bluuebunny/crossref_metadata_2025_split huggingface dataset:
FRET-based sensor for measuring adenine nucleotide binding to AMPK
Authors: Nahed Roland Abi , Pelosse Martin , Aulicino Francesco , Cottaz Florine , Berger Imre , Schlattner Uwe 
Published: September 2023

AbstractAMP-activated protein kinase (AMPK) has evolved to detect a critical increase in cellular AMP/ATP and ADP/ATP concentration ratios as a signal for limiting energy supply. Such energy stress then leads to AMPK activation and downstream events that maintain cellular energy homeostasis. AMPK activation by AMP, ADP or pharmacological activators involves a conformational switch within the AMPK heterotrimeric complex. We have engineered an AMPK-based sensor, AMPfret, which translates the activating conformational switch into a fluorescence signal, based on increased fluorescence resonance energy transfer (FRET) between donor and acceptor fluorophores. Here we describe how this sensor can be used to analyze direct AMPK activation by small moleculesin vitrousing a fluorimeter, or to estimate changes in the energy state of cells using standard fluorescence or confocal microscopy.
SPAG7 deletion causes intrauterine growth restriction, resulting in adulthood obesity and metabolic dysfunction
Authors: Flaherty Stephen E , Bezy Olivier , Paulhus Brianna LaCarubba , Song LouJin , Piper Mary , Pang Jincheng , Park Yoson , Asano Shoh , Lien Yu-Chin , Griffin John D , Robertson Andrew , Opsahl Alan , Hirenallur-Shanthappa Dinesh , Ahn Youngwook , Pashos Evanthia , Simmons Rebecca A , Birnbaum Morris J , Wu Zhidan 
Published: September 2023

SUMMARYFrom a forward mutagenetic screen to discover mutations associated with obesity, we identified mutations in thespag7gene linked to metabolic dysfunction in mice. Here we show that SPAG7 KO mice are born smaller and develop obesity and glucose intolerance in adulthood. This obesity does not stem from hyperphagia, but a decrease in energy expenditure. The KO animals also display reduced exercise tolerance and muscle function due to impaired mitochondrial function. Furthermore, SPAG7-deficiency in developing embryos leads to intrauterine growth restriction, brought on by placental insufficiency, likely due to abnormal development of the placental junctional zone. This insufficiency leads to loss of SPAG7-deficient fetuses in utero and reduced birth weights of those that survive. We hypothesize that a “thrifty phenotype” is ingrained in SPAG7 KO animals during development that leads to adult obesity. Collectively, these results indicate that SPAG7 is essential for embryonic development and energy homeostasis later in life.
Enriched Single-Nucleus RNA-Sequencing reveals unique attributes of distal convoluted tubule cells
Authors: Su Xiao-Tong , Reyes Jeremiah V. , Lackey Anne E. , Maeoka Yujiro , Cornelius Ryan J. , McCormick James A. , Yang Chao-Ling , Jung Hyun Jun , Welling Paul A. , Nelson Jonathan W. , Ellison David H. 
Published: September 2023

AbstractBackgroundThe distal convoluted tubule (DCT) comprises two subsegments, DCT1 and DCT2, with different functional and molecular characteristics. The functional and molecular distinction between these segments, however, has been controversial.MethodsTo understand the heterogeneity within the DCT population with better clarity, we enriched for DCT nuclei by using a mouse line combining “Isolation of Nuclei TAgged in specific Cell Types” and NCC (sodium chloride cotransporter)-driven inducible Cre recombinase. We sorted the fluorescently labeled DCT nuclei using Fluorescence-Activated Nucleus Sorting, and performed single nucleus transcriptomics.ResultsAmong 25,183 DCT cells, 70% were from DCT1 and 30% from DCT2. Additionally, there was a small population (<1%) enriched in proliferation-related genes, such asTop2a, Cenpp, and Mki67.Both DCT1 and DCT2 express NCC, magnesium transport genes are more abundant along DCT1; whereas calcium, electrogenic sodium and potassium transport genes are more abundant along DCT2. The transition between these two segments are gradual with a transitional zone where DCT1 and DCT2 cells are interspersed. The expression of the homeobox genes is not consistent between all DCT cells, suggesting that they develop along different trajectories.ConclusionTranscriptomics analysis of an enriched rare cell population using genetically targeted approach offers better clarification of the function and classification. The DCT segment is short, yet, can be separated into two sub-types that serve distinct functions, and are speculated to derive from different origins during development.Significance StatementHigh-resolution snRNAseq data indicate a clear separation between primary sites of calcium and magnesium handling within DCT. Both DCT1 and DCT2 expressSlc12a3, but these subsegments serve distinctive functions, with more abundant magnesium handling genes along DCT1 and more calcium handling genes along DCT2. The data also provides insight into the plasticity of the distal nephron-collecting duct junction, formed from cells of separate embryonic origins. By focusing/changing gradients of gene expression, the DCT can morph into different physiological cell states on demand.
Transcranial magnetic stimulation of primary motor cortex elicits a site-specific immediate transcranial evoked potential
Authors: Beck Mikkel Malling , Christiansen Lasse , Madsen Mads Alexander Just , Jadidi Armita Faghani , Vinding Mikkel Christoffer , Thielscher Axel , Bergmann Til Ole , Siebner Hartwig Roman , Tomasevic Leo 
Published: September 2023

AbstractBackgroundTranscranial evoked potentials (TEPs) measured via electroencephalography (EEG) are widely used to study the cortical responses to transcranial magnetic stimulation (TMS). Immediate transcranial evoked potentials (i-TEPs) have been obscured by pulse and muscular artifacts. Thus, the TEP peaks that are commonly reported have latencies that are too long to be caused by direct excitation of cortical neurons.MethodsIn 14 healthy individuals, we recorded i-TEPs evoked by a single biphasic TMS pulse targeting the primary motor hand area (M1HAND) or parietal or midline control sites. Sampling EEG at 50 kHz enabled us to reduce the duration of the TMS pulse artifact to a few milliseconds, while minor adjustments of the TMS coil tilt or position enabled us to avoid cranial muscular twitches during the experiment.ResultsWe observed an early positive EEG deflection starting after approx. 2 ms combined with a series of peaks with an inter-peak interval of ∼1.1-1.4 ms in electrodes overlying the stimulated sensorimotor region. This multi-peak i-TEP response was only evoked by TMS of the M1HANDregion and was modified by changes in stimulation intensity and current direction.DiscussionSingle-pulse TMS of the M1HANDevokes an immediate local multi-peak response at the cortical site of stimulation. Our results suggest that the observed i-TEP patterns are genuine cortical responses evoked by TMS caused by synchronized excitation of pyramidal neurons in the targeted precentral cortex. This notion needs to be corroborated in future studies, including further investigations into the potential contribution of instrumental or physiological artifacts.
Structural mechanisms for VMAT2 inhibition by tetrabenazine
Authors: Dalton Michael P. , Cheng Mary Hongying , Bahar Ivet , Coleman Jonathan A. 
Published: September 2023

ABSTRACTThe vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson’s disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2’s importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here we report a 3.1 Å resolution cryo-EM structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington’s chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
Placebo treatment entails resource-dependent downregulation of negative inputs
Authors: Rauh Jonas , Mostauli Arasch , Gamer Matthias , Büchel Christian , Rief Winfried , Brassen Stefanie 
Published: September 2023

