bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization
Authors: Tuddenham John F. , Taga Mariko , Haage Verena , Roostaei Tina , White Charles , Lee Annie , Fujita Masashi , Khairallah Anthony , Green Gilad , Hyman Bradley , Frosch Matthew , Hopp Sarah , Beach Thomas G. , Corboy John , Habib Naomi , Klein Hans-Ulrich , Soni Rajesh Kumar , Teich Andrew F. , Hickman Richard A. , Alcalay Roy N. , Shneider Neil , Schneider Julie , Sims Peter A. , Bennett David A. , Olah Marta , Menon Vilas , De Jager Philip L. 
Published: June 2022

AbstractHuman microglia play a pivotal role in neurological diseases, but few targeted therapies that directly modulate microglial state or function exist due to an incomplete understanding of microglial heterogeneity. We use single-cell RNA sequencing to profile live human microglia from autopsies or surgical resections across diverse neurological diseases and central nervous system regions. We observe a central divide between oxidative and heterocyclic metabolism and identify subsets associated with antigen presentation, motility, and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypesin situwith an RNAscope-immunofluorescence pipeline and leverage our dataset as a classification resource, finding that iPSC model systems recapitulate substantialin vivoheterogeneity. Finally, we identify and validate candidates for chemically inducing subtype-specific statesin vitro, showing that Camptothecin downregulates the transcriptional signature of disease-enriched subsets and upregulates a signature previously shown to be depleted in Alzheimer’s.
Illumination of a progressive allosteric mechanism mediating the glycine receptor activation
Authors: Shi Sophie , Lefebvre Solène N , Peverini Laurie , Cerdan Adrien , Gielen Marc , Changeux Jean-Pierre , Cecchini Marco , Corringer Pierre-Jean 
Published: June 2022

AbstractPentameric ligand-gated ion channel mediate signal transduction at chemical synapses by transiting between resting and open states upon neurotransmitter binding. Here, we investigate the gating transition of the glycine receptor fluorescently labeled at the extracellular-transmembrane interface by voltage-clamp fluorimetry (VCF). Fluorescence reports a glycine-elicited conformational transition that precedes pore opening. Low concentrations of glycine, partial agonists or specific mixtures of glycine and strychnine trigger the full fluorescence signal while weakly activating the channel. Molecular dynamic simulations of a partial agonist bound-closed Cryo-EM structure show a highly dynamic personality: a marked structural flexibility at both the extracellular-transmembrane interface and the orthosteric site, generating docking properties that recapitulate VCF data. Data thus illuminate a progressive gating transition towards activation, displaying structural plasticity with novel implication concerning the mechanism of action of allosteric effectors.
ECM-derived biophysical cues mediate interstitial flow-induced sprouting angiogenesis
Authors: Chang Chia-Wen , Shih Hsiu-Chen , Cortes-Medina Marcos , Beshay Peter E. , Avendano Alex , Seibel Alex J. , Liao Wei-Hao , Tung Yi-Chung , Song Jonathan W. 
Published: June 2022

AbstractSprouting angiogenesis is orchestrated by an intricate balance of biochemical and mechanical cues in the local microenvironment. Interstitial flow has been established as a potent regulator of angiogenesis. Similarly, extracellular matrix (ECM) physical properties, such as stiffness and microarchitecture, have also emerged as important mediators of angiogenesis. Yet, the interplay between interstitial flow and ECM physical properties in the initiation and control of angiogenesis is poorly understood. Using a 3-D microfluidic tissue analogue of angiogenic sprouting with defined interstitial flow, we found that the addition of hyaluronan (HA) to collagen-based matrices significantly enhances sprouting induced by interstitial flow compared to responses in collagen-only hydrogels. We confirmed that both the stiffness and matrix pore size of collagen-only hydrogels were increased by the addition of HA. Interestingly, interstitial flow-potentiated sprouting responses in collagen/HA matrices were not affected when functionally blocking the HA receptor CD44. In contrast, enzymatic depletion of HA in collagen/HA matrices with hyaluronidase (HAdase) resulted in decreased stiffness, pore size, and interstitial flow-mediated sprouting to the levels observed in collagen-only matrices. Taken together, these results suggest that HA enhances interstitial flow-mediated angiogenic sprouting through its alterations to collagen ECM stiffness and pore size.
The oncogenic fusion protein EWS-FLI1 promotes premature ageing of biomolecular condensates by catalyzing fibril formation
Authors: Selig Emily E. , Romero-Moreno Alma K. , Akula Shivani , Xu Xiaoping , Libich David S. 
Published: June 2022

