Bedrock fracture systems facilitate weathering, allowing fresh mineral surfaces to interact with corrosive waters and biota from Earth’s surface, while simultaneously promoting drainage of chemically equilibrated fluids. We show that topographic perturbations to regional stress fields explain bedrock fracture distributions, as revealed by seismic velocity and electrical resistivity surveys from three landscapes. The base of the fracture-rich zone mirrors surface topography where the ratio of horizontal compressive tectonic stresses to near-surface gravitational stresses is relatively large, and it parallels the surface topography where the ratio is relatively small. Three-dimensional stress calculations predict these results, suggesting that tectonic stresses interact with topography to influence bedrock disaggregation, groundwater flow, chemical weathering, and the depth of the “critical zone” in which many biogeochemical processes occur. Authors: J. St. Clair, S. Moon, W. S. Holbrook, J. T. Perron, C. S. Riebe, S. J. Martel, B. Carr, C. Harman, K. Singha, D. deB. Richter

Magnetic domain walls are boundaries between regions with different configurations of the same magnetic order. In a magnetic insulator, where the magnetic order is tied to its bulk insulating property, it has been postulated that electrical properties are drastically different along the domain walls, where the order is inevitably disturbed. Here we report the discovery of highly conductive magnetic domain walls in a magnetic insulator, Nd2Ir2O7, that has an unusual all-in-all-out magnetic order, via transport and spatially resolved microwave impedance microscopy. The domain walls have a virtually temperature-independent sheet resistance of ~1 kilohm per square, show smooth morphology with no preferred orientation, are free from pinning by disorders, and have strong thermal and magnetic field responses that agree with expectations for all-in-all-out magnetic order. Authors: Eric Yue Ma, Yong-Tao Cui, Kentaro Ueda, Shujie Tang, Kai Chen, Nobumichi Tamura, Phillip M. Wu, Jun Fujioka, Yoshinori Tokura, Zhi-Xun Shen

The Griffiths singularity in a phase transition, caused by disorder effects, was predicted more than 40 years ago. Its signature, the divergence of the dynamical critical exponent, is challenging to observe experimentally. We report the experimental observation of the quantum Griffiths singularity in a two-dimensional superconducting system. We measured the transport properties of atomically thin gallium films and found that the films undergo superconductor-metal transitions with increasing magnetic field. Approaching the zero-temperature quantum critical point, we observed divergence of the dynamical critical exponent, which is consistent with the Griffiths singularity behavior. We interpret the observed superconductor-metal quantum phase transition as the infinite-randomness critical point, where the properties of the system are controlled by rare large superconducting regions. Authors: Ying Xing, Hui-Min Zhang, Hai-Long Fu, Haiwen Liu, Yi Sun, Jun-Ping Peng, Fa Wang, Xi Lin, Xu-Cun Ma, Qi-Kun Xue, Jian Wang, X. C. Xie

We compare estimates of peer effects on worker output in laboratory experiments and field studies from naturally occurring environments. The mean study-level estimate of a change in a worker’s productivity in response to an increase in a co-worker’s productivity (γ) is γ^ = 0.12 (SE = 0.03, nstudies = 34), with a between-study standard deviation τ = 0.16. The mean estimated γ^-values are close between laboratory and field studies (γ^lab−γ^field = 0.04, P = 0.55, nlab = 11, nfield = 23), as are estimates of between-study variance τ2 (τ^lab2−τ^field2=−0.003, P = 0.89). The small mean difference between laboratory and field estimates holds even after controlling for sample characteristics such as incentive schemes and work complexity (γ^lab−γ^field = 0.03, P = 0.62, nsamples = 46). Laboratory experiments generalize quantitatively in that they provide an accurate description of the mean and variance of productivity spillovers. Authors: Daniel Herbst, Alexandre Mas

