bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Organellar Mapping in yeast reveals extensive protein localization changes during ER stress
Authors: Platzek Anna , Schessner Julia P , Odehnalová Klára , Borner Georg H H , Schuck Sebastian 
Published: February 2025

AbstractSophisticated techniques are available for systematic studies of yeast cell biology. However, it remains challenging to investigate protein subcellular localization changes on a proteome-wide scale. Here, we apply Dynamic Organellar Maps (DOMs) by label-free mass spectrometry to detect localization changes of native, untagged proteins during endoplasmic reticulum (ER) stress. We find that hundreds of proteins shift between cellular compartments. For example, we show that numerous secretory pathway proteins accumulate in the ER, thus defining the extent and selectivity of ER retention of misfolded proteins. Furthermore, we identify candidate cargo proteins of the ER reflux pathway, determine constituents of reticulon clusters that segregate from the remainder of the ER and provide evidence for altered nuclear pore complex composition and nuclear import. These findings uncover protein relocalization as a major aspect of cellular reorganization during ER stress and establish DOMs as a powerful discovery tool in yeast.
Opposing control of the respiratory brainstem on multiple timescales achieved by transmitter co-release from the locus coeruleus
Authors: Varga Adrienn G. , Reid Brandon T. , Maletz Sebastian N. , Dossat Amanda M. , Levitt Erica S. 
Published: February 2025

SummaryThe locus coeruleus (LC) provides widespread noradrenergic (NAergic) modulation throughout the brain to influence a wide range of functions, including breathing. Although both anatomical and physiological evidence supports the involvement of the LC in both the upstream integration and the downstream modulation of breathing, the circuitry behind the latter is unknown. Here, we show that NAergic LC neurons send projections to the Kӧlliker-Fuse nucleus (KF), a critical site in the control of breathing. Long duration activation of NAergic LC neuron terminals in pontine slices induces persistent inhibitory and excitatory NA currents or increases firing rate in postsynaptic KF neurons. Short stimulation on the other hand leads to the VGluT2-dependent release of glutamate that may be co-released with NA in a monosynaptic circuit. Together these results demonstrate that LC neurons can exert flexible, opposing effects on different timescales via glutamatergic and NAergic signaling onto a key respiratory brainstem nucleus.
Cell motility influences microfluidics capturing in scRNA-seq
Authors: López-Escobar Lara , Nascimento Ana M. , Figueiredo Luisa M. 
Published: February 2025

SUMMARYMicrofluidic isolation methods for single-cell RNA sequencing (scRNA-seq) have primarily been designed for immotile cells, with limited consideration for motile cells, such as those with flagella or cilia. By studying the encapsulation efficiency of the flagellatedTrypanosoma bruceiusing the 10x Genomics platform, we found that maintaining parasites at room temperature results in a low encapsulation yield. We implemented a rapid cooling method to 0ºC prior to encapsulation, which reduced parasite motility and preventing undesired transcriptomic change. This allowed for a representative scRNA-seq dataset, avoiding the disproportionate loss of the most motile forms. This study highlights the challenges of using motile cells in microfluidic systems and the biases caused by losing specific subpopulations, emphasizing the need for optimized protocols for non-standard mammalian cells.PLAIN LANGUAGE SUMMARYSingle-cell RNA sequencing (scRNA-seq) is a powerful technique used to study individual cells, but most methods have been designed for cells that do not move. This can be a challenge when working with motile cells, likeTrypanosoma brucei, a flagellated parasite responsible for sleeping sickness. In our study, we found that these parasites are poorly captured in microfluidic systems, such as the 10x Genomics platform, when kept at room temperature. Their movement reduces the efficiency of encapsulation, leading to biased results. To overcome this, we developed a simple cooling method that quickly lowers the temperature to 0°C before processing. This reduces parasite motility, improving capture rates while minimizing unwanted changes in gene expression. By applying this approach, we obtained a representative transcriptomic dataset, ensuring that all parasite forms were included. Our findings highlight the importance of adapting microfluidic techniques for motile cells to avoid losing key subpopulations and ensure accurate biological insights.
Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes
Authors: Antunes Luiza Berenguer , Isebe Tony , Kutova Oksana , Cestari Igor 
Published: February 2025

