bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein-coding mutation inAdcy3increases adiposity and alters emotional behaviors sex-dependently in rats
Authors: Fitzpatrick Mackenzie , Szalanczy Alexandria , Beeson Angela , Vora Anusha , Scott Christina , Grzybowski Michael , Klotz Jason , Der Nataley , Chen Rong , Geurts Aron M. , Woods Leah C. Solberg 
Published: June 2024

1AbstractObjectiveAdenylate cyclase 3 (Adcy3)has been linked to both obesity and major depressive disorder (MDD). Our lab identified a protein-coding variant in the 2ndtransmembrane (TM) helix ofAdcy3in rats, and similar obesity variants have been identified in humans. The current study investigates the role of a TM variant in adiposity and behavior.MethodsWe used CRISPR-SpCas9 to mutate the TM domain ofAdcy3in WKY rats (Adcy3mut/mut). We also created a heterozygous knockout rat in the same strain (Adcy3+/-). Wild-type (WT), Adcy3+/-, and Adcy3mut/mutrats were fed a high-fat diet for 12 weeks. We measured body weight, fat mass, glucose tolerance, food intake, metabolism, emotion-like behaviors, and memory.ResultsAdcy3+/-and Adcy3mut/mutrats weighed more than WT rats due to increased fat mass. There were key sex differences: adiposity was driven by increased food intake in males but by decreased energy expenditure in females. Adcy3mut/mutmales displayed increased passive coping and decreased memory while Adcy3mut/mutfemales displayed increased anxiety-like behavior.ConclusionsThese studies show that the ADCY3 TM domain plays a role in protein function, thatAdcy3may contribute to the relationship between obesity and MDD, and that sex influences the relationships betweenAdcy3, metabolism, and behavior.Study Importance QuestionsWhat is already known about this subject?Adcy3has been linked to both obesity and depression in humans, with protein-coding variants in the transmembrane domain leading to increased obesity. Yet the underlying mechanisms are unknown, and it is unknown if the sameAdcy3variants can cause both obesity and depression.RodentAdcy3knockout models show increased adiposity and altered emotional behaviors, but no rodent models have assessed the role of protein-coding variants inAdcy3.Very few studies have assessed sex differences.What are the new findings in your manuscript?This is the first study to assess the role of a protein-coding variant in the transmembrane domain ofAdcy3, showing increases in both obesity and emotion-like behaviors in a rat model.We observed striking sex differences, where male and female rats had different factors driving their adiposity and different patterns of altered behavior.How might your results change the direction of research or the focus of clinical practice?Understanding the role ofAdcy3in obesity and MDD may lead to improved treatments for both diseases.Improving our understanding of the sex differences caused by the sameAdcy3mutation emphasizes the importance of studying both sexes and paves the way for personalized medicine approaches.
SETD1A-dependent EME1 transcription drives PARPi sensitivity in HR deficient tumour cells
Authors: Sweatman Ellie , Bayley Rachel , Selemane Richad , Higgs Martin R. 
Published: June 2024

ABSTRACTBackgroundCells deficient in DNA repair factors breast cancer susceptibility 1/2 (BRCA1/2) or ataxia-telangiectasia mutated (ATM) are sensitive to poly-ADP ribose polymerase (PARP) inhibitors. Building on our previous findings, we asked how the lysine methyltransferase SETD1A contributed to PARP inhibitor-mediated cell death and determined the mechanisms responsible.MethodsWe used cervical, breast, lung and ovarian cancer cells bearing mutations inBRCA1orATMand depleted SETD1A using siRNA or CRISPR/Cas9. We assessed the effects of the PARPi Olaparib on cell viability, homologous recombination, and DNA repair. We assessed underlying transcriptional perturbations using RNAseq. We also used data from The Cancer Genomics Atlas (TCGA) to investigate overall patient survival.ResultsLoss of SETD1A from both BRCA1-deficient and ATM-deficient cancer cells was associated with resistance to Olaparib, explained by an partial restoration of homologous recombination. Mechanistically, SETD1A-dependent transcription of the crossover junction endonuclease EME1 correlated with sensitivity to Olaparib in these cells. Accordingly, when SETD1A or EME1 was lost, BRCA1 or ATM-mutated cells became resistant to Olaparib, and homologous recombination was partially restored.ConclusionsLoss of SETD1A or EME1 may explain why patients develop resistance to PARP inhibitors in the clinic.
Unraveling Lineage Roadmaps and Cell Fate Determinants to Postnatal Neural Stem Cells and Ependymal cells in the Developing Ventricular Zone
Authors: Zheng Jianqun , Chen Yawen , Hu Yukun , Lin Jie , Zhu Yujian , Xu Manlin , Song Weihong , Chen Xi 
Published: June 2024

