bluuebunny/crossref_metadata_2025_split huggingface dataset:
Notch is Required for Neural Progenitor Proliferation During Embryonic Eye Regrowth
Authors: Guerin Dylan J. , Gutierrez Belen , Zhang Baoyi , Tseng Kelly Ai-Sun 
Published: February 2024

ABSTRACTThe ability of an organism to regrow tissues is regulated by various signaling pathways. One such pathway that has been studied widely both in the context of regeneration and development is the Notch signaling pathway. Notch signaling is required for development of the eye and regeneration of tissues in multiple organisms but it is unknown if Notch plays a role in the regulation ofXenopus laevisembryonic eye regrowth. We found that Notch1 is required for eye regrowth and regulates retinal progenitor cell proliferation. Chemical and molecular inhibition of Notch1 significantly decreased eye regrowth through reducing retinal progenitor cell proliferation without affecting retinal differentiation. Temporal inhibition studies showed that Notch function is required during the first day of regrowth. Interestingly, Notch1 loss-of-function phenocopied the effects of the inhibition of the proton pump, V-ATPase, where retinal proliferation but not differentiation was blocked during eye regrowth. Overexpression of a form of activated Notch1, the Notch intracellular domain (NICD) was sufficient to rescue loss of eye regrowth due to V-ATPase inhibition, suggesting that Notch acts downstream of V-ATPase. These findings highlight the importance of the Notch signaling pathway in eye regeneration and its role in inducing retinal progenitor cell proliferation in response to injury.
HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis
Authors: Cömert Cagla , Kjær-Sørensen Kasper , Hansen Jakob , Carlsen Jasper , Just Jesper , Meaney Brandon F. , Østergaard Elsebet , Luo Yonglun , Oxvig Claus , Schmidt-Laursen Lisbeth , Palmfeldt Johan , Fernandez-Guerra Paula , Bross Peter 
Published: February 2024

SummaryMitochondrial proteostasis is critical for cellular function and survival. HSP60 is a molecular chaperone that interacts with more than 260 mitochondrial matrix proteins to assist in their folding and few genetic variants of HSP60 are compatible with life. The few reported human patients with HSP60 variants show phenotypes of neurodevelopmental delay associated with brain hypomyelination. It is currently unknown how deficiency of the HSP60 links to hypomyelination. Here, we studied the onset and progression of HSP60 deficiency in: (1) a HSP60 mutation-inducible cell system, (2) skin fibroblasts from patients with disease-associated HSP60 variants, and (3) zebrafish HSP60 knockout larvae. Collectively, we show how HSP60 deficiency leads to pervasive dysfunctions: (1) downregulated mitochondrial matrix proteome, (2) transcriptional activation of cytosolic stress responses, (3) and lipid accumulation with dysregulated cholesterol biosynthesis. In zebrafish larvae HSP60 deficiency induced early developmental abnormalities. Our comprehensive data identifies HSP60 as a master regulator of mitochondrial proteostasis and suggests a pivotal effect of HSP60 dysfunction on myelination through dysregulation of cholesterol biosynthesis.HighlightsHSP60 deficiency disrupts mitochondrial matrix proteins activating stress responsesDisrupted matrix proteome impairs catabolism causing acetyl-CoA shortageHSP60 deficiency dysregulates cytosolic cholesterol synthesisHsp60 deficiency causes developmental abnormalities in zebrafish larvaeDysregulated cholesterol synthesis links HSP60 deficiency to hypomyelinationGraphical abstract
Quantification of beta cell carrying capacity in prediabetes
Authors: Woller Aurore , Tamir Yuval , Bar Alon , Mayo Avi , Rein Michal , Godneva Anastasia , Cohen Netta Mendelson , Segal Eran , Toledano Yoel , Shilo Smadar , Gonze Didier , Alon Uri 
Published: February 2024

