bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling the physiological impact of aberrant folded-state protein filamentation in cells
Authors: Levin Tal , Garcia-Seisdedos Hector , Lobov Arseniy , Wojtynek Matthias , Alexandrov Alexander , Jona Ghil , Levi Dikla , Medalia Ohad , Levy D. Emmanuel 
Published: September 2024

AbstractThe formation of large polymeric structures such as cytoskeletal and enzyme filaments is crucial for normal cellular function. However, such filaments can also form due to mutations that create self-interactions at the surface of symmetric proteins. Often, the proteins forming these structures maintain a folded state and thereby differ from aggregates and amyloids that involve misfolding. We refer to this type of assemblies asagglomeratesto mark this difference. While cells have quality control mechanisms to identify, buffer, and eliminate misfolded proteins, it is unclear whether similar mechanisms exist for agglomerates, or whether agglomerates are toxic to cells. Here, we profiled the physiological impact of mutation-induced folded-state protein filamentation in yeast cells. First, we devised a simple strategy to distinguish fluorescently labeled proteins forming agglomerates versus aggregates. We then profiled exogenous protein agglomerates in terms of their recognition by known quality control mechanisms, their effects on specific cellular processes and overall fitness onS. cerevisiaecultures. We found that agglomerates do not colocalize with the proteostasis machinery and do not result in measurable fitness defects. Proteomics profiling of cells expressing the wild type protein, agglomerating or misfolded variants revealed a consistent picture, with only minor, agglomerate-size-dependent changes observed and linked to the cell-wall and plasma-membrane proteins. Overall, our findings indicate that agglomerates form mostly benign structures in cells when compared to aggregates, and thereby offer a promising route for synthetic biology applications.Graphical Abstract
Alpha-2 agonism of the locus coeruleus impairs learning driven by negative prediction error
Authors: Lui Simon K. C. , Brink Ashleigh K. , Corbit Laura H. 
Published: September 2024

AbstractRefining previous learning when environmental contingencies change is a critical adaptive function. Studies have shown that systemic noradrenaline (NA) manipulations, as well as optogenetic manipulations of the locus coeruleus (LC), the primary source of forebrain NA, can strengthen long-term retention of appetitive extinction. To determine whether the contribution of NA is specific to extinction or extends to other forms of learning where reward is less than expected, we suppressed LC activity with clonidine, an α2A-adrenergic receptor agonist, in two tasks: compound extinction, where two previously rewarded cues are paired and no longer rewarded, and overexpectation, where animals are presented with two previously rewarded cues but receive a single reward rather than the expected two. In compound extinction, we found no differences between groups in training, extinction, or a spontaneous recovery test. However, animals that received clonidine reacquired responding to the previously extinguished cue significantly faster than saline animals, suggesting weakened extinction learning. In overexpectation testing, the saline group responded significantly less to a stimulus that had undergone overexpectation relative to a control stimulus, indicating that they had recalibrated their estimation of reward magnitude following training where reward was less than expected. In contrast, clonidine-treated animals did not differ in responding to the overexpectation versus control stimuli, suggesting that clonidine impaired learning resulting from overexpectation. These results demonstrate that activity of the LC is important for learning to reduce responding in both extinction and overexpectation paradigms.
Enhancer adoption by an LTR retrotransposon generates viral-like particles causing developmental limb phenotypes
Authors: Glaser Juliane , Cova Giulia , Fauler Beatrix , Prada-Medina Cesar A. , Stanislas Virginie , Phan Mai H.Q. , Schöpflin Robert , Aktas Yasmin , Franke Martin , Andrey Guillaume , Paliou Christina , Laupert Verena , Chan Wing-Lee , Wittler Lars , Mielke Thorsten , Mundlos Stefan 
Published: September 2024

