bluuebunny/crossref_metadata_2025_split huggingface dataset:
LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis
Authors: Lewis Renard , Sinigiani Virginia , Koos Krisztian , Bersaglieri Cristiana , Ashiono Caroline , Santoro Raffaella , Ciaudo Constance , Horvath Peter , Sharma Puneet , Kutay Ulrike 
Published: December 2024

SummaryIn most eukaryotic cells, euchromatin is localized in the nuclear interior, whereas heterochromatin is enriched at the nuclear envelope (NE). This conventional chromatin organization is established by heterochromatin tethering to the NE, however its importance for cellular homeostasis is largely unexplored. Peripheral heterochromatin localization relies on redundant NE-tethering systems. One tether is constituted by the lamin B receptor (LBR) in mammals, but the enigmatic nature of the other tethers has hampered functional analyses. Here we demonstrate that the downregulation of abundant, ubiquitous NE proteins can induce the global detachment of heterochromatin from the NE. Among these factors, we identify LBR and LAP2 as major players in bulk heterochromatin attachment to the NE in pluripotent and differentiated mammalian cells. Their loss leads to repositioning of heterochromatin to the nuclear interior, changes in chromatin accessibility, deregulation of gene expression including activation of antiviral innate immunity, and defects in cell fate determination.
A 36-base hairpin within lncRNADRAIC, modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes
Authors: Hao Xiaoxiao , Chen Yuechuan , Sahu Divya , Przanowska Róża K. , Weidmann Chase A. , Nardi Isaac , Weeks Kevin M. , Dutta Anindya 
Published: December 2024

AbstractThe 1.7 kb DRAIC long noncoding RNA inhibits tumor growth, inhibits cancer cell invasion, migration, colony formation and interacts with IKK (IκB kinase) subunits, inhibiting the phosphorylation and degradation of the NF-κB inhibitor, IκB, to suppress the activation of NF-κB. Whether these activities are all linked is unclear. We used SHAPE-MaP to obtain the secondary structure of the lncRNA to perform structure-functions studies which identified the minimal region of DRAIC necessary for repressing NF-κB. A 36-nucleotide hairpin (A+B) within DRAIC inhibits NF-κB, inhibits IκB phosphorylation and binds specifically with the IKKα coiled- coil domain with a very high affinity: KDof ∼1-5 nM. This interaction weakens the dimerization of of the coiled coil domains of two IKK subunits, a dimerization that is indispensable for IKK activity. A+B is sufficient and necessary to inhibit the oncogenic phenotypes in multiple cancer cell-lines, demonstrating that interaction with IKK and inhibition of NF-κB is key for cancer suppression by DRAIC. Presence of this critical hairpin is modulated by alternative splicing the extends exon 4 to exon 4a of DRAIC and the expression of exon 4a in lung tumors is associated with low NF-κB activity. This is also the first demonstration that a short RNA can disrupt coiled- coil dimerization.
Grin2aAblation Distinctly Reshapes PV+ and SST+ Interneuron circuits in the Medial Prefrontal Cortex to Amplify Gamma Oscillations
Authors: Hosseini Hassan , Evans-Martin Sky , Jones Kevin S. 
Published: December 2024

AbstractSchizophrenia (SCZ) is a debilitating mental health disorder marked by cognitive deficits, especially in executive functions, which are often resistant to treatment. TheGRIN2Agene encodes the GluN2A subunit of N-methyl-D-aspartate (NMDA) receptor. Rare coding mutations inGRIN2A, such as protein-truncating variants, increase susceptibility to SCZ by ∼20-fold. However, the effects on network dynamics and the function of GABAergic interneurons (INs) in the medial prefrontal cortex (mPFC) remain unclear. In this study, we use brain slices fromGrin2amutant mice to investigate inhibitory synaptic and oscillatory activity driven by parvalbumin-positive (PV+) and somatostatin-positive (SST+) INs. Our findings reveal significant alterations in synaptic currents and inhibitory modulation arise from GluN2A deficiency. Specifically, both heterozygous and knockoutGrin2amutants exhibit impaired synaptic transmission and release properties of INs inputs, including changes in release probability and evoked quantal events to layer V pyramidal neurons. Genotype-dependent alterations were observed in the frequency, kinetics, and amplitude of excitatory and inhibitory postsynaptic currents. Immunohistochemical analysis showed an increased density of PV+ and SST+ INs in theGrin2amutants, consistent with an overall increase in inhibitory tone. Additionally, optogenetic stimulation revealed a dynamic shift for inducing gamma-band oscillations through PV+ INs. Overall, our study highlights the essential role of GluN2A-containing NMDA receptors in modulating inhibitory tone and maintaining network stability in the mPFC of adult mice and elucidates a pathophysiological mechanism that might contribute to cognitive deficits often observed in SCZ patients.
On the variation of structural divergence among residues in enzyme evolution
Authors: Echave Julian , Carpentier Mathilde 
Published: December 2024

