bluuebunny/crossref_metadata_2025 huggingface dataset:
Amygdala GABA Neurons: Gatekeepers of Stress and Reproduction
Authors: Yu Junru , Farjami Saeed , Nechyporenko Kateryna , Li Xiao Feng , Yaseen Hafsa , Lin Yanyan , Ye Jinbin , Hollings Owen , de Burgh Ross , O’Byrne Kevin T. , Tsaneva-Atanasova Krasimira , Voliotis Margaritis
Published: January 2025

Stress can disrupt menstrual cycles, cause infertility, and lead to other reproductive disorders. The posterodorsal medial amygdala (MePD) processes stress signals and regulates the gonadotropin-releasing hormone (GnRH) pulse generator through GABAergic inhibitory projections to the hypothalamus. However, how stress is processed in the MePD - especially involving its dense GABAergic and Urocortin-3 (UCN3) neurons - remains poorly understood.

In this study, we combinein vivoGRadient-INdex (GRIN) lens mini-endoscopic calcium imaging (to track neuronal activity), optogenetics, clustering analysis, and computational modeling to investigate MePD circuitry. Our findings reveal two anti-correlated GABAergic sub-populations in the MePD that dictate responses to both UCN3 neuron stimulation and restraint stress. Our computational modeling suggests that mutual inhibition between these GABAergic groups drives this anti-correlated activity and predicts how these interactions shape downstream responses to stimulation of GABAergic and UCN3 neurons.

We test these predictions using optogenetics and confirm that GABAergic neurons operate downstream of the UCN3 population, playing a crucial role in transmitting UCN3 signals to regulate luteinizing hormone (LH) pulse frequency. Our study is the first to show how GABAergic neurons in the amygdala mediate stress effects on reproductive health, uncovering key neural mechanisms linking emotional and reproductive functions.
Polymerase mutations underlie early adaptation of H5N1 influenza virus to dairy cattle and other mammals
Authors: Dholakia Vidhi , Quantrill Jessica L. , Richardson Samuel , Pankaew Nunticha , Brown Maryn D. , Yang Jiayun , Capelastegui Fernando , Masonou Tereza , Case Katie-Marie , Aejian Jila , Staller Ecco , Sheppard Carol M. , Brown Ian H. , Smith Claire M. , Iqbal Munir , Digard Paul , Barclay Wendy S. , Pinto Rute M. , Peacock Thomas P. , Goldhill Daniel H.
Published: January 2025

In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds and other mammals including humans. Here, we present molecular and virological evidence that the cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes that enabled better replication in bovine cells, as well as cells of other mammalian species including humans and pigs. We find evidence of several mammalian adaptations gained early in the evolution of these viruses in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show this mutation adapts the virus to co-opt bovine ANP32 proteins and thereby enhances virus replication in bovine and primary human airway cells. Importantly, we show that ongoing evolution during 2024 in the PB2 gene, including a convergently arising D740N substitution, further increases polymerase activity in a range of mammalian cells. Thus, the continued circulation of H5N1 in dairy cattle allows virus adaption improving replicative ability in cattle and increasing zoonotic spillover risk.
A glycerol oxidase from Norway spruce (Picea abiesL. Karst.) expands biochemical and structural attributes of the GMC oxidoreductase superfamily
Authors: Paasela Tanja , Schwenner Naike , Zhao Hongbo , Sun Mengyi , Haataja Topi , Karppi Johanna , Vaattovaara Aleksia , Master Emma , Sandgren Mats , Kärkönen Anna , Tenkanen Maija
Published: January 2025

Investigations to uncover the versatility of carbohydrate active enzymes belonging to the auxiliary activity family 3 (AA3) have focused on microbial enzymes. Plant genomes also harbor AA3 encoding genes, and reverse genetics approaches have shown their importance in plant development. To date, however, detailed biochemical characterizations and structures of plant AA3 enzymes have not been reported.

Here, we describe screening AA3 encoding genes from Norway spruce and the first in-depth biochemical and structural characterization of a plant AA3 oxidase,PaAOX1.PaAOX1 was crystallized, and the structure was solved by X-ray crystallography.

PaAOX1 demonstrated highest oxidase activity against glycerol. It oxidized glycerol to glyceraldehyde, then further to glyceric acid, and showed preference for L-glyceraldehyde over D-glyceraldehyde. Despite the low sequence similarity with fungal alcohol oxidases, it had all the structural features of the typical AA3 enzyme.

