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Results 1 through 20 out of 2160

in category biophysics

 

1: Transduction of the Geomagnetic Field as Evidenced from Alpha-band Activity in the Human Brain

Connie X Wang, Isaac A Hilburn et al.

7,894 downloads (posted 20 Oct 2018)

Magnetoreception, the perception of the geomagnetic field, is a sensory modality well-established across all major groups of vertebrates and some invertebrates, but its presence in humans has been tested rarely, yielding inconclusive results. We report here a strong, specific human brain response to ecologically-relevant rotations of Earth-strength magnetic fields. Following geomagnetic stimulation, a drop in amplitude of EEG alpha oscillations (8-13 Hz) occurred in a repeatable manner. Termed alpha event-related desynchronization (alpha-ERD), such a response is associated with sensory and cognitive processing of external stimuli. Biophysical tests showed that the neural response was sensitive to the dynamic components and axial alignment of the field but also to the static components and polarity of the field. This pattern of results implicates ferromagnetism as the biophysical basis for the sensory transduction and provides a basis to start the behavioral exploration of human magnetoreception.

https://rxivist.org/papers/34939
https://doi.org/10.1101/448449

2: Recording of "sonic attacks" on U.S. diplomats in Cuba spectrally matches the echoing call of a Caribbean cricket

Alexander L Stubbs, Fernando Montealegre-Z

7,754 downloads (posted 04 Jan 2019)

Beginning in late 2016, diplomats posted to the United States embassy in Cuba began to experience unexplained health problems including ear pain, tinnitus, vertigo, and cognitive difficulties which reportedly began after they heard strange noises in their homes or hotel rooms. In response, the U.S. government dramatically reduced the number of diplomats posted at the U.S. embassy in Havana. U.S. officials initially believed a sonic attack might be responsible for their ailments. The sound linked to these attacks, which ...

https://rxivist.org/papers/40995
https://doi.org/10.1101/510834

3: Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy

Shawn Q. Zheng, Eugene Palovcak et al.

5,845 downloads (posted 04 Jul 2016)

Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. Improving the accuracy and efficiency of motion correction can lead to further resolution improvement. Based on observations that the electron beam induces doming of the thin vitreous ice layer, we developed an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. I...

https://rxivist.org/papers/31058
https://doi.org/10.1101/061960

4: Achieving Better Than 3 Å Resolution By Single Particle Cryo-EM At 200 keV

Mark A Herzik, Mengyu Wu et al.

5,365 downloads (posted 25 May 2017)

Technical and methodological advances in single-particle cryo-electron microscopy (cryo-EM) have expanded the technique into a resolution regime that was previously only attainable by X-ray crystallography. Although single-particle cryo-EM has proven to be a useful technique for determining the structures of biomedically relevant molecules at near-atomic resolution, nearly 98% of the structures resolved to better than 4 Å resolution have been determined using 300 keV transmission electron microscopes (TEMs). We demonstr...

https://rxivist.org/papers/30823
https://doi.org/10.1101/141994

5: RELION-3: new tools for automated high-resolution cryo-EM structure determination

Jasenko Zivanov, Takanori Nakane et al.

5,110 downloads (posted 19 Sep 2018)

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides hig...

https://rxivist.org/papers/32792
https://doi.org/10.1101/421123

6: Cryo-EM structure of haemoglobin at 3.2 A determined with the Volta phase plate

Maryam Khoshouei, Mazdak Radjainia et al.

4,860 downloads (posted 15 Nov 2016)

With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way (ref. 1). These cameras are superior to previous detectors in coping with the intrinsically low contrast of radiation-sensitive organic materials embedded in amorphous ice, and so they have enabled the structure determination of several macromolecular assemblies to atomic or near-atomic resolution. According to one theoretical estimation, a few thousand images should suffice for calculating...

https://rxivist.org/papers/30975
https://doi.org/10.1101/087841

7: Real-time cryo-EM data pre-processing with Warp

Dimitry Tegunov, Patrick Cramer

4,250 downloads (posted 14 Jun 2018)

The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens is currently largely uncoupled from subsequent data evaluation, correction and processing. Therefore, the acquisition strategy is difficult to optimize during data collection, often leading to suboptimal microscope usage and disappointing results. Here we provide Warp, a software for real-time evaluation, correction, and processing of cryo-EM data during their acquisition. Warp evaluates and monitors key parameters for each recorded mic...

https://rxivist.org/papers/17549
https://doi.org/10.1101/338558

8: Direct visualization of transcriptional activation by physical enhancer-promoter proximity

Hongtao Chen, Miki Fujioka et al.

4,101 downloads (posted 11 Jan 2017)

A long-standing question in metazoan gene regulation is how remote enhancers communicate with their target promoters over long distances. Combining genome editing and quantitative live imaging we simultaneously visualize physical enhancer-promoter communication and transcription in Drosophila embryos. Enhancers regulating pair rule stripes of even-skipped expression activate transcription of a reporter gene over a distance of 150 kb. We show in individual cells that activation only occurs after the enhancer comes into c...

https://rxivist.org/papers/30923
https://doi.org/10.1101/099523

9: Sub-2 Å Ewald Curvature Corrected Single-Particle Cryo-EM

Yong Zi Tan, Sriram Aiyer et al.

