bluuebunny/crossref_metadata_2025 huggingface dataset:
MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury
Authors: Leroy Victoria , Manual Kollareth Denny J. , Tu Zhenxiao , Valisno Jeff Arni C. , Woolet-Stockton Makena , Saha Biplab , Emtiazjoo Amir M. , Rackauskas Mindaugas , Moldawer Lyle L. , Efron Philip A. , Cai Guoshuai , Atkinson Carl , Upchurch Gilbert R. , Sharma Ashish K.
Published: January 2024

Rationale

Patients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes.

Objectives

We examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI.

Methods

Single-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT),cebpb-/-(MDSC-deficient),Mertk-/-or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice.

Measurements and Main Results

A significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent incebpb-/-LandMertk-/-mice. Adoptive transfer of M-MDSCs incebpb-/-mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients.In vitrostudies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner.

Conclusions

Our results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.
Mitotic waves in frog egg extracts: Transition from phase waves to trigger waves
Authors: Puls Owen , Ruiz-Reynés Daniel , Tavella Franco , Jin Minjun , Kim Yeonghoon , Gelens Lendert , Yang Qiong
Published: January 2024

Cyclin-dependent kinase 1 (Cdk1) activity rises and falls throughout the cell cycle, a cell-autonomous process known as mitotic oscillations. These oscillators can synchronize when spatially coupled, providing a crucial foundation for rapid synchronous divisions in large early embryos likeDrosophila(∼0.5 mm) andXenopus(∼1.2 mm). While diffusion alone cannot achieve such long-range coordination, recent studies have proposed two types of mitotic waves, phase and trigger waves, to explain the phenomena. How the waves establish over time for efficient spatial coordination remains unclear. UsingXenopus laevisegg extracts and a Cdk1 FRET sensor, we observe a transition from phase waves to a trigger wave regime in an initially homogeneous cytosol. Adding nuclei accelerates such transition. Moreover, the system transitions almost immediately to this regime when externally driven by metaphase-arrested extracts from the boundary. Employing computational modeling, we pinpoint how wave nature, including speed-period relation, depends on transient dynamics and oscillator properties, suggesting that phase waves appear transiently due to the time required for trigger waves to entrain the system and that spatial heterogeneity promotes entrainment. Therefore, we show that both waves belong to a single biological process capable of coordinating the cell cycle over long distances.
3D Bioprinting of Human Neural Tissues with Functional Connectivity
Authors: Yan Yuanwei , Li Xueyan , Gao Yu , Mathivanan Sakthikumar , Kong Linghai , Tao Yunlong , Dong Yi , Li Xiang , Bhattacharyya Anita , Zhao Xinyu , Zhang Su-Chun
Published: January 2024

Probing how the human neural networks operate is hindered by the lack of reliable human neural tissues amenable for dynamic functional assessment of neural circuits. We developed a 3D bioprinting platform to assemble tissues with defined human neural cell types in a desired dimension using a commercial bioprinter. The printed neuronal progenitors differentiate to neurons and form functional neural circuits in and between tissue layers with specificity within weeks, evidenced by the cortical-to-striatal projection, spontaneous synaptic currents and synaptic response to neuronal excitation. Printed astrocyte progenitors develop into mature astrocytes with elaborated processes and form functional neuron-astrocyte networks, indicated by calcium flux and glutamate uptake in response to neuronal excitation under physiological and pathological conditions. These designed human neural tissues will likely be useful for understanding the wiring of human neural networks, modeling pathological processes, and serving as platforms for drug testing.
Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage
Authors: Cooper Jacob C.
Published: January 2024

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species’ evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan- American lineage, the avian genus of martins (Progne). Despite containing species with distributions that go from continent-spanning to locally endemic, I found limited evidence for niche divergence across the breeding distributions ofProgne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestralPrognehad a relatively broad ecological niche, similar to extant basalPrognelineages, and several geographically localized descendant species occupy only portions of the larger ancestralProgneniche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread, continental species (Southern MartinP. elegansvs. Gray-breasted MartinP. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple MartinP. subisandP. chalybea. I analyzed populations ofP. subisseparately, as a microcosm ofProgneevolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages. Even taxa that appear unique in terms of habitat or behavior may still not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.
CHOIR improves significance-based detection of cell types and states from single-cell data
Authors: Sant Cathrine , Mucke Lennart , Corces M. Ryan
Published: January 2024

Clustering is a critical step in the analysis of single-cell data, as it enables the discovery and characterization of putative cell types and states. However, most popular clustering tools do not subject clustering results to statistical inference testing, leading to risks of overclustering or underclustering data and often resulting in ineffective identification of cell types with widely differing prevalence. To address these challenges, we present CHOIR (clusteringhierarchyoptimization by iterative random forests), which applies a framework of random forest classifiers and permutation tests across a hierarchical clustering tree to statistically determine which clusters represent distinct populations. We demonstrate the enhanced performance of CHOIR through extensive benchmarking against 14 existing clustering methods across 100 simulated and 4 real single-cell RNA-seq, ATAC-seq, spatial transcriptomic, and multi-omic datasets. CHOIR can be applied to any single-cell data type and provides a flexible, scalable, and robust solution to the important challenge of identifying biologically relevant cell groupings within heterogeneous single-cell data.
Investigation of neural functional connectivity in thick acute mouse brain slices with novel multi-region 3D neural probe arrays
Authors: Smith Wesley Charles , Naumkina Zoia , Shin Hyo Geun , Chae Ui Kyu , Lee SeungHun , Park Jung-Hoon , Cho Yak Dol , Woo Ji Wan , Kwon Seok Kyu , Oh Soo Jin , Nam Min-Ho , Kim Tae Song , Cho Il Joo
Published: January 2024

There are significant limitations in investigating complex neural circuitsin vivo, including drawbacks to midline-adjacent surgeries, limited accessibility to deep brain regions and number of feasible regional targets for simultaneous recordings, and analytical or experimental biases from recording one columnar plane. On the other hand, recording extracellular neural signalsex vivoorin vitrousing planar microelectrode arrays (MEAs) only permits slice surface recordings, and since conventional slices under 400 μm-thick or dissociated cultures are used, no experiments contain a physiological multi-region circuit, drastically limiting conclusions about connectivity and pharmacology. Using thick, tract-preserving acute brain slices to record otherwise unassailable neural circuitsex vivocombines the strengths of both types of experiments, but is assumed to precipitate ischemic injury due to oxygen scarcity within the slice. Here, we report the first application of custom, multi-region silicon neural probe arrays to record spontaneous activity & optogenetically-induced functional connectivity acrosshe mesocorticolimbic pathway within tract-preserving 800 μm sagittal mouse brain slices, compared with 400 μm slices, among three brain regions: the ventral tegmental area (VTA), ventral striatum (VS), & medial prefrontal cortex (mPFC). We show that most single-unit signals are an order of magnitude below the noise floor seen using silicon probesin vivo, providing unit yields far higher than previously assumed, allowing for a deep functional understanding of acute slice condition compared to the assumed deterioration due to ischemia. Overall, our method allows for acute circuit manipulations beyond what is available in vivo, with far more information than conventional slice preparations.
Extracellular RNA induce neutrophil recruitment via endothelial TLR3 during venous thrombosis after vascular injury
Authors: Najem Maria Y. , Rys Ryan N. , Laurance Sandrine , Bertin François-René , Gourdou-Latyszenok Virginie , Gourhant Lénaïck , Le Gall Lauriane , Le Corre Rozenn , Couturaud Francis , Blostein Mark D. , Lemarié Catherine A.
Published: January 2024

Background

Venous thromboembolism is associated with endothelial cell activation that contributes to the inflammation-dependent activation of the coagulation system. Cellular damages are associated with the release of different species of extracellular RNA (eRNA) involved in inflammation and coagulation. TLR3, which recognizes (viral) double-stranded RNA, single-stranded RNA, and also self-RNA fragments might be the receptor of these eRNA during venous thromboembolism. We investigate how eRNA regulate endothelial function through TLR3 and contribute to venous thromboembolism.

Methods and Results

Thrombus formation and size in WT and TLR3 deficient (-/-) mice were monitored by ultrasonography after venous thrombosis using the FeCl3and stasis models. Mice were treated with RNase1, poly(I:C) or RNA extracted from murine endothelial cells (eRNA). Gene expression and signaling pathway activation were analyzed in HEK293T cells overexpressing TLR3 in response to eRNA or in HUVECs transfected with a siRNA against TLR3. Plasma clot formation on treated HUVECs was analyzed. Thrombosis exacerbated RNA release in vivo and increased RNA content within the thrombus. RNase1 treatment reduced thrombus size compared to vehicle-treated mice. Poly(I:C) and eRNA treatments increased thrombus size in WT mice, but not in TLR3-/-mice, by bolstering neutrophil recruitment. Mechanistically, TLR3 activation in endothelial cells promotes CXCL5 secretion and neutrophil recruitment in vitro. eRNA triggered plasma clot formation. eRNA mediate these effects through TLR3-dependent activation of NFκB.

Conclusions

We show that eRNA and TLR3 activation enhance venous thromboembolism through neutrophil recruitment and secretion of CXCL5.
A Vector System Encoding Histone H3 Mutants Facilitates Manipulations of the Neuronal Epigenome
Authors: Warren Sophie , Xiong Sen , Robles Daisy , Baizabal José-Manuel
Published: January 2024

The differentiation of developmental cell lineages is associated with genome-wide modifications in histone H3 methylation. However, the causal role of histone H3 methylation in transcriptional regulation and cell differentiation has been difficult to test in mammals. The experimental overexpression of histone H3 mutants carrying lysine-to-methionine (K-to-M) substitutions has emerged as an alternative tool for inhibiting the endogenous levels of histone H3 methylation at specific lysine residues. Here, we leverage the use of histone K-to-M mutants by creating Enhanced Episomal Vectors that enable the simultaneous depletion of multiple levels of histone H3 lysine 4 (H3K4) or lysine 9 (H3K9) methylation in projection neurons of the mouse cerebral cortex. Our approach also facilitates the simultaneous depletion of H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3, respectively) in cortical neurons. In addition, we report a tamoxifen-inducible Cre-FLEX system that allows the activation of mutant histones at specific developmental time points or in the adult cortex, leading to the depletion of specific histone marks. The tools presented here can be implemented in other experimental systems, such as humanin vitromodels, to test the combinatorial role of histone methylations in developmental fate decisions and the maintenance of cell identity.
Explorations of using a convolutional neural network to understand brain activations during movie watching
Authors: Sohn Wonbum , Di Xin , Liang Zhen , Zhang Zhiguo , Biswal Bharat B.
Published: January 2024

Neuroimaging studies increasingly use naturalistic stimuli like video clips to trigger complex brain activations, but the complexity of such stimuli makes it difficult to assign specific functions to the resulting brain activations, particularly for higher-level content like social interactions. To address this challenge, researchers have turned to deep neural networks, e.g., convolutional neural networks (CNNs). CNNs have shown success in image recognition due to their different levels of features enabling high performance. In this study, we used pre-trained VGG-16, a popular CNN model, to analyze video data and extract hierarchical features from low-level shallow layers to high-level deeper layers, linking these activations to different levels of activation of the human brain. We hypothesized that activations in different layers of VGG-16 would be associated with different levels of brain activation and visual processing hierarchy in the brain. We were also curious about which brain regions would be associated with deeper convolutional layers in VGG-16. The study analyzed a functional MRI (fMRI) dataset where participants watched the cartoon movie Partly Cloudy. Frames of the videos were fed into VGG-16, and activation maps from different kernels and layers were extracted. Time series of the average activation patterns for each kernel were created and fed into a voxel-wise model to study brain activations. Results showed that lower convolutional layers (1stconvolutional layer) were mostly associated with lower visual regions, but some kernels (6, 19, 24, 42, 55, and 58) surprisingly showed associations with activations in the posterior cingulate cortex, part of the default mode network. Deeper convolutional layers were associated with more anterior and lateral portions of the visual cortex (e.g., the lateral occipital complex) and the supramarginal gyrus. Analyzing activation features associated with different brain regions showed the promise and limitations of using CNNs to link video content to brain functions.
Testing retrogenesis and physiological explanations for tract-wise white matter aging: links to developmental order, fibre calibre, and vascularization
Authors: Robinson Tyler D. , Chad Jordan A. , Sun Yutong L. , Chang Paul T. H. , Chen J. Jean
Published: January 2024

To understand the consistently observed spatial distribution of white-matter (WM) aging, developmentally driven theories termed “retrogenesis” have gained traction, positing that the order of WM tract development predicts the order of declines. Regions that develop first are expected to deteriorate the last, i.e. “last-in-first-out”. Alternatively, regions which develop most rapidly may also decline most rapidly in aging, or “gains-predict-loss”. The validity of such theories remains uncertain, in part due to lack of clarity on the definition of developmental order. Importantly, our recent findings suggest that WM aging is also associated with physiological parameters such as perfusion, which may be linked to fibre metabolic need, which in turn varies with fibre size. Here we address the extent to which the degree of WM aging is determined by development trajectory (i.e. retrogenesis) and/or by physiological state. We obtained microstructural and perfusion measures using data from the Human Connectome Project in Aging (HCP-A), complemented by a meta-analysis involving maps of fibre calibre and macrovascular volume. Our results suggest that (1) while tracts that appear last or finish myelinating first in development display the slowest aging, the pattern of aging is not fully explained by retrogenesis; in fact, time courses of tract emergence and myelination give rise to opposite associations with WM decline; (2) tracts that appear earlier also have higher mean axon calibre and are also associated with lower degrees of WM microstructural aging; (3) such tracts also tend to exhibit relatively sustained CBF with a higher rate of lengthening of the arterial transit times (ATT), suggestive of collateral blood supply. These findings were also sex dependent in a tract-specific manner. Future work will investigate whether these are ultimately influenced by each tract’s metabolic demand and the role of macrovascular collateral flow.
Structural determinants of co-translational protein complex assembly
Authors: Mallik Saurav , Venezian Johannes , Lobov Arseniy , Heidenreich Meta , Garcia-Seisdedos Hector , Yeates Todd O. , Shiber Ayala , Levy Emmanuel D.
Published: January 2024

The assembly of proteins into functional complexes is critical to life’s processes. While textbooks depict complex assembly as occurring between fully synthesized proteins, we know today that thousands of proteins in the human proteome assemble co-translationally during their synthesis. Why this process takes place, however, remains unknown. We show that co-translational assembly is governed by biophysical and structural characteristics of the protein complex, and involves mutually stabilized, intertwined subunits. Consequently, these subunits are also co-regulated across the central dogma, from transcription to protein degradation. Leveraging structural signatures with AlphaFold2-based predictions enables us to accurately predict co-translational assembly on a proteome-wide scale, which we validated by ribosome profiling, genetic perturbations, and smFISH experiments. Notably, the latter showed that co-translationally assembling subunits exhibit co-localized mRNAs. This work unveils a fundamental connection between protein structure and the translation process, highlighting the overarching impact of three-dimensional structure on gene expression, mRNA localization, and proteostasis.

One Sentence Summary

Protein complexes with topologically intertwined subunits require co-translational assembly and synchronized proteostasis of subunits, with implications in protein stability, mRNA localization, and evolution.

Graphical Abstract
SOX9-regulated matrix proteins predict poor outcomes in patients with COVID-19 and pulmonary fibrosis
Authors: Pearmain Laurence , Jokl Elliot , Simpson Kara , Birchall Lindsay , Ou Yaqing , Lawless Craig , Simpson Angela , Mann Lizzie , Scott Nick , Shah Rajesh , Venkateswaran Rajamiyer , Stanel Stefan , Hayton Conal , Rivera-Ortega Pilar , Hansbro Phil , Hanley Neil A , Blaikley John F , Hanley Karen Piper
Published: January 2024

