bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Import Defects Drive Cell Cycle Dysregulation in Neurodegeneration
Authors: Plessis-Belair Jonathan , Russo Taylor , Riessland Markus , Sher Roger B 
Published: January 2025

AbstractNeurodegenerative diseases (NDDs) and other age-related disorders have been classically defined by a set of key pathological hallmarks. Two of these hallmarks, cell cycle dysregulation (CCD) and nucleocytoplasmic transport (NCT) defects, have long been debated as being either causal or consequential in the pathology of accelerated aging. Specifically, aberrant cell cycle activation in post-mitotic neurons has been shown to trigger neuronal cell death pathways and cellular senescence. Additionally, NCT has been observed to be progressively dysregulated during aging and in neurodegeneration, where the increased subcellular redistribution of nuclear proteins such as TAR DNA-Binding Protein-43 (TDP43) to the cytoplasm is a primary driver of many NDDs. However, the functional significance of NCT defects as either a primary driver or consequence of pathology, and how the redistribution of cell cycle machinery contributes to neurodegeneration, remains unclear. Here, we describe that pharmacological inhibition of importin-β nuclear import is capable of perturbing cell cycle machinery both in mitotic neuronal cell lines and post-mitotic primary neuronsin vitro. OurNemfR86Smouse model of motor neuron disease, characterized by nuclear import defects, further recapitulates the hallmarks of CCD in mitotic cell lines and in post-mitotic primary neuronsin vitro, and in spinal motor neuronsin vivo. The observed CCD is consistent with the transcriptional and phenotypical dysregulation observed in neuronal cell death and cellular senescence in NDDs. Together, this evidence suggests that impairment of nuclear import pathways resulting in CCD may be a common driver of pathology in neurodegeneration.Graphical AbstractGraphical Abstract:Overview of Dysregulated Cell Cycle Mechanisms in Neuronal Cells. A nuclear import block drives cell cycle re-entry from G0, culminating in cell cycle arrest at G1/S. This cell cycle arrest is associated with activation of CKIs from the INK locus (p15, p16, p18, p19) and Cip/Kip (p21, p27) which act on specific CDK/Cyclin complexes. This activity is further associated with the G1/S downregulation E2F and stathmins, resulting in microtubule dysregulation and cell cycle arrest.
Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf
Authors: Schleicher Jan T. , Claassen Manfred 
Published: January 2025

AbstractMotivationSingle-cell RNA sequencing (scRNA-seq) allows for the detailed analysis of dynamic cellular processes. In particular, this has been enabled by the estimation of RNA velocity, the derivative of gene expression, from separate count matrices for different splice states, which provides information about a cell’s immediate future even in snapshot data. Useful velocity estimates strongly depend on accurate counts for spliced and unspliced transcripts. Velocyto remains the standard tool for spliced and unspliced mRNA molecule quantification. However, despite considerable advances in scRNA-seq protocols, velocyto has not been updated to account for peculiarities of new protocols, such as popular approaches based on 5’ chemistry.ResultsTo address this shortcoming, we present tidesurf, a command line tool for the quantification of spliced and unspliced transcript molecules from scRNA-seq libraries. Employing it on four different publicly available 10x Genomics Chromium datasets, we show the accuracy on various datasets generated with either 3’ or 5’ chemistry, whereas velocyto’s results are highly erroneous for the latter. Considering broader applicability, our results highlight tidesurf as a potential replacement for velocyto.Availability and implementationA Python implementation of tidesurf is available from PyPI and atgithub.com/janschleicher/tidesurf. Code for reproducing the analyses is available at github.com/janschleicher/tidesurf projects.
Theoretical and Empirical Performance of Pseudo-likelihood-based Bayesian Inference of Species Trees under the Multispecies Coalescent
Authors: Sapoval Nicolae , Liu Zejian , Tamiji Mehrdad , Li Meng , Nakhleh Luay 
Published: January 2025

AbstractLikelihood-based inference under the multispecies coalescent provides accurate estimates of species trees. However, maximum likelihood and Bayesian inference are both computationally very demanding. Pseudo-likelihood has been previously proposed as a computationally efficient alternative to full phylogenetic likelihood calculations in the context of maximum likelihood estimation. However, theoretical and practical aspects of pseudo-likelihood in the context of Bayesian inference have not been explored. In this work, we provide strong theoretical guarantees and an empirical evaluation of pseudo-likelihood-based Bayesian inference of species trees under the multispecies coalescent. Our contributions are threefold. First, we prove a bound on the convergence rate for species tree topology inference and a Bernstein-von Mises result for branch lengths under model misspecification. Second, we provide an empirical comparison of full- and pseudo-likelihood-based Bayesian inference on synthetic data. Finally, we demonstrate the practical scalability of pseudo-likelihood-based inference by analyzing two biological datasets.
ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions
Authors: Schroeder Jeremy W. , Wolfe Michael B. , Freddolino Lydia 
Published: January 2025

AbstractDetermining where transcriptional regulators bind within a genome is paramount to understanding how gene expression is regulated. Historically, position weight matrices (PWMs) have been used to define the binding preferences of DNA binding proteins1. However, PWMs treat the identity of each base in a sequence as an independent and additive measure of binding preference, which can limit their utility2. Models that consider higher order interactions between nearby bases yield greater success in predicting proteins’ binding to DNA, but for many proteins there is still substantial room for improvement in predicting and understanding the determinants of proteins’ binding to DNA3. In addition to DNA sequence motifs, structural motifs (e.g., a narrow minor groove width) are important determinants of binding for some DNA-binding proteins4. Despite the initial success of algorithms using structural features of DNA to predict binding properties of proteins from either ChIP-seq or SELEX data5–8, there remains a need for ade novostructural motif discovery framework which can be applied to data from a variety of experimental designs. Here, we present a unified workflow, capable of utilizing virtually any type of data representing sequence coverage or enrichment (e.g. ChIP-seq, RNA-seq, SELEX, etc.), to discover short structural motifs with explanatory power for a protein’s DNA binding preference. We couple the DNAshapeR algorithm9with our own information-theoretic approach tode novomotif discovery, and wrap shape and sequence motif inference and model selection into a single tool called ShapeME. Application of our structural motif discovery algorithm to proteins with ChIP-seq data in ENCODE datasets reveals a subset of proteins where short structural motifs outperform the best PWM for that protein as determined from the JASPAR database, or as identified by the sequence motif elicitation tool STREME. Our approach offers a powerful and versatile framework for inferring structural DNA binding motifs, and will complement current sequence-based motif elicitation tools in discovery of protein-DNA interaction principles. A web-based interface to ShapeME is available athttps://seq2fun.dcmb.med.umich.edu/shapeme, with full source code available athttps://github.com/freddolino-lab/ShapeME.
Lower corticalFKBP5DNA methylation at key enhancer sites is associated with older age and higher gene expression in schizophrenia
Authors: Edmond Katrina Z. , Kaul Dominic , Yusupov Natan , Ködel Maik , Sauer Susann , Fröhlich Anna S. , Tao Ran , Kleinman Joel E. , Weinberger Daniel R. , Hyde Thomas M. , Czamara Darina , Binder Elisabeth B. , Matosin Natalie 
Published: January 2025

ABSTRACTAn increasingly compelling body of literature indicates the glucocorticoid receptor cochaperone FK506-binding protein 51 (FKBP51) is a promising target for novel psychiatric therapeutics. However, the mechanisms regulating the correspondingFKBP5gene directly in the human brain remain largely unknown yet are needed to facilitate the development of precise mechanism-based treatment approaches. Here, we examinedFKBP5DNA methylation patterns in postmortem human brain samples from the dorsolateral prefrontal cortex of individuals who lived with a major psychiatric disorder (schizophrenia, major depression, or bipolar disorder; n=329) and controls n=231. We identified that cytosine-phosphate-guanine-dinucleotide (CpG) specificFKBP5DNA methylation is altered in psychiatric disorders across theFKBP5locus, and that these changes are differentially associated with age and genotype (rs1360780 CCvsCT/TT). Individuals with schizophrenia had significantly lower levels of DNA methylation in the proximal enhancer ofFKBP5, which also negatively correlated withFKBP5gene expression. These changes were also associated with predicted glucocorticoid response elements (GREs) in the proximal enhancer, but not other transcription factor binding sites. This evidence supports that in the human cortex,FKBP5DNA methylation is associated with both genetic and ageing effects, and that the associations between these factors vary at a diagnosis-specific level in psychopathology. This may have implications for developingFKBP5-targeted therapeutics and defining a subgroup of patients who will benefit from such treatments.
The Effects of Pressure and Temperature on the Thermodynamics of α-Helices
Authors: Makhatadze George I. , Moustouka Caitlyn , Coffin Carleton , Tzul Franco O. 
Published: January 2025

AbstractIn light of the recent realization that a large fraction of microbial biomass lives under high hydrostatic pressure, there is a renewed interest in understanding molecular details by which proteins in these organisms modulate their functional native state. The effects of pressure on protein stability are defined by the volume changes between native and denatured states. The conformational ensemble of the denatured state can depend on several extrinsic variables, such as pH and ionic strength of solvent, temperature, and pressure. The effect of the latter on the elements of the secondary structures, and α-helical structures has been inconclusive. This has been largely due to the inherent difficulties of high-pressure experiments. Here, we adapted the method of choice, circular dichroism spectroscopy, on a well-established series of model peptides to study helical structure formation, while focusing on the pressure and temperature dependencies of the helix-coil transition. We find that at low temperatures, pressure stabilizes the helical structure, suggesting that the volume of the helix-coil transition is positive. However, at higher temperatures (>40°C), the volume changes become negative, and pressure destabilizes the helical structure.
Genomic and Transcriptomic Characterization of Carbohydrate-Active Enzymes in the Anaerobic FungusNeocallimastix camerooniivar. constans
Authors: Blair Elaina M. , Navaratna Tejas A. , Ahern Colleen B. , Ragunathan Ramya , Brown Jennifer L. , Mondo Stephen J. , Lipzen Anna , Hanafy Radwa A. , LaButti Kurt , Talag Jayson , Barry Kerrie , Chovatia Mansi , Wang Mei , Gonzalez Jessy , Peng Xuefeng , Grigoriev Igor V. , O’Malley Michelle A. 
Published: January 2025

AbstractAnaerobic gut fungi effectively degrade lignocellulose in the guts of large herbivores, but there remains a limited number of isolated, publicly available, and sequenced strains that impede our understanding of the role of anaerobic fungi within microbial communities. We isolated and characterized a new fungal isolate,Neocallimastix camerooniivar. constans, providing a transcriptomic and genomic understanding of its ability to degrade diverse carbohydrates. This anaerobic fungal strain was stably cultivated for multiple yearsin vitroamong members of an initial enrichment microbial community derived from goat feces, and it demonstrated the ability to pair with other microbial members, namely archaeal methanogens to produce methane from lignocellulose. Genomic analysis revealed a higher number of predicted carbohydrate-active enzymes encoded in theN. camerooniivar. constans genome compared to most other sequenced anaerobic fungi. The carbohydrate-active enzyme profile for this isolate contained 660 glycoside hydrolases, 160 carbohydrate esterases, 194 glycosyltrasferases, and 85 polysaccharide lyases. Differential gene expression analysis showed the upregulation of thousands of genes (including predicted carbohydrate-active enzymes) whenN. camerooniivar. constans was grown on lignocellulose (reed canary grass) compared to less complex substrates, such as cellulose (filter paper), cellobiose, and glucose. AlphaFold was used to predict functions of transcriptionally active yet poorly annotated genes, revealing feruloyl esterases that likely play an important role in lignocellulose degradation by anaerobic fungi. The combination of this strain’s genomic and transcriptomic characterization, omics-informed structural prediction, and robustness in microbial co-culture make it a well-suited platform to conduct future investigations into bioprocessing and enzyme discovery.
Biomarkers of pesticide exposure predict Depressive Symptoms in rural and urban workers of the Maule Region, Chile
Authors: Lucero Boris , Muñoz-Quezada María Teresa , Canales-Johnson Andrés , Carrasco Cynthia , Rodríguez María Victoria , Reid Tannelle , Méndez Pablo , Adonis Jandy , Bekinschtein Tristan A. 
Published: January 2025

AbstractBackgroundAgricultural workers are routinely exposed to pesticides, which are associated with a range of adverse health outcomes, including potential impacts on mental health such as depressive symptoms. In the Maule region of Chile, an area characterized by intensive pesticide use, this study investigates the association between exposure to organophosphate (OP) pesticides and the prevalence of depressive symptoms among agricultural workers.MethodsWe conducted a longitudinal study with 78 participants, comprising agricultural workers occupationally exposed to pesticides and nearby urban non-agricultural workers. Pesticide exposure was assessed through six dialkyl phosphate (DAP) metabolites in four repeated urine samples over two years. Depressive symptoms were evaluated using the CES-D scale and affect using the PANAS scale. Sociodemographic, health, and exposure-related variables were included as covariates. Generalized Estimating Equations (GEE) were employed to investigate dose-response relationships between pesticide exposure and depressive symptoms.ResultsNo reliable differences in urinary DAP, DEAP, and DMP metabolite concentrations were observed directly when testing between rural and urban workers, however, dose-response analyses revealed that cumulative exposure to diethyl alkyl phosphates (DEAPs) was associated with depressive symptoms (CI=0.0003–0.0127, p = 0.040). Over time, positive affect increased among rural workers, whereas urban workers reported significantly lower negative affect in 2023. Further analyses showed problematic alcohol consumption (CI=0.018–3.707, p = 0.048) as a predictor of depressive symptoms.ConclusionsPesticide exposure extends beyond occupational settings to include environmental sources or food residues, as shown by comparable exposure levels in rural and urban participants and consistent measurements over two years. Chronic exposure to DEAPs was predictive of depressive symptoms, emphasizing the importance of biomarkers for assessing cumulative exposure. Public health interventions, stricter regulations, and awareness programs are needed to address the mental health risks of pesticide exposure. Further research should explore genetic and environmental factors influencing susceptibility to mental health.
SHINE: SERS-based Hepatotoxicity detection using Inference from Nanoscale Extracellular vesicle content
Authors: Parlatan Ugur , Boudreau Luke , Torun Hulya , Fan Letao , Aygun Ugur , Gokaltun Ayse Aslihan , Akin Demir , Usta O. Berk , Demirci Utkan 
Published: January 2025

AbstractExtracellular vesicles (EV) are becoming crucial tools in liquid biopsy, diagnostics, and therapeutic applications, yet their nanoscale characterization remains challenging. In this context, the detection of drug-induced liver injury,i.e., hepatotoxicity, through extracellular vesicle molecular content remains an unexplored frontier. To this end, we present a label-free surface-enhanced Raman (SERS) spectroscopy approach, which provides rapid EV content analysis under ten minutes and requires only 1.3 microliters of sample. Using hepatic cultures as a model, our platform captures distinct and reproducible EV molecular changes in response to acetaminophen-induced hepatoxicity. Our platform achieves exceptional accuracy with root mean squared error values as low as 3.80%, establishing strong correlations between EV spectra and conventional toxicity biomarkers. Unlike previous EV-SERS studies limited to vesicle identification and disease markers, this approach reveals EV drug-response signatures strongly correlated with conventional toxicity markers. These findings establish EVs as dynamic reporters of cellular drug responses and demonstrate use of SERS-based EV detection of hepatotoxicity.
Aβ-induced distress of astrocytes triggers Alzheimer disease pathology through non-canonical δ secretase activity
Authors: Schmidt Vanessa , Ziemlinska Ewelina , Obrebski Tomasz , Zurawska-Plaksej Ewa , Cendrowski Jaroslaw , Hempstead Barbara L , Willnow Thomas E , Malik Anna R 
Published: January 2025

ABSTRACTThe importance of astrocytes for Alzheimer disease (AD) pathology is increasingly appreciated, yet the mechanisms whereby this cell type impacts neurodegenerative processes remain elusive. In a genetic mouse model with diminished astrocyte stress response, even low levels of amyloid-β trigger astrocyte reactivity, resulting in brain inflammation and massive amyloid and tau pathologies. This dysfunctional response of astrocytes to amyloid-β acts through activation of δ secretase, a stress-induced protease implicated in both amyloid and tau-related proteolytic processing. Our findings identify a failed astrocyte stress response to amyloid-β as an early inducer of amyloid and tau co-morbidity, a noxious process in AD acting through a unique non-canonical secretase pathway.
Gene regulatory mechanisms underlying evolutionary adaptations of homologous neuronal cell types
Authors: Millán-Trejo Andrea , Mora-Martínez Carlos , Tarazona-Sánchez Adrián , Lloret-Fernández Carla , Alis Rafael , Jordán Antonio , Barrios Arantza , Flames Nuria 
Published: January 2025

