bluuebunny/crossref_metadata_2025_split huggingface dataset:
Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome
Authors: Jager Shelley , Zeller Martin , Pashkova Anna , Schulte Douwe , Damoc Eugen , Reiding Karli R. , Makarov Alexander A. , Heck Albert J.R. 
Published: July 2024

AbstractRecently, a conceptually new mass analyzer was introduced by pairing a quadrupole Orbitrap mass spectrometer with an asymmetric track lossless (Astral™) analyzer. This system provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. This instrument allows a narrow-window data-independent (nDIA) strategy, improving sensitivity and reproducibility even when using very short LC gradients. Although this represents a new technical milestone in peptide-centric proteomics, this new system has not yet been evaluated for the analyses of very complex and clinically important proteomes, such as represented by the plasma glycoproteome. Here, we evaluated the Orbitrap Astral mass spectrometer for the analysis of the plasma glycoproteome, and pioneer a dedicated nDIA workflow, themed nGlycoDIA. With substantially adjusted parameters and varying collision energies, nGlycoDIA has clear benefits for plasma glycoproteomics. We tested our method both in glycopeptide enriched and crude plasma, leading to the identification of more than 3000 unique glycoPSMs from 181 glycoproteins, covering a dynamic range of 7 orders of magnitude in the enriched plasma sample in just 40 minutes. In addition, we detect for the first time several glycosylated cytokines that have a reported plasma concentration in the ng/L range. Furthermore, shortening the gradient to 10 min still allows the detection of almost 2500 unique glycoPSMs from enriched plasma, indicating that high-throughput indepth clinical plasma glycoproteomics may be within reach.
Harnessingin vivoSynthesis of Bioactive Multiarylmethanes inEscherichia colivia Oxygen-Mediated Free Radical Reaction Induced by Simple Phenols
Authors: Wang Donglou , He Jiangbo , Chen Yonghong , Liu Boran , Wu Zhuang , Pan Xuerong , Niu Xuemei 
Published: July 2024

ABSTRACTBackgroundXanthenes and multi-aryl carbon core containing compounds represent different types of complex and condensed architectures that have impressive wide range of pharmacological, industrial and synthetic applications. Moreover, indoles as building blocks were only found in naturally occurring metabolites with di-aryl carbon cores and in chemically synthesized tri-aryl carbon core containing compounds. Up to date, rare xanthenes with indole bearing multicaryl carbon core have been reported in natural or synthetic products. The underlying mechanism of fluores-cein-like arthrocolins with tetra-arylmethyl core were synthesized in an engineeredEscherichia colifed with toluquinol remained unclear.ResultsIn this study, the Keio collection of single gene knockout strains of 3901 mutants ofE. coliBW25113, together with 14 distinctE. colistrains, was applied to explore the origins of endoge-nous building blocks and the biogenesis for arthrocolin assemblage. Deficiency in bacterial res-piratory and aromatic compound degradation genesubiX,cydB,sucAandssuEinhibited the mu-tant growth fed with toluquinol. Metabolomics of the cultures of 3897 mutants revealed that only disruption oftnaAinvolving in transforming tryptophan to indole, resulted in absence of arthro-colins. Further media optimization, thermal cell killing and cell free analysis indicated that a non-enzyme reaction was involved in the arthrocolin biosynthesis inE. coli. Evaluation of redox potentials and free radicals suggested that an oxygen-mediated free radical reaction was respon-sible for arthrocolins formation inE. coli. Regulation of oxygen combined with distinct phenol derivatives as inducer, 31 arylmethyl core containing metabolites including 13 new and 8 biolog-ical active, were isolated and characterized. Among them, novel arthrocolins withp-hydroxylbenzene ring from tyrosine were achieved through large scale of aerobic fermentation and elucidated x-ray diffraction analysis. Moreover, most of the known compounds in this study were for the first time synthesized in a microbe instead of chemical synthesis. Through feeding the rat with toluquinol after colonizing the intestines of rat withE. coli, arthrocolins also ap-peared in the rat blood.ConclusionOur findings provide a mechanistic insight intoin vivosynthesis of complex and condensed ar-throcolins induced by simple phenols and exploits a quinol based method to generate endoge-nous aromatic building blocks, as well as a methylidene unit, for the bacteria-facilitated synthesis of multiarylmethanes.
Effect of curcumin and 5-bromoindole-3-carboxaldehyde on the inhibition of Quorum sensing-dependent virulence factors inPseudomonas aeruginosa
Authors: González Gabriel Martínez , Contreras Rodolfo García , Alvarado-Salazar Juan Andres , García Valdés Israel , Valdés Nilda García , Lugo Gutiérrez Denisse Alejandra , Bustamante Martínez Ingrid Lizeth , Tescucano Alonso Alonso Ruben , Ramirez-Villalva Alejandra , Almeida Villegas Jorge Angel 
Published: July 2024