AbstractMammalian genomes are scattered with transposable elements (TEs). TEs are epigenetically silenced to prevent harmful effects caused by either global activation leading to genome instability or insertional mutation disturbing gene transcription. However, whether the activation of a single element can contribute to pathological phenotypes without directly affecting gene expression is largely unknown. Here, we show that tissue-specific expression of a TE in the embryo leads to the production of viral-like particles (VLPs) which can affect organ formation. Failure to silence an LTR retrotransposon inserted upstream of theFgf8gene results in its co-expression withFgf8in the developing embryo. While local gene regulation is unaffected, the LTR retrotransposon participates in chromatin folding at the locus and adopts the expression of the regulatory domain it is located in. This drives the production of VLPs in theFgf8-expressing cells of the developing limb, triggering apoptotic cell death at the time of digit outgrowth and resulting in a limb malformation resembling human ectrodactyly. This phenotype can be rescued by knock-out or knock-in of the retrotransposon causing mutations preventing its full retroviral cycle. Insertion of the same element at other developmental loci faithfully recapitulates expression according to the neighboring regulatory activity. Our findings provide a mechanism by which TE insertion is incorporated into the local genomic regulatory landscape and show how VLP production in post-implantation embryos can interfere with organ formation.
SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots
Authors: Uruci Sidrit , Hoitsma Nicole M. , Solér-Oliva María E. , Bayona-Feliu Aleix , Gaggioli Vincent , García-Rubio María L. , Lo Calvin S.Y. , Bakker Collin , Marinello Jessica , Manolika Eleni Maria , Capranico Giovanni , Luijsterburg Martijn S. , Luger Karolin , Aguilera Andrés , Taneja Nitika 
Published: September 2024

ABSTRACTDNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series ofin vitroandin vivoexperiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.
Diversification and conservation of DNA binding specificities of SPL family of transcription factors
Authors: Li Miaomiao , Yao Tao , Galli Mary , Lin Wanru , Zhou Yilin , Chen Jin-Gui , Gallavotti Andrea , Huang Shao-shan Carol 
Published: September 2024

AbstractSQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors inArabidopsis thaliana, providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins. Comparative analysis between the paralogs AtSPL9 and AtSPL15 revealed differences in their binding motifs, suggesting divergent regulatory functions. Additionally, we expanded our investigation to homologs of AtSPL9/15 inZea mays(ZmSBP8/30) andTriticum aestivum(TaSPL7/13), identifying conserved and unique DNA-binding patterns across species. These findings provide key resources for understanding the molecular mechanisms of SPL transcription factors in regulating plant development and evolution across different species.
CD34+ Stromal Cell/Telocytes Demonstrate a Dynamic Pattern of Distribution During Healing of Post-Infarcted Myocardium in Middle-Aged Sprague-Dawley Rats
Authors: Schneider Daniel T. , Dedkov Eduard I. 
Published: September 2024

ABSTRACTIntroductionMyocardial CD34+ stromal cells/telocytes (SC/TCs) have been recently recognized as a novel resident cell which may play an important role in the repair process following acute myocardial infarction (MI). This study aims to determine the spatiotemporal dynamics of CD34+ SC/TCs within the left ventricular (LV) wall during the late inflammatory and proliferative phases of post-MI scar formation.MethodsA large transmural MI was induced in middle-aged, Sprague-Dawley rats by permanent ligation of the left anterior descending coronary artery. To recognize proliferating cells, rats were infused with 5-bromo-2’-deoxyuridine (BrdU) in a dose of 12.5 mg/kg/day for 72 hours via intraperitoneal osmotic minipumps on day 0, 4, or 11 after surgery. The rats were euthanized on day 3, 7 and 14 after MI, and their hearts were processed for histology and immunostaining.ResultsThree days after MI, CD34+ SC/TCs were absent within the necrotic myocardial tissue but were visible around the surviving cardiac myocytes (CMs) bordering the infarcted region, including those remaining in subepicardial and subendocardial regions, and in the adventitia of residual coronary vessels. Seven days after MI, many of the CD34+ SC/TCs located at the periphery of the developing scar appeared enlarged and contained the BrdU labeling, indicating the cell proliferation. At the same time, elongated CD34+ SC/TCs, which lacked BrdU labeling, were noticed closer to the necrotic zone residing in the interstitial areas between the intact basement membranes left from resorbed CMs, suggesting their migratory activity. Fourteen days after MI, CD34+ SC/TCs were distributed throughout the entire post-infarcted region except for the areas occupied by necrotic tissue, myofibroblast-rich granulation tissue, and the fibroelastic thickenings of the endocardium affected by an MI. Furthermore, accumulated clusters of flattened CD34+ SC/TCs cells were apparent in the areas where the edges of surviving CMs extend into the fibrotic portion of the scar.ConclusionThese findings, for the first time, demonstrate that a population of myocardial CD34+ SC/TCs follow a dynamic pattern of spatiotemporal distribution within the healing myocardium suggesting their direct involvement in post-MI repair process and scar formation.
Somatic Transthyretin-Related Proteins in C. elegans Govern Reproductive Longevity by Sustaining Sperm Integrity and Timely Ovulation
Authors: Wu Tingshan , Lyu Haochen , Wang Zhao , Jiang Zhaoyang , Qi Yingchuan B. 
Published: September 2024

