@article{8019, abstract = {Synaptic plasticity is essential for the function of neural systems. It sets up initial circuitry and adjusts connection strengths according to the maintenance requirements of its host networks. Like all things biological, synaptic plasticity must rely on genetic programs to provide the molecular components of its machinery to integrate ongoing, often multi-sensory experience without destabilising effects. Because of its fundamental importance to healthy behaviour, understanding plasticity is thought to hold the key to understanding the brain. There are innumerable ways to approach this topic and a complete review of its status quo would be impossible. In the current issue we dig into some of the finer points of synaptic plasticity, starting small, at the level of genes, and slowly zooming out to synapses, populations of synapses, and finally entire systems and brain regions. At each level, we tried to represent different perspectives, different systems, and approaches to the same questions to give a broad sampling of how synaptic plasticity is being studied.}, author = {Vogels, Tim P and Griffith, Leslie C}, issn = {0959-4388}, journal = {Current Opinion in Neurobiology}, pages = {A1--A5}, publisher = {Elsevier}, title = {{Editorial overview: Neurobiology of learning and plasticity 2017}}, doi = {10.1016/j.conb.2017.04.002}, volume = {43}, year = {2017}, } @article{8017, abstract = {nhibitory neurons, although relatively few in number, exert powerful control over brain circuits. They stabilize network activity in the face of strong feedback excitation and actively engage in computations. Recent studies reveal the importance of a precise balance of excitation and inhibition in neural circuits, which often requires exquisite fine-tuning of inhibitory connections. We review inhibitory synaptic plasticity and its roles in shaping both feedforward and feedback control. We discuss the necessity of complex, codependent plasticity mechanisms to build nontrivial, functioning networks, and we end by summarizing experimental evidence of such interactions.}, author = {Hennequin, Guillaume and Agnes, Everton J. and Vogels, Tim P}, issn = {0147-006X}, journal = {Annual Review of Neuroscience}, number = {1}, pages = {557--579}, publisher = {Annual Reviews}, title = {{Inhibitory plasticity: Balance, control, and codependence}}, doi = {10.1146/annurev-neuro-072116-031005}, volume = {40}, year = {2017}, } @article{8075, abstract = {Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.}, author = {Podlaski, William F and Seeholzer, Alexander and Groschner, Lukas N and Miesenböck, Gero and Ranjan, Rajnish and Vogels, Tim P}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, title = {{Mapping the function of neuronal ion channels in model and experiment}}, doi = {10.7554/elife.22152}, volume = {6}, year = {2017}, } @article{807, abstract = {On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.}, author = {Andrae, Magdalena and Villányi, Márton}, issn = {10222588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {2}, pages = {274 -- 280}, publisher = {VÖB}, title = {{Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung}}, doi = {10.31263/voebm.v70i2.1898}, volume = {70}, year = {2017}, } @inproceedings{8129, abstract = {Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function. Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.}, author = {Costa, Rui Ponte and Assael, Yannis M. and Shillingford, Brendan and Freitas, Nando de and Vogels, Tim P}, booktitle = {Advances in Neural Information Processing Systems}, issn = {10495258}, location = {Long Beach, CA, United States}, pages = {272--283}, publisher = {Neural Information Processing Systems Foundation}, title = {{Cortical microcircuits as gated-recurrent neural networks}}, volume = {30}, year = {2017}, } @article{817, abstract = {Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging.}, author = {Turoňová, Beata and Schur, Florian and Wan, William and Briggs, John}, journal = {Journal of Structural Biology}, number = {3}, pages = {187--195}, publisher = {Academic Press}, title = {{Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å}}, doi = {10.1016/j.jsb.2017.07.007}, volume = {199}, year = {2017}, } @article{8237, abstract = {Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells.}, author = {Ilieva, Kristina M. and Fazekas-Singer, Judit and Achkova, Daniela Y. and Dodev, Tihomir S. and Mele, Silvia and Crescioli, Silvia and Bax, Heather J. and Cheung, Anthony and Karagiannis, Panagiotis and Correa, Isabel and Figini, Mariangela and Marlow, Rebecca and Josephs, Debra H. and Beavil, Andrew J. and Maher, John and Spicer, James F. and Jensen-Jarolim, Erika and Tutt, Andrew N. and Karagiannis, Sophia N.