AbstractPseudomonas aerugoinosais a bacterium that causes important nosocomial diseases with high mortality and is classified within the bacteria of the acronym ESKAPE. The virulence ofPsuedomonas aeruginosais mediated by Quorum sensing, a cellular communication system that allows it to modulate the expression of virulence factors such as elastase, protease, siderophores, biofilm, alginate among others, through the LasI / LasR, RhlI / RhlR and PQS systems. Quorum inhibition allows an antivirulence strategy, where it has been shown that molecules such as curmunin and carboxaldehydes have considerable activity for this purpose. In the present work, the ability to inhibit Quorum Sensing-dependent virulence factors inPseudomonas aeruginosawas evaluated using curcumin and 5- bromoindole-3-carboxaldehyde. The strains evaluated are Pa01, Pa14 and ATCC 27853 at concentrations (1 and 5 µg/ml) for curcumin and (30, 50 and 100 µg/ml) for 5-bromoindole-3-carboxaldehyde. 5-Bromoindole-3-carboxaldehyde significantly inhibited the production of pyocyanin in Pa01 (92.5% at 100 µg/ml), elastase in Pa01 (79.85% at 100 µg/ml), protease in Pa01 (92.8% at 50 µg/ml) and alginate in ATCC 27853 (76.16% at 100 µg/ml). Curcumin showed substantial inhibition of pyocyanin in ATCC 27853 (100% at 5 µg/ml), elastase in Pa14 (56.19% at 5 µg/ml), protease in Pa01 (87.04% at 5 µg/ml) and alginate in Pa01 (48.26% at 5 µg/ml). These findings suggest the potential of these compounds as antivirulence agents, to combatP. aeruginosainfections.
A trimeric USP11/USP7/TCEAL1 complex stabilizes RNAPII during early transcription to sustain oncogenic gene expression
Authors: Dehmer Markus , Gallant Peter , Herold Steffi , Cossa Giacomo , Conte Francesca , Koster Jan , Sauer Florian , Schülein-Völk Christina , Ade Carsten P. , Vidal Raphael , Kisker Caroline , Versteeg Rogier , Beli Petra , Vos Seychelle M. , Eilers Martin , Büchel Gabriele 
Published: July 2024

AbstractDuring early transcription, RNA polymerase II (RNAPII) undergoes a series of structural transitions controlled by cyclin-dependent kinases. Whether protein ubiquitylation and proteasomal degradation affect the fate of RNAPII close to promoters is less well understood. Here we show that the deubiquitylating enzyme USP11 and its heterodimeric partner USP7 form a trimeric complex with TCEAL1, a member of the poorly understood TCEAL (TCEA/TFIIS-like) protein family. TCEAL1 shares sequence homology with the RNAPII interaction domain of the TCEA/TFIIS elongation factor, which controls the fate of backtracked RNAPII. TCEAL1 stabilizes complexes of USP11 with USP7 and with RNAPII. TCEAL1 is recruited to core promoters when transcription elongation is blocked and globally enhances the chromatin association of RNAPII during early transcription. Mechanistically, the USP11/USP7/TCEAL1 complex competes with TFIIS for binding to core promoters and protects RPB8, an essential subunit of RNAPII, from degradation, likely preventing excessive TFIIS-mediated transcript cleavage and RNAPII disassembly. In neuroblastoma and other tumors, TCEAL1-dependent genes define a TGF beta-dependent gene expression program that is characteristic for mesenchymal and invasive tumor cell types, suggesting that the USP11/USP7/TCEAL1 trimer stabilizes RNAPII during early transcription to support a critical oncogenic gene expression program (190 words).
A bacterial TIR-based immune system senses viral capsids to initiate defense
Authors: Roberts Cameron G. , Fishman Chloe B. , Banh Dalton V. , Marraffini Luciano A. 
Published: July 2024

