bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giant pyramidal neurons of the primary motor cortex express vasoactive intestinal polypeptide (VIP), a known marker of cortical interneurons
Authors: Teymornejad Sadaf , Worthy Katrina H. , Rosa Marcello G. P. , Atapour Nafiseh 
Published: January 2024

AbstractVasoactive intestinal polypeptide (VIP) is known to be present in a subclass of cortical interneurons that are involved in the disinhibition of excitatory pyramidal neurons. Here, using three different antibodies, we demonstrate that VIP is also present in the giant layer 5 pyramidal (Betz) neurons which are characteristic of the limb and axial representations of the marmoset primary motor cortex (cytoarchitectural area 4ab). No VIP staining was observed in smaller layer 5 pyramidal cells present in the primary motor facial representation (cytoarchitectural area 4c), or in premotor cortex (e.g. the caudal subdivision of the dorsal premotor cortex, A6DC), indicating the selective expression of VIP in Betz cells. The most intense VIP staining occurred in the largest Betz cells, located in the medial part of A4ab. VIP in Betz cells was colocalized with neuronal specific marker (NeuN) and a calcium-binding protein parvalbumin (PV). PV also intensely labelled axon terminals surrounding Betz cell somata. Whereas Betz cells bodies were located in layer 5, VIP-positive (VIP+) interneurons were more abundant in the superficial cortical layers. They constituted about 5-7% of total cortical neuronal population, with the highest density observed in area 4c. Our results demonstrate the expression of VIP in the largest excitatory neurons of the primate cortex, which may offer new functional insights into the role of VIP in the brain, and also provide opportunities for genetic manipulation of Betz cells.
Memory consolidation during rest forms shortcuts in a cognitive map
Authors: Shearer Cal M. , Rawson Annalise B. , Barron Helen C. , O’Reilly Jill X. 
Published: January 2024

AbstractRest and sleep not only strengthen existing memories but also reorganise memories to generate new knowledge that extends beyond direct experience. However, it remains unclear bothhowmemories are reorganised and the effect of this reorganisation on behaviour. Here, we designed a novel protocol to casually manipulate memory consolidation during rest using awake, contextual targeted memory reactivation (TMR). We found that promoting memory consolidation during rest qualitatively reorganises memories byforming ‘shortcuts’ between memorieswhich have not been experienced together. These shortcuts in memory extend beyond direct experience to facilitate our ability to make novel inferences. A series of control tests indicate that inference performance cannot be explained by quantitative strengthening of the experienced component links but are rather explained by qualitative changes in the cognitive map which involve formation of new shortcuts. Interestingly, we show that representing a shortcut may come with limitations, as shortcuts cannot be readily updated in response to rapid changes in the environment. Together, these findings reveal how memories are reorganised during awake rest to construct a cognitive map of our environment, while highlighting the constraints set by a trade-off between efficient and flexible behaviour.
Synaptic Signatures and Disease Vulnerabilities of Layer 5 Pyramidal Neurons
Authors: Marcassa Gabriele , Dascenco Dan , Lorente-Echeverría Blanca , Daaboul Danie , Vandensteen Jeroen , Leysen Elke , Baltussen Lucas , Howden Andrew J. M. , de Wit Joris 
Published: January 2024

AbstractCortical layer 5 (L5) intratelencephalic (IT) and pyramidal tract (PT) neurons are embedded in distinct information processing pathways. The morphology, connectivity, electrophysiological properties, and role in behavior of these neurons have been extensively analyzed. However, the molecular composition of their synapses remains largely uncharacterized. Here, we dissect the protein composition of the excitatory postsynaptic compartment of L5 neurons in intact somatosensory circuits, using an optimized proximity biotinylation workflow with subsynaptic resolution. We find distinct synaptic signatures of L5 IT and PT neurons that are defined by proteins regulating synaptic organization and transmission, including cell-surface proteins (CSPs), neurotransmitter receptors and ion channels. In addition, we find a differential vulnerability to disease, with a marked enrichment of autism risk genes in the synaptic signature of L5 IT neurons compared to PT neurons. Our results align with human studies and suggest that the excitatory postsynaptic compartment of L5 IT neurons is notably susceptible in autism. Together, our analysis sheds light on the proteins that regulate synaptic organization and function of L5 neuron types and contribute to their susceptibility in disease. Our approach is versatile and can be broadly applied to other neuron types to create a protein-based, synaptic atlas of cortical circuits.
Subcellular localization of truncated MAGEL2 proteins: insight into the molecular pathology of Schaaf-Yang syndrome
Authors: Centeno-Pla Mónica , Alcaide-Consuegra Estefanía , Gibson Sophie , Prat-Planas Aina , Gutiérrez-Ávila Juan Diego , Grinberg Daniel , Urreizti Roser , Rabionet Raquel , Balcells Susanna 
Published: January 2024