AbstractBackgroundClinical trials of antidepressants show improvements in placebo groups of up to 80% compared to the real treatment arm. The mechanism underlying this clinically important effect has been linked to expectation induced goal-directed control. Here, we investigated how cognitive resources influence the effects of positive expectations on emotional processing.MethodsForty-nine healthy volunteers participated in a cross-over fMRI study, in which expectancy of positive emotional changes was induced by an alleged oxytocin nasal spray combined with verbal instruction. Participants performed a spatial cueing paradigm that manipulated the attention to emotional face distractors in the scanner and were characterized regarding their general ability to control attention.ResultsBehavioral findings showed placebo treatment to improve mood and to reduce distractibility by fearful over happy faces, specifically when more attentional resources were available to process faces. This aligned with neural changes in activation and functional coupling in lateral prefrontal-limbic networks indicating an expectation induced top-down regulation of aversive inputs. In addition, behavioral effects and prefrontal-parietal engagement directly correlated with trait ability to control attention.ConclusionsOur data show that placebo treatment combined with verbal instruction alone can improve mood and recruit top-down attentional selection. Changes in emotional processing critically depended on attentional context and individual control ability (i.e., contextual and general resources). These findings may be particularly relevant in patients with major depressive disorder, who often demonstrate a negativity bias and in whom placebo effects by verbal instructions alone may be limited due to reduced cognitive control capacity.
CREBBP lysine acetyltransferase domain mutations create zombie enzymes that alter chromatin loading dynamics and prevent EP300 redundancy
Authors: Yang Haopeng , Zhang Wenchao , Ravanmehr Vida , Mechaly Ariel , Regad Leslie , Haouz Ahmed , Chen Ruidong , Henderson Jared M. , Rojas Estela , Wilson Ashley , Parsons Sydney , Nastoupil Loretta , Davis R. Eric , Deng Qing , Samaniego Felipe , Rodrigues-Lima Fernando , Green Michael R. 
Published: September 2023

ABSTRACTEpigenetic regulation of gene expression is fundamental to cell state transitions. A prominent example of this is the epigenetically-regulated generation of transitory cells states within the germinal center (GC) reaction that are required for humoral immunity. The deregulation of these processes through somatic mutations can give rise to B-cell lymphoma, thus studying these mutations can provide insight into fundamental mechanisms underlying epigenetic regulation of gene expression as well as GC B-cell and lymphoma biology. Here we show that classes of mutations in theCREBBPlysine acetyltransferase gene result in different structure, catalytic activity and function. We discover that CREBBP and its paralog EP300 are dynamically and reciprocally loaded onto chromatin during a signal-responsive cell state transitions within the GC. Mutation ofCREBBPin GC-derived lymphoma interrupt signal-responsive CREBBP loading onto chromatin, while also inhibiting EP300 redundancy. These observations lead to a model in which CREBBP or EP300 loss of function through acetyltransferase domain mutations, which occur frequently in both hematopoietic and solid tumors, create a zombie enzyme that retards the function of the active paralog by binding limiting concentrations of transcription factor substrate and preventing signal-responsive enhancer activation.
CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making
Authors: Clapp Matthew , Bahuguna Jyotika , Giossi Cristina , Rubin Jonathan E. , Verstynen Timothy , Vich Catalina 
Published: September 2023

AbstractHere we introduce CBGTPy, a virtual environment for designing and testing goal-directed agents with internal dynamics that are modeled on the cortico-basal-ganglia-thalamic (CBGT) pathways in the mammalian brain. CBGTPy enables researchers to investigate the internal dynamics of the CBGT system during a variety of tasks, allowing for the formation of testable predictions about animal behavior and neural activity. The framework has been designed around the principle of flexibility, such that many experimental parameters in a decision making paradigm can be easily defined and modified. Here we demonstrate the capabilities of CBGTPy across a range of single and multi-choice tasks, highlighting the ease of set up and the biologically realistic behavior that it produces. We show that CBGTPy is extensible enough to apply to a range of experimental protocols and to allow for the implementation of model extensions with minimal developmental effort.Author summaryWe introduce a toolbox for producing biologically realistic simulations of the cortico-basal ganglia-thalamic dynamics during a variety of experimental tasks. The purpose is to foster the theory-experiment cycle, offering a tool for generating testable predictions of behavioral and neural responses that can be validated experimentally, in a framework that allows for simple updating as new experimental evidence emerges. We outline how our toolbox works and demonstrate its performance on a set of normative cognitive tasks.
The potential of plasma HLA peptides beyond neoepitopes
Authors: Wahle Maria , Thielert Marvin , Zwiebel Maximilian , Skowronek Patricia , Zeng Wen-Feng , Mann Matthias 
Published: September 2023