PaAOX1 has a novel activity among the characterized AA3s, and it showed a new structural arrangement of the region surrounding the catalytic center. Our findings contribute to a deeper understanding of the structural and functional aspects of enzymes in the GMC superfamily, and especially of alcohol oxidases, expanding the knowledge from fungi to plants.
Human milk-derived extracellular vesicles promote the heat shock response in polarized microglia
Authors: Storm Jasmyne A. , Lu Jueqin , Obtial Mon Francis , Wijenayake Sanoji
Published: January 2025

Proteotoxic stress induces microglia polarization and attenuates cytoprotective, pro-survival cellular cascades. Milk-derived extracellular vesicles (MEVs) are lipid-coated nanovesicles that combat pro-inflammation in peripheral cells and tissues; however, the cytoprotective potential of MEVs remains unknown in brain macrophages. We investigated whether MEVs reduce neuroinflammation in human microglia by activating the heat shock response (HSR). The HSR triggers the upregulation of molecular chaperones (heat shock proteins; HSPs) to restore proteostasis by refolding or degrading misfolded aggregates. MEVs were isolated from unpasteurized human donor milk. Human microglia clone 3 (HMC3) cells were primed with 10 ng/mL IFN-γ to induce polarization, and a subset of cells were supplemented with 200 µg of MEVs. The abundance of HSF1 and candidate HSPs (Hsp70, Hsp90, Hsp40, Hsp27) were analyzed via RT-qPCR and western immunoblotting at 6h, 12h, and 24h post-MEV supplementation. We found that MEV supplementation promoted the HSR in polarized microglia, compared to homeostatic cells. Furthermore, MEVs increased the duration of the HSR in response to pro-inflammatory stress, exerting robust and continued pro-survival benefits.
Rev-RRE activity modulates HIV-1 replication and latency reactivation: Implications for viral persistence and cure strategies
Authors: Dzhivhuho Godfrey A. , Jackson Patrick E. H. , Honeycutt Ethan S. , da Silva Mesquita Flavio , Huang Jing , Hammarskjold Marie-Louise , Rekosh David
Published: January 2025

The HIV-1 Rev-RRE regulatory axis plays a crucial role in viral replication by facilitating the nucleo-cytoplasmic export and expression of viral mRNAs with retained introns. In this study, we investigated the impact of variation in Rev-RRE functional activity on HIV-1 replication kinetics and reactivation from latency. Using a novel HIV-1 clone with an interchangeable Rev cassette, we engineered viruses with different Rev functional activities and demonstrated that higher Rev-RRE activity confers greater viral replication capacity while maintaining a constant level of Nef expression. In addition, a low Rev activity virus rapidly acquired a compensatory mutation in the RRE that significantly increased Rev-RRE activity and replication. In a latency model, proviruses with differing Rev-RRE activity levels varied in the efficiency of viral reactivation, affecting both initial viral release and subsequent replication kinetics. These results demonstrate that activity differences in the Rev-RRE axis among different viral isolates have important implications for HIV replication dynamics and persistence. Importantly, our findings indicate that bolstering Rev/RRE activity could be explored as part of latency reversal strategies in HIV cure efforts.

Author Summary

The activity of the HIV-1 Rev-RRE axis is essential for viral replication and varies among primary viral isolates. However, the role of this for viral fitness, evolution, and persistence has not previously been investigated. Our results show that duringin vitroreplication, there is a selective fitness advantage for viruses with higher Rev-RRE activity and that HIV has the ability to fine tune this regulatory system with minimal sequence changes. Additionally, the maintenance of Nef expression in low Rev activity viruses suggests a potential mechanism for balancing immune evasion and replication capacity in different selection landscapes within a host. We also show that viruses with low Rev-RRE activity are more difficult to reverse from latency than viruses with higher Rev-RRE activity. Thus, differences in provirus Rev-RRE activity may be a barrier to developing effective latency reversal strategies. These findings provide new insights into the complex roles that the Rev/RRE axis plays in functionality, viral fitness, evolution, and persistence.
Benchmark of Wide Range of Pairwise Distance Metrics for Automated Classification of Mouse Mutant Phenotypes from Flow Cytometry Data
Authors: May M. , Hewitt T. , Mashford B. , Hammill D. , Davies A. , Andrews T. D.
Published: January 2025

Precision medicine requires a comprehensive mapping of genotype to phenotype to provide patients with individually tailored treatment. However, when using flow cytometry to identify phenotypes, such as the quantity of various immune cell populations in tissue and blood used to identify autoimmune disorders, it is often unclear which cellular phenotypes are from healthy and disease individuals, especially when including the effects of population diversity, due to the high-dimensional nature of the data. To identify and segregate healthy phenotype from various disease phenotypes, we use pairwise distance metrics between each sample’s cell populations. By comparing distance metrics between C57BL/6 clone mice with mutations of known phenotype, we find that cosine similarity is best suited for segregating wildtype from mutant samples while respecting minute differences in already small cell populations, and that standardised Euclidean distance is best suited for machine-learning input due to its sensitivity. Both metrics outperform other tested metrics (including Aitchison, Euclidean, Manhattan, Earth-Movers Distance, and squared Euclidean). We demonstrate the utility of these different pairwise metrics through their application to a classification task of known mutant phenotypes: using an existing FACS phenotype dataset derived from X000 inbred C57BL/6 mice that harbour potentially phenotypic genetic variation introduced through ENU mutagenesis of individual pedigree-founding G0 male mice.
Bacteria induce an amoeboid phase in coccolithophores that persists after bloom collapse
Authors: Zweifel Sophie T. , Henshaw Richard J. , Müller Oliver , Keegstra Johannes M. , Pioli Roberto , Martínez-Pérez Clara , Alcolombri Uria , Clerc Estelle , Stocker Roman
Published: January 2025

