bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractCoccolithophores, 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

AbstractIn 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.
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

AbstractDuring 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

SUMMARYInterorgan 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

AbstractAnthocyanins 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

AbstractLearning 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

AbstractProteins 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

ABSTRACTLipid 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

ABSTRACTDuring 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

ABSTRACTThe 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 & NOTEWORTHYMultichannelin 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

SummaryRNA 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

ABSTRACTIn 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

AbstractBacteria 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

AbstractTissue 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.