AbstractPrediabetes, a subclinical state of high glucose, carries a risk of transition to diabetes. One cause of prediabetes is insulin resistance, which impairs the ability of insulin to control blood glucose. However, many individuals with high insulin resistance retain normal glucose due to compensation by enhanced insulin secretion by beta cells. Individuals seem to differ in their maximum compensation level, termed beta cell carrying capacity, such that low carrying capacity is associated with a higher risk of prediabetes and diabetes. Carrying capacity has not been quantified using a mathematical model and cannot be estimated directly from measured glucose and insulin levels in patients, unlike insulin resistance and beta cell function which can be estimated using HOMA-IR and HOMA-B formula.Here we present a mathematical model of beta cell compensation and carrying capacity, and develop a new formula called HOMA-C to estimate it from glucose and insulin measurements. HOMA-C estimates the maximal potential beta cell function of an individual, rather than the current beta cell function. We test this approach using longitudinal cohorts of prediabetic people, finding 10-fold variation in carrying capacity. Low carrying capacity is associated with higher risk of transitioning to diabetes. We estimate the timescales of beta cell compensation and insulin resistance using large datasets, showing that, unlike previous mathematical models, the new model can explain the slow rise in glucose over decades. Our mathematical understanding of beta cell carrying capacity may help to assess the risk of prediabetes in each individual.
NMDtxDB: Data-driven identification and annotation of human NMD target transcripts
Authors: Britto-Borges Thiago , Gehring Niels , Boehm Volker , Dieterich Christoph 
Published: February 2024

AbstractThe nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use general established rules. We introduce a dataset with 4 cell lines and combinations for SMG5, SMG6 and SMG7 knockdowns or SMG7 knockout. Based on this dataset, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information from Ensembl, Gencode consensus RiboSeq ORFs and OpenProt to enhance the CDS annotation of novel transcript isoforms. 302,889 transcripts were obtained from the transcriptome assembly process, out of which, 48,213 contain a premature stop codon and 6,433 are significantly up regulated in three or more comparisons of NMD active vs deficient cell lines.We present an in-depth view on these results through the NMDtxDB database, which is available athttps://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow athttps://github.com/dieterich-lab/NMDtxDBandhttps://github.com/dieterich-lab/nmd-wf.
Chromosome segment scanning for gain- or loss-of-function screening (CHASING) and its application in metabolic engineering
Authors: Xia Yan , Sun Lichao , Liang Zeyu , Han ZhongRao , Li Jing , Guo Yingjie , Dong Pengyu , Huo Yi-Xin , Guo Shuyuan 
Published: February 2024

AbstractConstructing a library of thousands of single-gene knockout or interference strains is a powerful tool to understand the relation between genotype and phenotype, but it is labor and cost intensive. Powered by the computer-aided gene annotation and functional grouping of non-essential genes, we showed that targeting a single gene directly to a specific observed phenotype could be quickly achieved for a specific microorganism via constructing a library of strains containing single chromosome-segment-deletion per strain. As a proof-of-concept, a genome-scale library consisting of 70 chromosome-segment-deletion strains forB. subtiliswas constructed by CRISPR-based methods and strains with six loss-of- and gain-of-function phenotypes were screened out. To facilitate the rapid genotyping, we developed a web tool to visualize the potential targets of each chromosome segment associated with a particular function, successfully identifying the genes for valuable representative phenotypes. To apply the library to metabolic engineering, the hosts with improved production capacity of acetoin and lycopene were screened in the presence of pathway genes. This work demonstrated the significance of our strategy ofchromosome segment scanning for gain- or loss-of-function screening(CHASING)on functional genomics investigation, robust chassis engineering, and chemical overproduction.Abstract FigureTOC
Label-free and reference region-free X-ray cross-β index for quantifying protein aggregates of neurodegenerative diseases
Authors: Suresh Karthika , Dahal Eshan , Badano Aldo 
Published: February 2024