Coccolithophores, who contribute approximately 1-10% of phytoplankton biomass, are crucial players in the ocean’s biogeochemical cycles. Significant contributions come from bloom-forming species includingGephyrocapsa huxleyi(formerlyEmiliania huxleyi),which has served as a model system for investigating algal-bacterial and agal-viral interactions as well as algal fitness responses to environmental changes. Coccolithophores follow a biphasic lifecycle, existing as motile haploid and non-motile diploid phases. Here we characterize a third, ‘amoeboid’ phase, using a combination of light, electron and phase amplitude modulation (PAM) microscopy. Using time-resolved imaging we captured the rapid morphological transition from a spherical haploid to an elongated motile amoeboid cell. Cell tracking revealed slower and more directional swimming compared to haploid cells. Amoeboid metamorphosis was triggered by exposure to bacteria, including strains isolated fromG. huxleyiblooms and knownG. huxleyipathogens, but not by a range of classical phytoplankton stressors, including viral infection and oxidative stress. Further, the sub-population of haploids which switched to the amoeboid phase persisted past the rapid crash of the haploid population. This amoeboid phase was only observed in the primary bloom-forming coccolithophore speciesG. huxleyiandGeopharycapsa oceanicain stationary phase when exposed to high bacterial concentrations, typical of late-stage algal bloom events. Photophysiology of amoeboid cells was confirmed to be unaltered via PAM microscopy, indicating these cells are metabolically active. These findings highlight a previously uncharacterized morphotype in this important phytoplankton species and suggest that the amoeboid phase could be a bacteria-resistant morphotype following algal bloom collapse.
The superior colliculus gates dopamine responses to conditioned stimuli in visual classical conditioning
Authors: Zhang Yan-Feng , Dufour Jean-Philippe , Zatka-Haas Peter , Redgrave Peter , Black Melony J , Lak Armin , Mann Ed , Cragg Stephanie J , Abraham Wickliffe C , Reynolds John NJ
Published: January 2025

In classical Pavlovian conditioning, it is well-established that midbrain dopamine neurons respond to conditioned stimuli (CS) that predict a reward. However, how the dopamine neurons associate a neutral CS to a reward remains unknown. Here, we show that the superior colliculus (SC) develops neuronal responses to a visual CS during conditioning, which in turn drive the responses of dopamine neurons. Visual responses in the SC were only potentiated when a behaviorally meaningful time interval separated the visual stimulus and reward. Potentiation also required the convergence of visual, dopamine and serotonin inputs to the SC. Importantly, blocking potentiation of the visual response was sufficient to suppress the dopamine responses following a CS. These results reveal a mechanism for how the brain forms associations between unconditioned stimuli and behaviorally meaningful visual information during classical conditioning.
Conditional Denoising Diffusion Probabilistic Models with Attention for Subject-Specific Brain Network Synthesis
Authors: Ajith Meenu , Calhoun Vince D.
Published: January 2025

The development of diffusion models, such as Glide, DALLE 2, Imagen, and Stable Diffusion, marks a significant advancement in generative AI for image synthesis. In this paper, we introduce a novel framework for synthesizing intrinsic connectivity networks (ICNs) by utilizing the nonlinear capabilities of denoising diffusion probabilistic models (DDPMs). This approach builds upon and extends traditional linear methods, such as independent component analysis (ICA), which are commonly used in neuroimaging studies. A central contribution of our work is the integration of attention mechanisms into conditional DDPMs, enabling the generation of subject-specific 3D ICNs. Conditioning the resting-state fMRI (rs-fMRI) data on the corresponding ICNs enables the extraction of individualized brain connectivity patterns, effectively capturing within-subject and between-subject variability. Unlike prior models limited to 2D visualization, this framework generates 3D representations, providing a more comprehensive depiction of ICNs. The model’s performance is validated on an external dataset to prevent over-fitting and for overall generalizability. Furthermore, comparative evaluations also demonstrate that the proposed DDPM-based approach outperforms state-of-the-art generative models in producing more detailed and accurate ICNs, as validated through qualitative assessments.
Targeted stimulation of motor cortex neural ensembles drives learned movements
Authors: Wu An , Chen Qiyu , Yu Bin , Chae Soyoung , Tan Zijing , Ramot Assaf , Komiyama Takaki
Published: January 2025

During the execution of learned motor skills, the neural population in the layer 2/3 (L2/3) of the primary motor cortex (M1) expresses a reproducible spatiotemporal activity pattern. It is debated whether M1 actively participates in generating the activity pattern or it only passively reflects patterned inputs. Furthermore, it is unclear whether this learned activity pattern causally drives the learned movement. We addressed these issues usingin vivotwo-photon calcium imaging combined with holographic optogenetic stimulation of specific ensembles of M1 L2/3 neurons in mice engaged in a skilled lever-press task. We briefly and synchronously stimulated ∼20 neurons whose activity onset in voluntary trials precedes movement onsets. This stimulation, despite lacking temporal patterns, induced movements that resembled the learned movement, while producing spatiotemporal activity patterns in other M1 neurons not directly stimulated that resembled the activity during the voluntary learned movement. Trial-by-trial variability of optogenetically triggered population activity in the non-target neurons correlated with the variability in the induced movements. These trial-by-trial variabilities were predicted by the initial state of M1 population activity immediately preceding the optogenetic stimulation. Stimulation of the neurons whose activity followed voluntary movement onsets failed to induce the learned movement. Thus, the learned activity pattern in M1 L2/3 can be generated when the M1 network is prepared at the optimal initial state and receives precise triggering inputs, supporting the active role of M1 in learned activity generation. The resulting activity pattern then causally drives the learned movement.
Gut epithelium modifies enteric behaviors during nutritional adversity via distinct peptidergic signaling axes
Authors: Sural Surojit , Walker Zion , Hobert Oliver
Published: January 2025

Interorgan signaling events are emerging as key regulators of behavioral plasticity. The foregut and hindgut circuits of theC. elegansenteric nervous system (ENS) control feeding and defecation behavior, respectively. Here we show that epithelial cells in the midgut integrate feeding state information to control these behavioral outputs by releasing distinct neuropeptidergic signals. In favorable conditions, insulin and non-insulin peptides released from midgut epithelia activate foregut and hindgut enteric neurons, respectively, to sustain normal feeding and defecation behavior. During food scarcity, altered insulin signaling from sensory neurons activates the transcription factor DAF-16/FoxO in midgut epithelia, which blocks both peptidergic signaling axes to the ENS by transcriptionally shutting down the intestinal neuropeptide secretion machinery. Our findings demonstrate that midgut epithelial cells act as integrators to relay internal state information to distinct parts of the enteric nervous system to control animal behavior.
The miR156/SPL9 interaction mode regulates the anthocyanin accumulation in potato
Authors: Li Nan , Nie Hushuai , Wu Xiaojuan , Wang Peijie , Ma Yu , Yang Enze , Wu Juan , Zhang Zhicheng , Xie Rui , Wang Dan , Ma Yanhong
Published: January 2025

Anthocyanins are an essential class of flavonoids that represent a large group of plant secondary metabolites. microRNAs (miRNAs) can target TFs related to anthocyanin synthesis and inhibit their expression, thereby affecting the expression level of key downstream structural genes and ultimately regulating the synthesis and accumulation of anthocyanins in plants. Nevertheless, the regulatory function of miR156a in anthocyanin synthesis, especially in potatoes, has yet to be investigated. In this study, the miR156a and its target geneStSPL9were screened and analyzed from small RNA sequencing, degradome sequencing and transient expression assay. The function of miR156a in anthocyanin synthesis of potato tuber was investigated. Overexpression of miR156a (OE-miR156a) in potato tubers promoted anthocyanin synthesis while concurrently reducing flavonoid synthesis compared with wild-type (WT) potatoes. The miR156a-silenced tubers (STTM-miR156a) achieved using short tandem target mimics (STTM) contained significantly lower anthocyanin content and increased flavonoid accumulation compared to WT and OE-miR156a. Notably, overexpression ofStSPL9in potato yielded identical results. The relative expression levels of the anthocyanin-related structural genesPAL,4CL,CHS,CHI,F3H,DFR, andUFGTin STTM-miR156a transgenic potato tubers showed the opposite trend to that observed in OE-miR156a potato tubers, as demonstrated by RNA sequencing and quantitative real-time PCR (qRT-PCR). The integrated analysis of the transcriptome and metabolome revealed that the accumulation of flavonoids and flavonols in STTM-miR156a was significantly increased than in the wild type, whereas the contents of anthocyanins and phenolic acids were notably reduced. Further analysis showed that the expression ofCHS,FG2,BEATH, andCYP75Awere up-regulated in STTM-miR156a, andHCTwas downregulated, which resulted in a reduced accumulation of methyl 4-caffeoylquinate, a phenolic acid metabolite. Therefore, it is demonstrated that miR156a indirectly modulates the expression ofCHS,BEATH,CYP75A,HCT, andFG2by targeting and degrading its target geneStSPL9and otherSPLgenes, thus influencing anthocyanin accumulation in potato tuber. This study provides valuable insights into the complex regulatory network governing anthocyanin biosynthesis inSolanumspecies.
Accumbal acetylcholine signals associative salience
Authors: Zhang Zhewei , Costa Kauê Machado , Zhuo Yizhou , Li Guochuan , Li Yulong , Schoenbaum Geoffrey
Published: January 2025

Learning in dynamic environments requires animals to not only associate cues with outcomes but also to determine cue salience, which modulates how quickly related associations are updated. While dopamine (DA) in the nucleus accumbens core (NAcc) has been implicated in learning associations, the mechanisms of salience are less understood. Here, we tested the hypothesis that acetylcholine (ACh) in the NAcc encodes cue salience. We conducted four odor discrimination experiments in rats while simultaneously measuring accumbal ACh and DA. We found that ACh developed characteristic dips to cues over learning before DA signals differentiated cues by value, with these dips persisting through value decreases and developing faster during meta-learning. The dips reflected the cue salience across learning stages and tasks, as predicted by a hybrid attentional associative learning model that integrated principles from the Mackintosh and Pearce-Hall models, suggesting that accumbal ACh signals encode salience and potentially gate the learning process.
High-throughput protein binder discovery by rapid in vivo selection
Authors: Styles Matthew J. , Pixley Joshua A. , Wei Tongyao , Basile Christopher , Lu Shannon S. , Dickinson Bryan C.
Published: January 2025

Proteins that selectively bind to a target of interest are foundational components of research pipelines1,2, diagnostics3, and therapeutics4. Current immunization-based5,6, display-based7–14, and computational approaches15–17,18for discovering binders are laborious and time-consuming – taking months or more, suffer from high false positives – necessitating extensive secondary screening, and have a high failure rate, especially for disordered proteins and other challenging target classes. Here we establish Phage-Assisted Non-Continuous Selection of Protein Binders (PANCS-binders), anin vivoselection platform that links the life cycle of M13 phage to target protein binding though customized proximity-dependent split RNA polymerase biosensors, allowing for complete and comprehensive high-throughput screening of billion-plus member protein variant libraries with high signal-to-noise. We showcase the utility of PANCS-Binders by screening multiple protein libraries each against a panel of 95 separate therapeutically relevant targets, thereby individually assessing over 1011protein-protein interaction pairs, completed in two days. These selections yielded large, high-quality datasets and hundreds of novel binders, which we showed can be affinity matured or directly used in mammalian cells to inhibit or degrade targets. PANCS-Binders dramatically accelerates and simplifies the binder discovery process, the democratization of which will help unlock new creative potential in proteome-targeting with engineered binder-based biotechnologies.
FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis
Authors: Lange Mike , Wölk Michele , Doubravsky Cody E. , Hendricks Joseph M. , Kato Shunji , Otoki Yurika , Styler Benjamin , Nakagawa Kiyotaka , Fedorova Maria , Olzmann James A.
Published: January 2025

Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidationin vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.
The SinR•SlrR heteromer attenuates transcription of a long operon of flagellar genes inBacillus subtilis
Authors: Mishra Ayushi , Jackson Abby , Wang Xindan , Kearns Daniel B.
Published: January 2025

During growth,Bacillus subtilisdifferentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27 kb longfla/cheflagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA•DegU that activates thefla/chepromoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR•SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer on the genome. We identified two sites within thefla/cheoperon that were both necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.
Diurnal Modulation of Locus Coeruleus Noradrenergic Neurons in Anesthetized Adult Male Rats
Authors: Rae Rosaria J. , Baker Nathaniel L. , Irwin Zachary T. , Shea Stephen D. , McMahon Lori L.
Published: January 2025

The locus coeruleus (LC) is the primary source of noradrenaline (NA) in brain and its activity is essential for learning, memory, stress, arousal, and mood. LC-NA neuron activity varies over the sleep-wake cycle, with higher activity during wakefulness, correlating with increased CSF NA levels. Whether spontaneous and burst firing of LC-NA neurons during active and inactive periods is controlled by mechanisms independent of wakefulness and natural sleep, is currently unknown. Here, using multichannelin vivoelectrophysiology under anesthesia, we assessed LC-NA neuron firing in adult male Fisher 344 rats at two different times of day- ZT4- the inactive period (light phase) and ZT16-the active period (dark phase)- independent of contributions from behavioral arousal and natural sleep. In the dark phase, LC-NA neurons exhibit increased average firing rate during baseline compared to the light phase. Using a relatively weak foot shock paradigm, we observed distinct populations of LC-NA neurons with some increasing, and others decreasing, their firing rate compared to baseline. Additionally, while spike frequency during spontaneous and evoked bursts is consistent across the dark-light phase, units recorded during the dark phase have more frequent bursts with a longer duration than those during the light phase. Our findings show that independent of wake state, LC-NA neurons exhibit intrinsic diurnal activity, and that the variability of response to foot shock stimulation demonstrates a physiological heterogeneity of LC-NA neurons that is just beginning to be appreciated.

NEW & NOTEWORTHY

Multichannelin vivoelectrophysiology assesses activity of large populations of NA neurons within an intact LC. Recording activity under anesthesia eliminates influence of behavior and sleep on LC-NA neuron physiology. Our data show that LC-NA neurons have heightened firing and burst activity during the dark phase, suggesting a hardwired diurnal rhythm. Additionally, LC-NA neurons have variable evoked firing highlighting heterogeneity, consistent with a contemporary view that LC physiology is more complex than previously appreciated.
Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters
Authors: Palacio Megan , Taatjes Dylan J.
Published: January 2025

RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator. TFs and Mediator contain intrinsically-disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a Real-time In-vitro Fluorescence Transcription assay (RIFT) for second-by-second visualization of RNAPII transcription at hundreds of promoters simultaneously. We show rapid RNAPII activation is IDR-dependent, without condensate formation. For example, the MED1-IDR can functionally replace a native TF, activating RNAPII with similar (not identical) kinetics; however, MED1-IDR squelches transcription as a condensate, but activates as a single-protein. TFs and Mediator cooperatively activate RNAPII bursting and re-initiation and surprisingly, Mediator can drive TF-promoter recruitment, without TF-DNA binding. Collectively, RIFT addressed questions largely intractable with cell-based methods, yielding mechanistic insights about IDRs, condensates, enhancer-promoter communication, and RNAPII bursting that complement live-cell imaging data.
Heterochromatinde novoformation and maintenance inPlasmodium falciparum
Authors: Pérez-Cantero Alba , Llorà-Batlle Oriol , Pelaez-Conde Ingrid , Martínez-Guardiola César , Cortés Alfred
Published: January 2025

In the malaria parasitePlasmodium falciparum,the expression of many genes is regulated by heterochromatin (HC) based on the histone mark tri-methylation of histone H3 lysine 9 (H3K9me3). HC assembly involves three distinct steps:de novonucleation, spreading and maintenance. Nucleation, which consists in formation of HC in a previously euchromatic region, determines at which specific regions of the genome HC occurs. This process is not well understood in malaria parasites. Here we investigated the DNA sequencecisdeterminants of HC nucleation inP. falciparum, using a screening approach based on integration of fragments from different heterochromatic genes into an euchromatic locus, followed by H3K9me3 chromatin immunoprecipitation (ChIP) analysis. We found that fragments ofvargene upstream regions nucleated HC efficiently, whereas fragments from thepfap2-gupstream region or from themspdbl2locus did not nucleate HC. Fragments from the beginning of the coding sequence (CDS) ofpfap2-gnucleated HC with low efficiency, as evidenced by nucleation requiring long fragments of ∼2 Kb and occurring only in a fraction of the parasites. These results demonstrate that the primary DNA sequence is a main determinant of HC nucleation inP. falciparum. We also studied HC maintenance at thepfap2-glocus, which demonstrated that specific parts of the upstream region, different from the regions competent for HC nucleation, are required for maintenance. Together, our results provide initial insight into how HC is directed to specific loci and maintained inP. falciparum.
A Class 1 OLD family nuclease encoded byVibrio choleraeis countered by a vibriophage-encoded direct inhibitor
Authors: Patel Kishen M. , Seed Kimberley D.
Published: January 2025

Bacteria are constantly threatened by their viral predators (phages), which has resulted in the development of defense systems for bacterial survival. One family of defense systems found widely across bacteria are OLD (for overcoming lysogeny defect) family nucleases. Despite recent discoveries regarding Class 2 and 4 OLD family nucleases and how phages overcome them, Class 1 OLD family nucleases warrant further study as there has only been one anti-phage Class 1 OLD family nuclease described to date. Here, we identify theVibrio cholerae-encoded Class 1 OLD family nuclease Vc OLD and describe its disruption of genome replication of the lytic vibriophage ICP1. Furthermore, we examine itsin vitroactivity, identifying Vc OLD as a DNA nickase. Finally, we identify the first direct inhibitor of a Class 1 OLD family nuclease, the ICP1-encoded Oad1. Our research further illuminates Class 1 OLD family nucleases’ role in phage defense and explores the dynamic arms race betweenV. choleraeand its predatory phage ICP1.
DrosophilaToll-2 controls homeotic domain formation and timing of folding
Authors: Alpar Lale , Pigache Rémi , Leroy Adrien , Ech-Chouini Mehdi , Pelletier Stéphane , Bellaïche Yohanns
Published: January 2025

Tissue compartmentalization is a fundamental feature of animal development, crucial for determining cell fate, growth, and organ morphogenesis. Hox genes play essential and conserved roles in specifying homeotic compartments along the antero-posterior axis of the body. Despite extensive characterization of homeotic gene regulation, the mechanisms underlying the formation, maintenance, and reshaping of homeotic compartments during development remain incompletely understood. Here, we investigate the role of the Toll-2 receptor in the formation and folding of the Deformed (Dfd) homeotic compartment, which produces the neck of adultDrosophila. We show that Toll-2 is essential for properly forming the bilateral Dfd compartment through the fusion of the two eye-antennal imaginal discs. Additionally, we find that Toll-2 regulates the timing of neck morphogenesis by promoting cell apoptosis and cell-cell rearrangements preceding neck folding. Last, we establish that Toll-2 independently and sequentially governs both homeotic compartment formation and the timing of its morphogenesis via PI3K and Src signaling, respectively. Altogether, our findings provide novel insights into the spatiotemporal regulation of homeotic compartment development.
A temperature sensitive mutant screen reveals translational stress-induced cell cycle regulation in a thermophilic archaeon
Authors: Foo Sherman , Kuo Yin-Wei , Traparić Jovan , Grogan Dennis W. , Baum Buzz
Published: January 2025