AbstractEwing sarcoma (EwS) is an aggressive pediatric cancer of bone and soft tissue. A chromosomal translocation that joins the low-complexity domain of EWS (EWSLCD) with the DNA-binding domain of FLI1 (FLI1DBD) creates EWS-FLI1, a fusion oncoprotein essential for EwS development and accounts for 85% of all EwS cases. EWS-FLI1 acts as an aberrant transcription factor and interferes with the normal functions of nucleic acid-binding proteins via multivalent interactions and biomolecular condensation. The FLI1DBD was found to directly interact with the EWSLCD causing enhanced phase separation and induced hardening of EWSLCD condensates. Three related ETS DBDs (ERG, ETV1 and PU.1) also induced EWSLCD condensate hardening. DNA binding blocked the interaction with the EWSLCD, and NMR spectroscopy confirmed that ETS DBDs interact with EWSLCD via the DNA-binding interface. Our results provide a physical basis for the dominant-negative effect EWS-FLI1 exerts on EWS and highlight the need for further investigations of the FLI1DBD-EWSLCD interaction in vivo.
GPU-Accelerated All-atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber
Authors: Harris Julie A. , Liu Ruibin , de Oliveira Vinicius Martins , Montelongo Erik Vaquez , Henderson Jack A. , Shen Jana 
Published: June 2022

AbstractConstant pH molecular dynamics (MD) simulations sample protonation states on the fly according to the conformational environment and user specified pH condition; however, the current accuracy is limited due to the use of implicit-solvent models or a hybrid solvent scheme. Here we report the first GPU-accelerated implementation, parameterization, and validation of the all-atom continuous constant pH MD (CpHMD) method with particle-mesh Ewald (PME) electrostatics in the Amber22 pmemd. cuda engine. The titration parameters for Asp, Glu, His, Cys, and Lys were derived for the CHARMM c22 and Amber ff14sb and ff19sb force fields. We then evaluated the PME-CpHMD method using the asynchronous pH replica-exchange titration simulations with the c22 force field for six benchmark proteins, including BBL, hen egg white lysozyme (HEWL), staphylococcal nuclease (SNase), thioredoxin, ribonuclease A (RNaseA), and human muscle creatine kinase (HMCK). The root-mean-square deviation from the experimental pKa’s of Asp, Glu, His, and Cys is 0.76 pH units, and the Pearson’s correlation coefficient for the pKa shifts with respect to model values is 0.80. We demonstrated that a finite-size correction or much enlarged simulation box size can remove a systematic error of the calculated pKa’s and improve agreement with experiment. Importantly, the simulations captured the relevant biology in several challenging cases, e.g., the titration order of the catalytic dyad Glu35/Asp52 in HEWL and the coupled residues Asp19/Asp21 in SNase, the large pKa upshift of the deeply buried catalytic Asp26 in thioredoxin, and the large pKa downshift of the deeply buried catalytic Cys283 in HMCK. We anticipate that PME-CpHMD offers proper pH control to improve the accuracies of MD simulations and enables mechanistic studies of proton-coupled dynamical processes that are ubiquitous in biology but remain poorly understood due to the lack of experimental tools and limitation of current MD simulations.
Regulation of Klebsiella pneumoniae mucoidy by the bacterial tyrosine kinase Wzc
Authors: Khadka Saroj , Ring Brooke , Krzeminski Lindsey R. , Hathaway Matthew , Walker Ryan S. , Mobley Harry L.T. , Mike Laura A. 
Published: June 2022