Pulmonary fibrosis is an increasing and major cause of death worldwide. Understanding the cellular and molecular mechanisms underlying the pathophysiology of lung fibrosis may lead to urgently needed diagnostic and prognostic strategies for the disease. SOX9 is a core transcription factor that has been associated with fibrotic disease, however its role and regulation in acute lung injury and/or fibrosis have not been fully defined. In this study we apply a hypothesis based approach to uncover unique SOX9-protein signatures associated with both acute lung injury and fibrotic progression. Usingin vivomodels of lung injury in the presence or absence of SOX9, our study shows SOX9 is essential to the damage associated response of alveolar epithelial cells from an early time-point in lung injury. In parallel, as disease progresses, SOX9 is responsible for regulating tissue damaging ECM production from pro-fibrotic fibroblasts. In determining thein vivorole of SOX9 we identified secreted ECM components downstream of SOX9 as markers of acute lung injury and fibrosis. To underscore the translational potential of our SOX9-regulated markers, we analysed serum samples from acute COVID19, post COVID19 and idiopathic pulmonary fibrosis (IPF) patient cohorts. Our hypothesis driven SOX9-panels showed significant capability in all cohorts at identifying patients who had poor disease outcomes. This study shows that SOX9 is functionally critical to disease in acute lung injury and pulmonary fibrosis and its regulated pathways have diagnostic, prognostic and therapeutic potential in both COVID19 and IPF disease.
An unconventional autophagic pathway that inhibits ATP secretion during apoptotic cell death
Authors: Terraza-Silvestre Elena , Villamuera Raquel , Bandera-Linero Julia , Letek Michal , Ramón-Barros Cristina , Moyano-Jimeno Clara , Oña-Sánchez Daniel , Pimentel-Muiños Felipe X.
Published: January 2024

Mobilization of Damage-Associated Molecular Patterns (DAMPs) determines the immunogenic properties of apoptosis, but the mechanisms that control DAMP exposure are still unclear. Here we describe an unconventional autophagic pathway that inhibits the release of ATP, a critical DAMP in immunogenic apoptosis, from dying cells. Mitochondrial BAK activated by BH3-only molecules interacts with prohibitins and stomatin-1 through its latch domain, indicating the existence of an interactome specifically assembled by unfolded BAK. This complex engages the WD40 domain of the critical autophagic effector ATG16L1 to induce unconventional autophagy, and the resulting LC3-positive vesicles contain ATP. Functional interference with the pathway increases ATP release during cell death, reduces ATP levels remaining in the apoptotic bodies, and improves phagocyte activation. These results reveal that an unconventional component of the autophagic burst that often accompanies apoptosis sequesters intracellular ATP to prevent its release, thus favoring the immunosilent nature of apoptotic cell death.
A dynamic functional connectivity toolbox for multiverse analysis
Authors: Burkhardt Micha , Gießing Carsten
Published: January 2024

Various methods for estimating dynamic functional connectivity from fMRI data and subsequent analyses through graph theoretic approaches have been introduced in recent years. But with many of the ground truths unknown, researchers are often faced with arbitrary yet defensible decisions for their analyses, which raises concerns about the reproducibility of results. We here aim to address this issue through the implementation of a wide array of dynamic functional connectivity methods in a unified Python software package, facilitating a diverse exploration of brain dynamics. Anchored in the framework of multiverse analysis, the present work further introduces a workflow for the systematic examination of various methodological decisions. The developed toolbox is supplemented by a graphical user interface for easy usability and accessibility if usage outside of a script-based Python analysis pipeline is desired. Further, extensive demo scripts are provided for researchers to easily adapt this approach for their own analyses.
Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition
Authors: Bhatt Aadra P. , Arnold Jason W. , Awoniyi Muyiwa , Sun Shan , Santiago Verônica Feijoli , Quintela Pedro Henrique , Walsh Kenneth , Ngobeni Renay , Hansen Brenna , Gulati Ajay , Carroll Ian M. , Azcarate-Peril M. Andrea , Fodor Anthony A. , Swann Jonathan , Bartelt Luther A.
Published: January 2024

