New publication in Nature Methods

Our paper entitled “Fast volumetric calcium imaging across multiple cortical layers using sculpted light” has been published in Nature Methods.

In this work, we present a novel method based on light sculpting that enables unbiased single and dual-plane high-speed (up to 160 Hz) calcium imaging, as well as in vivo volumetric calcium imaging of a mouse cortical column (500x500x500 µm) at single-cell resolution and fast volume rates (3 – 6 Hz). This is achieved by tailoring the point-spread function of our microscope to the structures of interest while maximizing the signal-to-noise ratio while using a home-built fiber laser amplifier with pulses that are synchronized to the imaging voxel speed. Together, these innovations have enabled the near-simultaneous in-vivo recording of calcium dynamics of several thousand active neurons across cortical layers and in the hippocampus of awake behaving mice.

Read the publication or a short summary.

Please also have a look at the press release of the Rockefeller University.

New publication in Cell

Our paper entitled “A force-induced directional switch of a molecular motor enables parallel microtubule bundle formation” by Maxim I. Molodtsov et al. has been published in Cell.

Microtubule-organizing centers (MTOCs) nucleate microtubules that can grow autonomously in any direction. To generate bundles of parallel microtubules originating from a single MTOC, the growth of multiple microtubules needs to coordinated, but the underlying mechanism is unknown. Here, we show that a conserved two-component system consisting of the plus-endtracker EB1 and the minus-end-directed molecular motor Kinesin-14 is sufficient to promote parallel microtubule growth. The underlying mechanism relies on the ability of Kinesin-14 to guide growing plus ends along existing microtubules. The generality of this finding is supported by yeast, Drosophila, and human EB1/Kinesin-14 pairs. We demonstrate that plus-end guiding involves a directional switch of the motor due to a force applied via a growing microtubule end. The described mechanism can account for the generation of parallel microtubule networks required for a broad range of cellular functions such as spindle assembly or cell polarization.

Read the publication or a short summary.

Please have also look at the Press Release from The Rockefeller University.

New publication in Nature Communications

Our paper entitled “Direct Detection of a Single Photon by Humans” by Tinsley J. N. et. al., has been published in Nature Communications.

In this study we have shown that humans are capable of detecting a single photon onto their eyes with a probability above chance. This was done by developing a quantum light source based on spontaneous parametric down-conversion (SPDC) which can generate single-photon states of light and combining it with a state-of-the-art psychophysics procedure. Thereby we could show that the human visual system including the post-processing performed by the retina and the brain can detect a single photon incident onto the eye.

Read the publication or a short summary.

Please have also a look at the Nature News article by Davide Castelvecchi as well as the articles on the L.A. Times, APA (German), (German), (Russian), (German), Bild der Wissenschaft (German), Scientific American, Nature Asia (Japanese), (German), Discover Magazine, Vozpopuli (Spanish), Innovations Report (German), (German), and (Russian).

New publication in J. Phys. Chem. B

Together with our colleagues at the Institute for Biophysical Dynamics at the University of Chicago, we have developed a method using infrared spectroscopy and atomistic modeling that would allow to better understand the mechanism behind the extreme ion selectivity and transport properties in ion channels. Our findings have recently been published in The Journal of Physical Chemistry B.

Location of the potassium channel KcsA in the cell membrane of bacteria. The schematic illustration on the right shows the changes in strength and direction of vibrational coupling inside the filter depending on the ion species, as found by the study. @David S. Goodsell & RCSB Protein Data Bank

Location of the potassium channel KcsA in the cell membrane of bacteria. The schematic illustration on the right shows the changes in strength and direction of vibrational coupling inside the filter depending on the ion species, as found by the study. @David S. Goodsell & RCSB Protein Data Bank

Ion channels are essential structures of life.

Ion channels are specialized pores in the cell membrane and move charged atoms known as ions in and out of cells, thereby controlling a wide variety of biological processes including brain function and heartbeat. Ion channels are generally selective for certain ions, allowing specific types of ions to flow through at very high rates, while hindering the flow of others. On the basis of this selective permeability, ion channels are classified as potassium channels, sodium channels, etc.