AbstractThe ventricular zone (VZ) is made up of adult neural stem cells (NSCs) and multi-ciliated ependymal cells (EPCs). Both NSCs and EPCs are derived from radial glial cells (RGCs). To date, the transcriptomic dynamics and the molecular mechanisms guiding the cell fate commitment during the differentiation remain poorly understood. In this study, we analysed the developing VZ at the single-cell resolution and identified three distinct cellular states of RGCs: bipotent glial progenitor cells (bGPCs), neonatal NSC-neuroblasts (nNSC-NBs) and neonatal EPCs (nEPCs). The differentiation from bGPCs to nNSC-NBs and nEPCs forms a continuous bifurcating trajectory. Further molecular analysis along the NSC branch unveiled a novel intermediate state of cells expressing oligodendrocyte precursor cell (OPC) and neuroblast (NB) marker genes. Several transcription factors (TFs) were proved to be essential for the EPC-lineage differentiation, with TFEB emerging as a key regulator dictating the bGPC fate. The activation of TFEB promoted differentiation towards NSC-NBs while restrained the trajectory towards EPCs. Our findings offer detailed insights into further understanding VZ development and lay the groundwork for investigating potential therapeutic strategies against VZ-related disorders, such as hydrocephalus and neurodegenerative diseases (NDDs).
PreyTouch: An Automated System for Prey Capture Experiments Using a Touch Screen
Authors: Eyal Regev , Shein-Idelson Mark 
Published: June 2024

AbstractThe ability to catch prey is crucial for survival and reproduction and is subject to strong natural selection across predators. In many animals, prey capture demands the orchestrated activation of multiple brain regions, demonstrating the intricate interplay between sensory processing, decision-making, and motor execution. This makes prey capture a prime paradigm in neuroscience. Further, its ubiquity across species makes it ideal for comparative research and for studying the evolution of cognition. However, despite recent technological advances in the collection and analysis of behavioral data, experimental approaches for studying prey catch are lagging behind. To bridge this gap, we created PreyTouch - a novel system for performing prey capture experiments on a touch screen. PreyTouch incorporates flexible presentation of prey stimulus, accurate monitoring of predator strikes and automated rewarding. The system’s real time processing enables closing the loop between predator movement and prey dynamics for studying predator-prey interactions. Further, the system is optimized for automated long-term experiments and features a web-ui for remote control and monitoring. We successfully validated PreyTouch by conducting long-term prey capture experiments on the lizardPogona Vitticeps. The acquired data revealed the existence of prey preferences, complex prey attack patterns, and fast learning of prey dynamics. The unique properties offered by PreyTouch combined with the ubiquity of prey capture behaviors across animals establish it as a valuable platform for comparatively studying animal cognition.
node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking
Authors: Mandros Panagiotis , Gallagher Ian , Fanfani Viola , Chen Chen , Fischer Jonas , Ismail Anis , Hsu Lauren , Saha Enakshi , DeConti Derrick K. , Quackenbush John 
Published: June 2024

1AbstractComputational methods in biology can infer large molecular interaction networks from multiple data sources and at different resolutions, creating unprecedented opportunities to explore the mechanisms driving complex biological phenomena. Networks can be built to represent distinct conditions and compared to uncover graph-level differences—such as when comparing patterns of gene-gene interactions that change between biological states. Given the importance of the graph comparison problem, there is a clear and growing need for robust and scalable methods that can identify meaningful differences. We introduce node2vec2rank (n2v2r), a method for graph differential analysis that ranks nodes according to the disparities of their representations in joint latent embedding spaces. Improving upon previous bag-of-features approaches, we take advantage of recent advances in machine learning and statistics to compare graphs in higher-order structures and in a data-driven manner. Formulated as a multi-layer spectral embedding algorithm, n2v2r is computationally efficient, incorporates stability as a key feature, and can provably identify the correct ranking of differences between graphs in an overall procedure that adheres to veridical data science principles. By better adapting to the data, node2vec2rank clearly outperformed the commonly used node degree in finding complex differences in simulated data. In the real-world applications of breast cancer subtype characterization, analysis of cell cycle in single-cell data, and searching for sex differences in lung adenocarcinoma, node2vec2rank found meaningful biological differences enabling the hypothesis generation for therapeutic candidates. Software and analysis pipelines implementing n2v2r and used for the analyses presented here are publicly available.
The use of thermostable fluorescent proteins for live imaging inSulfolobus acidocaldarius
Authors: Recalde Alejandra , Nabi Jasmin Abdul , Junker Pierre , van der Does Chris , Elsässer Jana , van Wolferen Marleen , Albers Sonja-Verena 
Published: June 2024

