bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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.
MacqD - A Deep Learning-based Model for Automatic Detection of Socially-housed Laboratory Macaques
Authors: Moat Genevieve J , Gaudet Trafit Maxime , Paul Julian , Bacardit Jaume , Ben Hamed Suliann , Poirier Colline
Published: December 2024

Despite advancements in video-based behaviour analysis and detection models for various species, existing methods are suboptimal to detect macaques in complex laboratory environments. To address this gap, we present MacqD, a modified Mask R-CNN model incorporating a SWIN transformer backbone for enhanced attention-based feature extraction. MacqD robustly detects macaques in their home-cage under challenging scenarios, including occlusions, glass reflections, and overexposure to light. To evaluate MacqD and compare its performance against pre-existing macaque detection models, we collected and analysed video frames from 20 caged rhesus macaques at Newcastle University, UK. Our results demonstrate MacqD's superiority, achieving a median F1-score of 99% for frames with a single macaque in the focal cage (surpassing the next-best model by 21%) and 90% for frames with two macaques. Generalisation tests on frames from a different set of macaques from the same animal facility yielded median F1-scores of 95% for frames with a single macaque (surpassing the next-best model by 15%) and 81% for frames with two macaques (surpassing the alternative approach by 39% ). Finally, MacqD was applied to videos of paired macaques from another facility and resulted in F1-score of 90%, reflecting its strong generalisation capacity. This study highlights MacqD's effectiveness in accurately detecting macaques across diverse settings.
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

Schizophrenia (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

Abstract

Structural 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

Fluorescent 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

Phasing 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

Single-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

We 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

The 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

This 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

Meiotic 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

The 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

Chondrosarcoma (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

DNA 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

Zinc 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

Integrin 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.
A specialized bacterial group II intron is a highly efficient retrotransposon
Authors: Gomes Lucie , Toffano-Nioche Claire , Gautheret Daniel , Costa Maria
Published: December 2024

Mobile group II introns are site-specific retrotransposons composed of a large self-splicing ribozyme and an intron-encoded reverse transcriptase that are widespread in bacterial and organellar genomes. Sequence and structural variations of the ribozyme and the associated reverse transcriptase define several lineages of bacterial group II introns. Interestingly, some of these intron families evolved different mobility strategies while others colonize particular genetic contexts. Here, we have investigated the mobility activity of anEscherichia coligroup II intron that is inserted into the stop codon of the stress-response genegroEL. Using mobility assays based on over-expression from a donor plasmid, we demonstrate that this intron is a highly efficient and site-specific retrotransposon, capable of colonizing thegroELgene of anE. colihost strain according to the insertion pattern observed in natural genomes. Furthermore, we provide evidence that a chromosomal copy of the full-length retrotransposon can be expressed from its native genetic locus to yield mobile retroelement particles. This intron constitutes a novel model system that could help reveal original mobility strategies used by some group II intron retrotransposons to colonize bacterial genomes.
PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis
Authors: Sahoo Subhransu S. , Ramanand Susmita G. , Cuevas Ileana C. , Gao Yunpeng , Lee Sora , Abbas Ahmed , Zhang Xunzhi , Kumar Ashwani , Koduru Prasad , Roy Sambit , Broaddus Russell R. , Bae-Jump Victoria L. , Gladden Andrew B. , Lea Jayanthi , Lucas Elena , Xing Chao , Kobayashi Akio , Mani Ram S. , Castrillon Diego H.
Published: December 2024

In most cancers, including endometrial cancer, tumor suppressor genes harboring inactivating mutations have been systematically cataloged. However, locus-specific epigenetic alterations contributing to cancer initiation and progression remain only partly described, creating knowledge gaps about functionally significant tumor suppressors and underlying mechanisms associated with their inactivation. Here, we show that PAX2 is an endometrial tumor suppressor recurrently inactivated by a distinct epigenetic reprogramming event not associated with promoter hypermethylation. PAX2 is expressed throughout normal endometrial glands; however, microscopic clones with PAX2 protein loss arise spontaneously in adulthood and progress to endometrial precancers and cancers. Here we show that PAX2 protein loss occurs via transcriptional silencing in 80% of endometrial cancers. Mechanistically, transcriptomic, epigenomic, 3D genomic, and machine learning analyses showed that silencing is associated with replacement of open/active chromatin features (H3K27ac/H3K4me3) with inaccessible/repressive features (H3K27me3). The spread of the H3K27me3 signal is restrained by cohesin loops, preventing transcriptional dysregulation of neighboring genes. Functionally, PAX2 loss promoted endometrial carcinogenesis by rewiring the transcriptional landscape via global enhancer reprogramming. Genetically engineered mouse models together with organoid and human cell line studies establishedPax2as an in vivo endometrial tumor suppressor that cooperates withPtento produce lethal cancers. Our discovery of a specific and recurring epigenetic alteration that transcriptionally silencesPAX2to initiate most endometrial cancers opens new lines of investigation into the origins of endometrial cancer with diverse implications for its diagnosis and treatment.

One Sentence Summary

We demonstrate that PAX2 is silenced by a highly recurrent epigenetic mechanism to initiate most endometrial cancers, establishing a novel mechanism of tumor suppressor inactivation.
Flow rapidly replenishes scarce nutrients to promote bacterial growth
Authors: Padron Gilberto C. , Modi Zil , Koch Matthias D. , Sanfilippo Joseph E.
Published: December 2024

In laboratory settings, bacteria grow in static culture with more nutrients than they require. However, bacteria in nature experience flowing environments that are nutrient limited. Using microfluidics and single cell imaging, we discover that flow promotes growth of the human pathogenPseudomonas aeruginosaat surprisingly low nutrient concentrations. In static environments, cells require high nutrient concentrations as they steadily consume non-renewable resources. In flowing environments, cells grow robustly at very low nutrient concentrations that are constantly replenished. Our simulation-guided experiments show how stopping flow halts growth within minutes and varying flow impacts growth gradients across bacterial populations. By precisely delivering nutrients using microfluidics, we learned that cells in flow can grow on glucose concentrations 1,000 times lower than those observed in typical laboratory experiments. The ultralow glucose concentrations sufficient for growth in flow closely align with the affinity of bacterial glucose transporters, suggesting that bacteria have evolved in flowing environments with scarce nutrients. Collectively, our results emphasize the limits of traditional culturing approaches and highlight how depleted environments can unexpectedly support bacterial growth.
Single-cell Organelle Extraction with Cellular Indexing
Authors: Lam Trinh , Su Alison , Gomez Martinez Ana E. , Fomitcheva-Khartchenko Anna , Herr Amy E.
Published: December 2024

Bulk methods to fractionate organelles lack the resolution to capture single-cell heterogeneity. While microfluidic approaches attempt to fractionate organelles at the cellular level, they fail to map each organelle back to its cell of origin—crucial for multiomics applications. To address this, we developed VacTrap, a high-throughput microfluidic device for isolating and spatially indexing single nuclei from mammalian cells. VacTrap consists of three aligned layers: (1) a Bis-gel microwells layer with a ‘trapdoors’ (BAC-gel) base, fabricated atop a through-hole glass slide; (2) a PDMS microwell layer to receive transferred nuclei; and (3) a vacuum manifold. VacTrap operation begins with cell lysis using DDF to release intact nuclei into the Bis-gel microwells, while cytoplasmic proteins are electrophoresed into the Bis-gel. Upon exposure to DTT and vacuum force, the trapdoors open, allowing nuclei to transfer to the PDMS microwells. VacTrap dissolves the trapdoors within 3-5 minutes and achieve synchronized nuclei transfer with 98% efficiency across 80% of trapdoors in a 256-microwell array, surpassing the <1% efficiency of passive transfer without vacuum. Morphology analysis confirmed preservation of organelle integrity throughout VacTrap operation. By enabling spatial indexing of nuclei back to their original cell, VacTrap provides a robust, high-throughput tool for single-cell multiomics applications.
Attention field as a cognitive-behavioral marker for demarcating internet- but not smoking-addiction from reward
Authors: Mao Mingxing , Cai Yaochun , Li Ye , Li Zhuoqun , Dong Wenshan , Wang Yuanyuan , Zhang Xilin
Published: December 2024