ABSTRACTKlebsiella pneumoniae is a frequent nosocomial pathogen associated with urinary tract infections (UTI), pneumonia, and septicemia. Two lineages of K. pneumoniae have emerged that challenge the treatment of these infections. One lineage includes hypervirulent strains, causing invasive community-acquired infections, and the other encompasses carbapenem-resistant isolates. Non-mucoid, carbapenem-resistant isolates are most frequently isolated from UTI. Therefore, we hypothesized that environmental conditions may drive K. pneumoniae adaptation to the urinary tract. We found that two rmp-positive, hypervirulent strains and two rmp-negative clinical UTI isolates all suppressed mucoidy when cultured in urine compared to rich LB medium without altering capsular polysaccharide (CPS) abundance. We then performed a transposon screen to identify genetic factors through which urine suppresses mucoidy. Due to variations within transposon hits, we performed whole genome sequencing on our hits and found 100% association between secondary mutations in Wzc and increased mucoidy. Wzc is an inner membrane tyrosine kinase that regulates CPS assembly. When Wzc mutations are encoded chromosomally we observed both increased mucoidy and increased cell-free extracellular polysaccharide (EPS). However, when Wzc mutations are expressed in trans we observed increased mucoidy without impacting CPS or cell-free EPS abundance. Functionally, one periplasmic mutation increased Wzc autophosphorylation, while four active site mutations reduced Wzc autophosphorylation. These four active site mutations are also sufficient to increase mucoidy in one of the rmp-negative clinical UTI isolates without affecting EPS abundance. Combined, these data implicate mutation-driven modulation of Wzc activity as a global, rmp-independent mechanism for increasing K. pneumoniae mucoidy, without altering EPS uronic acid content. Wzc activity may represent the lynchpin that coordinates both capsule biosynthesis and mucoidy, explaining why these two phenotypes have been historically intertwined.
Biosynthetic diversification of peptaibol mediates fungus-mycohost interactions
Authors: Fan Jie , Ren Jinwei , He Ruolin , Wei Peng-Lin , Li Yuanyuan , Li Wei , Chen Dawei , Druzhinina Irina S. , Li Zhiyuan , Yin Wen-Bing 
Published: June 2022

AbstractFungi have evolved a plethora of functionally diverse secondary metabolites (SMs) to enhance their adaptation to various environments. To understand how structurally diverse metabolites contribute to fungal adaptation, we elucidate fungus-mycohost specific interactions mediated by a family of polypeptides, i.e., peptaibols. We specified that peptaibol structural diversification was attributed to the nonspecific substrate recognition by the highly conserved peptaibol synthetases (PSs) in dead wood inhabiting mycoparasitic fungi from the genus Trichoderma. Exemplified by investigation of T. hypoxylon, we characterized a library of 19 amino acid residue peptaibols, named trichohypolins, containing 42 derivatives synthesized by a single PS enzyme (NPS1Th). Elimination of trichohypolin production by the deletion of nps1Th reduced the inhibitory activities of T. hypoxylon on at least 15 saprotrophic host fungi, indicating that peptaibols are essential for interactions of Trichoderma spp. with their mycohosts. Different antagonistic effects of five trichohypolin subfractions SF1–SF5 and two pure compounds trichohypolins A (1) and B (2) on saprotrophic host fungi revealed specific activities of peptaibol derivatives in mediating fungus-mycohost interaction. Our study provides insights into the role of metabolic diversity of biosynthetic pathways in interfungal interactions.
Microstructures of Ant Chemosensory Sensilla Support a Dual Function in Detecting Both Volatile and Contact-Mediated Cues
Authors: Gellert Hannah R. , Halley Daphné C. , Sieb Zackary J. , Smith Jody C. , Pask Gregory M. 
Published: June 2022