Among hyperthermophilic organisms,in vivoprotein localization is challenging due to the high growth temperatures that can disrupt proper folding and function of mostly mesophilic-derived fluorescent proteins. While protein localization in the thermophilic model archaeonS. acidocaldariushas been achieved using antibodies with fluorescent probes in fixed cells, the use of thermostable fluorescent proteins in thermophilic archaea has so far been unsuccessful.Given the significance of live protein localization in the field of archaeal cell biology, we aimed to identify fluorescent proteins for use inS. acidocaldarius. To achieve this, we expressed various previously published and optimized thermostable fluorescent proteins along with fusion proteins of interest and analyzed the cells using flow cytometry and (thermo-) fluorescent microscopy. Of the tested proteins, Thermal Green Protein (TGP) exhibited the brightest fluorescence when expressed in Sulfolobus cells. By optimizing the linker between TGP and a protein of interest, we could additionally successfully fuse proteins with minimal loss of fluorescence. TGP-CdvB and TGP-PCNA1 fusions displayed localization patterns consistent with previous immunolocalization experiments. These initial results in protein localization inS. acidocaldariusat high temperatures, combined with recent advancements in thermomicroscopy, open new avenues in the field of archaeal cell biology. This progress finally enables localization experiments in thermophilic archaea, which have so far been limited to mesophilic organisms.
Conformational Landscapes of a Class I Ribonucleotide Reductase Complex during Turnover Reveal Intrinsic Dynamics and Asymmetry
Authors: Xu Da , Thomas William C. , Burnim Audrey A. , Ando Nozomi 
Published: June 2024

AbstractUnderstanding the structural dynamics associated with enzymatic catalysis has been a long-standing goal of biochemistry. With the advent of modern cryo-electron microscopy (cryo-EM), it has become conceivable to redefine a protein’s structure as the continuum of all conformations and their distributions. However, capturing and interpreting this information remains challenging. Here, we use classification and deep-learning-based analyses to characterize the conformational heterogeneity of a class I ribonucleotide reductase (RNR) during turnover. By converting the resulting information into physically interpretable 2D conformational landscapes, we demonstrate that RNR continuously samples a wide range of motions while maintaining surprising asymmetry to regulate the two halves of its turnover cycle. Remarkably, we directly observe the appearance of highly transient conformations needed for catalysis, as well as the interaction of RNR with its endogenous reductant thioredoxin also contributing to the asymmetry and dynamics of the enzyme complex. Overall, this work highlights the role of conformational dynamics in regulating key steps in enzyme mechanisms.
The effects of L-carnitine and fructose in improved Ham’s F10 on sperm culture in idiopathic severe asthenospermia within 24h
Authors: Chang Dehui , Li Fudong , Kang Yindong , Yan Yixin , Kong Feiyan , Jiang Wei , Wang Dongxing , Cao Zhigang , Xu Liuting , Huang Chuang , Kang Yafen , Shang Xuejun , Zhang Bin 
Published: June 2024