SummaryGenome three-dimensional organization is essential for the coordination of eukaryote gene expression. The chromosomes of the pathogenTrypanosoma bruceicontain hundreds of silent variant surface glycoprotein (VSGs) genes in subtelomeric regions. However,T. bruceitranscribes a single VSG gene and periodically changes the VSG expressed by transcriptional or recombination mechanisms, altering its surface coat to escape host antibodies by antigenic variation. We show that VSG-rich silent subtelomeric regions form distinct chromosome compartments from transcribed regions, with subtelomeric compartments of different chromosomes co-interacting. We uncovered chromatin-associating factors at the boundaries of transcribed and silent compartments. Among these, repressor activator-protein 1 (RAP1) marks the compartment boundaries and spreads over silent regions. Inactivation of phosphatidylinositol phosphate 5-phosphatase removed RAP1 from compartment boundaries and subtelomeric regions, disrupting compartment assembly and derepressing all VSG genes. The data show spatial segregation of repressed from transcribed chromatin and phosphoinositides regulation of silent compartment assembly and genome organization.
DateBack, a digital open access repository of archaeobotanical data for reconstructing date palm history
Authors: Besseiche Margot , Chambraud Elora , Dabrowski Vladimir , Brandstätt Elisa , Sabot François , Bouchaud Charlène , Gros-Balthazard Muriel 
Published: February 2025

AbstractThe date palm (Phoenix dactyliferaL.) has been a cornerstone of oasis agrosystems in West Asia and North Africa for millenia, yet the timeline and processes of its domestication and spread remain poorly documented. Archaeobotanical remains provide critical insights into its cultivation history, but no comprehensive review or dedicated platform currently exists to synthesize and analyze these data.To address this gap, we conducted an extensive literature review and developedDateBack(https://cloudapps.france-bioinformatique.fr/dateback), a digital open access repository of archaeobotanical remains ofPhoenixspp. In its first version,DateBackrecords macroremains (e.g., seeds, fruits, stems, petioles) from prehistoric to Late Antiquity contexts in Southwest and South Asia.We assembled 140 entries from 99 archaeological sites across 110 references, along with a separate table of 55 radiocarbon-dated entries from 17 sites, refining chronological assessments. Most entries comprise charred seeds (55.7%), with a smaller proportion of charred vegetative parts or desiccated remains. Our findings highlight regional disparities in remain distribution, concentrated in the Levant and Gulf, while Saudi Arabia and southern Iran are underrepresented, and in data reliability, particularly dating resolution, complicating the reconstruction of date cultivation history. Our evidence shows that the earliest securely dated remains, indicating date consumption, appear in the Gulf around 5000 BCE, while cultivation emerges later, first in southern Mesopotamia and the northern Gulf in the 4thmillennium BCE, then in eastern Arabia and the Indus Valley in the 3rdmillennium BCE. The Levant presents challenges, with numerous presumed early finds but significant uncertainties, with secure evidence of cultivation only appearing by the late 2ndmillennium BCE, as in northwestern Arabia, while in the southern Arabian Peninsula, it is not attested until the 1stmillennium BCE.By compiling and standardizing archaeobotanical data,DateBackfacilitates advanced spatiotemporal analyses and supports additional archaeobotany-based research including ancient DNA studies. Moreover, the platform is dynamic, scalable, and collaborative, enhancing data integration and refinement, with future expansions planned to include additional periods (Islamic era and beyond), geographic regions (North Africa), and new types of evidence, such as plant microremains and iconography.
Gut3Gel: A High Throughput Mucus Model for Culturing Human Intestinal Microbiota
Authors: Vargas Natalia Suárez , Antunes Miguel , Sobral João , Silva Carolina , Sousa Francisco , Garbero Olga Valentina , Kolková Anna , Visai Livia , Medana Claudio , Visentin Sonja , Petrini Paola , van Uden Sebastião , Pacheco Daniela 
Published: February 2025

