bluuebunny/crossref_metadata_2025_split huggingface dataset:
PLCγ1 promotes phase separation of the T cell signaling clusters
Authors: Zeng Longhui , Palaia Ivan , Šarić Anđela , Su Xiaolei 
Published: July 2020

SummaryThe T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here we report that phospholipase PLCγ1 promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly crosslinks LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK and SLP76 activation. Intriguingly, a non-monotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction.
High-resolution line-scanning reveals distinct visual response properties across human cortical layers
Authors: Morgan Andrew T. , Nothnagel Nils , Petro Lucy. S. , Goense Jozien , Muckli Lars 
Published: July 2020

AbstractOur understanding of the human brain relies on advancing noninvasive brain imaging approaches. Characterization of the function of brain circuitry depends on the spatiotemporal correspondence at which recorded signals can be mapped onto underlying neuronal structures and processes. Here we aimed to address key first-stage questions of feasibility, reliability, and utility of line-scanning fMRI as a next generation non-invasive imaging method for human neuroscience research at the mesoscopic scale. Line-scanning can achieve high spatial resolution by employing anisotropic voxels aligned to cortical layers. The method can simultaneously achieve high temporal resolution by limiting acquisition to a very small patch of cortex which is repeatedly acquired as a single frequency-encoded k-space line. We developed multi-echo line-scanning procedures to record cortical layers in humans at high spatial (200 μm) and temporal resolution (100 ms) using ultra high-field 7T fMRI. Quantitative mapping allowed us to identify cortical layers in primary visual cortex (V1) and record functional signals from them while participants viewed movie clips. Analysis of these recordings revealed layer-specific V1 spatial and orientation tuning properties analogous to those previously observed in electrophysiological recordings of non-human primates. We have consequently demonstrated that line-scanning is a powerful non-invasive imaging technique for investigating mesoscopic functional circuits in human cortex.Graphical Abstract
Quantitative profiling of protease specificity
Authors: Ratnikov B. I. , Cieplak P. , Remacle A. G. , Nguyen E. , Smith J. W. 
Published: July 2020

AbstractProteases comprise an important class of enzymes, whose activity is central to many physiologic and pathologic processes. Detailed knowledge of protease specificity is key to understanding their function. Although many methodologies have been developed to profile specificities of proteases, few have the diversity and quantitative grasp necessary to fully define specificity of a protease, both in terms of substrate numbers and their catalytic efficiencies. We have developed a concept of “selectome”, which defines the set of substrates that uniquely represents specificity of a protease. We applied it to two closely related members of the Matrixin family – MMP-2 and MMP-9 by using substrate phage display coupled with Next Generation Sequencing and information theory-based data analysis. We have also derived a quantitative measure of substrate specificity, which accounts for both the numbers and relative catalytic efficiencies of substrates. Using these advances greatly facilitates uncovering selectivity between closely related members of protease families and provides insight into to the degree of contribution of catalytic cleft specificity to protein substrate recognition, thus providing basis to overcoming two of the major challenges in the field of proteolysis: 1) development of highly selective activity probes and inhibitors for studying proteases with overlapping specificities, and 2) distinguishing targeted proteolysis from bystander proteolytic events.
Type I Interferon regulates cytokine-delayed neutrophil apoptosis, reactive oxygen species production and chemokine expression via activation of p38 MAPK
Authors: Glennon-Alty Laurence , Moots Robert J , Edwards Steven W , Wright Helen L 
Published: July 2020

ABSTRACTInterferons (IFNs) are key regulators of a number of inflammatory conditions in which neutrophils play an important role in pathology, such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), where Type I IFNs are implicated in disease pathology. However, IFNs are usually generatedin vivotogether with other cytokines that also have immunoregulatory functions but such interactions are poorly-defined experimentally. We measured the effects of Type-I IFN (IFNα), elevated in both RA and SLE, on the functions of healthy neutrophils incubatedin vitroin the absence and presence of pro-inflammatory cytokines typically elevated in inflammatory diseases (TNFα, GM-CSF). IFNαalone had no effect on neutrophil apoptosis, however it did abrogate the anti-apoptotic effect of GM-CSF (18h, p< 0.01). The enhanced stabilty of the anti-apoptotic protein Mcl-1 and delayed activation of caspase activation normally regulated by GM-CSF were blocked by IFNα: this effect was mediated, in part, by activation of p38 MAPK, increased turnover of the anti-apoptotic protein Mcl-1 and cleavage of caspases. IFNαalone also primed ROS production alone and maintained the transient priming effect of TNF for up to 4h: it also down-regulated GM-CSF and TNFα-activated expression of CXCL1, CXCL2, CXCL3, CXCL8, CCL3 and CCL4, but in contrast increased the expression of CXCL10. These novel data identify complex regulatory signalling networks in which Type I IFNs profoundly alter the response of neutrophils to inflammatory cytokines. This is likely to have important consequencesin vivoand may explain the complexity and heterogeneity of inflammatory diseases such as RA, in which multiple cytokine cascades have been activated.
Comparative whole-genome approach to identify bacterial traits for microbial interactions
Authors: Zoccarato Luca , Sher Daniel , Miki Takeshi , Segrè Daniel , Grossart Hans-Peter 
Published: July 2020