4,090 downloads (posted 21 Apr 2018)

Single-particle cryogenic electron microscopy (cryo-EM) provides a powerful methodology for structural biologists, but the resolutions typically attained with experimentally determined structures have lagged behind microscope capabilities. Here, we have exploited several technical solutions to improve resolution, including sub-Angstrom pixelation, per-particle CTF refinement, and most notably a correction for Ewald sphere curvature. The application of these methods on micrographs recorded on a base model Titan Krios ena...

https://rxivist.org/papers/30260
https://doi.org/10.1101/305599

10: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

Dari Kimanius, Björn O Forsberg et al.

3,921 downloads (posted 19 Jun 2016)

By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming struc- tural biology. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the relion image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determinat...

https://rxivist.org/papers/31065
https://doi.org/10.1101/059717

11: Heterochromatin drives organization of conventional and inverted nuclei

Martin Falk, Yana Feodorova et al.

3,762 downloads (posted 09 Jan 2018)

The mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer shell. This inverted architecture likely converts rod nuclei into microlenses to facilitate nocturnal vision, and may relate to th...

https://rxivist.org/papers/30492
https://doi.org/10.1101/244038

12: A simple and robust procedure for preparing graphene-oxide cryo-EM grids

Eugene Palovcak, Feng Wang et al.

3,557 downloads (posted 27 Mar 2018)

Graphene oxide (GO) sheets have been used successfully as a supporting substrate film in several recent cryogenic electron-microscopy (cryo-EM) studies of challenging biological macromolecules. However, difficulties in preparing GO-covered holey carbon EM grids have limited its widespread use. Here, we report a simple and robust method for covering holey carbon EM grids with GO sheets and demonstrate that these grids are suitable for high-resolution single particle cryo-EM. GO substrates adhere macromolecules, allowing ...

https://rxivist.org/papers/30339
https://doi.org/10.1101/290197

13: CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou, Nikolaus Grigorieff

3,275 downloads (posted 16 Jun 2015)

CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope?s contrast transfer function (CTF) to an image?s amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of...

https://rxivist.org/papers/31125
https://doi.org/10.1101/020917

14: NanoJ-SQUIRREL: quantitative mapping and minimisation of super-resolution optical imaging artefacts

Siân Culley, David Albrecht et al.

3,232 downloads (posted 02 Jul 2017)

Most super-resolution microscopy methods depend on steps that contribute to the formation of image artefacts. Here we present NanoJ-SQUIRREL, an ImageJ-based analytical approach providing a quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same focal volume, this approach generates a quantitative map of super-resolution defects, as well as methods for their correction. To illustrate its broad applicability to super-resolution approa...

https://rxivist.org/papers/30758
https://doi.org/10.1101/158279

15: The deadly touch: protein denaturation at the water-air interface and how to prevent it

Edoardo D'Imprima, Davide Floris et al.

3,003 downloads (posted 25 Aug 2018)

Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation of the protein. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolde...

https://rxivist.org/papers/30202
https://doi.org/10.1101/400432

16: Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

Takanori Nakane, Dari Kimanius et al.

2,932 downloads (posted 22 Mar 2018)

Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. M...

https://rxivist.org/papers/30351
https://doi.org/10.1101/286856

17: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation

Bryan A Gibson, Lynda K Doolittle et al.

2,861 downloads (posted 18 Jan 2019)

Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin. The basic unit of chromatin is the nucleosome, where ~146 base pair increments of the genome are wrapped and compacted around the core histone proteins. Further genomic organization and compaction occur through higher order assembly of nucleosomes. This organization regulates many nuclear processes, and is controlled in part by histone post-transtranslational modifications and chromatin-binding proteins. Mech...

https://rxivist.org/papers/41939
https://doi.org/10.1101/523662

18: Gctf: real-time CTF determination and correction

Kai Zhang

2,795 downloads (posted 12 Jul 2015)

Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, I present a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination. Similar to alternative programs, the main target of Gctf is to maximize the cross-correlation of a simulated CTF with the power spectra of observed micrographs after background reduction. However, novel approaches in Gctf improve both speed and accuracy. In addi...

https://rxivist.org/papers/31126
https://doi.org/10.1101/022376

19: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution

Xiao Fan, Jia Wang et al.

2,699 downloads (posted 13 Nov 2018)

The fast development of single particle cryo-EM has made it more feasible to obtain the 3D structure of well-behaved macromolecules with molecular weight higher than 300 kDa at ~3 Å resolution. It remains a challenge to obtain high resolution structure of molecules smaller than 100 kDa using single particle cryo-EM, mainly due to the low contrast of the molecules embedded in vitreous ice. In this work, we applied the Cs-corrector-VPP coupled cryo-EM to study 52 kDa streptavidin (SA) protein supported on a thin layer of ...

https://rxivist.org/papers/36648
https://doi.org/10.1101/457861

20: Microfluidic protein isolation and sample preparation for high resolution cryo-EM

Claudio Schmidli, Stefan Albiez et al.

2,634 downloads (posted 21 Feb 2019)

High-resolution structural information is essential to understand protein function. Protein-structure determination needs a considerable amount of protein, which can be challenging to produce, often involving harsh and lengthy procedures. In contrast, the several thousands to a few million protein particles required for structure-determination by cryogenic electron microscopy (cryo-EM) can be provided by miniaturized systems. Here, we present a microfluidic method for the rapid isolation of a target protein and its dire...

https://rxivist.org/papers/44447
https://doi.org/10.1101/556068