bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances in stress and depression research
Authors: LeMoult Joelle , Battaglini Ashley M. , Grocott Bronwen , Jopling Ellen , Rnic Katerina , Yang Lisa 
Published: October 2022

Purpose of review
Stress plays a central role in the onset and course of depression. However, only a subset of people who encounter stressful life events go on to experience a depressive episode. The current review highlights recent advances in understanding when, why, and for whom the stress-depression link occurs, and we identify avenues for future research.

Recent findings
In the last 18 months, researchers have taken a more nuanced perspective on the biopsychosocial mechanisms critical to the stress–depression link. For example, examination of specific facets of emotion regulation, including emotion regulation flexibility and interpersonal emotion regulation, has been critical to understanding its role in depression. Similarly, refined investigations of social support allowed researchers to identify distinct – and occasionally opposite – outcomes depending on the context or manner in which the support was provided. Researchers also documented that the stress–depression link was enhanced by dysregulation of several stress-sensitive biological systems, such as the immune system, microbiome, endocrine system, and neuroanatomical substrates.

Summary
Recent studies highlight the importance of adopting a nuanced understanding of mechanisms and moderators that explain the stress–depression link. We also encourage continued engagement in collaborative, open science that uses multiple methods to study the full breadth of human diversity.
A method to estimate contact regions between hands and objects during human multi-digit grasping
Authors: Hartmann Frieder , Maiello Guido , Rothkopf Constantin A. , Fleming Roland W. 
Published: October 2022

ABSTRACTIn order to grasp an object successfully, we must select appropriate contact regions for our hands on the surface of the object. However, identifying such regions is challenging. Here, we describe a workflow to estimate contact regions from marker-based tracking data. Participants grasp real objects, while we track the 3D position of both the objects and the hand including the fingers’ joints. We first determine joint Euler angles from a selection of tracked markers positioned on the back of the hand. Then, we use state-of-the-art hand mesh reconstruction algorithms to generate a mesh model of the participant’s hand in the current pose and 3D position. Using objects that were either 3D printed, or 3D scanned—and are thus available as both real objects and mesh data—allows us to co-register the hand and object meshes. In turn, this allows us to estimate approximate contact regions by calculating intersections between the hand mesh and the co-registered 3D object mesh. The method may be used to estimate where and how humans grasp objects under a variety of conditions. Therefore, the method could be of interest to researchers studying visual and haptic perception, motor control, human-computer interaction in virtual and augmented reality, and robotics.SUMMARYWhen we grasp an object, multiple regions of the fingers and hand typically make contact with the object’s surface. Reconstructing such contact regions is challenging. Here, we present a method for approximately estimating contact regions, by combining marker-based motion capture with existing deep learning-based hand mesh reconstruction.
Biological connectomes as a representation for the architecture of artificial neural networks
Authors: Schmidgall Samuel , Schuman Catherine , Parsa Maryam 
Published: October 2022

AbstractGrand efforts in neuroscience are working toward mapping the connectomes of many new species, including the near completion of theDrosophila melanogaster. It is important to ask whether these models could benefit artificial intelligence. In this work we ask two fundamental questions: (1) where and when biological connectomes can provide use in machine learning, (2) which design principles are necessary for extracting a good representation of the connectome. Toward this end, we translate the motor circuit of theC. Elegansnematode into artificial neu-ral networks at varying levels of biophysical realism and evaluate the outcome of training these networks on motor and non-motor behavioral tasks. We demonstrate that biophysical realism need not be upheld to attain the advantages of using biological circuits. We also establish that, even if the exact wiring diagram is not retained, the architectural statistics provide a valuable prior. Finally, we show that while theC. Eleganslocomotion circuit provides a powerful inductive bias on locomotion problems, its structure may hinder performance on tasks unrelated to locomotion such as visual classification problems.
A minimally-invasive method for serial cerebrospinal fluid collection and injection in rodents with high survival rates
Authors: Han Jingrong Regina , Yang Yu , Wu Tianshu William , Shi Tao-Tao , Li Wenlu , Zou Yilong 
Published: October 2022

AbstractCerebrospinal fluid (CSF) is a clear fluid surrounding and nourishing the brain and spinal cord. Molecular profiling of the CSF is a common diagnostic approach for central nervous system (CNS) diseases, including infectious diseases, autoimmune disorders, brain hemorrhage and traumatic brain injury, CNS tumors, and Alzheimer’s disease1–10. Rodent models are critical for investigating CNS disease mechanisms and therapeutics, however, both collecting CSF and injecting materials into CSF in small animals are technically challenging and often result in high rates of postoperative mortality. Here, we present an easy-to-practice and cost-effective protocol with minimum instrument requirements to access the CSF in live rodents for collection and infusion purposes. By introducing a metal needle tool bent at a unique angle and length, we could steadily reach the CSF via the foramen magnum. Compared with prior methods, this protocol requires neither the operator to discern the changes in resistance from solid tissues while puncturing the needle, nor surgical opening of the skin and muscle covering the rodent neck. Using this method, we frequently obtain 5-15 μL of CSF from mice and 70-120 μL from rats to enable diverse downstream analyses including mass spectrometry. Due to the minimal invasiveness, this procedure allows iterative CSF collection from the same animal every few days – a major improvement over prior protocols that require extensive surgical operations. Moreover, we demonstrate that this method could be used for injecting desired solutions including dyes into mouse CSF with high success rates. Our method shortens the time required for CSF collection or injection to 3-5 minutes. Notably, we could reach near 100% postoperative recovery rates in both mice and rats even with repetitive collections. Together, we establish an efficient and minimally-invasive protocol for collecting CSF and inoculating reagents into the CSF in live rodents to enable various longitudinal studies at the forefronts of CNS investigation.
Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium
Authors: Isoe Yasuko , Nakamura Ryohei , Nonaka Shigenori , Kamei Yasuhiro , Okuyama Teruhiro , Yamamoto Naoyuki , Takeuchi Hideaki , Takeda Hiroyuki 
Published: October 2022

SummaryThe dorsal telencephalon (i.e. the pallium) exhibits high anatomical diversity across vertebrate classes. The mammalian dorsal pallium accommodates a six layered-structure, the neocortex, whereas the teleostean dorsal pallium possesses various compartmentalized structures among species. The development, function and evolution of the fish dorsal pallium remain unillustrated. Here, we analyzed the structure and epigenetic landscapes of cell lineages in the telencephalon of medaka fish (Oryzias latipes) which possesses a clearly delineated dorsal pallium (the Dd2 region). We found that different pallial regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a unique open chromatin pattern that preferentially targets synapse-related genes. Indeed, Dd2 shows a high density of synapses, which might reflect strong plasticity. Finally, we identified several transcription factors as candidate regulators for the Dd2, which are partially shared with the human neocortex and hippocampus.
Decoupling of mRNA and protein expression in aging brains reveals the age-dependent adaptation of specific gene subsets
Authors: Khatir Ines , Brunet Marie A. , Meller Anna , Amiot Florent , Patel Tushar , Lapointe Xavier , Lopez Jessica Avila , Guilloy Noe , Castonguay Anne , Husain Mohammed Amir , St-Germain Joannie , Boisvert François-Michel , Plourde Mélanie , Roucou Xavier , Laurent Benoit 
Published: October 2022

AbstractDuring aging, changes in gene expression are associated with decline in physical and cognitive abilities. Here, we investigated the connection between changes of mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that increase of mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex where we also observed an increase of cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, but also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.
A pathway to produce non-coding piRNAs from endogenous protein-coding regions supports Drosophila spermatogenesis
Authors: Iki Taichiro , Kawaguchi Shinichi , Kai Toshie 
Published: October 2022

SummaryPIWI-interacting (pi)RNA pathways control transposable elements (TEs) and endogenous genes in animal gonads, playing important roles in gamete formation. Here, we report a mechanism by which endogenous protein-coding regions, that normally provide their sequences for translation, serve as origins of non-coding piRNA biogenesis in Drosophila melanogaster testes. The products, namely endo-piRNAs, formed silencing complexes with Aubergine (Aub) in germ cells. Proximity proteome combined to functional analyses revealed a testis-specialized chaperone, Cyclophilin 40 (Cyp40), selectively increases endo-piRNA occupancy inside Aub-RISCs aside from other TE-related piRNAs. Moreover, Argonaute 2 (Ago2) activities were found critical for endo-piRNA production. We provide evidence that Ago2-bound short interfering (si)RNAs and micro(mi)RNAs specify precursors and direct endo-piRNA biogenesis. Consistently, Aub and Ago2 cooperate in spermatid differentiation and regulate endogenous genes via endo-piRNA-directed mRNA cleavage. Collectively, our data highlight that Drosophila testes employ a unique strategy to expand the diversity of germline piRNAs supporting late spermatogenesis.HeadlinesEndogenous protein-coding regions derive non-coding endo-piRNAsendo-piRNA and TE-piRNA are produced via distinct mechanismssiRNA and miRNA activities direct secondary piRNA biogenesisendo-piRNA pathway controls chromatin and sperm formation
Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
Authors: Jiang Xiuyun , Harker-Kirschneck Lena , Vanhille-Campos Christian , Pfitzner Anna-Katharina , Lominadze Elene , Roux Aurélien , Baum Buzz , Šarić Anđela 
Published: October 2022

AbstractESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.Author summaryESCRT-III proteins have the unique ability to cut membrane necks from within, which is needed for a vast number of cell remodelling events including the release of cargo-containing vesicles. ESCRT-III proteins exist in different forms, which can assemble into spiral and helical homopolymers of different curvatures, and they have been suggested to polymerize and depolymerize with each other in a staged manner to deform and cut membranes.We developed a computer model to explore the physical mechanisms behind vesicle budding driven by the staged assembly and disassembly of multiple elastic filaments. We identified rules that determine the outcomes of membrane remodelling, which depend on the relative physical features of the distinct filaments, the dynamics of their disassembly, and on the presence of cargo; thereby providing experimentally testable predictions. Our study provides new physical insights into the ESCRT-III-mediated vesicle budding process, at a single subunit level, and identifies the general design principles of nanomachines built from shapeshifting copolymers, which might also be realized in synthetic systems.
Visual evoked potentials as an early-stage biomarker in the rTg4510 tauopathy mouse model
Authors: Parka Aleksandra , Volbracht Christiane , Hall Benjamin , Bastlund Jesper F. , Nedergaard Maiken , Laursen Bettina , Botta Paolo , Sotty Florence 
Published: October 2022

AbstractTauopathies such as Alzheimer’s Disease (AD) and frontotemporal dementia (FTD) are characterized by formation of neurofibrillary tangles consisting of hyperphosphorylated tau protein. Early pathophysiological and functional changes related to neurofibrillary tangles formation are considered to occur prior to extensive neurodegeneration. Hyperphosphorylated tau has been detected in postmortem retinas of AD and FTD patients, and the visual pathway is an easily accessible system in a clinical setting. Hence, assessment of the visual function may offer the potential to detect consequences of early tau pathology in patients. In this study we explored the association between the visual system and functional consequences of tau pathology progression using a tauopathy rTg4510 mouse model. To this end, we recorded full-field electroretinography and visual evoked potentials in anesthetized and awake states at different ages. While retinal function remained mostly intact within all the age groups investigated, we detected significant changes in amplitudes of visual evoked potential responses in young rTg4510 mice exhibiting early tau pathology prior to neurodegeneration. These functional alterations in the visual cortex were positively correlated with pathological tau levels. Our findings suggest that visual processing could be useful as a novel electrophysiological biomarker for early stages of tauopathy.
Pathological crosstalk between AQP4-dependent ATP/Adenosine release and dopamine neurotransmission underlying depressive behavior during cocaine withdrawal
Authors: Okada S. , Kobayashi M. , Lee H. , Nuralifah C. , Morita M. 
Published: October 2022

AbstractOur previous study has demonstrated the AQP4-dependent ATP release and following elevation of extracellular adenosine in hippocampal slices during hypo-osmotic treatment. In the present study, we examined the crosstalk between AQP4-dependent adenosine elevation and dopaminergic neurotransmissions, especially focusing on the mouse depressive behavior during cocaine withdrawal. The depressive behavior was mitigated in AQP4 knockout mice, and was sensitive to adenosine A1receptor antagonists. Thus, the influence of cocaine withdrawal on the adenosine or dopamine elevation in the slices from the striatum or medial prefrontal cortex, which is the focus of depression was analyzed by the originally-developed biosensor cells, which elevates intracellular Ca2+in response to adenosine or dopamine. We have found that the evoked-dopamine release in the striatum is tonically suppressed via A1receptor in a AQP4 dependent manner, and this suppression is augmented by the cocaine withdrawal. In contrast, the evoked dopamine elevation in the medial prefrontal cortex was suppressed by treating slices with adenosine or an A1receptor antagonist, and the cocaine withdrawal abolished the suppression by A1receptor antagonist alone in an AQP4-dependent manner. Since a GABAAor group II metabotropic glutamate receptor antagonist occluded the suppression by A1receptor antagonist, it has been suggested that the glutamatergic and GABAergic terminals suppressing dopamine releases have A1receptors, which the cocaine withdrawal down-regulates in a AQP4-dependent manner. These results indicate that astrocytes modulate dopaminergic neurotransmissions via A1receptor in an AQP4-dependent manner, and suggest that cocaine causes depression by changing this modulation.
Time-of-day effects on motor learning
Authors: Truong Charlène , Ruffino Célia , Gaveau Jérémie , White Olivier , Hilt Pauline M. , Papaxanthis Charalambos 
Published: October 2022

AbstractWhile the time-of-day significantly impacts motor performance, its effect on motor learning has not yet been elucidated. Here, we investigated the influence of the time-of-day on skill acquisition (i.e., skill improvement immediately after a training-session) and consolidation (i.e., skill retention after a time interval). Three groups were trained at 10 a.m. (G10am), 3 p.m. (G3pm), or 8 p.m. (G8pm) on a finger-tapping task. We recorded the skill (i.e. the ratio between movement duration and accuracy), before and immediately after the training to evaluate skill acquisition, and after 24 hours, to measure skill consolidation. We did not observe any difference in acquisition according to the time of the day. However, we found an improvement in performance 24 hours after the evening training (G8pm) while the morning (G10am) and the afternoon (G3pm) groups deteriorated and stabilized their performance, respectively. Furthermore, two control experiments (G8wake and G8sleep) supported the idea that a night of sleep contributes to the skill consolidation of the evening group. These results show an influence of time-of-day on the consolidation process, with better consolidation when the training is carried out in the evening. This finding may have an important impact on the planning of training programs in sports, clinical, or experimental domains.
Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri
Authors: Torraca Vincenzo , White Richard J. , Sealy Ian M. , Mazon-Moya Maria , Duggan Gina , Willis Alexandra , Busch-Nentwich Elisabeth M. , Mostowy Serge 
Published: October 2022

ABSTRACTShigella flexneri is a human adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri is poorly understood. Zebrafish larvae, highly innovative for genomics, transcriptomics and genetic tractability, represent a valuable animal model to study human infections in vivo. Here we use a S. flexneri-zebrafish infection model to generate mRNA expression profiles of host response to S. flexneri infection at the whole animal level. The signature of early S. flexneri infection (detected at 6 hours post-infection) is dominated by immune response-related processes. Consistent with its clearance from the host, the signature of late S. flexneri infection (detected at 24 hours post-infection) is significantly changed, where only a small set of immune-related genes remain differentially expressed, including gpr84 which encodes a putative G-protein coupled receptor. Using mutant zebrafish lines generated by ENU, CRISPR mutagenesis and the F0 CRISPR knockout method, we show that gpr84-deficient larvae are more susceptible to S. flexneri infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and provide a community resource to investigate host response to S. flexneri infection.
Rapid Evolution of Colistin Resistance in a Bioreactor Model of Infection of Klebsiella pneumoniae
Authors: Jiménez-Castellanos Juan-Carlos , Waclaw Bartlomiej , Meynert Alison , Schneiders Thamarai 
Published: October 2022

SynopsisObjectivesWe seek to understand the dynamics of de novo resistant mutations arising during colistin treatment of an antibiotic-naïve population of K. pneumoniae.MethodsWe used a bioreactor model of infection and colistin treatment against the colistin susceptible K. pneumoniae Ecl8. Whole-genome sequencing and MIC profiling was used to characterize genetic and phenotypic state of the bacterial culture at three time points: before treatment, immediately after regrowth following challenge, and at the end point of the experiment. A mathematical model based on the birth-death process was used to gain further insights on the population dynamics of emerging resistant variants.ResultsWe find that, after an initial decline, the population recovers within 24h due to the evolution of highly resistant clones which exhibit MICs >100-fold higher than the parental strain. Recovery is caused by a small number of “founder cells” which have single point mutations mainly in the regulatory genes encoding crrB and pmrB. The mutants arise through spontaneous mutations prior to colistin treatment.ConclusionsDevelopment of colistin resistance during treatment of K. pneumoniae infections is readily achieved if colistin is used as a monotherapy.
A shared neural code for social interaction encoding and memory in the human superior temporal sulcus
Authors: Lee Masson Haemy , Chen Janice , Isik Leyla 
Published: October 2022

AbstractRecognizing and remembering social information is a crucial cognitive skill. Neural patterns in the superior temporal sulcus (STS) support our ability to perceive others’ social interactions. However, despite the prominence of social interactions in memory, the neural basis of retrieving social interactions is still unknown. To fill this gap, we investigated the brain mechanisms underlying memory of others’ social interactions during free spoken recall of a naturalistic movie. By applying machine learning-based fMRI encoding analyses to densely labeled movie and recall data we found that STS activity patterns evoked by viewing social interactions predicted neural responses to social interaction memories. This finding suggests that the STS contains high-level conceptual, representations of social interactions, and its reactivation underlies our ability to remember others’ interactions.