AbstractBackground and objectivesRecent advancements in therapies targeting various protein aggregates, ranging from oligomers to fibrils, in neurodegenerative diseases exhibit considerable promise. This underscores the imperative for robust quantitative methods capable of accurately detecting and quantifying these biomarker aggregates across different structural states, even when present in sparse quantities during the early stages of the disease continuum. In response to this exigency, we propose and assess an X-ray-based quantitative metric designed for the global and region-specific detection and quantification of oligomers and fibrils within tissues. This methodology proves applicable to a broad spectrum of neurodegenerative diseases, including Alzheimer’s and Parkinson’s. Notably, unlike positron emission tomography (PET)-based biomarker quantification methods, our approach obviates the need for a contrast agent or a reference region.MethodsWe assessed the proposed metric, termed X-ray cross-β aggregate index (XβAI), in a sheep brain model and brain tissue phantoms, incorporating synthetic oligomers and fibrils characterized against amyloid β-42 and α-synuclein aggregates. Detection of these biomarkers utilized laboratory-based monochromatic, and polychromatic X-ray sources, specifically targeting the cross-β substructure of protein aggregates. We employed a peak-location, knowledge-based material decomposition approach to extract target signals from the complex X-ray scattering spectrum originating from a mixture of tissue, water, and aggregate signals.ResultsClinically relevant quantities of oligomers and fibrils were detected in tissues from different brain regions using the laboratory-based X-ray scattering method, without the need for a contrast agent. The signals from protein aggregates were successfully recovered from composite X-ray scattering spectra through material decomposition, eliminating the need for a reference region. The area under the peak of the decomposed inter-β-strand signal correlated well with aggregate burden in synthetically diseased brain tissues. The X-ray cross-β aggregate index (XβAI) accurately quantified aggregate burden in heterogeneous tissues across various brain regions and effectively tracked the deposition increments in specific tissue regions.ConclusionOur study introduces a novel metric, for both regional and global quantification of protein aggregates linked to various protein misfolding diseases, including synucleinopathies.
No cardiac phase bias for threat perception under naturalistic conditions in immersive virtual reality
Authors: Klotzsche Felix , Motyka Paweł , Molak Aleksander , Sahula Václav , Darmová Barbora , Byrnes Conor , Fajnerová Iveta , Gaebler Michael 
Published: February 2024

AbstractPrevious studies have found that threatening stimuli are more readily perceived and more intensely experienced when presented during cardiac systole compared to diastole. Also, threatening stimuli are judged as physically closer than neutral ones. In a pre-registered study, we tested these effects and their interaction using a naturalistic (interactive, 3D) experimental design in immersive virtual reality: We briefly displayed threatening and non-threatening animals (four each) at varying distances (1.5–5.5 meters) to a group of young, healthy participants (n = 41), while recording their ECGs (electrocardiograms). Participants then pointed to the location where they had seen the animal (ca. 29k trials in total). Our pre-registered analyses indicated that perceived distances to both threatening and non-threatening animals did not differ significantly between cardiac phases – with Bayesian analysis supporting the null hypothesis. There was also no evidence for an association between subjective fear and perceived proximity to threatening animals. These results contrast with previous findings that used verbal or declarative distance measures in less naturalistic experimental conditions. Furthermore, our findings suggest that the cardiac phase-related variation in threat processing may not generalize across different paradigms and may be less relevant in naturalistic scenarios than under more abstract experimental conditions.Impact statementTo our knowledge, this is the first study to assess the influence of interoceptive cardiac signals on visual perception using naturalistic stimuli in immersive virtual reality. We based the design of our experiment on previous reports about threat processing biases and the role of the cardiac cycle but did not observe the expected effects. This poses the question of their generalizability from abstract settings to more naturalistic setups, featuring greater behavioral engagement and a richer sensory environment.
Histological comparison of repeated mild weight drop and lateral fluid percussion injury models of traumatic brain injury (TBI) in female and male rats
Authors: Vita Sydney M. , Cruise Shealan C. , Gilpin Nicholas W. , Molina Patricia E. 
Published: February 2024