The cell’s most ubiquitous gateways are potassium ion channels – the importance of this type of ion channels was underpinned in 2003 when Roderick MacKinnon received the Nobel Prize in Chemistry for resolving the first atomic structure of the bacterial KcsA potassium channel.

Despite a large body of work, the exact molecular details underlying ion selectivity and transport of the potassium channel remain unclear. Since conventional methods, such as X-ray crystallography, capture only averaged frozen structures, it is not possible to investigate how the dynamic of the protein could be involved in key aspects of their function.

New method to unravel the secret of ion channel selectivity

Our team, together with researchers at the Institute for Biophysical Dynamics (University of Chicago), have now used infrared (IR) spectroscopy coupled with molecular dynamic-based simulations of the obtained spectra to investigate the subtlest changes in the shape of the KcsA potassium channel that are induced by binding either potassium or the only 0.04 nanometers smaller sodium ion. This combination proved to be a powerful tool to disentangle convoluted IR spectra – which contain contributions from the whole protein – by assigning each part of the spectrum to the amino acids that contribute to it.

This new approach allows us to probe these mechanisms in a non-perturbative way, meaning without tedious and expensive isotope labeling strategies. Moreover, it opens the way to study the structure and dynamics of ion channels on their biologically relevant timescales by extending it to two-dimensional infrared spectroscopy.

The study shows for the first time that the combination of the two methods can be used to detect subtle conformational changes in large membrane proteins, such as the KcsA potassium channel. Furthermore, it opens the way to capture the dynamics of proteins in real time at atomic resolution, which has been impossible with standard techniques until now.

Read the publication or browse through our other publications.

Press releases about the topic by the MFPL and IMP.

Paul Stevenson, Christoph Götz, Carlos R. Baiz, Jasper Akerboom, Andrei Tokmakoff, and Alipasha Vaziri
Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
J. Phys. Chem. B 2015, 119 (18), pp 5824–5831 (Download)

New Publication in Analytical Chemistry

Together with our collaborator Markus Arndt we published in Analytical Chemistry on how to improve Laser-induced acoustic desorption (LIAD) for natural biochromophores. This methodology might enable us to use fragile biomolecules in Quantum-enhanced metrology experiments.

Link to Paper or look up other publications of our group.

Ugur Sezer, Lisa Wörner, Johannes Horak, Lukas Felix, Jens Tüxen, Christoph Götz, Alipasha Vaziri, Marcel Mayor, and Markus Arndt
Laser-induced acoustic desorption of natural and functionalized biochromophores
Anal. Chem., 2015, 87 (11), pp 5614–5619 (Download)

We welcome our new Postdoc Michael Taylor

Michael got his PhD in Physics from the University of Queensland, Australia, where he worked on new experimental strategies for optical tweezers. Most notably, he combined optical tweezers with techniques from quantum optics to break the quantum limit to measurement precision, and used holographic beam shaping to increase trapping stiffness.

Now he will begin developing a new fluorescent microscopy technology to image neuronal activity at greater depths.

Two New WWTF Grants

The Vaziri lab has successfully secured with colleagues at IMP and IMBA two grants in the WWTF’s Life Sciences Call 2014 – “IMAGING
Innovative Biological and Biomedical Applications of Novel Imaging Technologies”. The projects will be dedicated to building new super-resolution and high-speed whole-brain functional imaging techniques in behaving animals.

VBC Art&Science Contest 2014 winner from the Vaziri lab


Friederike Schlumm and Christoph Götz from the Vaziri lab won together with Isabel Grießhammer (IMBA) the VBC Art&Science Contest with their video:

“Incubate over night”

Incubation is a widely used method in research. Nevertheless, the underlying mechanisms are not well understood. In this project we aimed to visualize this crucial process. We therefore applied the imaging technique “stop-motion” to study an overnight incubation. Our results reveal new insights into scientific experiments.

Four teams participated, with four terrific art pieces, which were exhibited in our Cafeteria, and the VBCers were voting for the best piece.

See the other art pieces at: