bluuebunny/crossref_metadata_2025_split huggingface dataset:
Choice anticipation as gated accumulation of sensory predictions
Authors: Caie Brandon , Endres Dominik , Khan Aarlenne Z. , Blohm Gunnar 
Published: December 2023

AbstractPredictions are combined with sensory information when making choices. Accumulator models have conceptualized predictions as trial-by-trial updates to a baseline evidence level. These models have been successful in explaining the influence of choice history across-trials, however they do not account for how sensory information is transformed into choice evidence within-trials. Here, we derive a gated accumulator that models the onset of evidence accumulation as a combination of delayed sensory information and a prediction of sensory timing. To test how the delays interact with across-trial predictions, we designed a free choice saccade task where participants directed eye movements to either of two targets that appeared with variable delays and asynchronies. Despite instructions not to anticipate, participants responded prior to target onset on some trials. We reasoned that anticipatory responses may reflect a trade-off between inhibiting and facilitating the onset of evidence accumulation via a gating mechanism as target appearance became more likely. Using a choice history analysis, we found that anticipatory responses were more likely following repeated choices, despite task randomization, suggesting that the balance between anticipatory and sensory responses was driven by a prediction of sensory timing. By fitting the gated accumulator model to the data, we found that variance in within-trial fluctuations in baseline evidence best explained the joint increase of anticipatory responses and faster sensory-guided responses with longer delays. Thus, we conclude that a prediction of sensory timing is involved in balancing the costs of anticipation with lowering the amount of accumulated evidence required to trigger saccadic choice, which could be explained by history-dependence in the baseline dynamics of a gated accumulator.New and NoteworthyEvidence accumulation models are used to study how recent history impacts the processes underlying how we make choices. Biophysical evidence suggests that the accumulation of evidence is gated, however classic accumulator models do not account for this, so little is known about how recent history may influence the gating process. In this work, computational modeling and experimental data from a free choice saccade task argue that predictions of the timing of sensory information are important in controlling how evidence accumulation is gated, and that signatures of these predictions can be detected even in randomized task environments where history effects may not be expected.
Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome
Authors: López-Alfonzo Erika M. , Saurabh Ayush , Zarafshan Sahar , Pressé Steve , Martin Andreas 
Published: December 2023

SummaryThe 26S proteasome is the major eukaryotic protease responsible for protein quality control, proteostasis, and the modulation of numerous vital processes through the degradation of regulatory proteins. Commitment to degradation occurs when conserved pore loops in the proteasomal heterohexameric ATPase motor engage the flexible initiation region of a polyubiquitinated protein substrate for subsequent mechanical unfolding and translocation into a proteolytic chamber. Here, we usedin vitrobiochemical and single-molecule FRET-based assays with mutant reconstituted 26S proteasomes from yeast to characterize how the pore-1 loops of individual ATPase subunits in the AAA+ motor contribute to the different steps of substrate degradation and affect the proteasome conformational dynamics. We found that the pore-1 loop of the Rpt6 ATPase subunit plays particularly important roles in substrate capture, engagement, and unfolding, while the pore-1 loop of the Rpt4 ATPase is critical for providing sufficient grip for substrate unraveling and maintaining a processing-competent state of the proteasome. Interestingly, these pore-1-loop contributions correlate with their positions in the spiral-staircase arrangements of ATPase subunits in the substrate-free and substrate-degrading proteasome, providing new insights into the mechanisms of substrate processing by the 26S proteasome and related hexameric ATPase motors.
Targeting HLA-E Positive Cancers with a Novel NKG2A/C Switch Receptor
Authors: Sætersmoen Michelle , Kotchetkov Ivan S. , Torralba-Raga Lamberto , Mansilla-Soto Jorge , Sohlberg Ebba , Krokeide Silje Zandstra , Hammer Quirin , Sadelain Michel , Malmberg Karl-Johan 
Published: December 2023

AbstractHLA-E is overexpressed by approximately 80% of solid tumors, including malignant glioblastoma, and is emerging as a major checkpoint for NKG2A+CD8+T cells and NK cells in the tumor microenvironment and circulation. This axis operates side-by-side with PD-L1 to shut down effector responses by T and NK cells. Here, we engineered a novel chimeric A/C switch receptor, combining the strong HLA-E binding affinity of the NKG2A receptor ectodomain with the activating signaling of the NKG2C receptor endodomain. We found that A/C Switch-transduced NK and T cells displayed superior and specific cytotoxic function when challenged with tumor cells exhibiting medium to high HLA-E expression. Furthermore, A/C Switch-expressing human T cells demonstrated enhanced anti-tumor function in a xenograft model of glioblastoma. Importantly, the activity of the modified T cells was governed by an equilibrium between A/C Switch transduction level and HLA-E expression, creating a therapeutic window to safeguard against on-target off-tumor toxicities. Indeed, normal cells remained insensitive to A/C Switch engineered T cells even after pre-treatment with IFN-γ to induce HLA-E expression. We propose that this novel A/C switch receptor may operate alone to control tumor cells expressing high levels of HLA-E or in combination with other engineered specificities to overcome the suppressive NKG2A/HLA-E checkpoint.
Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Authors: Olmedillas Eduardo , Rajamanickam Roshan R. , Avalos Ruben Diaz , Sosa Fernanda A. , Zandonatti Michelle A. , Harkins Stephanie S. , Shresta Sujan , Hastie Kathryn M. , Saphire Erica Ollmann 
Published: December 2023

ABSTRACTThe 800 million human infections with SARS-CoV-2 and the likely emergence of new variants and additional coronaviruses necessitate a better understanding of the essential spike glycoprotein and the development of immunogens that foster broader and more durable immunity. The S2 fusion subunit is more conserved in sequence, is essential to function, and would be a desirable immunogen to boost broadly reactive antibodies. It is, however, unstable in structure and in its wild-type form, cannot be expressed alone without irreversible collapse into a six-helix bundle. In addition to the irreversible conformational changes of fusion, biophysical measurements indicate that spike also undergoes a reversible breathing action. However, spike in an open, “breathing” conformation has not yet been visualized at high resolution. Here we describe an S2-only antigen, engineered to remain in its relevant, pre-fusion viral surface conformation in the absence of S1. We also describe a panel of natural human antibodies specific for S2 from vaccinated and convalescent individuals. One of these mAbs, from a convalescent individual, afforded a high-resolution cryo-EM structure of the prefusion S2. The structure reveals a complex captured in an “open” conformation with greater stabilizing intermolecular interactions at the base and a repositioned fusion peptide. Together, this work provides an antigen for advancement of next-generation “booster” immunogens and illuminates the likely breathing adjustments of the coronavirus spike.
A Fluorogenic-Based Assay to Measure Chaperone-Mediated Autophagic Activity in Cells and Tissues
Authors: Jonnavithula Anila , Tandar Megan , Umar Mohammed , Orton Scott N. , Woodrum MacKenzie C , Mookherjee Sohom , Boudina Sihem , Symons J. David , Ghosh Rajeshwary 
Published: December 2023

ABSTRACTObjectivePathologies including cardiovascular diseases, cancer, and neurological disorders are caused by the accumulation of misfolded / damaged proteins. Intracellular protein degradation mechanisms play a critical role in the clearance of these disease-causing proteins. Chaperone mediated autophagy (CMA) is a protein degradation pathway that employs chaperones to bind proteins, bearing a unique KFERQ-like motif, for delivery to a CMA-specific Lysosome Associated Membrane Protein 2a (LAMP2a) receptor for lysosomal degradation. To date, steady-state CMA function has been assessed by measuring LAMP2A protein expression. However, this does not provide information regarding CMA degradation activity. To fill this dearth of tools / assays to measure CMA activity, we generated a CMA-specific fluorogenic substrate assay.MethodsA KFERQ-AMC [Lys-Phe-Asp-Arg-Gln-AMC(7-amino-4-methylcou-marin)] fluorogenic CMA substrate was synthesized from Solid-Phase Peptide Synthesis. KFERQ-AMC, when cleaved via lysosomal hydrolysis, causes AMC to release and fluoresce (Excitation:355 nm, Emission:460 nm). Using an inhibitor of lysosomal proteases, i.e., E64D [L-trans-Epoxy-succinyl-leucylamido(4-guanidino)butane)], responsible for cleaving CMA substrates, the actual CMA activity was determined. Essentially,CMA activity = (substrate)fluorescence- (substrate+E64D)fluorescence.To confirm specificity of the KFERQ sequence for CMA, negative control peptides were used.ResultsHeart, liver, and kidney lysates containing intact lysosomes were obtained from 4-month-old adult male mice. First, lysates incubated with KFERQ-AMC displayed a time dependent (0-5 hour) increase in AMC fluorescence vs. lysates incubated with negative control peptides. These data validate the specificity of KFERQ for CMA. Of note, liver exhibited the highest CMA (6-fold; p<0.05) > kidney (2.4-fold) > heart (0.4-fold) at 5-hours. Second, E64D prevented KFERQ-AMC degradation, substantiating that KFERQ-AMC is degraded via lysosomes. Third, cleavage of KFERQ-AMC and resulting AMC fluorescence was inhibited in Human embryonic kidney (HEK) cells and H9c2 cardiac cells transfected withLamp2avs. control siRNA. Further, enhancing CMA usingLamp2aadenovirus upregulated KFERQ degradation. These data suggest that LAMP2A is required for KFERQ degradation.Conclusion.We have generated a novel assay for measuring CMA activity in cells and tissues in a variety of experimental contexts.Abstract FigureGraphical AbstractProposed mechanism of KFERQ-AMC degradation via CMA
Inhibition ofO-GlcNAc transferase activates type I interferon-dependent antitumor immunity by bridging cGAS-STING pathway
Authors: Chen Jianwen , Zhao Bao , Dong Hong , Li Tianliang , Cheng Xiang , Gong Wang , Wang Jing , Zhang Junran , Xin Gang , Yu Yanbao , Lei Yu L. , Black Jennifer D. , Li Zihai , Wen Haitao 
Published: December 2023

AbstractTheO-GlcNAc transferase (OGT) is an essential enzyme that mediates proteinO-GlcNAcylation, a unique form of posttranslational modification of many nuclear and cytosolic proteins. Recent studies observed increased OGT andO-GlcNAcylation levels in a broad range of human cancer tissues compared to adjacent normal tissues, indicating a universal effect of OGT in promoting tumorigenesis. Here, we show that OGT is essential for tumor growth in immunocompetent hosts by repressing the cyclic GMP-AMP synthase (cGAS)-dependent DNA sensing pathway. We found that deletion of OGT (Ogt−/−) caused a marked reduction in tumor growth in both syngeneic tumor models and a genetic colorectal cancer (CRC) model induced by mutation of theApcgene (Apcmin). Pharmacological inhibition or genetic deletion of OGT induced a robust genomic instability (GIN), leading to cGAS-dependent production of the type I interferon (IFN-I) and IFN-stimulated genes (ISGs). As a result, deletion ofCgasorStingfromOgt−/−cancer cells restored tumor growth, and this correlated with impaired CD8+T cell-mediated antitumor immunity. Mechanistically, we found that OGT-dependent cleavage of host cell factor C1 (HCF-1) is required for the avoidance of GIN and IFN-I production in tumors. In summary, our results identify OGT-mediated genomic stability and activate cGAS-STING pathway as an important tumor cell-intrinsic mechanism to repress antitumor immunity.
Substrate recruitment via eIF2γ enhances catalytic efficiency of a holophosphatase that terminates the Integrated Stress Response
Authors: Yan Yahui , Shetty Maithili , Harding Heather P. , George Ginto , Zyryanova Alisa , Labbé Katherine , Mafi Amirhossein , Hao Qi , Sidrauski Carmela , Ron David 
Published: December 2023

AbstractDephosphorylation of pSer51 of the α subunit of translation initiation factor 2 (eIF2αP) terminates signalling in the integrated stress response (ISR). A trimeric mammalian holophosphatase comprised of a PP1 catalytic subunit, the conserved C-terminally located ∼70 amino acid core of a substrate-specific regulatory subunit (PPP1R15A/GADD34 or PPP1R15B/CReP) and G-actin (an essential co-factor) efficiently dephosphorylate eIF2αPin vitro. Unlike their viral or invertebrate counterparts, with whom they share the conserved 70 residue core, the mammalian PPP1R15s are large proteins of more than 600 residues. Genetic and cellular observations point to a functional role for regions outside the conserved core of mammalian PPP1R15A in dephosphorylating its natural substrate, the eIF2 trimer. We have combined deep learning technology, all-atom molecular dynamics simulations, X-Ray crystallography and biochemistry to uncover binding of the γ subunit of eIF2 to a short helical peptide repeated four times in the functionally-important N-terminus of human PPP1R15A that extends past its conserved core. Binding entails insertion of Phe and Trp residues that project from one face of an α-helix formed by the conserved repeats of PPP1R15A into a hydrophobic groove exposed on the surface of eIF2γ in the eIF2 trimer. Replacing these conserved Phe and Trp residues with Ala compromises PPP1R15A function in cells and in vitro. These findings suggest mechanisms by which contacts between a distant subunit of eIF2 and elements of PPP1R15A distant to the holophosphatase active site contribute to dephosphorylation of eIF2αPby the core PPP1R15 holophosphatase and to efficient termination of the ISR in mammals.
Plants perceive aerosols as an intensification of atmospheric dryness and react according to their isohydricity
Authors: Chi Chia-Ju Ellen , Grantz David A. , Burkhardt Juergen 
Published: December 2023

AbstractHygroscopic aerosols deposited to leaves are a local water vapor sink and can affect the water balance of plants by deliquescence and the formation of hydraulic films that penetrate into the stomata. Stomatal responses to aerosols and vapor pressure deficit(VPD) were investigated in two poplar clones grown hydroponically in ventilated greenhouses with and almost without ambient aerosols.With increasing VPD, transpiration increased in ANI, the more anisohydric clone, and decreased in ISO, the more isohydric clone, while aerosols had little effect. In ANI, stomatal conductance (gsw) and photosynthesis (A) decreased slightly with increasing VPD, but significantly with exposure to aerosols. Leaf carbon isotopes confirmed the long-term reduction in stomatal aperture by aerosols. In ISO, gswand A decreased strongly with increasing VPD. Aerosols had no effect on stomatal conductance in ISO, but increased the minimum leaf conductance and decreased the turgor loss point. In both clones, aerosols reduced stomatal density by >20%, indicating increased water scarcity.Aerosols enhance the transmission of atmospheric dryness to the leaf, with plant responses depending on their isohydricity. Sensitive stomatal closure of isohydric plants is an effective adaptation to atmospheric dryness, but aerosol accumulation mediates a liquid pathway for water loss that undermines stomatal control.
Improved bladder cancer antitumor efficacy with a recombinant BCG that releases a STING agonist
Authors: Um Peter K. , Praharaj Monali , Lombardo Kara A. , Yoshida Takahiro , Matoso Andres , Baras Alex S. , Zhao Liang , Srikrishna Geetha , Huang Joy , Prasad Pankaj , Kates Max , McConkey David , Pardoll Drew M. , Bishai William R. , Bivalacqua Trinity J. 
Published: December 2023

ABSTRACTDespite the introduction of several new agents for the treatment of bladder cancer (BC), intravesical BCG remains a first line agent for the management of non-muscle invasive bladder cancer. In this study we evaluated the antitumor efficacy in animal models of BC of a recombinant BCG known as BCG-disA-OE that releases the small molecule STING agonist c-di-AMP. We found that compared to wild-type BCG (BCG-WT), in both the orthotopic, carcinogen-induced rat MNU model and the heterotopic syngeneic mouse MB-49 model BCG-disA-OE afforded improved antitumor efficacy. A mouse safety evaluation further revealed that BCG-disA-OE proliferated to lesser degree than BCG-WT in BALB/c mice and displayed reduced lethality in SCID mice. To probe the mechanisms that may underlie these effects, we found that BCG-disA-OE was more potent than BCG-WT in eliciting IFN-β release by exposed macrophages, in reprogramming myeloid cell subsets towards an M1-like proinflammatory phenotypes, inducing epigenetic activation marks in proinflammatory cytokine promoters, and in shifting monocyte metabolomic profiles towards glycolysis. Many of the parameters elevated in cells exposed to BCG-disA-OE are associated with BCG-mediated trained innate immunity suggesting that STING agonist overexpression may enhance trained immunity. These results indicate that modifying BCG to release high levels of proinflammatory PAMP molecules such as the STING agonist c-di-AMP can enhance antitumor efficacy in bladder cancer.
Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies
Authors: Mmatli Masego , Mbelle Nontombi Marylucy , Fourie P. Bernard , Sekyere John Osei 
Published: December 2023