Undernutrition in children commonly disrupts the structure and function of the small intestinal microbial community, leading to enteropathies, compromised metabolic health, and impaired growth and development. The mechanisms by which diet and microbes mediate the balance between commensal and pathogenic intestinal flora remain elusive. In a murine model of undernutrition, we investigated the direct interactionsGiardia lamblia,a prevalent small intestinal pathogen, on indigenous microbiota and specifically on Lactobacillus strains known for their mucosal and growth homeostatic properties. Our research reveals thatGiardiacolonization shifts the balance of lactic acid bacteria, causing a relative decrease inLactobacillus spp. and an increase inBifidobacterium spp. This alteration corresponds with a decrease in multiple indicators of mucosal and nutritional homeostasis. Additionally, protein-deficient conditions coupled withGiardiainfection exacerbate the rise of primary bile acids and susceptibility to bile acid-induced intestinal barrier damage. In epithelial cell monolayers,Lactobacillus spp. mitigated bile acid-induced permeability, showing strain-dependent protective effects.In vivo, L. plantarum,either alone or within aLactobacillusspp consortium, facilitated growth in protein-deficient mice, an effect attenuated byGiardia, despite not inhibiting Lactobacillus colonization. These results highlight Giardia’s potential role as a disruptor of probiotic functional activity, underscoring the imperative for further research into the complex interactions between parasites and bacteria under conditions of nutritional deficiency.
Effects of D3-preferring agonist PD 128907 on compulsive behaviour and decision making as assessed by the 5C-CPT
Authors: Abdulkader Sara , Gigg John
Published: January 2024

Background

Repetitive rituals in OCD patients result from pathological doubt, which has been linked to dysfunction in decision-making. First-line drug treatments for OCD are selective serotonin reuptake inhibitors; however, 40% of OCD patients do not respond to these. As brain activity patterns in OCD resemble those in schizophrenic patients, this suggests a dopaminergic component, supported by data showing that the D2/D3 receptor agonist Quinpirole induces compulsive checking in male rats. OCD has proved difficult to model in rodents and the contribution of decision making to compulsive behaviour in such models has not been studied. The five-choice continuous performance task (5C-CPT) measures both decision making and compulsive behaviour, making it possible to evaluate whether OCD models show correlated changes in these two behaviours. Establishing this would provide a new model approach to help develop therapeutic agents for OCD.

Aims

The role of dopaminergic D3 receptors in decision making and compulsive behaviour was determined by testing the effect of the preferential D3 agonist PD 128907 on 5C-CPT performance measures. Oldham’s method was used to determine the presence of any rate-dependent effect.

Methods

Female Lister hooded rats were trained to criterion in the 5C-CPT (>70% accuracy, < 30% omission and < 40% false alarms). The effects of PD128907 (0.25-1 mg/kg) were then investigated under challenging task conditions.

Results

Oldham method revealed: a moderate positive association between baseline perseverative correct responses and the change at 0.05 mg/kg PD 128907; a strong positive association between baseline perseverative false alarm and the change at 0.2 mg/kg; a positive association between baseline total number of perseverative responses and the change at 0.05 mg/kg or 0.2 mg/kg PD 128907; a positive relationship between baseline accuracy and the change at 0.05 mg/kg PD 128907; and a moderate positive association between baseline correct response latency and the change at 0.05 mg/kg or 0.2 mg/kg PD 128907. The angle measurements and the direction of movement (clockwise or counterclockwise) showed how effective is one dose at increasing compulsive behaviour compared with other doses.

Conclusions

PD 128907 effects on compulsive like behaviour and decision making in poor performing female lister hooded rats with long correct response latency and high perseveration at baseline (vulnerable population) in the 5C-CPT task matches two key features of OCD compulsions in humans (perseveration and indecision), this suggests that PD 128907 is more effective than Quinpirole in simulating the brain network conditions that underpin OCD. This model could help to develop more successful pharmacological interventions and to generate data translatable to clinical studies.
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

Vasoactive 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

Rest 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

Cortical 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

Schaaf-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

Despite 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

Endosomal 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

Nuclear 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

Infection 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

Polycyclic 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.

IMPORTANCE

Polycyclic 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

A 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 Summary

Formulating adenoviral, AAV, and lentiviral vectors with hypertonic saline remarkably enhances lung gene transfer. (114 characters, including spaces)