bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluoxetine treatment during postnatal and juvenile temporal epochs evokes diametrically opposing changes in anxio-depressive behaviors, gene expression, mitochondrial function, and neuronal architecture in the medial prefrontal cortex
Authors: Ghai Utkarsha , Chachra Parul , Fanibunda Sashaina E. , Mendon Suchith , Bhaskaran Amogh , Sarkar Ambalika , Kukkemane Kowshik , Singh Vivek , Vaidya Vidita A. 
Published: December 2023

AbstractBackgroundThe selective serotonin reuptake inhibitor, fluoxetine is reported to evoke distinct effects on anxio-depressive behaviors based on the temporal window of administration. Here, we systematically addressed the influence of postnatal or juvenile fluoxetine treatment on anxio-depressive behavior, gene expression, mitochondrial biogenesis, and neuronal cytoarchitecture in adulthood.MethodsRat pups received postnatal fluoxetine (PNFlx) or juvenile fluoxetine (JFlx) treatment from postnatal day 2 (P2)-P21 or P28-48 respectively, and were assessed for changes in anxio-depressive behaviors, global gene expression, mitochondrial biogenesis/function, and dendritic cytoarchitecture in the medial prefrontal cortex (mPFC) in adulthood.ResultsPNFlx evoked long-lasting increases in anxio-depressive behaviors, whereas JFlx elicited persistent decreases in anxio-depressive behavior, accompanied by differential and minimally overlapping transcriptional changes in the mPFC in adulthood. We noted opposing changes in mitochondrial function and dendritic cytoarchitecture in the mPFC of PNFlx and JFlx animals, with a decline observed following PNFlx and an increase in response to JFlx treatment. Furthermore, the enhanced despair-like behavior in the PNFlx cohort was reversed by adult-onset treatment with nicotinamide, a precursor for NAD+which enhances mitochondrial bioenergetics.ConclusionsFluoxetine treatment in early postnatal versus juvenile windows evokes opposing and persistent effects on anxio-depressive behavior in adult male rats, along with differential effects on gene expression, mitochondrial function, and dendritic morphology in the mPFC. Collectively, our findings highlight two distinct temporal windows in which fluoxetine exposure programs starkly differing outcomes in mood-related behavior, and posits a role for altered bioenergetics within the mPFC in contributing to these distinctive changes in emotionality.
Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)
Authors: Moya Muñoz Gabriel G. , Brix Oliver , Klocke Philipp , Harris Paul D. , Luna Piedra Jorge R. , Wendler Nicolas D. , Lerner Eitan , Zijlstra Niels , Cordes Thorben 
Published: December 2023

AbstractOver the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and open-source Brick-MIC platform will be a valuable tool for many laboratories worldwide.
Amygdala habituation during exposure is associated with failure to reduce phobic symptoms
Authors: Lor Cindy S. , Karner Alexander , Zhang Mengfan , Kostorz Kathrin , Sladky Ronald , Scharnowski Frank 
Published: December 2023

AbstractExposure therapy is an established treatment for anxiety disorders but the mechanisms underpinning its effectiveness remain unclear. Two theories offer contrasting perspectives: the traditional habituation model posits that a form of stimulus desensitization is required during exposure, while the inhibitory learning model emphasizes the formation of new non-fearful associations. Crucially, while the former may manifest as amygdala habituation, the latter may not. To distinguish between the two models, this study uses functional magnetic resonance imaging to examine the amygdala responses of spider-fearful participants during fear exposure. We hypothesized that intervention success might align with stable or even increased amygdala activation – an indicator of active engagement and re-learning as proposed by the inhibitory learning model. Conversely, decreasing amygdala activity might not be a sign of reduced fear memory as proposed by the habituation model, but could signal mental detachment, leading to suboptimal treatment outcomes. Our results corroborated our hypotheses: individuals with escalating amygdala responses during exposure exhibited better clinical progress, while those showing amygdala ‘habituation’ benefited less. Our results strengthen the case for the inhibitory learning model and highlight that therapy may not aim to diminish fear per se but rather to engage patients in active processing and association formation.
The French flag problem revisited: Creating robust and tunable axial patterns without global signaling
Authors: Kremser Stephan , Vercelli Gabriel , Gerland Ulrich 
Published: December 2023

