larsson Daniel S D DS Barty Anton A Martin Andrew V AV Schorb Sebastian S Bostedt Christoph C Bozek John D JD Carron Sebastian S Ferguson Ken K Rolles Daniel D Rudenko Artem A Epp Sascha W SW Foucar Lutz L Rudek Benedikt B Erk Benjamin B Hartmann Robert R Kimmel Nils N Holl Peter P Englert Lars L Loh N Duane ND Chapman Henry N HN Andersson Inger I Hajdu Janos J Ekeberg Tomas T

Scientific data 20160801

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. Thi ...[more]

PMID: 27479514

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Project description:Ice nucleation is one of the most uncertain microphysical processes, as it occurs in various ways and on many types of particles. To overcome this challenge, we present a heterogeneous ice nucleation study on deposition ice nucleation and immersion freezing in a novel cryogenic X-ray experiment with the capability to spectroscopically probe individual ice nucleating and non-ice nucleating particles. Mineral dust type particles composed of either ferrihydrite or feldspar were used and mixed with organic matter of either citric acid or xanthan gum. We observed in situ ice nucleation using scanning transmission X-ray microscopy (STXM) and identified unique organic carbon functionalities and iron oxidation state using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in the new in situ environmental ice cell, termed the ice nucleation X-ray cell (INXCell). Deposition ice nucleation of ferrihydrite occurred at a relative humidity with respect to ice, RH i, between ∼120-138% and temperatures, T ∼ 232 K. However, we also observed water uptake on ferrihydrite at the same T when deposition ice nucleation did not occur. Although, immersion freezing of ferrihydrite both in pure water droplets and in aqueous citric acid occurred at or slightly below conditions for homogeneous freezing, i.e. the effect of ferrihydrite particles acting as a heterogeneous ice nucleus for immersion freezing was small. Microcline K-rich feldspar mixed with xanthan gum was also used in INXCell experiments. Deposition ice nucleation occurred at conditions when xanthan gum was expected to be highly viscous (glassy). At less viscous conditions, immersion freezing was observed. We extended a model for heterogeneous and homogeneous ice nucleation, named the stochastic freezing model (SFM). It was used to quantify heterogeneous ice nucleation rate coefficients, mimic the competition between homogeneous ice nucleation; water uptake; deposition ice nucleation and immersion freezing, and predict the T and RH i at which ice was observed. The importance of ferrihydrite to act as a heterogeneous ice nucleating particle in the atmosphere using the SFM is discussed.

Dataset Information

Open data set of live cyanobacterial cells imaged using an X-ray laser.

Publications

Open data set of live cyanobacterial cells imaged using an X-ray laser.

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