bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine
Authors: Belo Yael , Mielko Zack , Nudelman Hila , Afek Ariel , Ben-David Oshrit , Shahar Anat , Zarivach Raz , Gordan Raluca , Arbely Eyal 
Published: February 2019

AbstractThe signal transducer and activator of transcription 3 (STAT3) protein is activated by phosphorylation of a specific tyrosine residue (Tyr705) in response to various extracellular signals. STAT3 activity was also found to be regulated by acetylation of Lys685. However, the molecular mechanism by which Lys685 acetylation affects the transcriptional activity of STAT3 remains elusive. By genetically encoding the co-translational incorporation of acetyl-lysine into position Lys685 and co-expression with the Elk receptor tyrosine kinase, we were able to biochemically characterize site-specifically acetylated, and simultaneously acetylated and phosphorylated STAT3. We measured the effect of acetylation on the crystal structure, and DNA binding affinity and specificity of Tyr705-phosphorylated and non-phosphorylated STAT3. In addition, we monitored the deacetylation of acetylated Lys685 by reconstituting the mammalian enzymatic deacetylation reaction in live bacteria. Surprisingly, we found that acetylation, per se, had no effect on the crystal structure, and DNA binding affinity or specificity of STAT3, implying that the previously observed acetylation-dependent transcriptional activity of STAT3 involves an additional cellular component. In addition, we discovered that Tyr705-phosphorylation protects Lys685 from deacetylation in bacteria, providing a new possible explanation for the observed correlation between STAT3 activity and Lys685 acetylation.
Extracellular spike waveform dissociates four functionally distinct cell classes in primate cortex
Authors: Trainito Caterina , von Nicolai Constantin , Miller Earl K. , Siegel Markus 
Published: February 2019

SummaryUnderstanding the function of different neuronal cell types is key to understanding brain function. However, cell type diversity is typically overlooked in electrophysiological studies in awake behaving animals. Here, we show that four functionally distinct cell classes can be robustly identified from extracellular recordings in several cortical regions of awake behaving monkeys. We recorded extracellular spiking activity from dorsolateral prefrontal cortex (dlPFC), the frontal eye field (FEF), and the lateral intraparietal area of macaque monkeys during a visuomotor decision-making task. We employed unsupervised clustering of spike waveforms, which robustly dissociated four distinct cell classes across all three brain regions. The four cell classes were functionally distinct. They showed different baseline firing statistics, visual response dynamics, and coding of visual information. While cell class-specific baseline statistics were consistent across brain regions, response dynamics and information coding were regionally specific. Our results identify four waveform-based cell classes in primate cortex. This opens a new window to dissect and study the cell-type specific function of cortical circuits.
Cxcr4 desensitization is an essential regulatory mechanism controlling the extra-follicular B cell response
Authors: Alouche Nagham , Bonaud Amélie , Rondeau Vincent , Nguyen Julie , Cricks Etienne , Setterblad Niclas , Mahevas Matthieu , Balabanian Karl , Espéli Marion 
Published: February 2019

AbstractThe signaling axis formed by the chemokine CXCL12 and its receptor CXCR4 plays an important role in B cell development and activation and is finely regulated by a process termed desensitization. Mutations leading to a truncation of the C-terminus tail of CXCR4 and thus to a defective desensitization have been reported in two diseases, a rare immunodeficiency called the WHIM syndrome and a B cell plasmacytoma called Waldenstrom’s Macroglobulinemia (WM). How CXCR4 desensitization may impact B cell activation in the context of a T-independent extra-follicular response is still unknown. Here using a unique mouse model bearing an orthologous gain of function mutation ofCxcr4we report that Cxcr4 desensitization is an essential gatekeeper controlling B lymphocyte entry into cycle, plasma cell differentiation, migration and maturation upon Myd88-dependent signaling. Altogether, our results support an essential role for Cxcr4 desensitization in limiting the depth and width of the B cell extra-follicular response and PC development.
Modeling microbial communities using biochemical resource allocation analysis
Authors: Sharma Suraj , Steuer Ralf 
Published: February 2019

ABSTRACTTo understand the functioning and dynamics of microbial communities remains a fundamental challenge at the forefront of current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. Currently, however, there is a large chasm between ecologically-motivated descriptions of microbial growth used in ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed within systems and synthetic biology. Here, we seek to demonstrate how current biochemical resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parameterization. In particular, recent work on quantitative microbial growth and cellular resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. Biochemical resource allocation models go beyond Michaelis-Menten and Monod-type growth models, and allow to account for emergent properties that underlie the remarkable plasticity of microbial growth. We exemplify our approach using a coarse-grained model of cyanobacterial phototrophic growth, and demonstrate how the model allows us to represent physiological acclimation to different environments, co-limitation of growth by several nutrients, as well as emergent switches between alternative nutrient sources. Our approach has implications for building models of microbial communities to understand their interactions, dynamics and response to environmental changes.
GeNet: Deep Representations for Metagenomics
Authors: Rojas-Carulla Mateo , Tolstikhin Ilya , Luque Guillermo , Youngblut Nicholas , Ley Ruth , Schölkopf Bernhard 
Published: February 2019

