bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
Authors: Eldjárn Grímur Hjörleifsson , Ramsay Andrew , van der Hooft Justin J. J. , Duncan Katherine R. , Soldatou Sylvia , Rousu Juho , Daly Rónán , Wandy Joe , Rogers Simon 
Published: June 2020

AbstractSpecialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research.We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links.Author summaryIn this article, we introduce NPLinker, a software framework to link genomic and metabolomic data, to link microbial secondary metabolites to their producing genomic regions.Two of the major approaches for such linking are analysis of the correlation between sets of strains, and analysis of predicted features of the molecules. While these methods are usually used separately, we demonstrate that they are in fact complementary, and show a way to combine them to improve their performance.We begin by demonstrating a weakness in the most common method of strain correlation analysis, and suggest an improvement. We then introduce a new feature-based analysis method which, unlike most such methods, does not directly depend on the natural prodcut compound class. Finally, we demonstrate that the two are complementary and proceed to combine them into a single scoring function for genomic and metabolomic links, which shows improved performance over either of the individual approaches.Verification is done using curated databases of genomic and metabolomic data, as well as public data sets of microbial data including verified links.
Multivalent Clustering of Adhesion Ligands in Nanofiber-Nanoparticle Composites
Authors: Dems Dounia , Freeman Ronit , Coradin Thibaud , Stupp Samuel I. , Aimé Carole 
Published: June 2020

ABSTRACTBecause the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance ofca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing
Authors: Sanchez-Garcia R , Gomez-Blanco J , Cuervo A , Carazo JM , Sorzano COS , Vargas J 
Published: June 2020

AbstractCryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to obtain much cleaner and more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.
Immunoresolvents Support Skeletal Myofiber Regeneration via Actions on Myeloid and Muscle Stem Cells
Authors: Markworth James F. , Brown Lemuel A. , Lim Eunice , Floyd Carolyn , Larouche Jaqueline , Castor-Macias Jesus A. , Sugg Kristoffer B. , Sarver Dylan C. , Macpherson Peter C. D. , Davis Carol , Aguilar Carlos A. , Maddipati Krishna Rao , Brooks Susan V. 
Published: June 2020

AbstractSpecialized pro-resolving mediators (SPMs) actively limit inflammation and expedite its resolution. Here we profiled intramuscular lipid mediators following injury and investigated the role of SPMs in skeletal muscle inflammation and repair. Both eicosanoids and SPMs increased following myofiber damage induced by intramuscular injection of barium chloride or functional overload. Daily systemic administration of resolvin D1 (RvD1) limited the degree and duration of inflammation, enhanced regenerating myofiber growth, and improved recovery of muscle strength. RvD1 suppressed inflammatory cytokines, enhanced polymorphonuclear cell clearance, modulated muscle stem cells, and polarized macrophages to a more pro-regenerative subset. RvD1 had minimal direct impact onin-vitromyogenesis but directly suppressed myokine production and stimulated macrophage phagocytosis, showing that SPMs influence modulate both infiltrating myeloid and resident muscle cells. These data reveal the efficacy of immunoresolvents as a novel alternative to classical anti-inflammatory interventions in the management of muscle injuries to modulate inflammation while stimulating tissue repair.
Microengineered three-dimensional collagen fiber landscapes with independently tunable anisotropy and directionality
Authors: Ahmed Adeel , Joshi Indranil M. , Mansouri Mehran , Larson Stephen , Gholizadeh Shayan , Allahyari Zahra , Forouzandeh Farzad , Borkholder David A. , Gaborski Thomas R. , Abhyankar Vinay V. 
Published: June 2020