}, issn = {1664-3224}, journal = {Frontiers in Immunology}, publisher = {Frontiers}, title = {{Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields}}, doi = {10.3389/fimmu.2017.01112}, volume = {8}, year = {2017}, } @article{8236, abstract = {Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment.}, author = {Jensen-Jarolim, E. and Bax, H. J. and Bianchini, R. and Capron, M. and Corrigan, C. and Castells, M. and Dombrowicz, D. and Daniels-Wells, T. R. and Fazekas, Judit and Fiebiger, E. and Gatault, S. and Gould, H. J. and Janda, J. and Josephs, D. H. and Karagiannis, P. and Levi-Schaffer, F. and Meshcheryakova, A. and Mechtcheriakova, D. and Mekori, Y. and Mungenast, F. and Nigro, E. A. and Penichet, M. L. and Redegeld, F. and Saul, L. and Singer, J. and Spicer, J. F. and Siccardi, A. G. and Spillner, E. and Turner, M. C. and Untersmayr, E. and Vangelista, L. and Karagiannis, S. N.}, issn = {0105-4538}, journal = {Allergy}, number = {6}, pages = {866--887}, publisher = {Wiley}, title = {{AllergoOncology - the impact of allergy in oncology: EAACI position paper}}, doi = {10.1111/all.13119}, volume = {72}, year = {2017}, } @article{8239, abstract = {Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk.}, author = {Roth-Walter, Franziska and Bergmayr, Cornelia and Meitz, Sarah and Buchleitner, Stefan and Stremnitzer, Caroline and Fazekas, Judit and Moskovskich, Anna and Müller, Mario A. and Roth, Georg A. and Manzano-Szalai, Krisztina and Dvorak, Zdenek and Neunkirchner, Alina and Jensen-Jarolim, Erika}, issn = {2045-2322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure}}, doi = {10.1038/srep45067}, volume = {7}, year = {2017}, } @article{8240, abstract = {Background/Aim: Cancer cell lines are indispensible surrogate models in cancer research, as they can be used off-the-shelf, expanded to the desired extent, easily modified and exchanged between research groups for affirmation, reproduction or follow-up experiments. As malignant cells are prone to genomic instability, phenotypical changes may occur after certain passages in culture. Thus, cell lines have to be regularly authenticated to ensure data quality. In between experiments these cell lines are often stored in liquid nitrogen for extended time periods. Although freezing of cells is a necessary evil, little research is performed on how long-term storage affects cancer cell lines. Therefore, this study investigated the effects of a 28-year long liquid nitrogen storage period on BT474 cells with regard to phenotypical changes, differences in cell-surface receptor expression as well as cytokine and gene expressional variations. Methods: Two batches of BT474 cells, one frozen in 1986, the other directly purchased from ATCC were investigated by light microscopy, cell growth analysis, flow cytometry and cytokine as well as whole-transcriptome expression profiling. Results: The cell lines were morphologically indifferent and showed similar growth rates and similar cell-surface receptor expression. Transcriptome analysis revealed significant differences in only 26 of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and 22 down-regulated. Conclusion: This study demonstrates that even after very long periods of storage in liquid nitrogen, cancer cell lines display only minimal changes in their gene expression profiles. However, also such minor changes should be carefully assessed before continuation of experiments, especially if phenotypic alterations can be additionally observed.}, author = {Fazekas, Judit and Grunt, Thomas W. and Jensen-Jarolim, Erika and Singer, Josef}, issn = {1949-2553}, journal = {Oncotarget}, pages = {35076--35087}, publisher = {Impact Journals}, title = {{Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474}}, doi = {10.18632/oncotarget.16623}, volume = {8}, year = {2017}, } @article{8235, abstract = {Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients.}, author = {Fazekas-Singer, Judit and Berroterán-Infante, Neydher and Rami-Mark, Christina and Dumanic, Monika and Matz, Miroslawa and Willmann, Michael and Andreae, Fritz and Singer, Josef and Wadsak, Wolfgang and Mitterhauser, Markus and Jensen-Jarolim, Erika}, issn = {1949-2553}, journal = {Oncotarget}, pages = {83128--83141}, publisher = {Impact Journals}, title = {{Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials}}, doi = {10.18632/oncotarget.20914}, volume = {8}, year = {2017}, } @article{825, abstract = {What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.