SummaryHow nervous systems coordinate the generation of specific neuron types with gene expression plasticity and how these mechanisms impact cell type evolution is unknown. Here we useCaenorhabditisspecies to study neuron-type robustness, plasticity and evolution, using VC4 and VC5 cholinergic motoneurons as models. InC. elegans, we found that epigenetic silencing through histone 3 lysine 9 methylation (H3K9me) is necessary to suppress the expression of the serotonin reuptake genemod-5/Sert and a serotonergic phenotype in these cells. In contrast, we observed that VC4 and VC5 neurons in theAngariagroup of species of theCaenorhabditisgenus have evolved an intense serotonergic staining. This phenotype is caused by the emergence of a new enhancer in themod-5/Sert locus, which has been recruited to the ancestral neuron-type gene regulatory network. Enhancer transfer fromC. angariais sufficient to impose a constitutive serotonergic fate inC. elegans. Remarkably, acquiring this new trait modulates egg-laying responses to high levels of exogenous serotonin, which can be found in specific environments. Finally, we discovered that the repression of the serotonergic fate inC. elegansVC4 and VC5 neurons is indeed a plastic trait that can be adjusted in specific environmental growth conditions to elicit egg-laying behaviours similar to those observed inAngariaspecies. Our work identifies gene regulatory mechanisms that coordinate the generation of robust neuron-type-specific programs with plastic gene expression responses. These findings identify a gene regulatory framework underlying the evolution of neuron-type-specific features and the emergence of novel behaviours.
Mapping of Quorum Sensing Landscape of Commensal and Pathogenic Staphylococci Reveals a Largely Inhibitory Interaction Network
Authors: Gless Bengt H. , Sereika-Bejder Benjamin S. , Jensen Iben , Bojer Martin S. , Tsiko Katerina , Schmied Sabrina H. , Vitolo Ludovica , Toledo-Silva Bruno , De Vliegher Sarne , Ingmer Hanne , Olsen Christian A. 
Published: January 2025

AbstractStaphylococci utilize secreted autoinducing peptides (AIPs) to regulate group behaviour through a process called quorum sensing (QS). For staphylococcal pathogens such asS. aureus, QS regulates expression of major virulence factors and QS inhibition has been proposed as an alternative to antibiotics for treatment of infections with methicillin resistantS. aureus(MRSA). Here, we surveyed the interaction map between QS systems of the pathogensStaphylococcus aureus, Staphylococcus epidermidis, andStaphylococcus lugdunensisand the 36 currently known AIPs from 22 staphylococcal species. We identified seven of these ribosomally synthesized and post-translationally modified peptides (RiPPs) in this study and all synthetic peptides were assessed for their ability to modulate QS. The mapped interactions of >280 native QS pairings were divided into human- and animal-associated staphylococci showing substantial differences in inhibitory potencies between the groups. In particular, AIPs of the bovine-associated speciesS. simulansdisplayed potential as QS inhibitors in the strains investigated in this study and were therefore chosen as starting point for a structure–activity relationship study. This study provides insights into the requirements for QS interference, yielding the most potent inhibitors reported to date forS. epidermidisandS. lugdunensis. Further, we tested anS. simulansAIP as anti-virulence agent in an assay to assess risk of acquired suppression of the inhibitory effect, and we established an assay set-up to successfully monitoragrdeactivation of virulent MRSA by the QS inhibitor. Finally, a peptide was shown to attenuate skin infection caused by MRSA in a mouse model. Our results reveal a complex network of staphylococcal interactions and provide further impetus for the development of therapeutic strategies, based on QS modulation to target antibiotic-resistant pathogens.TOC Graphic
Emergence of binding and catalysis from a designed generalist binding protein
Authors: Chen Yuda , Bhattacharya Sagar , Bergmann Lena , Correy Galen J. , Tan Sophia , Hou Kaipeng , Biel Justin , Lu Lei , Bakanas Ian , Polizzi Nicholas F. , Fraser James S. , DeGrado William F. 
Published: January 2025

AbstractThe evolution of proteins that bind to small molecules and catalyze chemical transformations played a central role in the emergence of life. While natural proteins have finely tuned affinity for their primary ligands, they also often have weak affinities for other molecules. These interactions serve as starting points for the evolution of new specificities and functions. Inspired by this concept, we determined the ability of a simplede novoprotein to bind a set of diverse small molecules (< 300 Da) by crystallographic fragment screening. We then used this information to design one variant that binds fluorogenic molecule and another that acts as a highly efficient Kemp eliminase enzyme. Collectively, our work illuminates how the evolution of novel protein functions can emerge from existing proteins.