ABSTRACTDistinction of non-self from self is the major task of the immune system. Immunopeptidomics studies the peptide repertoire presented by the human leukocyte antigen (HLA) protein, usually on tissues. However, HLA peptides are also bound to plasma soluble HLA (sHLA), but little is known about their origin and potential for biomarker discovery in this readily available biofluid. Currently, immunopeptidomics is hampered by complex workflows and limited sensitivity, generally requiring several mL of plasma for the detection of hundreds of HLA peptides. Here, we take advantage of recent improvements in the throughput and sensitivity of mass spectrometry (MS)-based proteomics to develop a highly-sensitive, automated and economical workflow for HLA peptide analysis, termed Immunopeptidomics by Biotinylated Antibodies and Streptavidin (IMBAS). IMBAS-MS quantifies more than 5,000 HLA class I peptides from only 200 μL of plasma, in just 30 minutes. Our technology revealed that the plasma immunopeptidome of healthy donors is remarkably stable throughout a year and strongly correlated between individuals with overlapping HLA types. Immunopeptides originating from diverse tissues, including the brain, are proportionately represented. We conclude that sHLAs are a promising avenue for immunology and precision oncology.
High-confidence 3D template matching for cryo-electron tomography
Authors: Cruz-León Sergio , Majtner Tomáš , Hoffmann Patrick C. , Kreysing Jan Philipp , Tuijtel Maarten W , Schaefer Stefan L , Geißler Katharina , Beck Martin , Turoňová Beata , Hummer Gerhard 
Published: September 2023

AbstractCryo-electron tomography (CryoET) resolves individual macromolecules inside living cells. However, the complex composition and high density of cells challenge the faithful identification of features in tomograms. Here, we capitalize on recent advances in electron tomography and demonstrate that 3D template matching (TM) localizes a wide range of structures inside crowded eukaryotic cells with confidence 10 to 100-fold above the noise level. We establish a TM pipeline with systematically tuned parameters for automated, objective and comprehensive feature identification. High-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, lipid membranes and microtubules, and individual subunits, demonstrate that TM is generic. We resolve ∼100-kDa proteins, connect the functional states of complexes to their cellular localization, and capture vaults carrying ribosomal cargoin situ. By capturing individual molecular events inside living cells with defined statistical confidence, high-confidence TM greatly speeds up the CryoET workflow and sets the stage for visual proteomics.
International and regional spread of carbapenem-resistantKlebsiella pneumoniaein Europe
Authors: Silva Mabel Budia , Kostyanev Tomislav , Montaño Stefany Ayala , Ferrer-Acosta Jose Bravo , Garcia-Castillo Maria , Cantón Rafael , Goossens Herman , Rodriguez-Baño Jesus , Grundmann Hajo , Reuter Sandra 
Published: September 2023

AbstractKlebsiella pneumoniae,an opportunistic pathogen able to cause hospital- and community-acquired infections, is of particular concern due to the active spread of antibiotic resistance genes associated with mobile genetic elements such as plasmids and transposons. Carbapenem-resistantK. pneumoniae(CRKP) exhibit a higher mortality rate than carbapenem-susceptibleK. pneumoniaeinfections. In this COMBACTE-EURECA study, we present genomic data of 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018) and compared these with the previous EuSCAPE collection (2013-2014). All isolates were resistant (EUCAST criteria) to at least one carbapenem antibiotic. We identified 11 clonal complexes (CCs), with most isolates belonging to the high-risk clones CC258, CC101, CC11, and CC307.blaKPC-likewas the most prevalent carbapenemase-encoding gene (45%), along with the dominance of the CC258 lineage. Equally,blaOXA-48had a wide-ranging spread (39%), andblaNDMwas present in half of the ST11 isolates representing a particular lineage circulating in Greece. Two carbapenemase genes were found in 38 isolates (5.5%). Through the combination of both EURECA and EuSCAPE collections, we elucidated the evolution ofK. pneumoniaehigh-risk clones circulating in Europe. Dominating clones and their associated carbapenemase genes exhibit relevant regional differences, namely CC258 in Greece, Italy, and Spain, CC101 present in Serbia and Romania and CC14 in Türkiye. Due to the wide expansion of CRKP, genomic surveillance across Europe with projects such as EURECA provides crucial insights for risk mapping at geo-temporal scales and informs necessary adaptions to the local settings for implementation of control strategies.
Astrocytes modulate neuronal development by S100A6 signaling
Authors: Cinquina Valentina , Calvigioni Daniela , Piscitelli Fabiana , Keimpema Erik , Marzo Vincenzo Di , Verkhratsky Alexei , Harkany Tibor 
Published: September 2023