The homology of the archaeal and eukaryotic ribosome provides one of the key pieces of evidence that underpins the idea that eukaryotes acquired their core information processing machinery from archaea. Since this discovery, reverse genetics has been used to study the functions of many archaeal proteins with eukaryotic homologues. Yet, our general understanding of archaeal growth and division remains unclear, in part because of difficulties of carrying out unbiased genetic screens in archaea. Here, by overcoming several technical hurdles we have used a screen of temperature sensitive mutants inSulfolobus acidocaldariusto identify core regulators of cell growth and division. First, flow cytometry was used to define DNA content, identifying a set of mutants defective in cell cycle progression at elevated growth temperatures. Using genome sequencing and plasmid rescue, we then identified a point mutation in the large ribosomal subunit that inhibits translation and prevents entry into division following a shift to the restrictive temperature. This study reveals a link between translation and cell cycle control, and opens up the future possibility of using forward genetic screens in archaea to further our understanding of the similarities and differences in the cell biology of archaea, bacteria and eukaryotes.

Significance statement

Current knowledge of archaeal cell biology is limited by the lack of forward genetics.

Whole genome sequencing and plasmid rescue identifies causative mutation in a temperature sensitive mutant strain.

A mutation in a ribosomal subunit blocks translation to prevent entry into division.
Identification of low copy synaptic glycine receptors in the mouse brain using single molecule localisation microscopy
Authors: Camuso Serena , Vella Yana , Abadi Souad Youjil , Mille Clémence , Brône Bert , Specht Christian G
Published: January 2025

Glycine receptors (GlyRs) are heteropentameric chloride channels that mediate fast inhibitory neurotransmission in the brainstem and spinal cord, where they regulate motor and sensory processes. GlyRs are clustered at the post-synaptic membrane by a strong interaction of the β subunit with the scaffold protein gephyrin. Even though GlyRβ mRNA is highly expressed throughout the brain, the existence of synaptic GlyRs remains controversial as there is little conclusive evidence using conventional fluorescence microscopy and electrophysiological recordings. Here we exploit the high sensitivity and spatial resolution of single molecule localisation microscopy (SMLM) to investigate the presence of GlyRs at inhibitory synapses in the brain, focusing on several areas in the telencephalon, including hippocampus and striatum. Making use of a knock-in mouse model expressing endogenous mEos4b-tagged GlyRβ, we identified low-copy GlyR complexes at inhibitory synapses in different hippocampal regions. Dual-colour SMLM further revealed that the sparse GlyRs are integrated within the post-synaptic gephyrin domain, pointing to a possible role in maintaining the structural integrity of inhibitory synapses. In contrast, we found functionally relevant numbers of synaptic GlyRs at inhibitory synapses in the ventral striatum. Our results further highlight the strength of SMLM to detect few and sparsely distributed synaptic molecules in complex samples and to analyse their organisation with high spatial precision.
Plasmon-enhanced Brillouin light scattering spectroscopy for magnetic systems. II. Numerical simulations
Authors: Demydenko Yurii , Vasiliev Taras , Levchenko Khrystyna O. , Chumak Andrii V. , Lozovski Valeri
Published: January 2025

Brillouin light scattering (BLS) spectroscopy is a powerful tool for detecting spin waves in magnetic thin films and nanostructures. Despite comprehensive access to spin-wave properties, BLS spectroscopy suffers from the limited wave number of detectable spin waves and the typically relatively low sensitivity. In this paper, we present the results of numerical simulations based on the recently developed analytical model describing plasmon-enhanced BLS. Effective susceptibility is defined for a single plasmonic nanoparticle in the shape of an ellipsoid of rotation, for the sandwiched plasmonic nanoparticles separated by a dielectric spacer, as well as for the array of plasmonic resonators on the surface of a magnetic film. It is shown that the eccentricity of the metal nanoparticles, describing their shape, plays a leading role in enhancing the BLS signal. The optimal conditions for BLS enhancement are numerically defined for gold and silver plasmon systems for photons of different energies. The presented results define the roadmap for the experimental realization of plasmon-enhanced BLS spectroscopy.

Published by the American Physical Society
2025
Parity-violating marginal deformation of the 3D Gross-Neveu-Thirring model
Authors: Semenoff Gordon W. , Stewart Riley A.
Published: January 2025

A hybrid of the critical three-dimensional Gross-Neveu and Thirring models deformed by explicit parity-breaking operators is studied in the large-N expansion and using the renormalization group. The regime of coupling constants where the theory is stable is identified and criteria for the occurrence of fixed points in that regime are found. For a certain range of Chern-Simons level, we find stable charge-gapped phase with spontaneously broken approximate scale invariance and a parametrically light dilaton. The Chern-Simons level can be tuned to the stability edge, resulting in exact scale invariance which is spontaneously broken, accompanied by a massless dilaton. For another, narrow range of Chern-Simons levels, we find a conformal window where the theory flows to a Wilson-Fisher-like fixed point and is a novel (and rare) example of a nonsupersymmetric nontrivial parity- and time-reversal-violating three-dimensional conformal field theory with scalar, spinor, and vector fields.