AbstractThe human intestinal microbiota plays a crucial role in health and disease, yet recreating its complex interactionsin vitroremains a significant challenge. Gut3Gel introduced herein as a novelin vitromucus model, designed for culturing complex microbial communities without the need for anaerobic conditions. Intestinal microbiota samples from five donors were individually inoculated in Gut3Gel and cultured for 72 hours. Taxonomic composition assessment revealed that Gut3Gel sustains diverse microbial species and particularly promotes the growth of mucus-associated bacteria includingBifidobacterium,Lactobacillus, andFaecalibacterium. Microbial metabolic activity within Gut3Gel was confirmed by the increased production of acetate and butyrate, as well as of exopolysaccharides. Gut3Gel reproduces physiological features of intestinal mucus, providing a reproducible and scalable culturing platform. These features make Gut3Gel a promising tool for advancing microbiota research with potential applications in drug screening, microbiome mining, and high throughput testing of microbiome-modulating molecules.
Arabidopsis REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes
Authors: Wu Zhongshou , Xue Yan , Wang Shuya , Shih Yuan-Hsin , Zhong Zhenhui , Feng Suhua , Draper Jonathan , Lu Allen , Sha Jihui , Li Lu , Wohlschlegel James , Wu Keqiang , Jacobsen Steven E. 
Published: February 2025

AbstractDNA methylation plays crucial roles in gene regulation and transposon silencing. In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific loci is unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the proteinGENETICSDETERMINESEPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes to generate 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific loci. In the absence ofGDE1, Pol IV transcription complexes redistribute to sites bound by a different factor called REM8. These results suggest that REM proteins act as sequence specific DNA binding proteins that pattern siRNAs and methylation at specific sites in the genome, highlighting the role of genetic information in determining epigenetic patterns.
Social context and dopamine signaling converge in the mushroom body to drive impulsivity
Authors: Sabandal Paul Rafael , Kim Young-Cho , Sabandal John Martin , Han Kyung-An 
Published: February 2025

AbstractOrganisms adapt their behaviors flexibly in response to various internal and environmental factors. However, how and where these factors converge in the brain to alter behavior is not well understood. In this study, we examine how social context interacts with dopamine activity to influence inhibitory control inDrosophila. We found that, regardless of social context—whether isolated or in groups—wild-type flies consistently showed strong movement suppression in a go/no-go task that measures action restraint. In contrast, flies with enhanced dopamine activity suppressed their movements when tested alone or with potential mates but exhibited impulsive behaviors when exposed to same-sex peers. This social-context-dependent impulsivity was shown to rely on dopamine-D1 receptor-cAMP signaling in mushroom body (MB) neurons. Remarkably, activating the MB was sufficient to induce impulsivity, even without dopamine input or a social context. Our findings highlight MB as a critical hub where social context and dopamine signaling converge to regulate impulsive behavior inDrosophila.Signficance statementThis study demonstrates that impulsivity results from the interplay between elevated dopamine levels and social context, rather than dopamine alone, with the mushroom body (MB) serving as a key neural hub for integrating these signals inDrosophila. Social stimuli, such as the presence of same-sex peers, disrupt inhibitory control in a context-dependent manner, highlighting the importance of multimodal sensory inputs and MB activity. These findings challenge the isolation-focused approach in traditional impulsivity research and underscore the need to account for social influences when investigating cognitive processes and disorders like ADHD, autism, and substance use, where social settings often amplify symptoms.ClassificationGenetics / Neuroscience
Phage interactions may contribute to the population structure and dynamics of hydrothermal vent microbial symbionts
Authors: Hauer Michelle A. , Klier Katherine M. , Langwig Marguerite V. , Anantharaman Karthik , Beinart Roxanne A. 
Published: February 2025