ABSTRACTToll/interleukin-1 receptor (TIR) domains are present in immune systems that protect prokaryotes from viral (phage) attack. In response to infection, TIRs can produce a cyclic adenosine diphosphate-ribose (ADPR) signaling molecule, which activates an effector that depletes the host of the essential metabolite NAD+ to limit phage propagation. How bacterial TIRs recognize phage infection is not known. Here we describe the sensing mechanism for the staphylococcal Thoeris defense system, which consists of two TIR domain sensors, ThsB1 and ThsB2, and the effector ThsA. We show that the major capsid protein of phage Φ80α forms a complex with ThsB1 and ThsB2, which is sufficient for the synthesis of 1’’-3’ glycocyclic ADPR (gcADPR) and subsequent activation of NAD+ cleavage by ThsA. Consistent with this, phages that escape Thoeris immunity harbor mutations in the capsid that prevent complex formation. We show that capsid proteins from staphylococcal Siphoviridae belonging to the capsid serogroup B, but not A, are recognized by ThsB1/B2, a result that suggests that capsid recognition by Sau-Thoeris and other anti-phage defense systems may be an important evolutionary force behind the structural diversity of prokaryotic viruses. More broadly, since mammalian toll-like receptors harboring TIR domains can also recognize viral structural components to produce an inflammatory response against infection, our findings reveal a conserved mechanism for the activation of innate antiviral defense pathways.
Subtypes and proliferation patterns of small intestine neuroendocrine tumors revealed by single cell RNA sequencing
Authors: Someach Einav , Halder Debdatta , Spitzer Avishay , Barbolin Chaya , Tyler Michael , Halperin Reut , Biton Moshe , Tirosh Amit , Tirosh Itay 
Published: July 2024

AbstractNeuroendocrine tumors (NETs) occur primarily in the small intestine, lung and pancreas. Due to their rarity compared to other malignancies in these organs, their complex biology remains poorly understood, including their oncogenesis, tumor composition and the intriguing phenomena of mixed neuroendocrine non-neuroendocrine neoplasms (MiNEN). Here we profiled ten low-grade small intestine NET (SiNET) tumor samples as well as one mixed lung tumor by single-cell or single-nuclei RNA-seq. We find that SiNETs are largely separated into two distinct subtypes, in which the neuroendocrine cells upregulate epithelial or neuronal markers, respectively. Surprisingly, in both subtypes the neuroendocrine cells are largely non-proliferative while higher proliferation is observed in multiple non-malignant cell types. Specifically, B and plasma cells are highly proliferative in the epithelial-like SiNET subtype, potentially reflecting the outcome of high Migration Inhibitory Factor (MIF) expression in those tumors, which may constitute a relevant target. Finally, our analysis of a mixed lung neuroendocrine tumor identifies a population of putative progenitor cells that may give rise to both neuroendocrine and non-neuroendocrine (squamous) cells, potentially explaining the origin of the mixed histology. Taken together, our results provide important insights and hypotheses regarding the biology of neuroendocrine neoplasms.
Calcium phosphate nanoclusters modify periodontium remodeling and minimize orthodontic relapse
Authors: Cuylear Darnell L. , Fu Moyu L. , Chau Justin C. , Kharbikar Bhushan , Kazakia Galateia J. , Jheon Andrew , Habelitz Stefan , Kapila Sunil D. , Desai Tejal A. 
Published: July 2024