Light mechanical stimulation of hairy skin can induce a form of itch known as mechanical itch. This itch sensation is normally suppressed by inputs from mechanoreceptors; however, in many forms of chronic itch, including alloknesis, this gating mechanism is lost. Here we demonstrate that a population of spinal inhibitory interneurons that are defined by the expression of neuropeptide Y::Cre (NPY::Cre) act to gate mechanical itch. Mice in which dorsal NPY::Cre-derived neurons are selectively ablated or silenced develop mechanical itch without an increase in sensitivity to chemical itch or pain. This chronic itch state is histamine-independent and is transmitted independently of neurons that express the gastrin-releasing peptide receptor. Thus, our studies reveal a dedicated spinal cord inhibitory pathway that gates the transmission of mechanical itch. Authors: Steeve Bourane, Bo Duan, Stephanie C. Koch, Antoine Dalet, Olivier Britz, Lidia Garcia-Campmany, Euiseok Kim, Longzhen Cheng, Anirvan Ghosh, Qiufu Ma, Martyn Goulding

γ-Aminobutyric acid (GABA) is the major inhibitory transmitter in the mature brain but is excitatory in the developing cortex. We found that mouse zona incerta (ZI) projection neurons form a GABAergic axon plexus in neonatal cortical layer 1, making synapses with neurons in both deep and superficial layers. A similar depolarizing GABAergic plexus exists in the developing human cortex. Selectively silencing mouse ZI GABAergic neurons at birth decreased synaptic activity and apical dendritic complexity of cortical neurons. The ZI GABAergic projection becomes inhibitory with maturation and can block epileptiform activity in the adult brain. These data reveal an early-developing GABAergic projection from the ZI to cortical layer 1 that is essential for proper development of cortical neurons and balances excitation with inhibition in the adult cortex. Authors: Jiadong Chen, Arnold R. Kriegstein

Infections and inflammation can lead to cachexia and wasting of skeletal muscle and fat tissue by as yet poorly understood mechanisms. We observed that gut colonization of mice by a strain of Escherichia coli prevents wasting triggered by infections or physical damage to the intestine. During intestinal infection with the pathogen Salmonella Typhimurium or pneumonic infection with Burkholderia thailandensis, the presence of this E. coli did not alter changes in host metabolism, caloric uptake, or inflammation but instead sustained signaling of the insulin-like growth factor 1/phosphatidylinositol 3-kinase/AKT pathway in skeletal muscle, which is required for prevention of muscle wasting. This effect was dependent on engagement of the NLRC4 inflammasome. Therefore, this commensal promotes tolerance to diverse diseases. Authors: Alexandria M. Palaferri Schieber, Yujung Michelle Lee, Max W. Chang, Mathias Leblanc, Brett Collins, Michael Downes, Ronald M. Evans, Janelle S. Ayres

Dendritic cells can capture and transfer retroviruses in vitro across synaptic cell-cell contacts to uninfected cells, a process called trans-infection. Whether trans-infection contributes to retroviral spread in vivo remains unknown. Here, we visualize how retroviruses disseminate in secondary lymphoid tissues of living mice. We demonstrate that murine leukemia virus (MLV) and human immunodeficiency virus (HIV) are first captured by sinus-lining macrophages. CD169/Siglec-1, an I-type lectin that recognizes gangliosides, captures the virus. MLV-laden macrophages then form long-lived synaptic contacts to trans-infect B-1 cells. Infected B-1 cells subsequently migrate into the lymph node to spread the infection through virological synapses. Robust infection in lymph nodes and spleen requires CD169, suggesting that a combination of fluid-based movement followed by CD169-dependent trans-infection can contribute to viral spread. Authors: Xaver Sewald, Mark S. Ladinsky, Pradeep D. Uchil, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas T. Murooka, Michael A. Brehm, Dale L. Greiner, Leonard D. Shultz, Thorsten R. Mempel, Pamela J. Bjorkman, Priti Kumar, Walther Mothes

Cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS) detects intracellular DNA and signals through the adapter protein STING to initiate the antiviral response to DNA viruses. Whether DNA viruses can prevent activation of the cGAS-STING pathway remains largely unknown. Here, we identify the oncogenes of the DNA tumor viruses, including E7 from human papillomavirus (HPV) and E1A from adenovirus, as potent and specific inhibitors of the cGAS-STING pathway. We show that the LXCXE motif of these oncoproteins, which is essential for blockade of the retinoblastoma tumor suppressor, is also important for antagonizing DNA sensing. E1A and E7 bind to STING, and silencing of these oncogenes in human tumor cells restores the cGAS-STING pathway. Our findings reveal a host-virus conflict that may have shaped the evolution of viral oncogenes. Authors: Laura Lau, Elizabeth E. Gray, Rebecca L. Brunette, Daniel B. Stetson