AbstractDeep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts through the oxidation of chemical reductants in vent fluids. Hydrothermal vents also support unique viral communities that often exhibit high host-specificity and frequently integrate into host genomes as prophages; however, little is known about the role of viruses in influencing the chemosynthetic symbionts of vent foundation fauna. Here, we present a comprehensive examination of contemporary lysogenic and lytic bacteriophage infections, auxiliary metabolic genes, and CRISPR spacers associated with the intracellular bacterial endosymbionts of snails and mussels at hydrothermal vents in the Lau Basin (Tonga). Our investigation of contemporary phage infection among bacterial symbiont species and across distant vent locations indicated that each symbiont species interacts with different phage species across a large geographic range. However, our analysis of historical phage interactions via assessment of CRISPR spacer content suggested that phages may contribute to strain-level variation within a symbiont species. Surprisingly, prophages were absent from almost all symbiont genomes, suggesting that phage interactions with intracellular symbionts may differ from free-living microbes at vents. Altogether, these findings suggest that species-specific phages play a key role in regulating chemosynthetic symbionts via lytic infections, potentially shaping strain-level diversity and altering the composition and dynamics of symbiont populations.
A Critical Role for the Fascin Family of Actin Bundling Proteins in Axon Development, Brain Wiring and Function
Authors: Hardin Katherine R. , Penas Arjolyn B. , Joubert Shuristeen , Ye Changtian , Myers Kenneth R. , Zheng James Q. 
Published: February 2025

AbstractActin-based cell motility drives many neurodevelopmental events including guided axonal growth. Fascin is a major family of F-actin bundling proteins, but its role in axon development and brain wiring is unknown. Here, we report that fascin is required for axon development, brain wiring and function. We show that fascin is enriched in the motile filopodia of axonal growth cones and its inhibition impairs axonal extension and branching of hippocampal neurons in culture. We next provide evidence that fascin is essential for axon development and brain wiring usingDrosophila melanogasteras anin vivomodel.Drosophilaexpress a single ortholog of mammalian fascin called Singed (SN), which is highly expressed in the mushroom body (MB) of the central nervous system. We observe that loss of SN results in drastic MB disruption, highlighted by α- and β-lobe defects that are consistent with altered axonal guidance. SN-null flies also exhibit defective sensorimotor behaviors as assessed by the negative geotaxis assay. MB-specific expression of SN in SN-null flies rescues MB structure and sensorimotor deficits, indicating that SN functions autonomously in MB neurons. Together, our data from primary neuronal culture andin vivomodels highlight a critical role for fascin in brain development and function.Significance statementFascin is a major family of actin-binding proteins (ABPs) that crosslink and bundle actin filaments to underline membrane protrusions essential for cell motility and neuronal development.Inhibition of fascin in cultured cells causes it to dissipate from F-actin-rich membrane protrusions and become cytosolic, reduces filopodia formation, and decreases axon outgrowth and branching.In fruit flies, loss of the fascin orthologue, Singed, causes defects in brain development, specifically in mushroom body (MB) lobes, and leads to behavioral impairments which can be rescued upon MB-specific expression of Singed.
Hyperreflexia after corticospinal tract lesion reflects 1A afferent circuit changes not increased KCC2 hyperexcitability
Authors: Bethea Thelma , Adegbenro Temitope , Martin John H. 
Published: February 2025