AbstractWolpert’s French flag problem conceptualizes the task of forming axial patterns with broad regions in multicellular systems. Wolpert described two different solutions to his problem, the balancing model and thresholding of a morphogen gradient, both of which require global, long-range signaling between cells. Since global signaling becomes challenging in large multicellular systems, we computationally explore alternative solutions, which use only local cell-cell signaling and are simple enough to potentially be implemented in natural or synthetic systems. We employ cellular automata rules to describe local signal processing logics, and search for rules capable of robust and tunable axial patterning with evolutionary algorithms. This yields large sets of successful rules, which however display only few types of behavior. We introduce a rule alignment and consensus procedure to identify patterning modules that are responsible for the different behaviors. With these modules as building blocks, we then construct local schemes for axial patterning, which function also in the presence of noise and growth, and for patterns with a larger number of different regions. The regulatory logic underlying these modules could therefore serve as the basis for the design of synthetic patterning systems, and as a conceptual framework for the interpretation of biological mechanisms.
Whole-brain modelling supports the use of serotonergic psychedelics for the treatment of disorders of consciousness
Authors: Mindlin I , Herzog R , Belloli L , Manasova D , Monge-Asensio M , Vohryzek J. , Escrichs A. , Alnagger N , Núñez P , Kringelbach ML , Deco G , Tagliazucchi E , Naccache L , Rohaut B , Sitt JD , Sanz Perl Y 
Published: December 2023

AbstractDisorders of consciousness (DoC) are a challenging and complex group of neurological conditions characterised by absent or impaired awareness. The current range of therapeutic options for DoC patients is limited, offering few non-invasive pharmacological alternatives. This situation has sprung a growing interest in the development of novel treatments, such as the proposal to study the efficacy of 5HT2A receptor agonists (also known as psychedelics) to restore impaired consciousness. Given the ethical implications of exploring novel compounds in non-communicative individuals, we assessed in silico their effects in the whole-brain dynamics of DoC patients. We embedded the whole-brain activity of patients in a low-dimensional space, and then used this representation to visualise the effects of simulated neuromodulation across a range of receptors representing potential drug targets. Our findings show that activation of serotonergic and opioid receptors shifted brain dynamics of DoC patients towards patterns typically seen in conscious and awake individuals, and that this effect was mediated by the brain-wide density of activated receptors. These results showcase the role of whole-brain models in the discovery of novel pharmacological treatments for neuropsychiatric conditions, while also supporting the feasibility of accelerating the recovery of consciousness with serotonergic psychedelics.
Hyperoxia Induced Alteration of Chromatin Structure in Bone Marrow Derived Primary Mesenchymal Stromal Cells
Authors: Monroe Lauren A. , Kaonis Samantha , Calahan Natalie , Kabi Neda , Ghosh Soham 
Published: December 2023

ABSTRACTChromatin is a highly dynamic entity of the eukaryotic cell nucleus. New evidence is emerging in support of the notion that chromatin can locally and globally rearrange itself to adapt with the cellular microenvironmental changes. Such changes include oxidative stress such as supraphysiological oxygen level, found in hyperoxia. Although it is known that hyperoxia can result in DNA damage and alterations in cell function, it is not well understood how the chromatin architecture changes under such a condition and what the functional significance of such change entails. In this work we developed an imaging-based technique to visualize and characterize nanoscale chromatin remodeling under hyperoxia, created via hydrogen peroxide treatment. We found high spatiotemporal variability of remodeling in different chromatin domains such as the euchromatin, heterochromatin and interchromatin. Chromatin remodeling was hindered by the GSK126 mediated inhibition of methyltransferase EZH2, which regulates the chromatin compaction. Epigenetic modifications and DNA damage under hyperoxia was investigated, which was found affected by the pretreatment of GSK126. The developed techniques and findings inform us with new mechanistic insights of chromatin remodeling which might lead to new intervention strategies to target genotoxic hyper-oxidative stress, which is common in degenerative diseases and aging, and for cell therapy in regenerative medicine.
Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities
Authors: Sharma Ashutosh , Vijay Nagarjun 
Published: December 2023

AbstractThe diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at theFmlocus, resulting in the overexpression of theEDN3(a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by theIdlocus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of theIdlocus, its precise location and functional details remain elusive. Our study aims to precisely locate theIdlocus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of theIdlocus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined theIdlocus to a ∼1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that theIdlocus shares a common ancestry across all BBC breeds, much like theFmlocus. Selection signatures and highly differentiated BBC-specific SNPs within theMTAPgene position it as the prime candidate for theIdlocus withCCDC112and additional genes, suggesting a possible polygenic nature. Our results suggest that theIdlocus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.
Investigation of Biomedical Cell Image Cryptography Based on RC4 Technique
Authors: Jiang Song , Kumar Ela 
Published: December 2023

