Unusual spin-wave population in nickel after femtosecond laser pulse excitation

The spin-wave relaxation mechanisms after intense laser excitation in ferromagnetic nickel films are investigated with all-optical pump-probe experiments. Uniform precession (Kittel mode), Damon-Eshbach surface modes and perpendicular standing spin waves can be identified by their dispersion f(H). However, different to other ferromagnets f(H) deviates from the expected behavior. Namely, a mode discontinuity is observed, that can be attributed to a non-linear process. Above a critical field the power spectrum reveals a redistribution of the energy within the spin-wave spectrum populated.Comment: 7 pages, 6 figure

Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation

The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its β-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff’s base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation

Free backbone carbonyls mediate rhodopsin activation

Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins

The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L

X-linked retinitis pigmentosa (XLRP) is frequently caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. A complex splicing process acts on the RPGR gene resulting in three major isoforms: RPGR(ex1-19), RPGR(ORF15) and RPGR(skip14/15). We characterized the widely expressed, alternatively spliced transcript RPGR(skip14/15) lacking exons 14 and 15. Using the CRISPR/eSpCas9 system, we generated HEK293T cell lines exclusively expressing the RPGR(skip14/15) transcript from the endogenous RPGR gene. RPGR(ex1-19) and RPGR(ORF15) were knocked out. Immunocytochemistry demonstrated that the RPGR(skip14/15) protein localizes along primary cilia, resembling the expression pattern of RPGR(ex1-19). The number of cilia-carrying cells was not affected by the absence of the RPGR(ex1-19) and RPGR(ORF15) isoforms. Co-immunoprecipitation assays demonstrated that both RPGR(ex1-19) and RPGR(skip14/15) interact with PDE6D, further supporting that RPGR(skip14/15) is associated with the protein networks along the primary cilium. Interestingly, interaction complexes with INPP5E or RPGRIP1L were only detectable with isoform RPGR(ex1-19), but not with RPGR(skip14/15), demonstrating distinct functional properties of the major RPGR isoforms in spite of their similar subcellular localization. Our findings lead to the conclusion that protein binding sites within RPGR are mediated through alternative splicing. A tissue-specific expression ratio between RPGR(skip14/15) and RPGR(ex1-19) seems required to regulate the ciliary concentration of RPGR interaction partners

Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation

The second extracellular loop (EL2) of rhodopsin forms a cap over the binding site of its photoreactive 11-cis retinylidene chromophore. A crucial question has been whether EL2 forms a reversible gate that opens upon activation or acts as a rigid barrier. Distance measurements using solid-state 13C NMR spectroscopy between the retinal chromophore and the β4 strand of EL2 show that the loop is displaced from the retinal binding site upon activation, and there is a rearrangement in the hydrogen-bonding networks connecting EL2 with the extracellular ends of transmembrane helices H4, H5 and H6. NMR measurements further reveal that structural changes in EL2 are coupled to the motion of helix H5 and breaking of the ionic lock that regulates activation. These results provide a comprehensive view of how retinal isomerization triggers helix motion and activation in this prototypical G protein-coupled receptor. © 2009 Nature America, Inc. All rights reserved

RASSF1A promoter methylation and expression analysis in normal and neoplastic kidney indicates a role in early tumorigenesis