ABSTRACTFibrillar collagens are structural proteins in the extracellular matrix (ECM), and cellular processes, including differentiation, proliferation, and migration, have been linked to the orientation (directionality) and alignment (anisotropy) of collagen fibers. Given the importance of cell-substrate interactions in driving biological functions, several microfluidic approaches have demonstrated three-dimensional (3D) collagen gels with defined fiber properties that enable quantitative correlations between structural cues and observed cell responses. Although existing methods provide excellent definition over collagen fiber anisotropy, independent control over both anisotropy and directionality (that we collectively refer to as the collagen landscape) has not been demonstrated. Therefore, to advance collagen microengineering capabilities, we present a user-friendly approach that uses controlled fluid flows within a non-uniform microfluidic channel network to create well-defined collagen landscapes. We demonstrate capabilities including i) control over fiber anisotropy, ii) spatial gradients in fiber anisotropy, iii) defined fiber directionality, and iv) multi-material interfaces. We then show that cells respond to the microengineered topographic cues by aligning along the anisotropy domains and following fiber directionality. Finally, this platform’s modular capability is demonstrated by integrating an ultrathin porous parylene (UPP) membrane on the microengineered collagen as a mask to control cell-substrate interactions.
Repurposing the antidepressant sertraline as SHMT inhibitor to suppress serine/glycine synthesis addicted breast tumor growth
Authors: Geeraerts Shauni L. , Kampen Kim R. , Rinaldi Gianmarco , Gupta Purvi , Planque Mélanie , De Cremer Kaat , De Brucker Katrijn , Vereecke Stijn , Verbelen Benno , Vermeersch Pieter , Cassiman David , Fendt Sarah-Maria , Voet Arnout , Cammue Bruno P.A. , Thevissen Karin , De Keersmaecker Kim 
Published: June 2020

ABSTRACTMetabolic rewiring is a hallmark of cancer that supports tumor growth, survival and chemotherapy resistance. While normal cells often rely on extracellular serine and glycine supply, a significant subset of cancers becomes addicted to intracellular serine/glycine synthesis, offering an attractive drug target. Previously developed inhibitors of serine/glycine synthesis enzymes did not reach clinical trials due to unfavorable pharmacokinetic profiles, implying that further efforts to identify clinically applicable drugs targeting this pathway are required. In this study, we aimed to develop therapies that can rapidly enter the clinical practice by focusing on drug repurposing, as their safety and cost-effectiveness have been optimized before. Using a yeast model system, we repurposed two compounds, sertraline and thimerosal, for their selective toxicity against serine/glycine synthesis addicted breast cancer and T-cell acute lymphoblastic leukemia cell lines. Isotope tracer metabolomics, computational docking studies and an enzymatic activity assay revealed that sertraline and thimerosal inhibit serine/glycine synthesis enzymes serine hydroxymethyltransferase and phosphoglycerate dehydrogenase, respectively. In addition, we demonstrated that sertraline’s anti-proliferative activity was further aggravated by mitochondrial inhibitors, such as the antimalarial artemether, by causing G1-S cell cycle arrest. Most notably, this combination also resulted in serine-selective antitumor activity in breast cancer mouse xenografts. Collectively, this study provides molecular insights into the repurposed mode-of-action of the antidepressant sertraline and allows to delineate a hitherto unidentified group of cancers being particularly sensitive to treatment with sertraline. Furthermore, we highlight the simultaneous inhibition of serine/glycine synthesis and mitochondrial metabolism as a novel treatment strategy for serine/glycine synthesis addicted cancers.
Evidence for an expanded repertoire of electron acceptors for the anaerobic oxidation of methane in authigenic carbonates in the Atlantic and Pacific Ocean
Authors: Beckmann Sabrina , Farag Ibrahim F. , Zhao Rui , Christman Glenn D , Prouty Nancy G , Biddle Jennifer F 
Published: June 2020

AbstractAuthigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by 7 different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- andmcrA gene sequencing coupled with metagenomic analyses. These sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and −2 clades were abundant in the carbonates yet their typical syntrophic partners, sulfate reducing bacteria, were not significantly present. Our analysis indicated that methane oxidizers affiliated to the ANME-1 and −2 as well as to theCandidatusMethanoperedens clades, are capable of performing complete methane- and potentially short-chain alkane oxidations independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds in potential syntrophy with methane oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.
Cargo competition for a dimerization interface stabilizes a protease adaptor inCaulobacter crescentus
Authors: Kuhlmann Nathan J. , Doxsey Dylan , Chien Peter 
Published: June 2020