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Author: Stephen T. Jackson

by Kushagra Singhal, Jocelyne Vreede, Alireza Mashaghi, Sander J. Tans, Peter G. Bolhuis

How chaperones interact with protein chains to assist in their folding is a central open question in biology. Obtaining atomistic insight is challenging in particular, given the transient nature of the chaperone-substrate complexes and the large system sizes. Recent single-molecule experiments have shown that the chaperone Trigger Factor (TF) not only binds unfolded protein chains, but can also guide protein chains to their native state by interacting with partially folded structures. Here, we used all-atom MD simulations to provide atomistic insights into how Trigger Factor achieves this chaperone function. Our results indicate a crucial role for the tips of the finger-like appendages of TF in the early interactions with both unfolded chains and partially folded structures. Unfolded chains are kinetically trapped when bound to TF, which suppresses the formation of transient, non-native end-to-end contacts. Mechanical flexibility allows TF to hold partially folded structures with two tips (in a pinching configuration), and to stabilize them by wrapping around its appendages. This encapsulation mechanism is distinct from that of chaperones such as GroEL, and allows folded structures of diverse size and composition to be protected from aggregation and misfolding interactions. The results suggest that an ATP cycle is not required to enable both encapsulation and liberation.

by Peter K. Koo, Matthew Weitzman, Chandran R. Sabanaygam, Kenneth L. van Golen, Simon G. J. Mochrie

Resolving distinct biochemical interaction states when analyzing the trajectories of diffusing proteins in live cells on an individual basis remains challenging because of the limited statistics provided by the relatively short trajectories available experimentally. Here, we introduce a novel, machine-learning based classification methodology, which we call perturbation expectation-maximization (pEM), that simultaneously analyzes a population of protein trajectories to uncover the system of diffusive behaviors which collectively result from distinct biochemical interactions. We validate the performance of pEM in silico and demonstrate that pEM is capable of uncovering the proper number of underlying diffusive states with an accurate characterization of their diffusion properties. We then apply pEM to experimental protein trajectories of Rho GTPases, an integral regulator of cytoskeletal dynamics and cellular homeostasis, in vivo via single particle tracking photo-activated localization microcopy. Remarkably, pEM uncovers 6 distinct diffusive states conserved across various Rho GTPase family members. The variability across family members in the propensities for each diffusive state reveals non-redundant roles in the activation states of RhoA and RhoC. In a resting cell, our results support a model where RhoA is constantly cycling between activation states, with an imbalance of rates favoring an inactive state. RhoC, on the other hand, remains predominantly inactive.

by Matthias S. Keil

Power laws describe brain functions at many levels (from biophysics to psychophysics). It is therefore possible that they are generated by similar underlying mechanisms. Previously, the response properties of a collision-sensitive neuron were reproduced by a model which used a power law for scaling its inhibitory input. A common characteristic of such neurons is that they integrate information across a large part of the visual field. Here we present a biophysically plausible model of collision-sensitive neurons with η-like response properties, in which we assume that each information channel is noisy and has a response threshold. Then, an approximative power law is obtained as a result of pooling these channels. We show that with this mechanism one can successfully predict many response characteristics of the Lobula Giant Movement Detector Neuron (LGMD). Moreover, the results depend critically on noise in the inhibitory pathway, but they are fairly robust against noise in the excitatory pathway.

by Mauricio Santillana, André T. Nguyen, Mark Dredze, Michael J. Paul, Elaine O. Nsoesie, John S. Brownstein

We present a machine learning-based methodology capable of providing real-time (“nowcast”) and forecast estimates of influenza activity in the US by leveraging data from multiple data sources including: Google searches, Twitter microblogs, nearly real-time hospital visit records, and data from a participatory surveillance system. Our main contribution consists of combining multiple influenza-like illnesses (ILI) activity estimates, generated independently with each data source, into a single prediction of ILI utilizing machine learning ensemble approaches. Our methodology exploits the information in each data source and produces accurate weekly ILI predictions for up to four weeks ahead of the release of CDC’s ILI reports. We evaluate the predictive ability of our ensemble approach during the 2013–2014 (retrospective) and 2014–2015 (live) flu seasons for each of the four weekly time horizons. Our ensemble approach demonstrates several advantages: (1) our ensemble method’s predictions outperform every prediction using each data source independently, (2) our methodology can produce predictions one week ahead of GFT’s real-time estimates with comparable accuracy, and (3) our two and three week forecast estimates have comparable accuracy to real-time predictions using an autoregressive model. Moreover, our results show that considerable insight is gained from incorporating disparate data streams, in the form of social media and crowd sourced data, into influenza predictions in all time horizons.