AbstractOrthodontic relapse is one of the most prevalent concerns of orthodontic therapy. Relapse results in patients’ teeth reverting towards their pretreatment positions, which increases the susceptibility to functional problems, dental disease, and substantially increases the financial burden for retreatment. This phenomenon is thought to be induced by rapid remodeling of the periodontal ligament (PDL) in the early stages and poor bone quality in the later stages. Current therapies, including fixed or removable retainers and fiberotomies, have limitations with patient compliance and invasiveness. Approaches using biocompatible biomaterials, such as calcium phosphate polymer-induced liquid precursors (PILP), is an ideal translational approach for minimizing orthodontic relapse. Here, post-orthodontic relapse is reduced after a single injection of high concentration PILP (HC-PILP) nanoclusters by altering PDL remodeling in the early stage of relapse and improving trabecular bone quality in the later phase. HC-PILP nanoclusters are achieved by using high molecular weight poly aspartic acid (PASP, 14 kDa) and poly acrylic acid (PAA, 450 kDa), which resulted in a stable solution of high calcium and phosphate concentrations without premature precipitation.In vitroresults show that HC-PILP nanoclusters prevented collagen type-I mineralization, which is essential for the tooth-periodontal ligament (PDL)-bone interphase.In vivoexperiments show that the PILP nanoclusters minimize relapse and improve the trabecular bone quality in the late stages of relapse. Interestingly, PILP nanoclusters also altered the remodeling of the PDL collagen during the early stages of relapse. Furtherin vitroexperiments showed that PILP nanoclusters alter the fibrillogenesis of collagen type-I by impacting the protein secondary structure. These findings propose a novel approach for treating orthodontic relapse and provide additional insight into the PILP nanocluster’s structure and properties on collagenous structure repair.
Shifts in neural tuning systematically alter sensorimotor learning ability
Authors: Hayashi Takuji , Takiyama Ken , Smith Maurice A. , Nozaki Daichi 
Published: July 2024

AbstractSensorimotor learning can change the tuning of neurons in motor-related brain areas and rotate their preferred directions (PDs). These PD rotations are commonly interpreted as reflecting motor command changes; however, cortical neurons that display PD rotations also contribute to sensorimotor learning. Sensorimotor learning should, therefore, alter not only motor commands but also the tuning of neurons responsible for this learning, and thus impact subsequent learning ability. Here, we investigate this possibility with computational modeling and by directly measuring adaptive responses during sensorimotor learning in humans. Modeling shows that the PD rotations induced by sensorimotor learning, predict specific anisotropic changes in PD distributions that in turn predict a specific spatial pattern of changes in learning ability. Remarkably, experiments in humans then reveal large, systematic changes in learning ability in a spatial pattern that precisely reflects these model-predicted changes. We find that this pattern defies conventional wisdom and implements Newton’s method, a learning rule where the step size is inversely proportional rather than proportional to the learning gradient’s amplitude, limiting overshooting in the adaptive response. Our findings indicate that PD rotation provides a mechanism whereby the motor system can simultaneously learn how to move and learn how to learn.
Cell binding, uptake and infection of influenza A virus using recombinant antibody-based receptors
Authors: Adu Oluwafemi F. , Borau Milagros Sempere , Früh Simon , Karakus Umut , Weichert Wendy S. , Wasik Brian R. , Stertz Silke , Parrish Colin R. 
Published: July 2024

ABSTRACTHuman and avian influenza A viruses bind to sialic acid (Sia) receptors on cells as their primary receptors, and this results in endocytic uptake of the virus. While the role of Sia on glycoproteins and/or glycolipids for virus entry is crucial, the roles of the carrier proteins are still not well understood. Furthermore, it is still unclear how receptor binding leads to infection, including whether the receptor plays a structural or other roles beyond being a simple tether. To enable the investigation of the receptor binding and cell entry processes in a more controlled manner, we have designed a protein receptor for pandemic H1 influenza A viruses. The engineered receptor possesses the binding domains of an anti-HA antibody prepared as a single chain variable fragment (scFv) fused with the stalk, transmembrane and cytoplasmic sequences of the feline transferrin receptor type-1 (fTfR). When expressed in cells that lack efficient display of Sia due to a knockout of theSlc35A1gene which encodes for the Solute Carrier Family 35 transporter (SLC35A1), the anti-H1 receptor was displayed on the cell surface, bound virus or hemagglutinin proteins, and the virus was efficiently endocytosed into the cells. Infection occurred at similar levels to those seen after Sia reconstitution, and treatment with clathrin-mediated endocytosis (CME) inhibitors significantly reduced viral entry.IMPORTANCE.Influenza A viruses mostly circulate among avian reservoirs, and also can jump hosts to cause epidemics in mammals, including among humans. A key interaction of the viruses is with host cell Sia, which vary in chemical form, in their linkages within the oligosaccharide, and in the attachment to surface glycoproteins or glycolipids with different properties. Here we report a new method for examining the processes of receptor binding and uptake into cells during influenza A virus infection, by use of an engineered HA-binding membrane glycoprotein, where an antibody is used as the binding domain and the transferrin receptor uptake structures mediate efficient entry, which should allow us to test and manipulate the processes of cell binding, entry, and infection.
Ca2+-driven PDIA6 phase separation to ensure proinsulin quality control
Authors: Lee Young-Ho , Saio Tomohide , Watabe Mai , Matsusaki Motonori , Kanemura Shingo , Lin Yuxi , Mannen Taro , Kuramochi Tsubura , Iuchi Katsuya , Tajiri Michiko , Suzuki Kotono , Li Yan , Heo Yunseok , Kamada Yuka , Arai Kenta , Hashimoto Mayuko , Ninagawa Satoshi , Hattori Yoshikazu , Kumeta Hiroyuki , Takeuchi Airu , Abe Hiroya , Mori Eiichiro , Muraoka Takahiro , Okiyoneda Tsukasa , Akashi Satoko , Vendruscolo Michele , Inaba Kenji , Okumura Masaki 
Published: July 2024