AbstractTrial designTo study the effects of L-carnitine and fructose on semen parameters of severe asthenospermia patients by sperm culturing in vitro within 24h. We optimized the energy composition and antioxidant substances of sperm culture medium in vitro (based on Ham’s F10 culture medium) by orthogonal test for preparing high quality culture medium. Sperms of 60 patients with idiopathic severe asthenospermia were collected, and cultured in vitro within 24h, by Ham’s F10 culture medium added to different concentrations of L-carnitine and fructose and culture temperature, whose effects on sperm motility were observed to determine which is the most appropriate concentration and temperature.MethodsFor determining the appropriate concentration of L-carnitine and fructose and the suitable culture temperature in Ham’s F10 culture medium, the orthogonal experiments were carried out to optimize above three factors, which had great influence on sperm viability, survival rate, deformity rate and DNA fragmentation index (DFI).ResultsThe final concentration of L-carnitine and fructose was determined in terms of initial tests to assess the effects of different concentrations (4, 8, 12, and 16 mg/ml L-carnitine and 0.125, 0.250, 0.375, and 0.50 mg/ml fructose) on sperm viability and motility in culture. During the operation of processing and culturing sperms in vitro within 24h, orthogonal test showed that sperm viability was better at the final concentration of 8 mg/ml L-carnitine and 0.375 mg/mL fructose in improved Ham’s F10 culture medium at 36.5 ℃.ConclusionIdiopathic severe asthenospermia sperm can be effectively improved by the modified Ham’s F10 culture medium of the final concentration of 8 mg/ml L- carnitine and 0.375 mg/mL fructose in at 36.5 ℃ within 24h, which has shown better culture effect and is superior to Ham’s F10 basic medium.
PSSR2: a user-friendly Python package for democratizing deep learning-based point-scanning super-resolution microscopy
Authors: Stites Hayden , Manor Uri 
Published: June 2024

AbstractPSSR2 improves and expands on the previously established PSSR (Point-Scanning Super-Resolution) workflow for simultaneous super-resolution and denoising of undersampled microscopy data. PSSR2 is designed to put state-of-the-art technology into the hands of the general microscopy and biology research community, enabling user-friendly implementation of PSSR workflows with little to no programming experience required, especially through its integrated CLI and Napari plugin.
Mechanosensitive FHL2 tunes endothelial function
Authors: Seetharaman Shailaja , Devany John , Kim Ha Ram , van Bodegraven Emma , Chmiel Theresa , Tzu-Pin Shentu , Chou Wen-hung , Fang Yun , Gardel Margaret Lise 
Published: June 2024

AbstractEndothelial tissues are essential mechanosensors in the vasculature and facilitate adaptation to various blood flow-induced mechanical cues. Defects in endothelial mechanoresponses can perturb tissue remodelling and functions leading to cardiovascular disease progression. In this context, the precise mechanisms of endothelial mechanoresponses contributing to normal and diseased tissue functioning remain elusive. Here, we sought to uncover how flow-mediated transcriptional regulation drives endothelial mechanoresponses in healthy and atherosclerotic-prone tissues. Using bulk RNA sequencing, we identify novel mechanosensitive genes in response to healthy unidirectional flow (UF) and athero-prone disturbed flow (DF). We find that the transcription as well as protein expression of Four-and-a-half LIM protein 2 (FHL2) are enriched in athero-prone DF bothin vitroandin vivo. We then demonstrate that the exogenous expression of FHL2 is necessary and sufficient to drive discontinuous adherens junction morphology and increased tissue permeability. This athero-prone phenotype requires the force-sensitive binding of FHL2 to actin. In turn, the force-dependent localisation of FHL2 to stress fibres promotes microtubule dynamics to release the RhoGEF, GEF-H1, and activate the Rho-ROCK pathway. Thus, we unravelled a novel mechanochemical feedback wherein force-dependent FHL2 localisation promotes hypercontractility. This misregulated mechanoresponse creates highly permeable tissues, depicting classic hallmarks of atherosclerosis progression. Overall, we highlight crucial functions for the FHL2 force-sensitivity in tuning multi-scale endothelial mechanoresponses.
Lipogenic Lung Fibroblast-derived Extracellular Vesicles Mitigate Cigarette Smoke-Induced Chronic Obstructive Pulmonary Disease Pathologies through LAT1-mediated Alveolar Type II Cell Restoration
Authors: Fujimoto Shota , Hirano Yuta , Watanabe Naoaki , Matsubayashi Sachi , Inukai Shun , Nishioka Saiko , Yoshida Masahiro , Ito Saburo , Minagawa Shunsuke , Hara Hiromichi , Ohtsuka Takashi , Wiriyasermkul Pattama , Nagamori Shushi , Kuwano Kazuyoshi , Araya Jun , Fujita Yu 
Published: June 2024