AbstractStructural divergence varies among protein residues. Unlike the classic problem of substitution rate variation, this structural divergence variation has been largely ignored. Here we show that in enzymes structural divergence increases with both residue flexibility and distance from the active site. Although these factors are correlated, we demonstrate through modelling that the pattern arises from two independent types of constraints, non-functional and functional. Their relative importance varies across enzyme families: as functional constraints increase from 4% to 85%, non-functional constraints decrease from 96% to 15%, reshaping the divergence pattern. This analysis overturns two accepted views in protein evolution: First, evolutionary variation has been thought to mirror protein dynamics generally, but we show this similarity exists only when non-functional constraints dominate. Second, active site structural conservation has been attributed to functional constraints alone, but we show it stems largely from their location in rigid regions where non-functional constraints are high.
Dissecting the functional heterogeneity of glutamatergic synapses with high-throughput optical physiology
Authors: Barlow Samuel T. , Levy Aaron D. , Contreras Minerva , Anderson Michael C. , Blanpied Thomas A. 
Published: December 2024

AbstractFluorescent reporters for glutamate release and postsynaptic Ca2+signaling are essential tools for quantifying synapse functional heterogeneity across neurons and circuits. However, leveraging these probes for neuroscience requires scalable experimental frameworks. Here, we devised a high-throughput approach to efficiently collect and analyze hundreds of optical recordings of glutaamate release activity at presynaptic boutons in cultured rat hippocampal neurons. Boutons exhibited remarkable functional heterogeneity and could be separated into multiple functional classes based on their iGluSnFR3 responses to single action potentials, paired stimuli, and synaptic parameters derived from mean-variance analysis. Finally, we developed a novel all-optical assay of pre- and postsynaptic glutamatergic synapse function. We deployed iGluSnFR3 with a red-shifted, postsynaptically-targeted Ca2+sensor, enabling direct imaging and analysis of NMDA receptor-mediated synaptic transmission at large numbers of dendritic spines. This work enables direct observation of the flow of information at single synapses and should speed detailed investigations of synaptic functional heterogeneity.
Circadian regulation of key physiological processes by the RITMO1 clock protein in the marine diatomPhaeodactylum tricornutum
Authors: Manzotti Alessandro , Monteil Raphaël , Cheminant Navarro Soizic , Croteau Dany , Charreton Lucie , Hoguin Antoine , Strumpen Nils Fabian , Jallet Denis , Daboussi Fayza , Kroth Peter , Bouget François-Yves , Jaubert Marianne , Bailleul Benjamin , Bouly Jean-Pierre , Falciatore Angela 
Published: December 2024

SummaryPhasing biological and physiological processes to periodic light-dark cycles is crucial for the life of most organisms. Marine diatoms, as many phytoplanktonic species, exhibit biological rhythms, yet their molecular timekeepers remain largely uncharacterized. Recently, the bHLH-PAS protein RITMO1 has been proposed to act as a regulator of circadian rhythms.In this study, we first determined the physiological conditions to monitor circadian clock activity and its perturbation in the diatom model speciesPhaeodactylum tricornutumby using cell fluorescence as a circadian output. Employing ectopic overexpression, targeted gene mutagenesis, and functional complementation, we then investigated the role of RITMO1 in various circadian processes.Our findings reveal that RITMO1 significantly influences theP. tricornutumcircadian rhythms not only of cellular fluorescence, but also of photosynthesis and of the expression of clock-controlled genes, including transcription factors and putative clock input/output components. RITMO1 effects on rhythmicity are unambiguously detectable under free running conditions.By uncovering the complex regulation of biological rhythms inP. tricornutum, these results provide a key step in understanding the endogenous regulators of phytoplankton physiological responses to environmental changes. Furthermore, these studies position diatoms as instrumental and novel model systems for elucidating key mechanistic principles of oscillator functions in marine ecosystems.
BMI1-mediated heterochromatinization represses G-quadruplex DNA formation to maintain genomic stability during replication
Authors: Hanna Roy , Bernier Gilbert 
Published: December 2024