Attentional effect (AE), attention profile (AP), and attention field (AF) have been studied extensively, however, their roles in addiction and demarcating addiction from rewards remain unclear. Using a modified Posner-paradigm with two types of pre-rewarded-cues (addiction-related and addiction-unrelated) and four groups (smoking-dependents, internet-dependents, and respective HCs), we found that both AEs and APs were independent of either cue type or group, while AFs were interactively modulated by the two. AFs of addiction-related cues were narrower than those of addiction-unrelated cues for internet-dependents, but not for either smoking-dependents or HCs; AFs of internet-dependents (not smoking-dependents) were narrower than those of HCs for addiction-related cues, but not for addiction-unrelated cues. Significantly, internet-dependents’ reduced AFs can be simulated by the divisive-normalization computation, both of which closely tracked their addictive severities. Our findings identify a cognitive-behavioral marker for demarcating internet-addiction from rewarding, arguing against the notion that internet-addiction, or, more generally, non-substance-addiction, is ill-posed.
Patches: A Representation Learning framework for Decoding Shared and Condition-Specific Transcriptional Programs in Wound Healing
Authors: Beker Ozgur , Amador Dreyton , Pomarino Nima Jose Francisco , Van Deursen Simon , Woappi Yvon , Dumitrascu Bianca
Published: December 2024

Single-cell genomics enables the study of cell states and cell state transitions across biological conditions like aging, drug treatment, or injury. However, existing computational methods often struggle to simultaneously disentangle shared and condition-specific transcriptional patterns, particularly in experimental designs with missing data, unmatched cell populations, or complex attribute combinations. To address these challenges,Patchesidentifies universal transcriptomic features alongside condition-dependent variations in scRNA-seq data. Using conditional subspace learning, Patches enables robust integration, cross-condition prediction, and biologically interpretable representations of gene expression. Unlike prior methods, Patches excels in experimental designs with multiple attributes, such as age, treatment, and temporal dynamics, distinguishing general cellular mechanisms from condition-dependent changes. We appliedPatchesto both simulated data and real transcriptomic datasets from skin injury models, focusing on the effects of aging and drug treatment.Patchesrevealed shared wound healing patterns and condition-specific changes in cell behavior and extracellular matrix remodeling. These insights deepen our understanding of tissue repair and can identify potential biomarkers for therapeutic interventions, particularly in contexts where the experimental design is complicated by missing or difficult-to-collect data.
Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions
Authors: Sahu Vishal Kumar , Sur Subhayan , Agarwal Sanjana , Madhyastha Harish , Ranjan Amit , Basu Soumya
Published: December 2024

MicroRNAs (miRNAs) belong to a short endogenous class of non-coding RNAs which have been well studied for their crucial role in regulating cellular homeostasis. Their role in modulation of diverse biological pathways by intracellular or extracellular communication and interaction with DNA, RNA or protein, projects them or their targets as promising biomarkers and therapeutic agents. However, studying specific interactions in the extracellular or cell-free environment for drug discovery or biomarker establishment is resource-intensive. In this study, we derive a computational approach based on available experimental data to decipher patterns in miRNA-protein interactions in the cell-free milieu. We characterized the miRNA-protein interactome (miRPin,https://www.mirna.in/miRPin) and identified consensus sequences governing these interactions. The study establishes the role of multiple miRNAs and protein interactions present in cell-free environments leading to pathological conditions, viz., role of proteins like METTL3 and AGO2 etc. and miRNAs like hsa-miR-484 and hsa-miR-30 families, hsa-mir-126-5p etc. in association with multiple miRNAs in different cancer types, cardiovascular diseases, and neurological disorders. The findings outlined in the study may facilitate new avenues of therapeutic discovery leading to the understanding of cellular mechanisms underlying therapy relapse and drug resistance. By addressing these interactions in an extracellular environment may further gain insight into regulating disease initiation and progression, overcoming challenges related to drug efficacy and drug delivery in the presence of bilayer membranes with drug efflux pumps.
Laser Speckle Contrast Imaging of Hepatic Microcirculation
Authors: Zhukov Oleg , Postnov Dmitry D. , Hejn Kamilla H. , Ravnskjær Kim , Sosnovtseva Olga
Published: December 2024