AbstractThe decline in reproductive capability during adult life is critical for health, but its mechanism is elusive. We systematically analyzed the developmental role of an expanded TTR family of proteins, structurally analogous to mammalian thyroid hormone-transporting Transthyretin, and identified three paralogous proteins, TTR-15, TTR-16, and TTR-17, differentially expressed in somatic cells of the gonads and secreted around gametes inC. elegans. Simultaneous inactivation of TTR-15, TTR-16, and TTR-17 leads to a rapid reduction in reproductive capacity in middle age. While oocyte and sperm production remain unaffected in the triple mutants, late-onset infertility results from stalled ovulation. Mechanistically, the absence of TTR-15, TTR-16, and TTR-17 causes sperm to prematurely deplete the cytoplasmic pool of major sperm protein (MSP), released via non-conventional vesicle budding as a signal for ovulation. We propose that the somatic gonads play a central role in maintaining sperm integrity post-production and determining the duration of the reproductive age.HighlightsSystematic analysis of TTR family proteins reveals diverse expression and critical functions.TTR-15, TTR-16, and TTR-17 are secreted around gametes inC. elegans.TTR-15/16/17 triple KO exhibits middle-age onset infertility due to stalled ovulation.MSP, a signal for ovulation, is prematurely depleted from sperm in the absence of TTR-15/16/17.
Translation profiling of stress-induced small proteins reveals a novel link among signaling systems
Authors: Vellappan Sangeevan , Sun Junhong , Favate John , Jagadeesan Pranavi , Cerda Debbie , Shah Premal , Yadavalli Srujana S. 
Published: September 2024

AbstractSignaling networks allow adaptation to stressful environments by activating genes that counteract stressors. Small proteins (≤ 50 amino acids long) are a rising class of stress response regulators.Escherichia coliencodes over 150 small proteins, most of which lack phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we identify stress-induced small proteins using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, several of them transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, underscoring their physiological significance in low magnesium stress. Most remarkably, we elucidate an unusual connection via a small membrane protein YoaI, between major signaling networks – PhoR-PhoB and EnvZ-OmpR inE. coli, advancing our understanding of small protein regulators in cellular signaling.SynopsisRibo-RET identifies 17 small proteins induced under low magnesium (Mg2+) stress inE. coliMany of these proteins are transcriptionally activated by PhoQP signaling systemHalf of the stress-induced small proteins localize to the membraneDeletion or overexpression of specific small proteins affects growth under stressSmall protein YoaI connects PhoR-PhoB and EnvZ-OmpR signaling networks
Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils
Authors: Trubl Gareth , Leleiwi Ikaia , Campbell Ashley , Kimbrel Jeffrey A. , Bhattacharyya Amrita , Riley Robert , Malmstrom Rex R. , Blazewicz Steven J. , Pett-Ridge Jennifer 
Published: September 2024

AbstractBackgroundWet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment—driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable.ResultsTo investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phylaPseudomonadota,Acidobacteriota, andActinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions.ConclusionsOur study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.
Reconstruction of functional olfactory sensory tissue from embryonic nasal stem cells
Authors: Suzuki Kazuya , Wagai Fumi , Eiraku Mototsugu 
Published: September 2024

SummaryDuring the development of the olfactory epithelium (OE), olfactory sensory neurons (OSNs) express only one member of the odorant receptor (OR) gene family, and OSNs expressing the same OR converge their axons to the same set of glomeruli on the olfactory bulb (OB). The resulting odor maps allow mice to discriminate more than 100,000 different odorants using about 1,000 ORs. It remains elusive how odor maps are formed. Here, we show a means of forming OE organoids with pseudostratified structure from mouse embryonic OE stem cells. Single-cell RNA sequencing revealed that the OE organoids give rise to all the OE cellular lineages and undergo active neurogenesis. We also found that most OSNs in OE organoids exclusively express only one type of ORs and exhibit a unique molecular code of axon guidance-related genes that can discriminate between OR classes. Thus, OE organoids could be a useful model for studying olfactory nervous system development.
Creation of MLPA: A Multi-level Digital Twin Framework for Personalized Cancer Simulation and Treatment Optimization
Authors: Gu James , Chen Jake Y 
Published: September 2024