SummarySingle-stranded DNA secondary structures such as G-quadruplexes (G4s) can potentially disrupt transcription, replication, and repair. Using bio-informatic analysis, here we show that BMI1 is enriched at putative G4s flanked by heterochromatin domains, and thatBMI1knockdown in human dermal fibroblasts (HDFs) resulted in heterochromatin relaxation and G4 induction, followed by replication stress and genomic instability. In these cells, G4s co-localized with large 53BP1 and PCNA foci resembling replication catastrophes. Inhibiting transcription partly attenuated DNA damage, suggesting rescue of transcription-replication collisions at difficult-to-replicate sequences. InBMI1knockdown or pyridostatin-exposed HDFs, the Werner helicase accumulated and co-localized with G4s. AcuteWRNknockdown also resulted in G4 induction. In HDFs from Werner and Hutchinson-Gilford progeria syndromes, loss of heterochromatin and nuclear envelope anomalies were associated with G4 induction and DNA damage. Nuclear envelope anomalies were also prominent followingBMI1knockdown. These findings suggests that heterochromatin-mediated repression of G4s attenuates replication stress and genomic instability, and that this mechanism is shared across distinct progeroid models.
Engineered biological neural networks as basic logic operators
Authors: Küchler Joël , Vulić Katarina , Yao Haotian , Valmaggia Christian , Ihle Stephan J. , Weaver Sean , Vörös János 
Published: December 2024

AbstractWe present anin vitroneuronal network with controlled topology capable of performing basic Boolean computations, such as NAND and OR. Neurons cultured within polydimethylsiloxane (PDMS) microstructures on high-density microelectrode arrays (HD-MEAs) enable precise interaction through extracellular voltage stimulation and spiking activity recording. The architecture of our system allows for creating non-linear functions with two inputs and one output. Additionally, we analyze various encoding schemes, comparing the limitations of rate coding with the potential advantages of spike-timing-based coding strategies. This work contributes to the advancement of hybrid intelligence and biocomputing by offering insights into neural information encoding and decoding with the potential to create fully biological computational systems.
Genome-wide identification, characterization and expression analysis ofCsC3Hgene family in cucumber (Cucumis sativusL) under various abiotic stresses
Authors: Uddin Saleem , Gull Sadia , Mahmood Umer 
Published: December 2024

AbstractThe CCCH zinc finger (C3H) gene family plays a significant role in plant growth, development, and stress response mechanisms. In cucumber (Cucumis sativusL), the CsC3H gene family has been implicated in mediating responses to abiotic stresses, though its functional characterization remains underexplored. This study provides a comprehensive genome-wide identification, characterization, and expression analysis of the CsC3H gene family in cucumber, with a focus on their roles in stress tolerance. 38 CsC3H genes have been discovered, and detailed conserved motif and domain analyses revealed key structural features essential for their function. Phylogenetic analysis classified the CsC3H proteins into four distinct subfamilies (CsC3H I–IV), highlighting functional diversification. The gene duplication and expansion analysis indicated that the C3H gene family grew due to both tandem and segmental duplications, with segmental duplications playing a predominant role. qRT-PCR expression profiling revealed widespread expression of CsC3H genes across various cucumber tissues, with distinct differential expression patterns under waterlogging and hormonal treatments (NAA, ETH, MeJA). Notably, CsC3H9 was localized to the nucleus, indicating its potential involvement in regulating cellular processes under stress. These results offer novel information for future studies focused on leveraging genetic innovations to improve stress resilience in cucurbits and other crops while also offering new perspectives on the functional role of CsC3H genes in cucumber.
Exploring High LET Oxygen-Ion FLASH Radiation for Targeting Pancreatic Cancer in Vitro and In Vivo
Authors: Karle Celine , Filosa Domenico Ivan , Akbarpour Mahdi , Schuhmacher Nora , Brons Stephan , Cee Rainer , Schömers Christian , Scheloske Stefan , Petersson Kristoffer , Haberer Thomas , Abdollahi Amir , Debus Jürgen , Tessonnie Thomas , Moustafa Mahmoud , Mairani Andrea , Dokic Ivana 
Published: December 2024