Published by the American Physical Society
2025
Correlations Enable Lossless Ergotropy Transport
Authors: Simon Rick P. A. , Anders Janet , Hovhannisyan Karen V.
Published: January 2025

“A battery powers a device” can be read as “work stored in the battery is being transported to the device.” In quantum batteries, the total amount of stored work can be measured by ergotropy, which is the maximal work extractable by unitary operations. Transporting ergotropy is fundamentally different from transporting energy, and here we find that ergotropy can be even when the transmission channel is strictly energy conserving. We show that, generically, ergotropy transport is lossy whenever the two systems start uncorrelated. In contrast, for a large class of correlated initial states, transport can be gainful. Furthermore, a single correlated state can be used multiple times, allowing to transport without losses an order of magnitude more work than the battery capacity. Correlations are thus a useful resource for ergotropy transport, and we quantify how this resource is consumed during gainful transport.

Published by the American Physical Society
2025
Star Cluster Population of High Mass Black Hole Mergers in Gravitational Wave Data
Authors: Antonini Fabio , Romero-Shaw Isobel M. , Callister Thomas
Published: January 2025

Stellar evolution theories predict a gap in the black hole birth mass spectrum as the result of pair instability processes in the cores of massive stars. This gap, however, is not seen in the binary black hole masses inferred from gravitational wave data. One explanation is that black holes form dynamically in dense star clusters where smaller black holes merge to form more massive black holes, populating the mass gap. We show that this model predicts a distribution of the effective and precessing spin parameters, χeff and χp, within the mass gap that is insensitive to assumptions about black hole natal spins and other astrophysical parameters. We analyze the distribution of χeff as a function of primary mass for the black hole binaries in the third gravitational wave transient catalog. We infer the presence of a high mass and isotropically spinning population of black holes that is consistent with hierarchical formation in dense star clusters and a pair-instability mass gap with a lower edge at 44−4+6M⊙. We compute a Bayes factor B>104 relative to models that do not allow for a high mass population with a distinct χeff distribution. Upcoming data will enable us to tightly constrain the hierarchical formation hypothesis and refine our understanding of binary black hole formation.

Published by the American Physical Society
2025
Realization of Versatile and Effective Quantum Metrology Using a Single Bosonic Mode
Authors: Pan Xiaozhou , Krisnanda Tanjung , Duina Andrea , Park Kimin , Song Pengtao , Fontaine Clara Yun , Copetudo Adrian , Filip Radim , Gao Yvonne Y.
Published: January 2025

Quantum metrology offers the potential to surpass its classical counterpart, pushing the boundaries of measurement precision toward the ultimate Heisenberg limit. This enhanced precision is normally attained by utilizing large squeezed states or multiparticle entangled quantum states, both of which are often challenging to implement and prone to decoherence in real quantum devices. In this work, we present a versatile and on-demand protocol for deterministic parameter estimation that leverages two efficient state-transfer operations on a single bosonic mode. Specifically, we demonstrate this protocol in the context of phase estimation using the superposition of coherent states in the bosonic circuit quantum electrodynamics (cQED) platform. With low average photon numbers of only up to 1.76, we achieve quantum enhanced precision approaching the Heisenberg scaling, reaching a metrological gain of 7.5(6) dB. Importantly, we show that the gain or sensitivity range can be further enhanced on the fly by tailoring the input states, with different superposition weights, based on specific system constraints. The realization of this versatile and efficient scheme affords a promising path toward practical quantum enhanced sensing, not only for bosonic cQED hardware but also readily extensible to other continuous-variable platforms.

Published by the American Physical Society
2025
Synthesis and crystal structure of [Sr(urea)(NO3)2]
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Authors: Bektursinova Aysanem , Djumanazarova Zulfiya , Uzakbergenova Zamira , Ashurov Jamshid , Khan Akram A , Kadirova Shakhnoza , Torambetov Batirbay
Published: January 2025

The crystal structure of poly[di-μ2-nitrato-μ2-urea-strontium(II)], [Sr(NO3)2(CH4N2O)]
n
, was determined using single-crystal X-ray diffraction. Crystallizing in the orthorhombic space group Aba2, the asymmetric unit consists of an SrII cation, two nitrate anions, and two half urea molecules. The SrII cation adopts a distorted decahedral geometry coordinated by ten oxygen atoms, with Sr—O bond lengths ranging from 2.573 (3) to 2.847 (5) Å. The nitrate anions act as bidentate ligands, displaying both terminal and bridging coordination modes. The structure features a robust coordination network supported by hydrogen bonding. These results provide insight into the coordination behaviour of SrII with nitrate and urea ligands, contributing to the understanding of supramolecular architectures in metal–organic frameworks (MOFs).
Tetraphenylglycolide tetrahydrofuran monosolvate
Authors: Ndima Lubabalo , Hosten Eric Cyriel , Betz Richard
Published: January 2025

The title compound, C28H20O4·C4H4O, is the cyclic ester anhydride of benzilic acid. A disordered solvent molecule is present in the structure. The asymmetric unit contains half the acid-derived molecule. C—H...O contacts connect the constituents of the title compound into a three-dimensional network.