AbstractHyperreflexia, spasticity, and a loss of skilled motor function are consequences of spinal cord injury (SCI). Multiple potential mechanisms underpinning hyperreflexia have been reported, including: aberrant proprioceptive afferent (PA) sprouting, which could enhance reflex signaling; reduced GABAergic inhibitory presynaptic regulation of 1A terminals (GABApre); and increased excitability produced by reduced motor neuron membrane-bound potassium-chloride co-transporter #2 (KCC2), which has only studied after SCI and bilateral CST lesion. Here we examine how selective CST injury allows for specific investigation of the different mechanisms to determine their contributions to hyperreflexia. Hoffmann (H)-reflex rate-dependent depression (RDD) of the forelimb and hindlimb 5th-digit abductor muscles was used to assess hyperreflexia. We compared RDD in naïve and unilateral-PTX animals at 7-dpi and 42-dpi, supplemented with additional timed tests to examine the time-course of hyperreflexia development.Immunohistochemistry was used to identify PA synapses (VGlut1) and GABApre (GABApre), motor neurons (ChAT), and KCC2. Following unilateral PTX, which eliminates the CST from one hemisphere, we observed significant hyperreflexia in the contralesional forelimb only. Membrane-bound KCC2 was unchanged in contralesional cervical motor neurons. Whereas both cervical and lumbar motor neurons showed increased PA sprouting contralesionally, there was a concomitant increase in GABApre terminals for the lumbar not cervical cord. Our findings show that KCC2 is disassociated from hyperreflexia in the uniPTX model. Instead, forelimb hyperreflexia can be explained by cervical motor neuron PA sprouting and an uncompensated GABApre regulation.
Transcription factors instruct DNA methylation patterns in plant reproductive tissues
Authors: Xu Guanghui , Chen Yuhan , Wang Fuxi , Li En , Law Julie A. 
Published: February 2025

AbstractDNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to male or female reproductive tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. These findings not only reveal RIMs as the first sex-specific RdDM proteins but also establish a critical role for genetic information in targeting DNA methylation. This novel mode of targeting expands our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.
Composition and RNA binding specificity of metazoan RNase MRP
Authors: Liu Yuan , He Shiyang , Pyo Anzie , Zheng Shanshan , Chen Meijuan , Cheloufi Sihem , Slavov Nikolai , Marzluff William F , Murn Jernej 
Published: February 2025

AbstractRibonuclease (RNase) MRP is a conserved RNA-based enzyme that is essential for maturation of ribosomal RNA (rRNA) in eukaryotes. However, the composition and RNA substrate specificity of this multisubunit ribonucleoprotein complex in higher eukaryotes remain a mystery. Here, we identify NEPRO and C18ORF21 as constitutive subunits of metazoan RNase MRP. Both proteins are specific to RNase MRP and are the only ones distinguishing this enzyme from the closely related RNase P, which selectively cleaves transfer RNA-like substrates. We find that NEPRO and C18ORF21 each form a complex with all other subunits of RNase MRP, stabilize its catalytic RNA, and are required for rRNA maturation and cell proliferation. We harness our discovery to identify a full suite ofin vivoRNA targets of each enzyme, including positions of potential cleavage sites at nucleotide resolution. These findings resolve the general composition of metazoan RNase MRP, illuminate its RNA binding specificity, and provide valuable assets for functional exploration of this essential eukaryotic enzyme.
Mutations in ASH1L cause a neurodevelopmental disorder with sex differences in epilepsy and autism
Authors: Papendorp Carin M. , Nolan Elizabeth , Higashimori Haruki , Goicouria Luis , Pieplow Cosmo A. , Whitely Kirsten , Elacio Jennifer , Nie Duyu , Kavanaugh Brian , Best Carrie R. , Lizarraga Sofia B. , Liu Judy S. 
Published: February 2025

SummaryTo understand brain phenotypes associated with ASH1L, we used a mouse model, performing analysis in different genetic backgrounds: C57BL/6 and CD-1. We found that in both lines, ASH1L mutations result in seizures. Mice from both lines have microcephaly, and also less complex dendritic morphology. We also found differential effects of ASH1L between C57BL/6 and CD-1 strains on a number of different measures identifying aspects of ASH1L function that may be influenced by genetic background. When we analyzed human subjects based on biological sex, for epilepsy, intellectual disability, and ASD, we found sex differences in epilepsy and autism, with epilepsy predominantly in female and ASD in male subjects. Functional evaluation by whole cell patch clamp electrophysiology in mice demonstrated hyperexcitability female compared with male hippocampal CA1 neurons. Thus, the role of ASH1L in specific circuits may be sex-dependent leading to sexual dimorphic effects from haploinsufficiency of this gene.