AbstractMicrobial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a new trait-based approach, and applied it to 473 complete genomes (248 genera), representing a significant fraction of marine microbial communities. We identified genome functional clusters (GFCs) which condense bacterial diversity into groups with potentially common ecology and life history. Most GFCs revealed unique combinations of interaction traits, some widely distributed (e.g., antimicrobial activity), others less common (e.g., production of siderophores and phytohormones, biosynthesis and export of specific B vitamins). Specific GFCs, comprising Alpha- and Gammaproteobacteria, are predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Moreover, linked trait clusters (LTCs) identify traits that may have evolved together and point to specific modes of interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their ecosystem functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
Epithelial layer unjamming shifts energy metabolism toward glycolysis
Authors: DeCamp Stephen J. , Tsuda Victor M.K. , Ferruzzi Jacopo , Koehler Stephan A. , Giblin John T. , Roblyer Darren , Zaman Muhammad H. , Weiss Scott T. , DeMarzio Margherita , Park Chan Young , Ogassavara Nicolas Chiu , Mitchel Jennifer , Butler James P. , Fredberg Jeffrey J. 
Published: July 2020

AbstractIn development of an embryo, healing of a wound, or progression of a carcinoma, a requisite event is collective epithelial cellular migration. For example, cells at the advancing front of a wound edge tend to migrate collectively, elongate substantially, and exert tractions more forcefully compared with cells many ranks behind. With regards to energy metabolism, striking spatial gradients have recently been reported in the wounded epithelium, as well as in the tumor, but within the wounded cell layer little is known about the link between mechanical events and underlying energy metabolism. Using the advancing confluent monolayer of MDCKII cells as a model system, here we report at single cell resolution the evolving spatiotemporal fields of cell migration speeds, cell shapes, and traction forces measured simultaneously with fields of multiple indices of cellular energy metabolism. Compared with the epithelial layer that is unwounded, which is non-migratory, solid-like and jammed, the leading edge of the advancing cell layer is shown to become progressively more migratory, fluid-like, and unjammed. In doing so the cytoplasmic redox ratio becomes progressively smaller, the NADH lifetime becomes progressively shorter, and the mitochondrial membrane potential and glucose uptake become progressively larger. These observations indicate that a metabolic shift toward glycolysis accompanies collective cellular migration but show, further, that this shift occurs throughout the cell layer, even in regions where associated changes in cell shapes, traction forces, and migration velocities have yet to penetrate. In characterizing the wound healing process these morphological, mechanical, and metabolic observations, taken on a cell-by-cell basis, comprise the most comprehensive set of biophysical data yet reported. Together, these data suggest the novel hypothesis that the unjammed phase evolved to accommodate fluid-like migratory dynamics during episodes of tissue wound healing, development, and plasticity, but is more energetically expensive compared with the jammed phase, which evolved to maintain a solid-like non-migratory state that is more energetically economical.Two sentence summaryAt the leading front of an advancing confluent epithelial layer, each cell tends to migrate, elongate, and pull on its substrate far more than do cells many ranks behind, but little is known about underlying metabolic events. Using the advancing monolayer of MDCKII cells as a model of wound healing, here we show at single cell resolution that physical changes associated with epithelial layer unjamming are accompanied by an overall shift toward glycolytic metabolism.
Single neurons throughout human memory regions phase-lock to hippocampal theta
Authors: Schonhaut Daniel R. , Ramayya Ashwin G. , Solomon Ethan A. , Herweg Nora A. , Fried Itzhak , Kahana Michael J. 
Published: July 2020