AbstractEnormous data permeates various facets of social life, including public administration, community services, and scientific research, owing to the advent of new technologies. With the escalation of data transportation concerns, its significance in our daily lives has magnified. Particularly in the medical field, preserving information integrity during data transit has become an urgent priority. For instance, safeguarding massive electronic medical files like MRI images from cyberattacks and data loss poses a formidable challenge. Encryption and decryption techniques are employed as a solution. While numerous image types have undergone testing using cryptography techniques, biomedical images have received limited attention. In this article, We implemented RC4, pixel shuffling, and steganography to encrypt and decrypt cell images. Evaluating the encryption and decryption performance of these cell images involved testing cell viability, live/dead ratio, and morphology.
Calcyphosine is a microtubule-associated protein required for spindle formation and function
Authors: Setu Bipul , Nie Qian , Echele Grace , Spencer Susan A. 
Published: December 2023

AbstractCalcyphosine (CAPS) is a highly conserved but little explored calcium-binding protein that shows elevated expression in many forms of human cancer. Here we uncover a role for CAPS in spindle formation during mitosis. Our experiments suggest that CAPS is a microtubule-binding, spindle-associated protein that helps create the kinetochore fibers that bind and segregate chromosomes. Knockdown of CAPS causes a variety of defects during mitosis, including uncongressed chromosomes and multi-polar spindles, as well as high levels of apoptosis and a reduced mitotic index. We find that CAPS promotes microtubule bundling, both in vitro and in cells, and knockdown of CAPS leads to reduction of thick k-fibers in the mitotic spindle. The high level of CAPS observed in many forms of cancer suggests that CAPS may promote cell proliferation, but our results indicate that CAPS overexpression has little effect on the cell cycle. This suggests that the high level of CAPS expression may be a consequence of cancer, rather than a driving force for cell proliferation.
Nucleocytoplasmic transport rates are regulated by cellular processes that modulate GTP availability
Authors: Scott Kelsey L. , Halfmann Charles T. , Hoefakker Allison D. , Purkayastha Purboja , Wang Ting Ching , Lele Tanmay P. , Roux Kyle J. 
Published: December 2023

AbstractNucleocytoplasmic transport (NCT), the facilitated diffusion of cargo molecules between the nucleus and cytoplasm through nuclear pore complexes (NPCs), enables numerous fundamental eukaryotic cellular processes. Ran GTPase uses cellular energy in the direct form of GTP to create a gradient across the nuclear envelope (NE) that drives the majority of NCT. We report here that changes in GTP availability resulting from altered cellular physiology modulate the rate of NCT, as monitored using synthetic and natural cargo, and the dynamics of Ran itself. Cell migration, cell spreading and/or modulation of the cytoskeleton or its connection to the nucleus alter GTP availability and thus rates of NCT, regulating RNA export and protein synthesis. These findings support a model in which changes in cellular physiology that alter GTP availability can regulate the rate of NCT, impacting fundamental cellular processes that extensively utilize NCT.SummaryChanges in the availability of cellular GTP resulting from physiologically relevant processes, including cell migration and cell spreading, alter the rates of Ran-dependent nuclear import and export. Altered rates of nucleocytoplasmic transport regulate RNA localization and protein synthesis.
Chloroplast Genome Data ofTecticornia indica, a Hygrohalophytic C4 Plant Species
Authors: Sharpe Richard M. , Williamson-Benavides Bruce , Edwards Gerald E. , Dhingra Amit 
Published: December 2023

AbstractTecticornia indicais a hygrohalophytic, NAD-malic enzyme-type C4 plant species with near-aphyllous photosynthetic shoots. Total cellular DNA was extracted from the aphyllous shoots and branches ofTecticornia indicafor subsequent High Throughput Sequencing (HTS). Illumina HiSeq 2000 technology produced a total of 91,825,666 reads. Reads were trimmed and filtered to retain base calls corresponding to a 99.9% base call accuracy. Ade novoassembly produced 413,729 contigs and 45,238 scaffolds with a maximum length of 120,548 nucleotides, an N50of 881, and an average depth of coverage of 16.29 nucleotides. A subset of 2,196,299 reads were used for assembling the chloroplast genome at an average depth of coverage of 1,094 nucleotides. Sanger sequencing was performed to validate the LSC-IR-SSC junctions and to complete the missing regions of the chloroplast genome. The assembled chloroplast genome map andT. indicagenomic sequence is expected to facilitate genetics and genomic research focused on understanding function of genes involved in halophytic and drought tolerant traits.SPECIFICATIONS TABLEVALUE OF THE DATAGenomic sequence information ofTecticornia indicaand its chloroplast map will be useful for genomics research.Genomics and genetics scientists, bioinformatics and biotechnologists in the fields of photosynthesis, taxonomy and drought tolerance will benefit from these data.These data can be used in developing molecular markers and quantitative trait loci in identification and selection of halophyte and drought tolerance, taxonomic resolution, and variables in photosynthetic genes.
Transcription promotes discrete long-range chromatin loops besides organizing cohesin-mediated DNA folding
Authors: Chapard Christophe , Bastié Nathalie , Cournac Axel , Gadal Olivier , Koszul Romain , Beckouët Frédéric 
Published: December 2023