SummaryThis study showcases the feasibility of oxygen ion ultra-high dose rate irradiation for in vitro and in vivo experiments at the Heidelberg Ion-Beam Therapy Center. The results indicate comparable effectiveness to standard dose rate in pancreatic cancer cell killing and tumor control, highlighting its potential to address challenges in treating radio-resistant tumors.
Sex-specific fish recombination landscapes link recombination and karyotype evolution
Authors: Kivioja Teemu , Rastas Pasi 
Published: December 2024

AbstractMeiotic recombination is an ubiquitous feature of sexual reproduction across eukaryotes. While recombination has been widely studied both theoretically and experimentally, the causes of its variation across species are still poorly understood. Composing a coherent view across species has been difficult because of the differences in recombination map generation and reporting of the results. Thus, fundamental questions like why recombination rates differ between sexes (heterochiasmy) in many but not all species remain unanswered. Here we present the first collection of recombination maps that allows quantitative comparisons across a diverse set of species. We generated sex-specific high-density linkage maps for 40 fish species using the same computational pipeline. Comparing the maps revealed that the higher genome-wide recombination rate in females compared to males was linked to the karyotype of the species. The difference between the sexes in the positioning of the crossovers was also highly variable and unrelated to the difference in their total number. Especially in males, CpG content of the sequence was a strong indicator of the broad scale distribution of crossovers between and within chromosomes. More generally, the collection of recombination landscapes can serve as a link between the theoretical and experimental work on recombination.
Quantitative proteome of bacterial periplasmic predation reveals a prey damaging protease
Authors: Lai Ting F. , Jankov Denis , Grossmann Jonas , Roschitzki Bernd , Huwiler Simona G. 
Published: December 2024

AbstractThe rise of antimicrobial resistant pathogens calls for novel ways to kill and damage bacteria. A rich source for bacterial cell-damaging proteins is periplasmic predatory bacteriumBdellovibrio bacteriovorus, which invades, kills and subsequently exits the Gram-negative prey cell. An increased understanding of predatory protein function can be achieved by analyzing their relative abundance at key stages of predation. Here, we present the first quantitative proteome covering the complete predatory life cycle of the bacterial predatorB. bacteriovoruskillingEscherichia coli, quantifying 2195 predator proteins. From these proteins, nine protein clusters sharing similar expression patterns were identified. Towards the end of the life cycle when the predator exits prey remnants, we identified significant amounts of protease Bd2269. Gene knockout and heterologous expression experiments revealed that Bd2269 is involved in the prey exit process and damagesE. colifrom within. This quantitative predator proteome is a valuable resource to unravel bacterial predator-prey interactions and advances the search for novel antimicrobial enzymes.
Exploring Adenosine Analogues for Chondrosarcoma Therapy: In Vitro and In Vivo Insights
Authors: Lenté Marion , Aury-Landas Juliette , Taieb Mahdia , Bernay Benoît , Lhuissier Eva , Boumédiene Karim , Baugé Catherine 
Published: December 2024

AbstractChondrosarcoma (CS) is described as resistant to conventional chemotherapy and radiotherapy. The development of new therapeutic approaches is necessary. The aim of the present study is to validate the use of adenosine analogues as a new therapeutic strategy in the treatment of CS.Five adenosine analogues (aristeromycin, cladribine, clofarabine, formycin, and pentostatin) were evaluatedin vitroon several chondrosarcoma cell lines using both 2D cultures and 3D alginate bead models. Cell viability was assessed using Acridine Orange and DAPI staining, or ATP assay. Apoptosis was measured via Annexin V and Propidium Iodide staining, while cell cycle progression was analyzed with DAPI staining. The most promising compounds were further testedin vivousing a xenograft chondrosarcoma model in nude mice.Results showed that four analogues (aristeromycin, formycin, cladribine, and clofarabine) significantly reduced cell viability in 2D cell cultures. Of these, cladribine and clofarabine demonstrated potent efficacy in both 2D and 3D models by inducing apoptosis. Cladribine was further found to induce cell cycle arrest, leading to apoptosis-mediated cell death.In vivo, both cladribine and clofarabine exhibited substantial antitumor effects in a xenograft model.In conclusion, cladribine and clofarabine, which are already approved for clinical use in leukemia and multiple sclerosis, show promise as potential candidates for chondrosarcoma treatment. Their efficacy in preclinical models suggests these molecules could be repurposed for Phase II clinical trials in CS patients.
Methyl-CODEC enables simultaneous methylation and duplex sequencing
Authors: Liu Ruolin , Darbeheshti Farzaneh , Walsh Laurel , Li Rachel , Bae Jin H. , Zeggar Hayet Radia , Narayan Azeet , Xiong Kan , Makrigiorgos G. Mike , Adalsteinsson Viktor A. 
Published: December 2024

AbstractDNA mutations and methylation often contribute to disease development in a synergistic manner. While duplex sequencing is the most accurate method for detecting DNA mutations, it typically lacks the ability to simultaneously assess methylation or requires many reads. Here, we developed Methyl-CODEC to enable simultaneous methylation sequencing and duplex sequencing using single read pairs. To achieve this, Methyl-CODEC links an enzymatically deaminated sense strand to the reverse complement of the antisense strand, which is protected from conversion by using conversion-resistant dCTPs in the strand linking step of CODEC. Methyl-CODEC shows high concordance with standard enzymatic or bisulfite based whole genome methylation sequencing, while also uniquely preserving the original DNA sequence. This improves genetic sequencing accuracy, enables better alignment for next-generation sequencing (NGS), and distinguishes C>T mutations from unmethylated Cs. It also identifies rare mutations including those producing methylated Cs, which are enriched in CpG contexts. Methyl-CODEC opens new horizons for enhanced detection of biomarkers in cancer and molecular medicine.
Structural and functional characterization of the KHNYN extended-diKH domain for mediating ZAP antiviral activity
Authors: Youle Rebecca L , Lista María José , Bouton Clement , Kunzelmann Simone , Wilson Harry , Cottee Matthew A , Purkiss Andrew G , Morris Elizabeth R , Neil Stuart J D , Taylor Ian A , Swanson Chad M 
Published: December 2024

AbstractZinc finger antiviral protein (ZAP) binds CpG dinucleotides in viral RNA and targets them for decay. ZAP interacts with several cofactors to form the ZAP antiviral system, including KHNYN, a multidomain endoribonuclease required for ZAP-mediated RNA decay. However, it is unclear how the individual domains in KHNYN contribute to its activity. Here, we demonstrate that the KHNYN amino terminal extended-diKH (ex-diKH) domain is required for antiviral activity and present its crystal structure. The structure belongs to a rare group of KH-containing domains, characterized by a non-canonical arrangement between two type-1 KH modules, with an additional helical bundle. N4BP1 is a KHNYN paralog with an ex-diKH domain that functionally complements the KHNYN ex-diKH domain. Interestingly, the ex-diKH domain structure is present in N4BP1-like proteins in lancelets, which are basal chordates, indicating that it is evolutionarily ancient. While many KH domains demonstrate RNA binding activity, biolayer interferometry and electrophoretic mobility shift assays indicate that the KHNYN ex-diKH domain does not bind RNA. Furthermore, residues required for canonical KH domains to bind RNA are not required for KHNYN antiviral activity. By contrast, an inter-KH domain cleft in KHNYN is a potential protein-protein interaction site and mutations that eliminate arginine salt bridges at the edge of this cleft decrease KHNYN antiviral activity. This suggests that this domain could be a binding site for an unknown KHNYN cofactor.
The NPxY motifs in the β integrin regulates serotonin response and mechanosensation inC. elegans
Authors: Bumm Josh Haram , Lee Daniel Dogeon , Qiu Zhongqiang , Choi Angela , Kolluri Meghana , Olsen Michael J. , Wang Lianzijun , Lee Myeongwoo 
Published: December 2024

ABSTRACTIntegrin is an αβ heterodimeric receptor; its binding to the matrix recruits focal adhesions to two NPxY (Asn-Pro-x-Tyr) motifs, the putative tyrosine phosphorylation sites in the cytoplasmic domain. Here, we report a novel role forpat-3β integrin NPxY motifs inC. elegans. The double non-phosphorylatablepat-3(YYFF)mutant exhibited an egg-laying defect, accumulating more unlaid eggs in the uterus while still responding to serotonin or fluoxetine. The phosphomimetic distalpat-3(Y804E)mutant also displayed a reduced response to serotonin and fluoxetine, suggesting phosphorylation of the distal NPxY motif is associated with vulval contraction. Additionally, the non-phosphorylatablepat-3(Y792F),pat-3(YYFF), disruptivepat-3(Y792A), and phosphomimeticpat-3(Y804E)mutants exhibited mechanosensation defects, demonstrating that NPxY phosphorylation regulates sensory responses. Our results underscore the functional importance ofpat-3NPxY motifs in muscle and sensory neurons, potentially linking integrin NPxY motifs to muscle anomalies and mechanosensory functions.