The liver controls blood homeostasis and depends critically on adequate blood supply. While the global regulation of liver blood flow via the hepatic arterial buffer response is well established, the mechanisms governing hepatic sinusoidal hemodynamics remain elusive. We use laser speckle contrast imaging to investigate the hepatic microvascular blood flow in anesthetized rats. Laser speckle contrast imaging offers a spatial resolution of a few micrometers, enabling visualization of individual microvessels, and a temporal resolution sufficient to track flow dynamics. This allowed us to resolve individual sinusoids and venules on the liver surface and to detect a reduction of the blood flow following local Angiotensin-II injections. We show that the blood flow oscillates with frequencies within the range of 0.05–0.4 Hz, which may be linked to rhythmic contraction of upstream blood vessels. Our findings provide insights into vessel-specific liver microcirculationin vivo, offering new opportunities to explore vascular dysfunction mechanisms in metabolic liver diseases.
Atypical Visual Selective Attention in Children with Dyslexia: Evidence from N2pc and PD
Authors: Liu Hongyu , Sun Yulu , Wang Zimo , Guo Jialiang , Song Yan , Meng Xiangzhi
Published: December 2024

Efficient visual attention is fundamental to the development of reading abilities. Previous studies have identified visual attention impairments in individuals with dyslexia, particularly in visual attention span and sluggish attention shifting. However, findings regarding basic visual selective attention remain controversial. To address this issue, the present study provides event-related potential (ERP) evidence to verify whether children with developmental dyslexia (DD) suffered from deficits in visual selective attention. A pop-out visual search task was used to examine visual attentional patterns to a lateral target in 66 children (33 children with DD and 33 typically developing (TD) children) using electroencephalography. Compared to TD children, children with DD showed a larger and prolonged P1 component, as well as a larger target-evoked N2pc component. The larger P1 amplitude was associated with lower reading fluency while the larger N2pc amplitude was associated with poor reading comprehension performance. Interestingly, the target-elicited N2pc was followed by positivity (PDcomponent) in TD children but not in children with DD; however, the N2pc amplitude was correlated with the PDamplitude in children with DD. Children with DD show immature early attentional processing and may have an imbalance in the regulation of visual selective attention between attentional selection and suppression. Our findings provide ERP evidence for interpreting the underlying neural mechanism of visual selective attention in children with DD and may offer a new perspective for exploring the mechanism of visual attention deficits in dyslexia.

Research Highlights

In a pop-out visual search task, children with dyslexia exhibited a larger N2pc and an absent PDcomponent.

The absence of the PDcomponent in children with dyslexia may be associated with their larger N2pc amplitudes.

N2pc amplitude is associated with reading ability in children with dyslexia.

Children with dyslexia need to allocate more resources towards the target but also struggle to disengage from the attended location.
Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk
Authors: Gonzalez Freddy L. , Ranaivoson Hafaliana Christian , Andrianiaina Angelo , Andry Santino , Raharinosy Vololoniaina , Randriambolamanantsoa Tsiry Hasina , Lacoste Vincent , Dussart Philippe , Héraud Jean-Michel , Brook Cara E.
Published: December 2024

Kobuviruses (familyPicornaviridae, genusKobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g. SARS-related coronaviruses), a handful of prior reports catalog kobuvirus infection in bats and posit the role of bats as potential progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing significant public health threats. Here, we report detection of kobuvirus RNA in Malagasy fruit bat (Eidolon dupreanum) feces and undertake phylogenetic characterization of one full genome kobuvirus sequence, which nests within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species infection, further characterization of this clade is critical to accurate evaluation of future zoonotic threats.
Polaris: a universal tool for chromatin loop annotation in bulk and single-cell Hi-C data
Authors: Hou Yusen , Baguette Audrey , Blanchette Mathieu , Zhang Yanlin
Published: December 2024