SummaryThis research proposes a new personalized cancer modeling and treatment strategy: the Multi-level Parameterized Automata (MLPA), an innovative digital twin framework. The MLPA framework fully integrates macroscopic electronic health records (EHR) and microscopic genomic data for the first time, employing stochastic cellular automata to model tumor progression and treatment efficacy dynamically.The multi-scale strategy effectively enables MLPA to simulate complex cancer behaviors, including metastasis and pharmacological responses, with remarkable precision. The validation using bioluminescent imaging from mice demonstrates MLPA’s exceptional predictive power, achieving a state-of-the-art R² value of 0.93, improvement over previously reported conventional models, and fitting within 95% confidence intervals.The proposed MLPA framework accurately captures tumors’ characteristic S-shaped growth curve and shows high fidelity in simulating various scenarios, from natural progression to aggressive growth and drug treatment responses. MLPA’s ability to simulate drug effects through gene pathway perturbation, with predicted tumor cell counts being within a 2.5% equivalence margin interval, underscores its potential as a powerful method for precision oncology.The proposed MLPA framework not only offers a more reliable platform for exploring personalized treatment strategies, but also potentially transforms patient outcomes by optimizing therapy based on individual human biological profiles. As clinically adopted technology progresses towards precision medicine, MLPA stands at the forefront, offering new possibilities in cancer simulation and treatment optimization. The code and imaging dataset used is available athttps://github.com/alphamind-club/MLPA.
Effects ofNf1on sleep behavior are mediated through starvation caused by deficits in SARM1 dependent NAD+ metabolism
Authors: Sofela Folasade A. , Lopez Valencia Mariela , Jongens Thomas A. , Sehgal Amita 
Published: September 2024

SummaryNeurofibromatosis 1 (NF1) is a relatively common autosomal dominant disease which predisposes to the formation of tumors, and is also associated with behavioral phenotypes, including sleep disturbances. As loss of the NF1 protein has been recently associated with metabolic dysfunction, we explored the relationship between metabolic and behavioral phenotypes through metabolomic analysis ofDrosophila Nf1-null mutants.Nf1-null mutants exhibit a metabolic signature indicative of starvation, with diminished metabolites related to glucose, glycogen, and fatty acid processing and increased mRNA ofAkh, a hormone that promotes foraging during starvation. Reduced sleep inNf1-null mutants was rescued by genetic manipulation of the AKH pathway and by a high-sucrose diet, which also partially corrected hypolipidemia, suggesting that sleep loss is due to starvation-induced foraging. Interestingly, behavioral phenotypes can be recapitulated by loss of NF1 only in the periphery and trace to mitochondrial defects that include elevated levels of the NADase SARM1. Indeed, inhibition of SARM1 activity rescues sleep behavior inNf1-null flies. These findings suggest a novel connection between loss of NF1 and mitochondrial dysfunction caused by SARM1 hyperactivation, setting the scene for new pharmacological and dietary approaches that could provide relief to NF1 patients.
Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis
Authors: Jenkins Benjamin H. , Kilias Estelle S. , Savory Fiona R. , Sørensen Megan E. S. , Poirier Camille , Attah Victoria , Drew Georgia C. , Galindo Luis J. , Leonard Guy , Cameron Duncan D. , Brockhurst Michael A. , Milner David S. , Richards Thomas A. 
Published: September 2024

AbstractEndosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are largely unknown. Here, we describe an immune-like glycan-sensing/processing network, partly assembled through horizontal gene-transfers (HGTs), that enablesParamecium bursariato control its algal endosymbionts. Using phylogenetics, RNA-interference (RNAi), and metabolite exposure experiments, we show thatP. bursariaregulates endosymbiont destruction using glycan-sensing/processing – a system that includes a eukaryotic-wide chitin-binding chitinase-like protein (CLP) localized to the host phago-lysosome. RNAi ofCLPalters expression of eight glycan-processing genes, including two prokaryote-derived HGTs, during endosymbiont destruction. Furthermore, glycan-sensing/processing dynamically regulates endosymbiont number inP. bursaria, plasticity crucial to maximize host fitness across ecological conditions.CLPis homologous to a human phagocyte-associated innate immune factor, revealing how immune functions can be alternatively adapted and expanded, partly through HGT, enabling endosymbiotic control.Graphical Abstract