AbstractFunctional interactions between the hippocampus and cortex are critical for episodic memory. Neural oscillations are believed to coordinate these interactions, and in rodents, prefrontal neurons phase-lock to hippocampal theta oscillations during memory-guided behavior. We assessed inter-regional phase-locking to hippocampal oscillations in humans by recording 1,233 cortical and amygdala neurons and simultaneous hippocampal local field potentials in 18 neurosurgical patients. We identified 362 neurons (29.4%) from multiple regions that phase-locked to rhythmic hippocampal activity, predominantly at theta (2-8Hz) frequencies. Compared to baseline spiking, strong theta phase-locking coincided with regionally-specific increases in hippocampal theta power, local and hippocampal high frequency activity, and cross-frequency power correlations between the hippocampus and a phase-locked neuron’s local region. These results reveal that spike-time synchrony with hippocampal theta is a defining feature of cortico-hippocampal functional connections in humans. We propose that theta phase-locking could mediate flexible inter-regional communication to shape the content and quality of episodic memories.
Organic Dust Exposure Induces Stress Response and Mitochondrial Dysfunction in Monocytic Cells
Authors: Mahadev-Bhat Sanjana , Shrestha Denusha , Massey Nyzil , Karriker Locke A. , Kanthasamy Anumantha G. , Charavaryamath Chandrashekhar 
Published: July 2020

AbstractExposure to airborne organic dust (OD), rich in microbial pathogen-associated molecular patterns, has been shown to induce inflammatory responses in the lung resulting in changes in airway structure and function. A common manifestation in lung inflammation is the occurrence of altered mitochondrial structure and bioenergetics, consequently regulating mitochondrial ROS (mROS) and creating a vicious cycle of mitochondrial dysfunction.The role of mitochondrial dysfunction in airway diseases such as COPD and asthma is well known. However, whether OD exposure induces mitochondrial dysfunction largely remains unknown. Therefore, in this study, we tested a hypothesis that OD exposure induces mitochondrial stress using a human monocytic cell line (THP-1). We examined the mechanisms of organic dust extract (ODE) exposure-induced mitochondrial structural and functional changes in THP-1 cells.In addition, the effect of co-exposure to ethyl pyruvate (EP), a known anti-inflammatory agent, or mitoapocynin (MA), a mitochondria targeting NOX2 inhibitor was examined. Transmission electron microscopy images showed significant changes in cellular and organelle morphology upon ODE exposure. ODE exposure with and without EP co-treatment increased the mtDNA leakage into the cytosol. Next, ODE exposure increased the PINK1 and Parkin expression, cytoplasmic cytochrome c levels and reduced mitochondrial mass and cell viability, indicating mitophagy. MA treatment was partially protective by decreasing Parkin expression, mtDNA and cytochrome c release and increasing cell viability.
Revival of light-evoked neuronal signals in the post-mortem mouse and human retina
Authors: Abbas Fatima , Becker Silke , Jones Bryan W. , Mure Ludovic S. , Panda Satchidananda , Hanneken Anne , Vinberg Frans 
Published: July 2020

AbstractThe retina, a highly metabolic tissue in the central nervous system, consumes the most oxygen and energy stores in the body by tissue mass/volume. Consequently, it is not surprising that retinal ischemia leads to a rapid loss of retinal light responses and electrical transmission. In this study, we show that despite a swift decline of retinal light responses after circulatory death (decay time constant τ = ∼1-2 min), we were able to restore mouse rod and cone photoreceptor light signals from enucleated eyes up to 3 h postmortem with significantly better postmortem recovery of cone versus rod light responses. We also demonstrate that both rod and cone phototransduction are more resistant to postmortem enucleation delay than synaptic transmission to second order neurons (bipolar cells). Encouraged by these analyses and the lack of previously successful postmortem retinal light recordings from human foveal/macular photoreceptors, we attempted to restore light responses in the human macula using donor eyes harvested 0.5 – 5 hours postmortem. Here we show successful recordings of human macular cone photoresponses in samples obtained from eyes enucleated up to 5 hours postmortem. Comparing ‘freshly’ enucleated non-human primate eyes with human eyes enucleated and reoxygenated at different times after death, we show the exponential decay of the light response amplitudes has a time constant of 74 min. We find that both cause of death and donor age are useful parameters for predicting the recovery of retinal light responses in postmortem human macular tissue. Moreover, we present evidence that hypoxia and secondary acidosis, two modifiable factors, are primary contributors to the rapid loss of retinal light signaling after death. Finally, we show postmortem hypoxia rather than acidosis is the major cause of irreversible decay of the light response amplitudes. The criteria and methodology that we have established here for reviving electrical photoresponses in the postmortem human eye will serve as a new starting point for studying neurophysiology and disease in the human retina.
Striatal circuits support broadly opponent aspects of action suppression and production
Authors: Cruz Bruno F. , Soares Sofia , Paton Joseph J. 
Published: July 2020