AbstractBacterial protein degradation is a regulated process aided by protease adaptors that alter specificity of energy dependent proteases. InCaulobacter crescentus, cell-cycle dependent protein degradation depends on a hierarchy of adaptors, such as the dimeric RcdA adaptor which binds multiple cargo and delivers substrates to the ClpXP protease. RcdA itself is degraded in the absence of cargo and how RcdA recognizes its targets is unknown. Here we show that RcdA dimerization and cargo binding compete for a common interface. Cargo binding separates RcdA dimers and a monomeric variant of RcdA fails to be degraded, suggesting that RcdA degradation is a result of self-delivery. Based on HDX-MS studies showing that different cargo rely on different regions of the dimerization interface, we generate RcdA variants that are selective for specific cargo and show cellular defects consistent with changes in selectivity. Using the same interface for dimerization and cargo binding offers an ability to limit excess protease adaptors by self-degradation, while providing capacity for binding a range of substrates.Significance StatementEnergy-dependent proteases broadly regulate bacterial physiology and development. Adaptor proteins tune the substrate specificity of proteases to only degrade selective substrates during the bacterial life cycle and during times of cellular stress. In the process of delivering cargo to their respective proteases, adaptor proteins are inherently protected from degradation until the delivery is complete. How protease adaptors can recognize a wide range of cargo while maintaining stringent specificity and how this process results in stabilization of adaptors remains unclear. Here, we show that direct competition for distinct regions of the dimer interface of the RcdA adaptor by its cargo protects RcdA from degradation by the ClpXP protease, and that this interface can be selectively perturbed in a rational manner with biochemical and physiological consequences.HighlightsCargo binding of RcdA cargo competes with dimerizationDimerization of RcdA is necessary for self-degradation by ClpXPRcdA can deliver either cargo or other RcdA subunits to ClpXPDifferent regions of the dimerization interface are needed for different cargo
Drift and termination of spiral waves in optogenetically modified cardiac tissue at sub-threshold illumination
Authors: Hussaini Sayedeh , Venkatesan Vishalini , Biasci Valentina , Romero Sepúlveda José M. , Quiñonez Uribe Raúl A. , Sacconi Leonardo , Bub Gil , Richter Claudia , Krinski Valentin , Parlitz Ulrich , Majumder Rupamanjari , Luther Stefan 
Published: June 2020

AbstractThe development of new approaches to control cardiac arrhythmias requires a deep understanding of spiral wave dynamics. Optogenetics offers new possibilities for this. Preliminary experiments show that sub-threshold illumination affects electrical wave propagation in the mouse heart. However, a systematic exploration of these effects is technically challenging. Here, we use state-of-the-art computer models to study the dynamic control of spiral waves in a two-dimensional model of the adult mouse ventricle, using stationary and non-stationary patterns of sub-threshold illumination. Our results indicate a light intensity-dependent increase in cellular resting membrane potentials, which together with diffusive cell-cell coupling leads to the development of spatial voltage gradients over differently illuminated areas. A spiral wave drifts along the positive gradient. These gradients can be strategically applied to ensure drift-induced termination of a spiral wave, both in optogenetics and in conventional methods of electrical defibrillation.
Electro-Steric Mechanism of CLC-2 Chloride Channel Activation
Authors: De Jesús-Pérez José J. , Méndez-Maldonado G. Arlette , Gonzalez-Hernandez Irma L. , De la Rosa Victor , Gastélum-Garibaldi Roberto , Sánchez-Rodríguez Jorge E. , Arreola Jorge 
Published: June 2020

AbstractTwo-pore voltage-gated CLC chloride channels control neuronal and muscle excitability. They share a dimeric structure but their activation mechanism remains unresolved. Here we determine the step-by-step activation mechanism of the broadly expressed CLC-2 channel using homology modelling, molecular dynamic simulations and functional studies. We establish that a two-leaf gate formed by Tyr561-H2O-Glu213 flanked by Lys568/Glu174 and Lys212 closes the canonical pore. Activation begins when a hyperpolarization-propelled intracellular chloride occupies the pore and splits Tyr561-H2O-Glu213 by electrostatic/steric repulsion. Unrestrained Glu213 rotates outwardly to bind Lys212 but the pore remains closed. Protonation breaks the Glu213-Lys212 interaction while another chloride occupies the pore thus catalysing chloride exit via Lys212. Also, we found that the canonical pore is uncoupled from a cytosolic cavity by a Tyr561-containing hydrophobic gate that prevents Glu213 protonation by intracellular protons. Our data provide atomistic details about CLC-2 activation but this mechanism might be common to other CLC channels.
Adipose tissue macrophages orchestrate β cell adaptation in obesity through secreting miRNA-containing extracellular vesicles
Authors: Gao Hong , Luo Zhenlong , Jin Zhongmou , Ji Yudong , Ying Wei 
Published: June 2020