}, author = {Petritsch, Barbara}, issn = {10222588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare}, number = {2}, pages = {200 -- 207}, publisher = {VÖB}, title = {{Metadata for research data in practice}}, doi = {10.31263/voebm.v70i2.1678}, volume = {70}, year = {2017}, } @inproceedings{8299, abstract = {Permissionless blockchain-based cryptocurrencies commonly use proof-of-work (PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double spending attacks. However, both approaches have disadvantages: PoW leads to massive amounts of wasted electricity and re-centralization, whereas major stakeholders in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood (PoP), a mechanism that binds physical entities to virtual identities in a way that enables accountability while preserving anonymity. Afterwards we introduce PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a continuously fair and democratic wealth creation process which paves the way for an experimental basic income infrastructure.}, author = {Borge, Maria and Kokoris Kogias, Eleftherios and Jovanovic, Philipp and Gasser, Linus and Gailly, Nicolas and Ford, Bryan}, booktitle = {2017 IEEE European Symposium on Security and Privacy Workshops}, location = {Paris, France}, publisher = {IEEE}, title = {{Proof-of-personhood: Redemocratizing permissionless cryptocurrencies}}, doi = {10.1109/eurospw.2017.46}, year = {2017}, } @inproceedings{8306, abstract = {Bias-resistant public randomness is a critical component in many (distributed) protocols. Generating public randomness is hard, however, because active adversaries may behave dishonestly to bias public random choices toward their advantage. Existing solutions do not scale to hundreds or thousands of participants, as is needed in many decentralized systems. We propose two large-scale distributed protocols, RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted client to divide a set of randomness servers into groups for scalability, and it depends on the pigeonhole principle to ensure output integrity, even for non-random, adversarial group choices. RandHerd implements an efficient, decentralized randomness beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound in a one-time setup to arrange participants into verifiably unbiased random secret-sharing groups, which then repeatedly produce random output at predefined intervals. Our prototype demonstrates that RandHound and RandHerd achieve good performance across hundreds of participants while retaining a low failure probability by properly selecting protocol parameters, such as a group size and secret-sharing threshold. For example, when sharding 512 nodes into groups of 32, our experiments show that RandHound can produce fresh random output after 240 seconds. RandHerd, after a setup phase of 260 seconds, is able to generate fresh random output in intervals of approximately 6 seconds. For this configuration, both protocols operate at a failure probability of at most 0.08% against a Byzantine adversary.}, author = {Syta, E. and Jovanovic, P. and Kokoris Kogias, Eleftherios and Gailly, N. and Gasser, L. and Khoffi, I. and Fischer, M. J. and Ford, B.}, booktitle = {2017 IEEE Symposium on Security and Privacy}, isbn = {9781509055340}, issn = {2375-1207}, location = {San Jose, CA, United States}, pages = {444--460}, publisher = {IEEE}, title = {{Scalable bias-resistant distributed randomness}}, doi = {10.1109/SP.2017.45}, year = {2017}, } @inproceedings{8301, abstract = {Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that eliminates single points of failure, enforces transparency, and provides efficient verifiability of integrity and authenticity for software-release processes. Independent witness servers collectively verify conformance of software updates to release policies, build verifiers validate the source-to-binary correspondence, and a tamper-proof release log stores collectively signed updates, thus ensuring that no release is accepted by clients before being widely disclosed and validated. The release log embodies a skipchain, a novel data structure, enabling arbitrarily out-of-date clients to efficiently validate updates and signing keys. Evaluation of our CHAINIAC prototype on reproducible Debian packages shows that the automated update process takes the average of 5 minutes per release for individual packages, and only 20 seconds for the aggregate timeline. We further evaluate the framework using real-world data from the PyPI package repository and show that it offers clients security comparable to verifying every single update themselves while consuming only one-fifth of the bandwidth and having a minimal computational overhead.