ABSTRACTSchaaf-Yang syndrome (SYS) is an ultra-rare neurodevelopmental disorder caused by truncating mutations inMAGEL2. Heterologous expression of wild-type (WT) or a truncated (p.Gln638*) C-terminal HA-tagged MAGEL2 revealed a shift from a primarily cytoplasmic to a more nuclear localization for the truncated protein variant. We now extend this analysis to six additional SYS mutations on a N-terminal FLAG-tagged MAGEL2. Our results replicate and extend our previous findings, showing that all the truncated MAGEL2 proteins consistently display a predominant nuclear localization, irrespective of the C-terminal or N-terminal position and the chemistry of the tag. The variants associated with arthrogryposis multiplex congenita (AMC) display a more pronounced nuclear retention phenotype, suggesting a correlation between clinical severity and the degree of nuclear mis-localization. These results point to a neomorphic effect of truncated MAGEL2, which might contribute to the pathogenesis of SYS.
Genomic diversity of novel strains of mammalian gut microbiome derivedClostridiumXIVa strains is driven by mobile genetic element acquisition
Authors: Kamat Maya T. , Ormsby Michael J. , Humphrey Suzanne , Dixit Shivendra , Thümmler Katja , Lapsley Craig , Crouch Kathryn , Jukes Caitlin , Hulme Heather , Burchmore Richard , Meikle Lynsey M. , Pritchard Leighton , Wall Daniel M. 
Published: January 2024

AbstractDespite advances in sequencing technologies that enable a greater understanding of mammalian gut microbiome composition, our ability to determine a role for individual strains is hampered by our inability to isolate, culture and study such microbes. Here we describe highly unusualClostridiumXIVa group strains isolated from the murine gut. Genome sequencing indicates that these strains,Clostridium symbiosumLM19B and LM19R andClostridium clostridioformeLM41 and LM42, have significantly larger genomes than most closely related strains. Genomic evidence indicates that the isolated LM41 and LM42 strains diverge from most otherClostridiumXIVa strains and supports reassignment of these groups at genus-level. We attribute increasedC. clostridioformeLM41 and LM42 genome size to acquisition of mobile genetic elements including dozens of prophages, integrative elements, putative group II introns and numerous transposons including 29 identical copies of the IS66 transposase, and a very large 192 Kb plasmid. antiSmash analysis determines a greater number of biosynthetic gene clusters within LM41 and LM42 than in related strains, encoding a diverse array of potential novel antimicrobial compounds. Together these strains highlight the potential untapped microbial diversity that remains to be discovered within the gut microbiome and indicate that, despite our ability to get a top down view of microbial diversity, we remain significantly blinded to microbe capabilities at the strain level.
Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29 and Fam21
Authors: Romano-Moreno Miguel , Astorga-Simón Elsa N , Rojas Adriana L , Hierro Aitor 
Published: January 2024

AbstractEndosomal trafficking ensures the proper distribution of lipids and proteins to various cellular compartments, facilitating intracellular communication, nutrient transport, waste disposal, and the maintenance of cell structure. Retromer, a peripheral membrane protein complex, plays an important role in this process by recruiting the associated actin- polymerizing WASH complex to establish distinct sorting domains. The WASH complex is recruited through the interaction of the VPS35 subunit of retromer with the WASH complex subunit FAM21. Here, we report the identification of two separate fragments of Fam21 that interact with VPS35, along with a third fragment that binds to the VPS29 subunit of retromer. The crystal structure of VPS29 bound to a peptide derived from Fam21 shows a distinctive sharp bend that inserts into a conserved hydrophobic pocket with a binding mode similar to that adopted by other VPS29 effectors. Interestingly, despite the network of interactions between Fam21 and retromer occurring near the Parkinson’s disease-linked mutation (D620N) in VPS35, this mutation does not significantly impair the direct association with Fam21in vitro.
TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD
Authors: Bryce-Smith Sam , Brown Anna-Leigh , Mehta Puja R. , Mattedi Francesca , Mikheenko Alla , Barattucci Simone , Zanovello Matteo , Dattilo Dario , Yome Matthew , Hill Sarah E. , Qi Yue A. , Wilkins Oscar G. , Sun Kai , Ryadnov Eugeni , Wan Yixuan ,   NYGC ALS Consortium, Vargas Jose Norberto S. , Birsa Nicol , Raj Towfique , Humphrey Jack , Keuss Matthew , Ward Michael , Secrier Maria , Fratta Pietro 
Published: January 2024

AbstractNuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3’ end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3’UTR extensions (3’Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3’Exts occur in multiple transcription factors, such asELK1,SIX3,andTLX1,and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
Maternal n-3 enriched diet reprograms neurovascular transcriptome and blunts inflammation in neonate
Authors: Chumak Tetyana , Jullienne Amandine , Joakim Ek C. , Ardalan Maryam , Svedin Pernilla , Quan Ryan , Salehi Arjang , Salari Sirus , Obenaus Andre , Vexler Zinaida S , Mallard Carina 
Published: January 2024

AbstractInfection during perinatal period can adversely affect brain development, predispose infants to ischemic stroke and have lifelong consequences. We previously demonstrated that diet enriched in n-3 polyunsaturated fatty acids (PUFA) transforms brain lipid composition and protects from neonatal stroke. Vasculature is a critical interface between blood and brain providing a barrier to systemic infection. Here we examined whether maternal PUFA-enriched diets exert reprograming of endothelial cell signalling in 9-day old mice after endotoxin (LPS)-induced infection. Transcriptome analysis was performed on brain microvessels from pups born to dams maintained on 3 diets: standard, n-3 or n-6 enriched. N-3 diet enabled higher immune reactivity in brain vasculature, while preventing imbalance of cell cycle regulation and extracellular matrix cascades that accompanied inflammatory response in standard diet. LPS response in blood and brain was blunted in n-3 offspring. Cerebral angioarchitecture analysis revealed modified vessel complexity after LPS. Thus, n-3-enriched maternal diet partially prevents imbalance in homeostatic processes and alters inflammation rather than affects brain vascularization during early life. Importantly, maternal diet may presage offspring neurovascular outcomes later in life.
Critical analysis of polycyclic tetramate macrolactam biosynthetic cluster phylogeny and functional diversity
Authors: Harper Christopher P. , Day Anna , Tsingos Maya , Ding Edward , Zeng Elizabeth , Stumpf Spencer D. , Qi Yunci , Robinson Adam , Greif Jennifer , Blodgett Joshua A. V. 
Published: January 2024

ABSTRACTPolycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggests their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. Towards addressing the origins of this complexity and understanding its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs, and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically-important bacteria, includingStreptomycesandLysobacterspp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggests new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize practical limitations to genomics-based discovery by exposing hidden complexity.
High ionic strength vector formulations enhance gene transfer to airway epithelia
Authors: Cooney Ashley L. , Loza Laura Marquez , Najdawi Kenan , Brommel Christian M. , McCray Paul B. , Sinn Patrick L. 
Published: January 2024

ABSTRACTA fundamental challenge for cystic fibrosis (CF) gene therapy is ensuring sufficient ransduction of airway epithelia to achieve therapeutic correction. Hypertonic saline (HTS) is frequently administered to people with CF to enhance mucus clearance. HTS transiently disrupts epithelial cell tight unctions, but its ability to improve gene transfer has not been investigated. Here we asked if increasing the concentration of NaCl enhances the transduction efficiency of three gene therapy vectors: adenovirus, AAV, and lentiviral vectors. Vectors formulated with 3-7% NaCl exhibited markedly increased transduction for all hree platforms, leading to anion channel correction in primary cultures of human CF epithelial cells and enhanced gene transfer in mouse and pig airwaysin vivo. The mechanism of transduction enhancement nvolved tonicity but not osmolarity or pH. Formulating vectors with a high ionic strength solution is a simple strategy to greatly enhance efficacy and immediately improve preclinical or clinical applications.One Sentence SummaryFormulating adenoviral, AAV, and lentiviral vectors with hypertonic saline remarkably enhances lung gene transfer. (114 characters, including spaces)
Wnt signaling alters CTCF binding patterns and global chromatin structure
Authors: Nordin Anna , Chakraborty Chaitali , Jonasson Mattias , Dano Orgena , Zambanini Gianluca , Pagella Pierfrancesco , Remeseiro Silvia , Cantù Claudio 
Published: January 2024