SummaryImbalance between action suppression and production characterizes several basal ganglia (BG) disorders. Relatedly, the direct and indirect pathways of the BG are hypothesized to promote and suppress actions, respectively. Yet striatal direct (dMSNs) and indirect (iMSNs) medium spiny neurons are coactive around movement, apparently contradicting direct-indirect functional opponency. In the dorsolateral striatum of mice, we observed coactivation around movements, but elevated and diminished activity of iMSNs and dMSNs, respectively, during action suppression. Furthermore, relative activity of the two hemispheres evolved in opposite directions in the two pathways as the need to suppress movements to either side of the body developed over time. Lastly, optogenetic inhibition experiments revealed the necessity of iMSNs but not dMSNs for the proactive suppression of specific actions, and dMSNs but not iMSNs for generalized action vigor. These data demonstrate distinct yet still broadly opponent roles for the direct and indirect pathways in behavioral control.
Mechanotransduction and dynamic outflow regulation in trabecular meshwork requires Piezo1 channels
Authors: Yarishkin Oleg , Phuong Tam T. T. , Baumann Jackson M. , De Ieso Michael L. , Vazquez-Chona Felix , Rudzitis Christopher N. , Sundberg Chad , Lakk Monika , Stamer W. Daniel , Križaj David 
Published: July 2020

AbstractMechanosensitivity of the trabecular meshwork (TM) is a key determinant of intraocular pressure (IOP) yet our understanding of the molecular mechanisms that subserve it remains in its infancy. Here, we show that mechanosensitive Piezo1 channels modulate the TM pressure response via calcium signaling and dynamics of the conventional outflow pathway. Pressure steps evoked fast, inactivating cation currents and calcium signals that were inhibited by Ruthenium Red, GsMTx4 and Piezo1 shRNA. Piezo1 expression was confirmed by transcript and protein analysis, and by visualizing Yoda1-mediated currents and [Ca2+]ielevations in primary human TM cells. Piezo1 activation was obligatory for transduction of physiological shear stress and was coupled to reorganization of F-actin cytoskeleton and focal adhesions. The importance of Piezo1 channels as pressure sensors was shown by the GsMTx4 -dependence of the pressure-evoked current and conventional outflow function. We also demonstrate that Piezo1 collaborates with the stretch-activated TRPV4 channel, which mediated slow, delayed currents to pressure steps. Collectively, these results suggest that TM mechanosensitivity utilizes kinetically, regulatory and functionally distinct pressure transducers to inform the cells about force-sensing contexts. Piezo1-dependent control of shear flow sensing, calcium homeostasis, cytoskeletal dynamics and pressure-dependent outflow suggests a novel potential therapeutic target for treating glaucoma.Significance StatementTrabecular meshwork (TM) is a highly mechanosensitive tissue in the eye that regulates intraocular pressure through the control of aqueous humor drainage. Its dysfunction underlies the progression of glaucoma but neither the mechanisms through which TM cells sense pressure nor their role in aqueous humor outflow are understood at the molecular level. We identified the Piezo1 channel as a key TM transducer of tensile stretch, shear flow and pressure. Its activation resulted in intracellular signals that altered organization of the cytoskeleton and cell-extracellular matrix contacts, and modulated the trabecular component of aqueous outflow whereas another channel, TRPV4, mediated a delayed mechanoresponse. These findings provide a new mechanistic framework for trabecular mechanotransduction and its role in the regulation of fast fluctuations in ocular pressure, as well as chronic remodeling of TM architecture that epitomizes glaucoma.
Cryo-EM structures reveal a multistep mechanism of Hsp90 activation by co-chaperone Aha1
Authors: Liu Yanxin , Sun Ming , Myasnikov Alexander G. , Elnatan Daniel , Delaeter Nicolas , Nguyenquang Michael , Agard David A. 
Published: July 2020

AbstractHsp90 is a ubiquitous molecular chaperone that facilitates the folding and maturation of hundreds of cellular “client” proteins. The ATP-driven client maturation process is regulated by a large number of co-chaperones. Among them, Aha1 is the most potent activator of Hsp90 ATPase activity and thus dramatically affects Hsp90’s client proteins. To understand the Aha1 activation mechanism, we determined full-length Hsp90:Aha1 structures in six different states by cryo-electron microscopy, including nucleotide-free semi-closed, nucleotide-bound pre-hydrolysis, and semi-hydrolyzed states. Our structures demonstrate that the two Aha1 domains can each interact with Hsp90 in two different modes, uncovering a complex multistep activation mechanism. The results show that Aha1 accelerates the chemical step of ATP hydrolysis like a conventional enzyme, but most unusually, catalyzes the rate-limiting large-scale conformational changes of Hsp90 fundamentally required for ATP hydrolysis. Our work provides a structural framework to guide small molecule development targeting this critical modulator of client protein maturation.