AbstractWe introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and Centrifuge on datasets obtained from several sequencing technologies, in which dataset shift occurs. We show that GeNet obtains competitive precision and good recall, with orders of magnitude less memory requirements. Moreover, we show that a linear model trained on top of representations learned by GeNet achieves recall comparable to state-of-the-art methods on the aforementioned datasets, and achieves over 90% accuracy in a challenging pathogen detection problem. This provides evidence of the usefulness of the representations learned by GeNet for downstream biological tasks.
A practive faeces collection protocol for multidisciplinary research in wildlife science
Authors: Biswas Suvankar , Bhatt Supriya , Paul Shrutarshi , Modi Shrushti , Ghosh Tista , Habib Bilal , Nigam Parag , Talukdar Gautam , Pandav Bivash , Mondol Samrat 
Published: February 2019

AbstractFaecal samples have become important non-invasive source of information in wildlife biology and ecological research. Despite regular use of faeces, there is no universal protocol available for faeces collection and storage to answer various questions in wildlife biology. We collected 1408 faeces from ten different species using a dry sampling approach, and achieved 94.87% and 86.02% success rate in mitochondrial and nuclear marker amplifications. We also suggest a universal framework to use the same samples for different use. This protocol provides an easy, quick and cheap option to collect non-invasive samples from species living at different environmental conditions to answer multidisciplinary questions in wildlife biology.
Fracking and Ostwald ripening position the lumen of the mouse blastocyst
Authors: Dumortier Julien G. , Le Verge-Serandour Mathieu , Tortorelli Anna-Francesca , Mielke Annette , de Plater Ludmilla , Turlier Hervé , Maître Jean-Léon 
Published: February 2019

AbstractDuring mouse preimplantation development, the formation of the blastocoel, a fluid-filled lumen, breaks the radial symmetry of the blastocyst. What controls the formation and positioning of this basolateral lumen remains obscure. We find that accumulation of pressurized fluid fractures cell-cell contacts into hundreds of micron-size lumens. Microlumens eventually discharge their volumes into a single dominant lumen, which we model as a process akin to Ostwald ripening, underlying the coarsening of foams. Using chimeric mutant embryos, we tune the tracking of cell-cell contacts and steer the coarsening of microlumens, allowing us to successfully manipulate the final position of the lumen. We conclude that hydraulic fracture of cell-cell contacts followed by directed coarsening of microlumens sets the first axis of symmetry of the mouse embryo.
Modelling plastics exposure for the marine biota: Risk maps for fin whales in the Pelagos Sanctuary (North-Western Mediterranean)
Authors: Guerrini Federica , Mari Lorenzo , Casagrandi Renato 
Published: February 2019

AbstractThe Mediterranean basin is among the most impacted marine ecoregions globally, being at the same time semi-enclosed by densely populated countries and crossed by trafficked maritime routes. Such anthropogenic pressure threatens both the qual-ity of its waters and the high biodiversity living in them, making the role of Marine Protected Areas (MPAs) crucial for pre-serving species suitable habitats. Under the European Union Marine Strategy Framework Directive, marine litter has been recognized as one of the principal causes of marine pollution, and public awareness on its environmental and biological impacts is raising. Using a quantitative and data-driven modelling approach, here we assess the presence of plastic waste within the feeding grounds of the fin whale Balaenoptera physalus, an endangered cetacean for which there is increasing evidence of impacts due to microplastic ingestion. To this end, we analyze a decade (2000 - 2010) of advection patterns of marine plastic litter, modelled with a Lagrangian approach. Particles are released in the MPA Pelagos, the International Sanctuary for the Protection of Mediterranean Marine Mammals (North-Western Mediterranean, between France, Italy and Monaco), from different sources (i.e., untreated waste along coasts, plastic discharged from rivers and plastic pollution released along maritime shipping routes). Risk of exposure of fin whales to microplastic pollution is evaluated by interlacing plastic litter distribution maps obtained through modelling with maps of suitable habitats obtained from the elaboration of satellite chlorophyll-a data in species-specific visited areas. Our modelling results show that all the three main sources of plastic litter taken into account clearly contribute to impacting cetaceans in the Sanctuary, yet in a different manner. The procedure formalized here can be extended to assess the risk caused by plastic pollution in other MPAs as well as to evaluate possible impacts on other taxa, thus informing targeted actions to tackle the complex issue of marine litter.
Analysis of solid-state heparin samples by ATR-FTIR spectroscopy
Authors: Devlin Anthony , Mycroft-West Courtney J. , Guerrini Marco , Yates Edwin A. , Skidmore Mark A. 
Published: February 2019