AbstractEmerging research has revealed specific cellular aberrations in Chronic Obstructive Pulmonary Disease (COPD), with a particular focus on alveolar type 2 (AT2) cells, which play a pivotal role in the restoration of damaged lung tissue and promotion of normal cellular differentiation. Lipofibroblasts (LipoFBs), which are stromal fibroblasts that house lipid droplets, have been identified in close proximity to AT2 cells and have been demonstrated to support AT2 function. In this study, we present a comprehensive investigation into the therapeutic potential of extracellular vesicles (EVs) derived from LipoFBs (LipoFB-EVs) in COPD treatment. They effectively mitigate key COPD pathologies such as cellular senescence and inflammatory responses in lung epithelial cells. This is achieved by reducing reactive oxygen species (ROS) levels and modulating DNA damage response pathways. Moreover, LipoFB-EVs demonstrate antifibrotic properties by inhibiting TGF-β-induced myofibroblast differentiation, surpassing conventional antifibrotic drugs. They also aid in restoring impaired AT2 stem cells, which are crucial for lung homeostasis, by enhancing their viability, colony-forming ability, and proliferation. Furthermore, we identify the presence of L-type amino acid transporter 1 (LAT1) within LipoFB-EVs, which mediates amino acid uptake, particularly leucine transport, and contributes to the restoration of AT2 cell dysfunction. Importantly, the administration of LipoFB-EVs in murine models of COPD resulted in significant improvements in airway inflammation, remodeling, obstruction, cellular senescence, and alveolar emphysema induced by both short- and long-term CS exposure. Overall, our findings highlight the therapeutic potential of LipoFB-EVs as a novel regenerative therapy for COPD, offering promising avenues for future clinical interventions.
Pathogenic LRRK2 mutations cause loss of primary cilia and Neurturin in striatal Parvalbumin interneurons
Authors: Lin Yu-En , Jaimon Ebsy , Tonelli Francesca , Pfeffer Suzanne R. 
Published: June 2024

AbstractParkinson’s disease-associated, activating mutations in LRRK2 kinase block primary cilia formation in cell culture and in specific cell types in the brain. In the striatum that is important for movement control, about half of astrocytes and cholinergic interneurons, but not the predominant medium spiny neurons, lose their primary cilia. Here we show that Parvalbumin interneurons that are inhibitory regulators of movement also lose primary cilia. Without cilia, these neurons are not able to respond to Sonic hedgehog signals that normally induce the expression of Patched protein, and their numbers decrease. In addition, glial cell line-derived neurotrophic factor-related Neurturin expression is significantly decreased. These experiments highlight the importance of Parvalbumin neurons in cilia-dependent, neuroprotective signaling pathways and show that LRRK2 activation decreases Neurturin production, resulting in less neuroprotection for dopamine neurons.SummaryParvalbumin interneurons in the dorsal striatum lose primary cilia in mice harboring Parkinson’s-associated, activating mutations in LRRK2 kinase, resulting in loss of Hedgehog signaling and decreased production of neuroprotective, Glial cell line-derived neurotrophic factor-related Neurturin to support dopamine neurons.
The DNA Replication Checkpoint Targets the Kinetochore for Relocation of Collapsed Forks to the Nuclear Periphery
Authors: Maclay Tyler , Whalen Jenna , Johnson Matthew , Freudenreich Catherine H. 
Published: June 2024

AbstractHairpin forming expanded CAG/CTG repeats pose significant challenges to DNA replication which can lead to replication fork collapse. Long CAG/CTG repeat tracts relocate to the nuclear pore complex to maintain their integrity. Forks impeded by DNA structures are known to activate the DNA damage checkpoint, thus we asked whether checkpoint proteins play a role in relocation of collapsed forks to the nuclear periphery inS. cerevisiae. We show that relocation of a (CAG/CTG)130tract is dependent on activation of the Mrc1/Rad53 replication checkpoint. Further, checkpoint-mediated phosphorylation of the kinetochore protein Cep3 is required for relocation, implicating detachment of the centromere from the spindle pole body. Activation of this pathway leads to DNA damage-induced microtubule recruitment to the repeat. These data suggest a role for the DNA replication checkpoint in facilitating movement of collapsed replication forks to the nuclear periphery by centromere release and microtubule-directed motion.HighlightsThe DNA replication checkpoint initiates relocation of a structure-forming CAG repeat tract to the nuclear pore complex (NPC)The importance of Mrc1 (hClaspin) implicates fork uncoupling as the initial checkpoint signalPhosphorylation of the Cep3 kinetochore protein by Dun1 kinase allows for centromere release, which is critical for collapsed fork repositioningDamage-inducible nuclear microtubules (DIMs) colocalize with the repeat locus and are required for relocation to the NPCEstablishes a new role for the DNA replication and DNA damage checkpoint response to trigger repositioning of collapsed forks within the nucleus.