<p>Abstract</p> <p>Background</p> <p>Epigenetic silencing of the RAS association domain family 1A (<it>RASSF1A</it>) tumor suppressor gene promoter has been demonstrated in renal cell carcinoma (RCC) as a result of promoter hypermethylation. Contradictory results have been reported for <it>RASSF1A </it>methylation in normal kidney, thus it is not clear whether a significant difference between <it>RASSF1A </it>methylation in normal and tumor cells of the kidney exists. Moreover, RASSF1A expression has not been characterized in tumors or normal tissue as yet.</p> <p>Results</p> <p>Using combined bisulfite restriction analysis (COBRA) we compared RASSF1A methylation in 90 paired tissue samples obtained from primary kidney tumors and corresponding normal tissue. Bisulfite sequence analysis was carried out using both pooled amplicons from the tumor and normal tissue groups and subclones obtained from a single tissue pair. Expression of RASSF1A was analyzed by the use of tissue arrays and immunohistochemistry. We found significantly increased methylation in tumor samples (mean methylation, 20%) compared to corresponding normal tissues (mean methylation, 11%; <it>P </it>< 0.001). Densely methylated sequences were found both in pooled and individual sequences of normal tissue. Immunohistochemical analysis revealed a significant reduced expression of RASSF1A in most of the tumor samples. Heterogeneous expression patterns of RASSF1A were detected in a subgroup of histologically normal tubular epithelia.</p> <p>Conclusion</p> <p>Our methylation and expression data support the hypothesis that <it>RASSF1A </it>is involved in early tumorigenesis of renal cell carcinoma.</p

Tracked 3D ultrasound and deep neural network-based thyroid segmentation reduce interobserver variability in thyroid volumetry

Thyroid volumetry is crucial in the diagnosis, treatment, and monitoring of thyroid diseases. However, conventional thyroid volumetry with 2D ultrasound is highly operator-dependent. This study compares 2D and tracked 3D ultrasound with an automatic thyroid segmentation based on a deep neural network regarding inter- and intraobserver variability, time, and accuracy. Volume reference was MRI. 28 healthy volunteers (24—50 a) were scanned with 2D and 3D ultrasound (and by MRI) by three physicians (MD 1, 2, 3) with different experience levels (6, 4, and 1 a). In the 2D scans, the thyroid lobe volumes were calculated with the ellipsoid formula. A convolutional deep neural network (CNN) automatically segmented the 3D thyroid lobes. 26, 6, and 6 random lobe scans were used for training, validation, and testing, respectively. On MRI (T1 VIBE sequence) the thyroid was manually segmented by an experienced MD. MRI thyroid volumes ranged from 2.8 to 16.7ml (mean 7.4, SD 3.05). The CNN was trained to obtain an average Dice score of 0.94. The interobserver variability comparing two MDs showed mean differences for 2D and 3D respectively of 0.58 to 0.52ml (MD1 vs. 2), −1.33 to −0.17ml (MD1 vs. 3) and −1.89 to −0.70ml (MD2 vs. 3). Paired samples t-tests showed significant differences for 2D (p = .140, p = .002 and p = .002) and none for 3D (p = .176, p = .722 and p = .057). Intraobsever variability was similar for 2D and 3D ultrasound. Comparison of ultrasound volumes and MRI volumes showed a significant difference for the 2D volumetry of all MDs (p = .002, p = .009, p <.001), and no significant difference for 3D ultrasound (p = .292, p = .686, p = 0.091). Acquisition time was significantly shorter for 3D ultrasound. Tracked 3D ultrasound combined with a CNN segmentation significantly reduces interobserver variability in thyroid volumetry and increases the accuracy of the measurements with shorter acquisition times

Protocols to Code: Formal Verification of a Next-Generation Internet Router

We present the first formally-verified Internet router, which is part of the SCION Internet architecture. SCION routers run a cryptographic protocol for secure packet forwarding in an adversarial environment. We verify both the protocol's network-wide security properties and low-level properties of its implementation. More precisely, we develop a series of protocol models by refinement in Isabelle/HOL and we use an automated program verifier to prove that the router's Go code satisfies memory safety, crash freedom, freedom from data races, and adheres to the protocol model. Both verification efforts are soundly linked together. Our work demonstrates the feasibility of coherently verifying a critical network component from high-level protocol models down to performance-optimized production code, developed by an independent team. In the process, we uncovered critical bugs in both the protocol and its implementation, which were confirmed by the code developers, and we strengthened the protocol's security properties. This paper explains our approach, summarizes the main results, and distills lessons for the design and implementation of verifiable systems, for the handling of continuous changes, and for the verification techniques and tools employed