AbstractNeuronal morphogenesis relies on intercellular signaling. Astrocytes release metabolites, trophic, and guidance factors to promote neuronal differentiation. In contrast, the mechanisms by which astrocytes could limit and stabilize neuronal connectivity remain less explored. Here, we show cortical astrocytes to express and release S100A6, a Ca2+-binding protein (‘calcyclin’). Simultaneously, the majority of cortical neurons express abona fidebinding partner for S100A6, calcyclin-binding protein (CaCyBp). In neurons, CaCyBp maintains unfolded protein response, thereby controlling proteostasis. When released, S100A6 inhibits CaCyBp signaling, thus slowing protein turnover, and inhibiting neuritogenesis. S100A6-CaCyBp signaling during gestation and lactation is sensitive to the mother’s nutritional status, particularly eicosapentaenoic acid intake. Thus, a member of the S100 protein family acts as an astroglia-derived morphogen, whose action on neurons is modulated by environmental factors.
Distinct basal ganglia contributions to learning from implicit and explicit value signals in perceptual decision-making
Authors: Balsdon Tarryn , Pisauro M. Andrea , Philiastides Marios G. 
Published: September 2023

AbstractMetacognitive evaluations of confidence provide an estimate of decision accuracy that could guide learning in the absence of explicit feedback. We examine how humans might learn from this implicit feedback in direct comparison with that of explicit feedback, using simultaneous EEG-fMRI. Participants performed a motion direction discrimination task where stimulus difficulty was increased to maintain performance, with intermixed explicit- and no-feedback trials. We isolate single-trial estimates of post-decision confidence using EEG decoding, and find these neural signatures re-emerge at the time of feedback together with separable signatures of explicit feedback. We identified these signatures of implicit versus explicit feedback along a dorsal-ventral gradient in the striatum, a finding uniquely enabled by an EEG-fMRI fusion. These two signals are then integrated into an aggregate representation in the external globus pallidus, which broadcasts updates to improve cortical decision processing via the thalamus and insular cortex, irrespective of the source of feedback.
Nighttime-specific gene expression changes in suprachiasmatic nucleus and habenula are associated with resiliency to chronic social stress
Authors: Narain Priyam , Petković Aleksa , Šušić Marko , Haniffa Salma , Drou Nizar , Arnoux Marc , Anwar Mariam , Chaudhury Dipesh 
Published: September 2023

AbstractThe molecular mechanisms that link stress and circadian rhythms still remain unclear. The habenula (Hb) is a key brain region involved in regulating diverse types of emotion-related behaviours while the suprachiasmatic nucleus (SCN) is the body’s central clock. To investigate the effects of chronic social stress on transcription patterns, we performed gene expression analysis in the Hb and SCN of stress naive and stress exposed mice. Our analysis revealed a large number of differentially expressed genes and enrichment of synaptic and cell signalling pathways between resilient and stress-naïve mice at ZT16 in both the Hb and SCN. This transcriptomic signature was nighttime-specific and observed only in stress-resilient mice. In contrast, there were relatively few differences between the stress-susceptible and stress-naïve groups across timepoints. Our results reinforce the functional link between diurnal gene expression patterns and differential responses to stress, thereby highlighting the importance of temporal expression patterns in homeostatic stress responses.