AbstractThe endoplasmic reticulum (ER) plays key roles in protein quality control1,2and dynamic Ca2+storage3,4in eukaryotic cells. However, the protein homeostasis (proteostasis) system that regulates these ER functions is still incompletely characterised. Previous study revealed the importance of oligomerization in the function PDIA1, an ER-resident disulfide isomerase and molecular chaperone, regulates oligomeric states in accordance with client folding5. This result suggests that at least some of the 20 members of other PDI family may undergo regulated self-assembly in order to optimally function. Here, we show that Ca2+triggers the phase separation of PDIA6 into liquid-like condensates. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the Ca2+-driven condensation of PDIA6 recruits PDIA3 and proinsulin, thus increasing their local concentrations. This process results in the 30-fold enhancement of proinsulin folding and in the inhibition of proinsulin aggregation. Our findings shed light on a condensation-driven Ca2+-mediated proteostasis cascade in the ER by revealing how the efficiency of the protein folding process can be enhanced within quality control granules.
Cryo-EM structures of ρ1 GABAAreceptors with antagonist and agonist drugs
Authors: Fan Chen , Cowgill John , Howard Rebecca J. , Lindahl Erik 
Published: July 2024

AbstractThe family of ρ-type GABAAreceptors includes potential therapeutic targets in several neurological conditions, and features distinctive pharmacology compared to other subtypes. Here we combine structures, recordings and simulations to characterize the binding and conformational impact of the drugs THIP (a non-opioid analgesic), CGP36742 (phosphinic acid inhibitor) and GABOB (an anticonvulsant) on a human ρ1 GABAAreceptor. We identify a distinctive binding pose of THIP in ρ1 versus neuronal α4β3δ GABAAreceptors, offering a rationale for its inverse effects on these subtypes. CGP36742 binding is similar to the canonical ρ-type inhibitor TPMPA, supporting a shared mechanism of action among phosphinic acid inhibitors. Binding of GABOB is similar to that of GABA, but produces a mixture of primed and desensitized states, likely underlying its weaker agonist activity. Together, these results elucidate interactions of a ρ-type GABAAreceptor with therapeutic drugs, offering mechanistic insights and a prospective basis for further pharmaceutical development.
Disruption of CAD oligomerization by pathogenic variants
Authors: Del Caño-Ochoa Francisco , Ramadane-Morchadi Lobna , Eixerés Lluís , Moreno-Morcillo María , Fernández-Leiro Rafael , Ramón-Maiques Santiago 
Published: July 2024

ABSTRACTCAD is a multi-enzymatic protein essential for initiating the de novo biosynthesis of pyrimidine nucleotides, forming large hexamers whose structure and function are not fully understood. Defects in CAD result in a severe neurometabolic disorder that is challenging to diagnose. We developed a cellular functional assay to identify defective CAD variants, and in this study, we characterized five pathogenic missense mutations in CAD’s dihydroorotase (DHO) and aspartate transcarbamylase (ATC) domains. All mutations impaired enzymatic activities, with two notably disrupting the formation of DHO dimers and ATC trimers. Combining crystal structures and AlphaFold predictions, we modeled the hexameric CAD complex, highlighting the central role of the DHO and ATC domains in its assembly. Our findings provide insight into CAD’s stability, function, and organization, revealing that correct oligomerization of CAD into a supramolecular complex is required for its function in nucleotide synthesis and that mutations affecting this assembly are potentially pathogenic.