AbstractAnts and other eusocial insects emit and receive chemical signals to communicate important information within the colony. In ants, nestmate recognition, task allocation, and reproductive distribution of labor are largely mediated through the detection of cuticular hydrocarbons (CHCs) that cover the exoskeleton. With their large size and limited volatility, these CHCs are believed to be primarily detected through direct contact with the antennae during behavioral interactions. Here we use scanning electron microscopy to investigate the unique morphological features of CHC-sensitive basiconic sensilla of two ant species, the black carpenter ant Camponotus pennsylvanicus and the Indian jumping ant Harpegnathos saltator. These basiconic sensilla possess an abundance of small pores typical of most insect olfactory sensilla, but also have a large concave depression at the terminal end. Basiconic sensilla are enriched at the distal segments of the antennae in both species, further supporting their proposed role in contact chemosensation. A survey of these sensilla across other ant subfamilies shows varied microstructures at their tips, but each possess surface textures that would also increase sensory surface area. These unique ant chemosensory sensilla represent yet another example of how specialized structures have evolved to serve the functional requirements of eusocial communication.
Exploring the culturable bacterial diversity and its hydrocarbon degrading potentiality isolated from the Oxygen Minimum Zone Sediments of Bay of Bengal
Authors: Prasannakumar ChinnamaniKumar 
Published: June 2022

AbstractUnderstanding biota distribution in oxygen minimum zone can help guide further exploration of potentially unusual habitats. The present study explores the culturable bacterial fractions in the oxygen minimum zone sediments of Bay of Bengal. The 16S rRNA gene sequences of 30 morphologically distinct bacterial colonies isolated form oxygen minimum zone of Bay of Bengal reveals 25 phylo-types, predominated by Proteobacteria (83.3%) and Actinobacteria (16.6%). Over all, Alphaproteobacteria and Gammaproteobacteria dominated the culturable fraction in this study. The overall pair-wise distances of bacterial isolates of Bay of Bengal is two times lesser when compared to overall pair-wise distance of bacterial isolates from oxygen minimum zone of Arabian Sea indicating relatively low genetic distances in Bay of Bengal. Not even 1% of bacterial cells in oxygen minimum zone of Bay of Bengal are culturable. We found that oxygen concentration alone could not be a deciding factor of culturable bacterial diversity in oxygen minimum zone. More than 50% bacterial isolates of present study is an active degraders of hydrocarbons. Higher similarity of 16S rRNA sequences produced in this study with that of previously reported efficient hydrobonoclastic bacterial isolates like Vibrio diazotrophicus, Vibrio cyclotrophicus, Pseudomonas poae, Marinobacter hydrocarbonoclasticus, Marinobacter flavimaris and Alcanivorax borkumensis further strengthens the evidence of hydrocarbon presence in Bay of Bengal sediments. This study is first of its time addresses the diversity of culturable bacterial fractions in oxygen minimum zone sediments of Bay of Bengal. Higher number of bacterial isolates from oxygen minimum zone of Bay of Bengal has carbonoclastic potentialities implying that they may play an important role in in situ hydrocarbon degradation in oxygen minimum zone of Bay of Bengal.
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties
Authors: Ragaller Franziska , Andronico Luca , Sykora Jan , Kulig Waldemar , Rog Tomasz , Urem Yagmur Balim , Amaro Mariana , Abhinav  , Danylchuk Dmytro I. , Klymchenko Andrey , Hof Martin , Vattulainen Ilpo , Sezgin Erdinc 
Published: June 2022

AbstractThe plasma membrane serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades several environment-sensitive probes have been popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we studied the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration, phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
CryoEM Structures of the Nitrogenase Complex During Catalytic Turnover
Authors: Rutledge Hannah L. , Cook Brian D. , Nguyen Hoang P. M. , Herzik Mark A. , Tezcan Akif 
Published: June 2022

AbstractThe enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multi-electron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here we report the cryogenic electron microscopic interrogation of the nitrogenase complex under enzymatic turnover conditions, which has enabled the structural characterization of the nitrogenase reaction intermediates at high resolution for the first time. Our structures show that asymmetry governs all aspects of nitrogenase mechanism including ATP hydrolysis, protein-protein interactions, and catalysis. Furthermore, they reveal several previously unobserved, mechanistically relevant conformational changes near the catalytic iron-molybdenum cofactor that are correlated with the nucleotide-hydrolysis state of the enzyme.One-sentence summaryHigh-resolution cryoEM structures of the nitrogenase complex obtained under turnover provide new mechanistic insights.
Human adenylyl cyclase 9 is auto-stimulated by its isoform-specific C-terminal domain and equipped with paradigm-switching mechanisms
Authors: Chen Zhihao , Antoni Ferenc A. 
Published: June 2022