}, author = {Nikitin, Kirill and Kokoris Kogias, Eleftherios and Jovanovic, Philipp and Gasser, Linus and Gailly, Nicolas and Khoffi, Ismail and Cappos, Justin and Ford, Bryan}, booktitle = {Proceedings of the 26th USENIX Conference on Security Symposium}, isbn = {9781931971409}, location = {Vancouver, Canada}, pages = {1271–1287}, publisher = {USENIX Association}, title = {{CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds}}, year = {2017}, } @article{8446, abstract = {Solid‐state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross‐polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide‐protonated proteins from approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly.}, author = {Fraga, Hugo and Arnaud, Charles‐Adrien and Gauto, Diego F. and Audin, Maxime and Kurauskas, Vilius and Macek, Pavel and Krichel, Carsten and Guan, Jia‐Ying and Boisbouvier, Jerome and Sprangers, Remco and Breyton, Cécile and Schanda, Paul}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {19}, pages = {2697--2703}, publisher = {Wiley}, title = {{Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins}}, doi = {10.1002/cphc.201700572}, volume = {18}, year = {2017}, } @article{8445, abstract = {Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.}, author = {Kurauskas, Vilius and Izmailov, Sergei A. and Rogacheva, Olga N. and Hessel, Audrey and Ayala, Isabel and Woodhouse, Joyce and Shilova, Anastasya and Xue, Yi and Yuwen, Tairan and Coquelle, Nicolas and Colletier, Jacques-Philippe and Skrynnikov, Nikolai R. and Schanda, Paul}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Slow conformational exchange and overall rocking motion in ubiquitin protein crystals}}, doi = {10.1038/s41467-017-00165-8}, volume = {8}, year = {2017}, } @article{8444, abstract = {Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.}, author = {Dehez, François and Schanda, Paul and King, Martin S. and Kunji, Edmund R.S. and Chipot, Christophe}, issn = {0006-3495}, journal = {Biophysical Journal}, keywords = {Biophysics}, number = {11}, pages = {2311--2315}, publisher = {Elsevier}, title = {{Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity}}, doi = {10.1016/j.bpj.2017.09.019}, volume = {113}, year = {2017}, } @article{9065, abstract = {Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a prominent transition from the canted antiferromagnetic state to the weak ferromagnetic (WFM) state. A comprehensive analysis was conducted to examine the isotropic and anisotropic regimes and probe the easy magnetization axis along the a b plane. The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior, and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field regime. This indicates that the orientation of the easy axis of the FM component is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs. We compared the coefficients of the magnetic susceptibility tensors and captured the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic behavior for fields with values above the field value of the WFM transition.}, author = {Nauman, Muhammad and Hong, Yunjeong and Hussain, Tayyaba and Seo, M. S. and Park, S. Y. and Lee, N. and Choi, Y. J. and Kang, Woun and Jo, Younjung}, issn = {2469-9950}, journal = {Physical Review B}, number = {15}, publisher = {American Physical Society}, title = {{In-plane magnetic anisotropy in strontium iridate Sr2IrO4}}, doi = {10.1103/physrevb.96.155102}, volume = {96}, year = {2017}, } @article{9165, abstract = {Advances in colloidal synthesis allow for the design of particles with controlled patches. This article reviews routes towards colloidal locomotion, where energy is consumed and converted into motion, and its implementation with active patchy particles. A special emphasis is given to phoretic swimmers, where the self-propulsion originates from an interfacial phenomenon, raising experimental challenges and opening up opportunities for particles with controlled anisotropic surface chemistry and novel behaviors.}, author = {Aubret, A. and Ramananarivo, S. and Palacci, Jérémie A}, issn = {1359-0294}, journal = {Current Opinion in Colloid & Interface Science}, pages = {81--89}, publisher = {Elsevier}, title = {{Eppur si muove, and yet it moves: Patchy (phoretic) swimmers}}, doi = {10.1016/j.cocis.2017.05.007}, volume = {30}, year = {2017}, }