AbstractThe widely used anticoagulant pharmaceutical, heparin, is a polydisperse, heterogeneous polysaccharide. Heparin is one of the essential medicines defined by the World Health Organisation but, during 2007-2008, was the subject of adulteration. The intrinsic heterogeneity and variability of heparin makes it a challenge to monitor its purity by conventional means. This has led to the adoption of alternative approaches for its analysis and quality control, some of which are based on multivariate analysis of 1H NMR spectra, or exploit correlation techniques. Such NMR spectroscopy-based analyses, however, require costly and technically demanding NMR instrumentation. Here, an alternative approach based on the use of attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR) combined with multivariate analysis is proposed. FTIR-ATR employs more affordable and easy-to-use technology and, when combined with multivariate analysis of the resultant spectra, readily differentiates between glycosaminoglycans of different types, between heparin samples of distinct animal origins and enables the detection of both known heparin contaminants, such as over-sulphated chondroitin sulfate (OSCS), as well as other alien sulphated polysaccharides in heparin samples to a degree of sensitivity comparable to that achievable by NMR. The approach will permit the rapid and cost-effective monitoring of pharmaceutical heparin at any stage of the production process and indeed, in principle, the quality control of any heterogeneous or variable material.
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota
Authors: Aranda-Díaz Andrés , Obadia Benjamin , Thomsen Tani , Hallberg Zachary F. , Tüzün Güvener Zehra , Casey Huang Kerwyn , Ludington William B. 
Published: February 2019

AbstractDespite decades of investigation into how antibiotics affect isolated bacteria, it remains highly challenging to predict consequences for communities in complex environments such as the human intestine. Interspecies interactions can impact antibiotic activity through alterations to the extracellular environment that change bacterial physiology. By measuring key metabolites and environmental pH, we determined that metabolic cross-feeding among members of the fruit fly gut microbiota drives changes in antibiotic sensitivityin vitro. Co-culturing ofLactobacillus plantarumwithAcetobacterspecies induced tolerance to rifampin. Mechanistically, we found that acetobacters counter the acidification driven byL. plantarumproduction of lactate, and that pH shifts during stationary phase were sufficient to drive rifampin tolerance inL. plantarummonocultures. The keyLactobacillusphysiological parameter related to tolerance was a reduction in lag time exiting stationary phase, opposite to a previously identified mode of tolerance to ampicillin inE. coli. Lactobacillustolerance to erythromycin also depended on growth status and pH, suggesting that our findings generalize to other antibiotics. Finally, tolerance ofL. plantarumto rifampin varied spatially across the fruit fly gut. This mechanistic understanding of the coupling among interspecies interactions, environmental pH, and antibiotic tolerance enables future predictions of growth and the effects of antibiotics in more complex communities and within hosts.
Structural and binding studies of human CAMKK2 kinase domain bound to small molecule ligands
Authors: Profeta Gerson S. , dos Reis Caio V. , Godoi Paulo H. C. , Fala Angela M. , Sartori Roger , Salmazo Anita P. T. , Ramos Priscila Z. , Massirer Katlin B. , Elkins Jonathan M. , Drewry David H. , Gileadi Opher , Couñago Rafael M. 
Published: February 2019

AbstractCalcium/Calmodulin-dependent Protein Kinase Kinase 2 (CAMKK2) acts as a signaling hub, receiving signals from various regulatory pathways and decoding them via phosphorylation of downstream protein kinases - such as AMPK (AMP-activated protein kinase) and CAMK types I and IV. CAMKK2 relevance is highlighted by its constitutive activity being implicated in several human pathologies. However, at present, there are no specific small-molecule inhibitors available for this protein kinase. Moreover, CAMKK2 and its closest human homologue, CAMKK1, are thought to have overlapping biological roles. Here we present six novel co-structures of CAMKK2 bound to potent ligands identified from a library of ATP-competitive kinase inhibitors. Isothermal titration calorimetry (ITC) revealed that binding to some of these molecules is enthalpy driven. We expect our results to further advance current efforts to discover small molecule kinase inhibitors specific to each human CAMKK.
Structure-based methyl resonance assignment with MethylFLYA
Authors: Pritišanac Iva , Würz Julia , Alderson T. Reid , Güntert Peter 
Published: February 2019