AbstractHuman transmembrane adenylyl cyclase 9 (AC9) is not regulated by heterotrimeric G proteins. Key to the resistance to stimulation by Gs-coupled receptors (GsR) is auto-inhibition by the COOH-terminal domain (C2b). The present study investigated the role of the C2b domain in the regulation of cyclic AMP production by AC9 in HEK293FT cells expressing the Glosensor22F cyclic AMP-reporter protein. Surprisingly, we found C2b to be essential for sustaining the basal output of cyclic AMP by AC9. A human mutation (E326D) in the parallel coiled-coil formed by the signalling helices of AC9 dramatically increased basal activity, which was also dependent on the C2b domain. Intriguingly, the same mutation enabled stimulation of AC9 by GsRs. In summary, auto-regulation by the C2b domain of AC9 sustains its basal activity and quenches activation by GsR. Thus AC9 appears to be tailored to support constitutive activation of cyclic AMP effector systems. A switch from this paradigm to stimulation by GsRs may be occasioned by conformation changes at the coiled-coil or removal of the C2b domain.
Comprehensive functional annotation of metagenomes and microbial genomes using a deep learning-based method
Authors: Maranga Mary , Szczerbiak Pawel , Bezshapkin Valentyn , Gligorijevic Vladimir , Chandler Chris , Bonneau Richard , Xavier Ramnik J , Kosciolek Tomasz , Vatanen Tommi 
Published: June 2022

AbstractComprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. Still, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling and deep learning-based functional annotations from DeepFRI. We validate DeepFRI functional annotations by comparing them to orthology-based annotations from eggNOG on a set of 1,070 infant metagenome samples from the DIABIMMUNE cohort. Using the workflow, we have generated a sequence catalogue of 1.9 million non-redundant microbial genes. The functional annotations revealed 70% concordance between GO annotations predicted by DeepFRI and eggNOG. However, DeepFRI improved the annotation coverage, with 99% of the gene catalogue obtaining GO molecular function annotations, albeit less specific compared to eggNOG. Additionally, we construct pan-genomes in a reference-free manner using high-quality metagenome assembled genomes (MAGs) and analyse the associated annotations. eggNOG annotated more genes on well-studied organisms such as Escherichia coli while DeepFRI was less sensitive to taxa. This workflow will contribute to novel understanding of the functional signature of the human gut microbiome in health and disease as well as guide future metagenomics studies.
Characterization of the continuous transcriptional heterogeneity in Wilms’ tumors using unsupervised machine learning
Authors: Trink Yaron , Urbach Achia , Dekel Benjamin , Hohenstein Peter , Goldberger Jacob , Kalisky Tomer 
Published: June 2022

ABSTRACTWilms’ tumors are pediatric malignancies that are thought to arise from faulty kidney development. To date, the course of treatment depends on manual histopathological classification which is difficult since the tumors differ between patients in a continuous manner. Here, we used three computational approaches to characterize the continuous heterogeneity of Wilms’ tumors. We first chose a published dataset of microarray gene expression measurements from high-risk blastemal-type Wilms’ tumors. Then, we used Pareto Task Inference to show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with “stromal”, “epithelial”, and “blastemal” characteristics, that resemble the un-induced mesenchyme, the Cap mesenchyme, and early epithelial structures of the fetal kidney. We confirmed this by fitting a generative probabilistic “grade of membership” model whereby each tumor is represented as a unique mixture of three hidden “topics” with blastemal, stromal, and epithelial characteristics. Finally, we used cellular deconvolution to show that each tumor is composed of a unique mixture of cell populations resembling the un-induced mesenchyme, the cap mesenchyme, and the early epithelial structures of the fetal kidney. We anticipate that these methodologies will pave the way for more quantitative strategies for tumor stratification and classification.