AbstractObesity induces an adaptive expansion of β cell mass and insulin secretion abnormality. Here, we explore a novel role of adipose tissue macrophages (ATMs) in mediating obesity-induced β cell function and proliferation through releasing miRNA-containing extracellular vesicles (EVs). ATM EVs derived from obese mice notably suppress insulin secretion in bothin vivoandin vitroexperiments, whereas there are more proliferating β cells in the islets treated with obese ATM EVs. Depletion of miRNAs blunts the ability of obese ATM EVs to regulate β cell responses. miR-155, a highly enriched miRNA within obese ATM EVs, exerts profound regulation on β cell functions, as evidenced by impaired insulin secretion and increased β cell proliferation after miR-155 overexpression in β cells. By contrast, knockout of miR-155 can attenuate the regulation of obese ATM EVs on β cell responses. We further demonstrate that the miR-155-Mafbaxis plays a critical role in controlling β cell responses. Taken together, these studies show a novel mechanism by which ATM-derived EVs act as endocrine cargoes delivering miRNAs and subsequently mediating β cell adaptation and functional dysfunction in obesity.
CK2 inhibits TIMELESS nuclear export and modulates CLOCK transcriptional activity to regulate circadian rhythms
Authors: Cai Yao D. , Xue Yongbo , Truong Cindy C. , Del Carmen-Li Jose , Ochoa Christopher , Vanselow Jens T. , Murphy Katherine A. , Li Ying H. , Liu Xianhui , Kunimoto Ben L. , Zheng Haiyan , Zhao Caifeng , Zhang Yong , Schlosser Andreas , Chiu Joanna C. 
Published: June 2020

AbstractCircadian clocks orchestrate daily rhythms in organismal physiology and behavior to promote optimal performance and fitness. InDrosophila, key pacemaker proteins PERIOD (PER) and TIMELESS (TIM) are progressively phosphorylated to perform phase-specific functions. Whereas PER phosphorylation has been extensively studied, systematic analysis of site-specific TIM phosphorylation is lacking. Here, we identified phosphorylation sites of PER-bound TIM by mass spectrometry, given the importance of TIM as a modulator of PER function in the oscillator. Among the twelve TIM phosphorylation sites we identified, at least two of them are critical for circadian timekeeping as mutants expressing non-phosphorylatable mutations exhibit altered behavioral rhythms. In particular, we observed that CK2-dependent phosphorylation of TIM(S1404) promotes nuclear accumulation of PER-TIM heterodimers by inhibiting the interaction of TIM and nuclear export component, Exportin 1 (XPO1). We postulate that proper level of nuclear PER-TIM accumulation is necessary to facilitate kinase recruitment for the regulation of daily phosphorylation rhythm and phase-specific transcriptional activity of CLOCK (CLK). Our results highlight the contribution of phosphorylation-dependent nuclear export of PER-TIM heterodimers to the maintenance of circadian periodicity and identify a new mechanism by which the negative elements of the circadian oscillator (PER-TIM) regulate the positive elements (CLK-CYC). Finally, since the molecular phenotype oftim(S1404A) non-phosphorylatable mutant exhibits remarkable similarity to that of a mutation in humantimelessthat underlies Familial Advanced Sleep Phase Syndrome (FASPS), our results revealed an unexpected parallel between the functions ofDrosophilaand human TIM and may provide new insights into the molecular mechanisms underlying human FASPS.Significance StatementPhosphorylation is a central mechanism important for the regulation of circadian physiology across organisms. The molecular oscillator is composed of pacemaker proteins that undergo elaborate phosphorylation programs to regulate phase-specific functions. InDrosophila, phosphorylation of TIMELESS (TIM) has been recognized as critical for its function in the oscillator, but a systematic analysis of TIM phosphorylation is lacking. Here, we identified twelveDrosophilaTIM phosphorylation sites by mass spectrometry and showed that phosphorylation at TIM(S1404) is necessary for maintaining 24-hour rhythms. Finally, since the molecular phenotype oftim(S1404A) non-phosphorylatable fly mutant exhibits remarkable similarity to that of a mutation in humantimelessthat underlies FASPS, our results may provide new insights into the molecular underpinnings of human FASPS.