AbstractThe multi-layered arrangement of eukaryotic genomes and chromosome spatial organization dynamics are of functional importance for gene expression, DNA replication and segregation. SMC complexes are essential instruments of chromosome folding by carrying out long range intra-chromatid DNA looping. Cohesin, in addition to tether sister chromatids, also ensures dynamic regulation of gene expression in mammals by promoting interaction between distal regulatory elements and promoters whereas transcription affects genome folding in numerous organisms and in multiple ways. Here, we comprehensively dissect the relative contributions of transcription and cohesin complexes, as well as their interplay, on the yeastS. cerevisiaegenome organization through DNA borders and loops. Transcription activation specifically induces appearance of DNA borders and loops, independently of SMC complexes, while also directly interfering in addition with cohesin-mediated loop expansion.
ESM-PVP: Identification and classification of phage virion proteins with a large pretrained protein language model and an MLP neural network
Authors: Li Bowen , Liang Guanxiang 
Published: December 2023

AbstractBacteriophages, also known as phages, are essential for the stability of the microbiome system due to their ability to infect prokaryotes, another significant component of the microbiome. Thus, understanding the functions of phage proteins could help us unravel the nature of phages and their roles in the microbiome. However, limited by the low throughput of experimental techniques, a vast number of phage proteins remain unannotated in terms of their functions. Computational methods are expected to solve this restriction due to their high throughput and cost-effectiveness. In this study, we focused on one aspect of functional annotation for phage proteins, the identification and classification of phage virion proteins, and the integration of a large pretrained protein language model and an MLP neural network dramatically improved the performance of these two tasks. Additionally, we compared our model with some previous deep learning models using a newly collected, independent benchmark dataset, demonstrating the strong generalization ability of our model for both tasks. The source codes of ESM-PVP and the software for the PVP identification task have been uploaded to:https://github.com/li-bw18/ESM-PVP.
Diversity and connectivity of principal neurons in the lateral and basal nuclei of the mouse amygdala
Authors: Reéb Zsófia , Magyar Dániel , Weisz Filippo , Fekete Zsuzsanna , Müller Kinga , Vikór Attila , Péterfi Zoltán , Andrási Tibor , Veres Judit M. , Hájos Norbert 
Published: December 2023

ABSTRACTThe basolateral amygdala is a non-layered cortical structure playing a role in various cognitive processes. Despite many studies focusing on local information processing within the circuits of the basolateral amygdala, the characteristics of excitatory principal neurons (PNs) are still not fully revealed. Here, we combined neuroanatomical, electrophysiological, and tracing techniques to determine the single-cell features, dendritic and axonal projections of PNs within the lateral (LA) and basal amygdala (BA). Using a mouse reporter line, we found that cholecystokinin (CCK) expression defines two spatially and functionally segregated groups of PNs both in the LA and BA. PNs in CCK-positive (CCK+) areas of the LA (LAa) had small somata and short dendrites which matched their single-cell electrophysiological properties. PNs in CCK-negative (CCK-) areas of the LA (LAp) and all BA had similarly ramified dendrites and single-cell features with some differences. Importantly, the dendritic arbors of PNs were restricted to the subnuclei defined by CCK expression, which corresponded to various extra-amygdalar afferents indicating specific inputs on distinct PN groups. Axonal arborization patterns of PNs within the basolateral amygdala and surrounding areas showed consistency to their soma location. For instance, BA PNs that projected to the medial prefrontal cortex but not to the lateral nucleus of the central amygdala were present in CCK+ areas. In contrast, those BA PNs that projected to the lateral part of the central nucleus were found in the subnucleus lacking CCK. Our study revealed that the basolateral amygdala is composed of functionally different subnuclei with specific inputs and outputs. This structural arrangement may empower the LA and BA to flexibly channel processed information toward their downstream regions, which can be a key requirement for diverse amygdala functions in cognitive operation.