Archiv 2018

Gastgeber: R. J. Dwayne Miller

DIALS for ED: Adapting X-ray software for electron diffraction integration

MPSD Seminar
In recent years, electron diffraction has arisen as an alternative to X-ray diffraction for structural studies on threedimensional crystals. Promising features of the technique include complete data sets from a few or even singlenanocrystals, sensitivity to the charged state of ions and the relatively low expense of the apparatus. Experimentalprotocols and detector technologies are improving, so that data collection using the rotation method, dominant inX-ray crystallography, is now feasible in a cryoTEM. This convergence of experimental techniques has beenaccompanied by repurposing of analysis tools: robust and sophisticated algorithms developed over decades forX-ray diffraction integration software can be now employed to tackle electron diffraction data. Nevertheless, thegeometry of the electron diffraction experiment incurs specific challenges to address in the analysis. Here, thediffraction integration package DIALS is discussed, highlighting particular adaptations that were made to thesoftware for various example cases of electron diffraction, particularly on protein crystals. The experience gainedindicates that integration of good quality ED data can be straightforward, but the bottleneck remains with collectionof such good data, which relies on careful calibration and understanding of the instrument. Improved apparatus willameliorate this issue and future studies to develop improved models for details including dynamic diffraction andabsorption are anticipated. [mehr]
Elementary steps of proton transfer between acids and bases occur on ultrafast time scales. To elucidate the microscopic mechanisms of proton transfer many research groups have applied time-resolved spectroscopy utilizing a class of organic molecules called photoacids. In this talk I will provide an overview of results obtained by my research team on photoacid molecules with ultrafast infrared spectroscopy as a local probing technique. Whereas profound insight in aqueous proton transfer pathways in acid-base neutralization have been achieved in recent years, the underlying reasons for photoacidity have remained unsolved. Recent developments will be discussed how to tackle this unsolved question using the technique of soft-x-ray spectroscopy as an alternative local probe. For this liquid flatjet technology appears to be a highly promisingmethodological approach. [mehr]

Donatas Zigmantas - Revealing lowest functional states and excitation dynamics in bacterial photosynthetic reaction centers

MPSD ARD Seminar

Liquid-Phase Electron Microscopy of Cells and Nanomaterials in Liquid

MPSD Seminar
Transmission electron microscopy (TEM) has traditionally been associated with the study of thin solid samples in vacuum. With the availability of reliable thin membranes of silicon nitride, TEM of liquid specimens has become accessible with nanoscale resolution in the past decade [1]. The usage of scanning transmission electron microscopy (STEM) presents a novel concept to study membrane proteins within whole mammalian cells in their native liquid environment [2]. The cells in liquid are placed in a microfluidic chamber enclosing the sample in the vacuum of the electron microscope, and are then imaged with STEM. It is not always necessary to enclose the cells in the microfluidic chamber. For many studies, it is sufficient to obtain information from the thin outer regions of the cells, and those can be imaged with high resolution using environmental scanning electron microscopy (ESEM) with STEM detector [3]. A third option is to cover a liquid specimen under a thin membrane of graphene providing the thinnest possible layer [4]. Liquid STEM was used to explore the formation of HER2 homodimers at the single-molecule level in intact SKBR3 breast cancer cells in liquid state [3]. HER2 is a membrane protein and plays an important role in breast cancer aggressiveness and progression. Data analysis based on calculating the pair correlation function from individual HER2 positions revealed remarkable differences its functional state between rare- and bulk cancer cells with relevance for studying the role of cancer cell heterogeneity in drug response. We discovered a small sub-populations of cancer cells with a different response to a prescription drug [5]. Liquid STEM was also used to explore the behavior of nanoparticles in liquid in time-lapse experiments. It was discovered that nanoparticle movement in close proximity of the supporting silicon nitride membrane was three orders of magnitude slower than what was expected on the basis of Brownian motion for a bulk liquid [6], pointing to the existence of a layer of highly ordered liquid at the membrane. References [1] de Jonge, N. and Ross, F.M. Nat. Nanotechnol., 6, 695-704 (2011) [2] de Jonge, N., et al. Proc. Natl. Acad. Sci., 106, 2159-2164 (2009) [3] Peckys, D.B., et al. Sci. Adv., 1, e1500165 (2015) [4] Dahmke, I.N., et al. ACS Nano, 11, 11108-11117 (2017) [5] Peckys, D.B., et al. Mol. Biol. Cell, 28, 3193-3202 (2017) [6] Verch, A., et al. Langmuir, 31, 6956–6964 (2015) [mehr]
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