AbstractThe emergence of colistin and carbapenem-resistantKlebsiella pneumoniaeisolates presents a significant global health threat. This study investigates the resistance mechanisms in sixK. pneumoniaeand fourEnterobactersp. isolates lacking carbapenemases ormcrgenes using genomics and transcriptomics. The ten isolates were classified into three categories: non-carbapenemase-producing, carbapenem-resistant strains (n = 4), non-mcr–producing colistin-resistant strains (n = 5), and one isolate susceptible to both antibiotics.The analysis included phenotypic characterization using MicroScan ID/AST, enzyme (MCR and Metallo β-lactamase) and efflux pump inhibition (EPI) assays. Whole-genome sequencing, RNA sequencing, and bioinformatics tools were employed in subsequent analysis. Most of theK. pneumoniaewere ST307 with KL102 and O1/O2V2 serotypes. MicroScan revealed multidrug resistance, and AMR analysis identified numerous ARGs inK. pneumoniae.Enterobacterspecies possessed fewer resistance genes; nevertheless, they encoded virulence factors and gene mutations, potentially impacting the AST profile.K. pneumoniaeARGs were mainly plasmid-borne, with IncFIB(K)/IncFII(K) in Kp_15 harbouring up to nineteen ARGs. Virulence factors included biofilm formation, capsule production, and type IV secretion. Epigenomic investigations revealed prevalent type I (M1.Ecl34977I) and type II (M.Kpn34618Dcm) restriction modification sites. Compared to international isolates, the study isolates phylogenetically clustered more closely with Chinese strains. Transcriptomics showed high efflux pump activity in carbapenem-resistant isolates, confirmed by EPI. Further, mutations were identified in outer membrane proteins. Colistin-resistant isolates exhibited high capsule production, efflux pump, and putative glycotransferase activity, potentially influencing their phenotypes.In conclusion, genomic and transcriptional analyses enhanced our understanding of adaptive mechanisms in clinical multidrug-resistant pathogens, posing significant public health challenges.
Simulations reveal that beta burst detection may inappropriately characterize the beta band
Authors: Langford Zachary D , Wilson Charles R E 
Published: December 2023

ABSTRACTIn neurophysiological research, the traditional view of beta band activity as sustained oscillations is being reinterpreted as transient bursts. Bursts are characterized by a distinct wavelet shape, high amplitude, and, most importantly, brief temporal occurrence. The primary method for their detection relies on a threshold-based analysis of spectral power, and this presents two fundamental issues. First, the threshold selection is effectively arbitrary, being influenced by both local and global factors in the signal. Second, the method necessarily detects temporal events, as such it is susceptible to misidentifying sustained signals as transient bursts. To address these issues, this study systematically explores burst detection through simulations, shedding light on the method’s robustness across various scenarios. Although the method is effective in detecting transients in numerous cases, it can be overly sensitive, leading to spurious detections. Moreover, when applied to simulations featuring exclusively sustained events, the method frequently yields events exhibiting characteristics consistent with a transient burst interpretation. By simulating an average difference in power between experimental conditions, we illustrate how apparent burst rate differences between conditions can emerge even in the absence of actual burst rate disparities, and even in the absence of bursts. This capacity to produce misleading outcomes challenges the reinterpretation of sustained beta oscillations as transient bursts and prompts a critical reassessment of the existing literature.New and NoteworthyNeurophysiological research is experiencing a transformative shift in understanding beta band activity, moving away from the notion of sustained oscillations towards recognizing the significance of transient bursts. Here we show how the methods to detect such bursts are prone to spurious detections and can blur the distinction between sustained signals and transient bursts. Further, in realistic scenarios these methods can produce apparent behavioral associations where no such association exists.
Task dependent coarticulation of movement sequences
Authors: Kalidindi Hari Teja , Crevecoeur Frederic 
Published: December 2023

AbstractCombining individual actions into sequences is a hallmark of everyday activities. Classical theories propose that the motor system forms a single specification of the sequence as a whole, leading to coarticulation of the different elements. In contrast, recent neural recordings challenge this idea and suggest independent execution of each element specified separately. Here we show that separate or coarticulated sequences can result from the same task-dependent controller, without implying different representations in the brain. Simulations show that planning for multiple reaches simultaneously allows separate or coarticulated sequences depending on instructions about intermediate goals. Human experiments in a two-reach sequence task validated this model. Furthermore, in co-articulated sequences, the second goal influenced long-latency stretch responses to external loads applied during the first reach, demonstrating the involvement of the sensorimotor network supporting fast feedback control. Overall, our study establishes a computational framework for sequence production that highlights the importance of feedback control in this essential motor skill.