AbstractMethyl groups provide crucial NMR probes for investigating protein structure, dynamics and mechanisms in systems that are too large for NMR with uniform isotope labeling. This requires the assignment of methyl signals in the NMR spectra to specific methyl groups in the protein, an expensive and time-consuming endeavor that limits the use of methyl-based NMR for large proteins. To resolve this bottleneck, several methyl resonance assignment methods have been developed. These approaches remain limited with regard to complete automation and/or the extent and accuracy of the assignments. Here, we present the completely automated MethylFLYA method for the assignment of methyl groups. MethylFLYA requires as input exclusively methyl-methyl nuclear Overhauser effect spectroscopy (NOESY) peak lists. The algorithm was applied to five proteins of 28–358 kDa mass with a total of 708 isotope-labeled methyl groups. Manually made 1H/13C reference assignments were available for 674 methyls. The available experimental peak lists contained NOESY cross peaks for 614 methyls. MethylFLYA confidently assigned 488 methyls, i.e. 79% of those with NOESY data. Of these assignments, 460 agreed with the reference, 5 were different (and 23 concerned methyls without reference assignment). For three proteins of 28, 81, and 358 kDa, all confident assignments by MethylFLYA were correct. We furthermore show that, for high-quality NOESY spectra, automatic picking of NOE signals followed by resonance assignment with MethylFLYA can yield results that are comparable to those obtained for manually prepared peak lists, indicating the feasibility of unbiased, fully automatic methyl resonance assignment starting directly from the NMR spectra. This renders MethylFLYA an advantageous alternative to existing approaches for structure-based methyl assignment. MethylFLYA assigns, for most proteins, significantly more methyl groups than other algorithms, has an average error rate of 1%, modest runtimes of 0.4–1.2 h for the five proteins, and flexibility to handle arbitrary isotope labeling patterns and include data from other types of NMR spectra.
Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins
Authors: Zhang Haiyang , Petrie Meghan V. , He Yiwei , Peace Jared M. , Chiolo Irene E. , Aparicio Oscar M. 
Published: February 2019

ABSTRACTChromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. Sites undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. InS. cerevisiae, replication origins occupy characteristic subnuclear localizations that anticipate their initiation timing during S phase. Here, we link localization of replication origins in G1 phase with Fkh1 activity, which is required for their early replication timing. Using a Fkh1-dependent origin relocalization assay, we determine that execution of Dbf4-dependent kinase function, including Cdc45 loading, results in dynamic relocalization of a replication origin from the nuclear periphery to the interior in G1 phase. Origin mobility increases substantially with Fkh1-driven relocalization. These findings provide novel molecular insight into the mechanisms that govern dynamics and spatial organization of DNA replication origins and possibly other functional DNA elements.
Impaired M-current in KCNQ2 Encephalopathy Evokes Dyshomeostatic Modulation of Excitability
Authors: Simkin Dina , Searl Timothy J. , Piyevsky Brandon N. , Forrest Marc , Williams Luis A. , Joshi Vaibhav , Zhang Hongkang , Ryan Steven J. , Schwake Michael , Robertson Gabriella L. , Penzes Peter , Laux Linda C. , McManus Owen B. , Dempsey Graham T. , Millichap John J. , George Alfred. L. , Kiskinis Evangelos 
Published: February 2019

ABSTRACTMutations in KCNQ2, which encodes a pore-forming K+ channel subunit responsible for neuronal M-current, cause neonatal epileptic encephalopathy, a complex disorder presenting with severe early-onset seizures and impaired neurodevelopment. The condition is exceptionally difficult to treat, partially because the effects of KCNQ2 mutations on the development and function of human neurons are unknown. Here, we used induced pluripotent stem cells and gene editing to establish a disease model, and measured the functional properties of patient-derived neurons using electrophysiological and optical approaches. We find that while patient-derived excitatory neurons exhibit reduced M-current early, they develop intrinsic and network hyperexcitability progressively. This hyperexcitability is associated with faster action potential repolarization, larger afterhyperpolarization, and a functional enhancement of large conductance Ca2+-activated K+ (BK) channels. These properties facilitate a burst-suppression firing pattern that is reminiscent of the interictal electroencephalography pattern in patients. Importantly, we were able to phenocopy these excitability features in control neurons only by chronic but not acute pharmacological inhibition of M-current. Our findings suggest that dyshomeostatic mechanisms compound KCNQ2 loss-of-function and lead to alterations in the neurodevelopmental trajectory of patient-derived neurons. Our work has therapeutic implications in explaining why KCNQ2 agonists are not beneficial unless started at an early disease stage.