AbstractWnt signaling plays a pivotal role during development, stem cell maintenance, and tissue homeostasis. Upon Wnt pathway activation, β-catenin translocates to the nucleus where it binds the TCF/LEF transcription factors to drive the context-specific expression of Wnt target genes. Coordinating gene expression programs in vertebrates requires a complex interplay between the regulatory and the 3D organization of the genome. However, the impact of Wnt signaling on genome structure has been poorly explored. Here we investigated how Wnt signaling activation influences the binding patterns of CTCF, one of the core architectural proteins that helps establish the 3D genome organization be demarcating topologically associated domains (TAD). This study uncovered a series of CTCF rearrangements under Wnt, that we termed RUW. Notably, RUW sites that were gained upon Wnt activation were typically dependent on β-catenin and were characterized by both CTCF and TCF/LEF binding. Accordingly, many CTCF RUWs aligned with β-catenin binding patterns, and β-catenin and CTCF co-localized in vivo in discreet nuclear puncta only upon pathway activation. Genome-wide investigation of CTCF-mediated 3D genomic interactions upon Wnt pathway stimulation supported the role of the identified RUWs in mediating Wnt-dependent chromatin loops. Lastly, targeted disruption of selected CTCF binding sites demonstrated their functional contribution to Wnt target gene regulation, implicating regulation of the 3D genomic structure in the execution of transcriptional programs orchestrated by developmental pathways.
Dynamic transient brain states in preschoolers mirror parental report of behavior and emotion regulation
Authors: Toffoli Lisa , Zdorovtsova Natalia , Epihova Gabriela , Duma Gian Marco , Del Popolo Cristaldi Fiorella , Pastore Massimiliano , Astle Duncan E. , Mento Giovanni 
Published: January 2024

AbstractThe temporal dynamics of resting-state networks (RSNs) may represent an intrinsic functional repertoire supporting cognitive control performance across the lifespan (Kupis et al., 2021). However, little is known about brain dynamics during the preschool period, which is a sensitive time window for cognitive control development. The fast timescale of synchronization and switching characterizing cortical network functional organization gives rise to quasi-stable patterns (i.e., brain states) that recur over time. These can be inferred at the whole-brain level using Hidden Markov Models (HMMs), an unsupervised machine learning technique that allows the identification of rapid oscillatory patterns at the macro-scale of cortical networks (Vidaurre et al., 2018). The present study used a HMM technique to investigate dynamic neural reconfigurations and their associations with behavioral (i.e., parental questionnaires) and cognitive (i.e., neuropsychological tests) measures in typically developing preschoolers (4-6 years old). We used high density EEG to better capture the fast reconfiguration patterns of the HMM-derived metrics (i.e., switching rates, entropy rates, transition probabilities and fractional occupancies). Our results revealed that the HMM-derived metrics were reliable indices of individual neural variability and differed between boys and girls. However, only brain state transition patterns toward prefrontal and default-mode brain states, predicted differences on parental-report questionnaire scores. Overall, these findings support the importance of resting-state brain dynamics as functional scaffolds for behavior and cognition. Brain state transitions may be crucial markers of individual differences in cognitive control development in preschoolers.KeypointsHMM-derived metrics are reliable hallmarks of individual neural variability and show gender-related differences.Brain state transition patterns toward prefrontal and default-mode brain states predict differences on parental-report questionnaires scores.Brain state transitions may be crucial markers of individual differences in cognitive control development in preschoolers.
NeuroCSF: an fMRI method to measure contrast sensitivity function in human visual cortex
Authors: Goulet Laurie , Farivar Reza 
Published: January 2024

AbstractThe contrast sensitivity function (CSF) describes a range of spatial frequencies (SF) that are detectable at a given level of contrast and is a very valuable tool both in clinical and fundamental research. However, despite its immense value, the full potential of the CSF has not been utilized in every aspect of clinical research due to time limits and patient factors. We propose neuroCSF as a new method for measuring the CSF across the visual field directly from brain activity, and with minimal demand from participants. NeuroCSF is a computational model that estimates voxel-wise CSF parameters (i.e., peak contrast sensitivity, peak spatial frequency, and spatial frequency bandwidth) from functional magnetic resonance imaging (fMRI) signals, under controlled visual stimulation conditions. The approach extends the population spatial frequency tuning (Aghajari, Vinke, & Ling, 2020) and population receptive field (Dumoulin & Wandell, 2008) methods to provide the first characterization of a full CSF using neuroimaging. We observe that across early visual areas (V1, V2 and V3), the CSF peak spatial frequency and spatial frequency cutoff are significantly higher for foveal eccentricity and decrease at parafoveal eccentricities. Conversely, SF bandwidth slowly increases with eccentricity, while peak contrast sensitivity remains constant with eccentricity for all early visual areas. Thus, cortical CSF estimates vary systematically with eccentricity. The neuroCSF approach opens new perspectives for the study of cortical visual functions in various disorders where the CSF is impacted, such as amblyopia, traumatic brain injury, and multiple sclerosis.