by Nidhi Tyagi, Edward J Farnell, Colin M Fitzsimmons, Stephanie Ryan, Edridah Tukahebwa, Rick M Maizels, David W Dunne, Janet M Thornton, Nicholas Furnham

Allergic reactions can be considered as maladaptive IgE immune responses towards environmental antigens. Intriguingly, these mechanisms are observed to be very similar to those implicated in the acquisition of an important degree of immunity against metazoan parasites (helminths and arthropods) in mammalian hosts. Based on the hypothesis that IgE-mediated immune responses evolved in mammals to provide extra protection against metazoan parasites rather than to cause allergy, we predict that the environmental allergens will share key properties with the metazoan parasite antigens that are specifically targeted by IgE in infected human populations. We seek to test this prediction by examining if significant similarity exists between molecular features of allergens and helminth proteins that induce an IgE response in the human host. By employing various computational approaches, 2712 unique protein molecules that are known IgE antigens were searched against a dataset of proteins from helminths and parasitic arthropods, resulting in a comprehensive list of 2445 parasite proteins that show significant similarity through sequence and structure with allergenic proteins. Nearly half of these parasite proteins from 31 species fall within the 10 most abundant allergenic protein domain families (EF-hand, Tropomyosin, CAP, Profilin, Lipocalin, Trypsin-like serine protease, Cupin, BetV1, Expansin and Prolamin). We identified epitopic-like regions in 206 parasite proteins and present the first example of a plant protein (BetV1) that is the commonest allergen in pollen in a worm, and confirming it as the target of IgE in schistosomiasis infected humans. The identification of significant similarity, inclusive of the epitopic regions, between allergens and helminth proteins against which IgE is an observed marker of protective immunity explains the ‘off-target’ effects of the IgE-mediated immune system in allergy. All these findings can impact the discovery and design of molecules used in immunotherapy of allergic conditions.

by Farras Abdelnour, Susanne Mueller, Ashish Raj

Mesial temporal lobe epilepsy (TLE) is characterized by stereotyped origination and spread pattern of epileptogenic activity, which is reflected in stereotyped topographic distribution of neuronal atrophy on magnetic resonance imaging (MRI). Both epileptogenic activity and atrophy spread appear to follow white matter connections. We model the networked spread of activity and atrophy in TLE from first principles via two simple first order network diffusion models. Atrophy distribution is modeled as a simple consequence of the propagation of epileptogenic activity in one model, and as a progressive degenerative process in the other. We show that the network models closely reproduce the regional volumetric gray matter atrophy distribution of two epilepsy cohorts: 29 TLE subjects with medial temporal sclerosis (TLE-MTS), and 50 TLE subjects with normal appearance on MRI (TLE-no). Statistical validation at the group level suggests high correlation with measured atrophy (R = 0.586 for TLE-MTS, R = 0.283 for TLE-no). We conclude that atrophy spread model out-performs the hyperactivity spread model. These results pave the way for future clinical application of the proposed model on individual patients, including estimating future spread of atrophy, identification of seizure onset zones and surgical planning.

by Anja Winter, Ralf Schmid, Richard Bayliss

Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes. They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains. However, unlike other well-characterized groups of clan CD peptidases, there are no high-resolution structures of separases and the details of their regulation and substrate recognition are poorly understood. Here we undertook an in-depth bioinformatical analysis of separases from different species with respect to their similarity in amino acid sequence and protein fold in comparison to caspases, MALT-1 proteins (mucosa-associated lymphoidtissue lymphoma translocation protein 1) and gingipain-R. A comparative model of the single C-terminal caspase-like domain in separase from C. elegans suggests similar binding modes of substrate peptides between these protein subfamilies, and enables differences in substrate specificity of separase proteins to be rationalised. We also modelled a newly identified putative death domain, located N-terminal to the caspase-like domain. The surface features of this domain identify potential sites of protein-protein interactions. Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif. We envisage that findings from our study will guide structural and functional studies of this important protein family.

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b09740