AbstractTraumatic brain injury (TBI) heterogeneity has led to the development of several preclinical models, each modeling a distinct subset of outcomes. Selection of an injury model should be guided by the research question and the specific outcome measures of interest. Consequently, there is a need for conducting direct comparisons of different TBI models. Here, we used immunohistochemistry to directly compare the outcomes from two common models, lateral fluid percussion (LFP) and repeat mild weight drop (rmWD), on neuropathology in adult female and male Wistar rats. Specifically, we used immunohistochemistry to measure the effects of LFP and rmWD on cerebrovascular and tight junction disruption, inflammatory markers, mature neurons and perineuronal nets in the cortical site of injury, cortex adjacent to injury, dentate gyrus, and the CA2/3 area of the hippocampus. Animals were randomized into either LFP or rmWD groups. The LFP group received a craniotomy prior to LFP (or corresponding sham procedure) three days later, while rmWD animals underwent either weight drop or sham (isoflurane only) on each of those four days. After a recovery period of 7 days, animals were euthanized, and brains were harvested for analysis of RECA-1, claudin-5, GFAP, Iba-1, CD-68, NeuN, and wisteria floribunda lectin. Overall, our observations revealed that the most significant disruptions were evident in response to LFP, followed by craniotomy-only, while rmWD animals showed the least residual changes compared to isoflurane-only controls. These findings support consideration of rmWD as a mild, transient injury. LFP leads to longer-lasting disruptions that are more closely associated with a moderate TBI. We further show that both craniotomy and LFP produced greater disruptions in females relative to males at 7 days post-injury. These findings support the inclusion of a time-matched experimentally-naïve or anesthesia-only control group in preclinical TBI research to enhance the validity of data interpretation and conclusions.
The Switchmaze: an open-design device for measuring motivation and drive switching in mice
Authors: Hartmann Clara , Mahajan Ambika , Borges Vinicius , Razenberg Lotte , Thönnes Yves , Karnani Mahesh M. 
Published: February 2024

AbstractAnimals need to switch between motivated behaviours, like drinking, feeding or social interaction, to meet environmental availability, internal needs and more complex ethological needs such as hiding future actions from competitors. Inflexible, repetitive behaviours are a hallmark of many neuropsychiatric disorders. However, how the brain orchestrates switching between the neural mechanisms controlling motivated behaviours, or drives, is unknown. This is partly due to a lack of appropriate measurement systems. We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. Individual animals access the Switchmaze from the home-cage and choose between entering one of two chambers containing different goal objects or returning to the home-cage. Motivational switching is measured as a ratio of switching between chambers and continuous exploitation of one chamber. Behavioural transition analysis is used to further dissect altered motivational switching. As proof-of-concept, we show environmental manipulation, and targeted brain manipulation experiments which altered motivational switching without effect on traditional behavioural parameters. Chemogenetic inhibition of the prefrontal-hypothalamic axis increased the rate of motivation switching, highlighting the involvement of this pathway in drive switching. This work demonstrates the utility of open-design in understanding animal behaviour and its neural correlates.
A Cell Cycle-aware Network for Data Integration and Label Transferring of Single-cell RNA-seq and ATAC-seq
Authors: Liu Jiajia , Ma Jian , Wen Jianguo , Zhou Xiaobo 
Published: February 2024

ABSTRACTIn recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity and confounding factors. As we know, cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it’s not clear how it will work on the integrated single-cell multi-omics data. Here, we developed a Cell Cycle-Aware Network (CCAN) to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the out-standing performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
MYBL2 drives prostate cancer plasticity and identifies CDK2 as a therapeutic vulnerability in RB1-loss and neuroendocrine prostate cancer
Authors: German Beatriz , Singh Jagpreet N. , Fonseca Marcos AdS , Burkhart Deborah L. , Sheahan Anjali , Bergom Hannah , Morel Katherine L. , Beltran Himisha , Hwang Justin H. , Lawrenson Kate , Ellis Leigh 
Published: February 2024