Annotating chromatin loops is essential for understanding the 3D genome’s role in gene regulation, but current methods struggle with low coverage, particularly in single-cell datasets. Chromatin loops are kilo-to mega-range structures that exhibit broader features, such as co-occurring loops, stripes, and domain boundaries along axial directions of Hi-C contact maps. However, existing tools primarily focus on detecting localized, highly-concentrated, interactions. Furthermore, the wide variety of available chromatin conformation datasets is rarely utilized in developing effective loop callers. Here, we present Polaris, a universal tool that integrates axial attention with a U-shaped backbone to accurately detect loops across different 3D genome assays. By leveraging extensive Hi-C contact maps in a pretrain-finetune paradigm, Polaris achieves consistent performance across various datasets. We compare Polaris against existing tools in loop annotation from both bulk and single-cell data and find that Polaris outperforms other programs across different cell types, species, sequencing depths, and assays.
Sex-specific transcriptome dynamics ofAnopheles gambiaeduring embryonic development
Authors: Kalita Agata Izabela , Marois Eric , Rühle Frank , Keller Valsecchi Claudia Isabelle
Published: December 2024

Malaria-transmitting mosquitoes are extremely sexually dimorphic in their anatomy and behaviour. Sex-specific gene expression inAnopheles gambiaeis well-studied in adult stages, but its onset during embryogenesis, apart from sex-determination factors likeYob, remains largely unknown. Here, we report a comprehensive single-embryo transcriptome atlas ofA. gambiaemales and females to understand the earliest stages of establishing the sex-specific expression networks. Our dataset reveals embryonic RNA isoform diversity including a global shift towards distal alternative polyadenylation (APA) sites during the maternal-to-zygotic genome transition. Sex-biased gene expression and alternative splicing are limited during embryogenesis, with most sex-specific patterns emerging post- embryonically. X chromosome dosage compensation is established shortly after zygotic genome activation concomitant with direct binding of the master regulator protein SOA to X- linked promoters. Unlike the dosage compensation regulators inDrosophilaor mammals, SOA operates in a one-step fashion, directly binding CA-rich promoter motifs without prioritizing certain gene groups over others. We propose that theAnophelesdosage compensation system represents an evolutionary endpoint of a gene-by-gene regulatory mechanism that evolved to a chromosome-wide scale.
Chicken shank color determined byInhibition of dermal melanin(ID) is mediated by a structural variation regulatingCDKN2Aexpression
Authors: Li Jingyi , Wang Lei , Yang Sendong , Zhou Xin , Gou Qinli , Cai Jinping , Yang Hongrui , Wang Qiaohua , Li Shijun
Published: December 2024

It is well established that the color of a chicken’s shank is primarily determined by four genetic loci. Among these, theInhibition of dermal melanin(ID) locus, which suppresses black pigmentation in the dermal layer of the shank, is the sole sex-linked mutation and its molecular mechanisms remained elusive. In this study, a resource family with segregating shank colors was constructed. A genome-wide association study utilizing FarmCPU software identified a top-associated SNP located on the Z chromosome. Subsequent linkage mapping further refined the candidate region, enabling the screening of the candidate structural variation. The candidate structural variation is associated with the yellow shank and characterized by a 143 bp deletion accompanied by a 2 bp insertion. Within the same Topologically Associating Domain, only theCDKN2Agene showed differential expression. Functional studies, including CRISPR/Cas9-edited cells, provided evidence that this mutation regulatesCDKN2Atranscription and is responsible for theIDshank color in chickens. The absence of melanocytes is likely due to their apoptosis. This study completes the puzzle of chicken shank color genetics and paves the way for the application of theIDmutation in the auto-sexing of chicks which is intensively needed in layer and broiler industries.
Non-Hermitian multiterminal phase-biased Josephson junctions
Authors: Cayao Jorge , Sato Masatoshi
Published: December 2024

We study non-Hermitian Josephson junctions formed by multiple superconductors and discover the emergence of exceptional points entirely determined by the interplay of the distinct superconducting phases and non-Hermiticity due to normal reservoirs. In particular, in Josephson junctions with three and four superconductors, we find stable lines and surfaces of exceptional points protected by non-Hermitian topology and highly tuneable by the superconducting phases. We also discover that, in Josephson junctions formed by laterally coupled superconductors, exceptional points can result from hybridized Andreev bound states and lead to the enhancement of supercurrents controlled by dissipation. Our work unveils the potential of multiterminal Josephson junctions for realizing higher-dimensional topological non-Hermitian superconducting phenomena.

Published by the American Physical Society
2024