AbstractPhenotypic plasticity is a recognized mechanism driving therapeutic resistance in prostate cancer (PCa) patients. While underlying molecular causations driving phenotypic plasticity have been identified, therapeutic success is yet to be achieved. To identify putative master regulator transcription factors (MR-TF) driving phenotypic plasticity in PCa, this work utilized a multiomic approach using genetically engineered mouse models of prostate cancer combined with patient data to identify MYBL2 as a significantly enriched transcription factor in PCa exhibiting phenotypic plasticity. Genetic inhibition ofMybl2using independent murine PCa cell lines representing phenotypic plasticity demonstratedMybl2loss significantly decreased in vivo growth as well as cell fitness and repressed gene expression signatures involved in pluripotency and stemness. Because MYBL2 is currently not druggable, a MYBL2 gene signature was employed to identify cyclin-dependent kinase-2 (CDK2) as a potential therapeutic target. CDK2 inhibition phenocopied genetic loss ofMybl2and significantly decreased in vivo tumor growth associated with enrichment of DNA damage. Together, this work demonstrates MYBL2 as an important MR-TF driving phenotypic plasticity in PCa. Further, high MYBL2 activity identifies PCa that would be responsive to CDK2 inhibition.SignificancePCa that escapes therapy targeting the androgen receptor signaling pathways via phenotypic plasticity are currently untreatable. Our study identifies MYBL2 as a MR-TF in phenotypic plastic PCa and implicates CDK2 inhibition as novel therapeutic target for this most lethal subtype of PCa.
Disruption of DLL4/NOTCH1 Causes Dysregulated PPARγ/AKT Signaling in Pulmonary Arterial Hypertension
Authors: Awad Keytam S. , Wang Shuibang , Dougherty Edward J. , Keshavarz Ali , Demirkale Cumhur Y. , Yu Zu Xi , Miller Latonia , Elinoff Jason M. , Danner Robert L. 
Published: February 2024

AbstractPulmonary arterial hypertension (PAH) is a progressive cardiopulmonary disease characterized by vascular remodeling of small pulmonary arteries. Endothelial dysfunction in advanced PAH is associated with proliferation, apoptosis resistance, and endothelial to mesenchymal transition (EndoMT) due to aberrant signaling. DLL4, a cell membrane associated NOTCH ligand, activates NOTCH1 signaling and plays a pivotal role maintaining vascular integrity. Inhibition of DLL4 has been associated with the development of pulmonary hypertension, but the mechanism is incompletely understood. Here we report thatBMPR2silencing in PAECs activated AKT and decreased DLL4 expression. DLL4 loss was also seen in lungs of patients with IPAH and HPAH. Over-expression of DLL4 in PAECs inducedBMPR2promoter activity and exogenous DLL4 increasedBMPR2mRNA through NOTCH1 activation. Furthermore, DLL4/NOTCH1 signaling blocked AKT activation, decreased proliferation and reversed EndoMT inBMPR2– silenced PAECs and ECs from IPAH patients. PPARγ, suppressed by BMPR2 loss, was induced and activated by DLL4/NOTCH1 signaling in bothBMPR2-silenced and IPAH PAECs, reversing aberrant phenotypic changes, in part through AKT inhibition. Finally, leniolisib, a well-tolerated oral PI3K8/AKT inhibitor, decreased cell proliferation, induced apoptosis and reversed markers of EndoMT inBMPR2-silenced PAECs. Restoring DLL4/NOTCH1/PPARγ signaling and/or suppressing AKT activation may be beneficial in preventing or reversing the pathologic vascular remodeling of PAH.