bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient alterations in nucleosome distribution and sensitivity to nuclease define the THP-1 monocyte to macrophage transition
Authors: Benoit Jane M , Buck Brandon , Khadem Mahdi , Bass Hank W. , Dennis Jonathan Hancock
Published: February 2025

The monocyte to macrophage transition is marked by alterations to both the structure and function of the genome, including changes in histone post-translational modifications, DNA methylation, 3D nuclear architecture, and expression of lineage specific genes. The nucleosome is the fundamental organizational unit of the eukaryotic genome and underpins both genome structure and function. However, nucleosome dynamics at promoters, which are essential for transcriptional regulation, are understudied in cellular differentiation. We conducted high-resolution chromatin structure profiling at promoters in the THP-1 cell line at eight different time points spanning PMA-induced monocyte to macrophage differentiation. We found that fewer than 10% of nucleosomes within promoters were redistributed during differentiation and only a subset of these were associated with immediate transcriptional alterations. Nucleosomes within the promoters of PMA-responsive genes were strongly positioned prior to differentiation and experienced minimal alterations during differentiation thus implying the existence of a pre-differentiation primed chromatin state. Additionally, we observed pronounced alterations in nucleosome sensitivity to MNase digestion within one hour of PMA-induced differentiation and the emergence of a highly resistant phenotype in fully differentiated cells. We found that resistance is correlated with active chromatin marks, transcription factor binding, gene expression, and higher order chromatin structure demonstrating that it is a useful measure of both genome structure and function. Together this suggests that, unlike more stable nucleosome distribution, transient sensitivity alterations may underpin new genomic functions in differentiating cells. Our results offer a framework for understanding how chromatin structural alterations potentiate cellular differentiation in a monocyte model and use methodology that is widely applicable to other systems.
Peroxisome proliferator-activated receptor gamma (PPARG)-mediated myocardial salvage in acute myocardial infarction managed with left ventricular unloading and coronary reperfusion
Authors: Visker Joseph R. , Tseliou Eleni , Kyriakopoulos Christos P. , Hamouche Rana , Yin Michael , Ling Jing , Shankar Thirupura S. , Kwan Eugene , Cedeno-Rosaria Luis , Velasco-Silva Jesse N. , Sideris Konstantinos , Kwak Hyoin , Hillas Yanni , Yannias Eleni , Maneta Eleni , Srinivasan Harini , Padilla Laisha , Polishchuck Georgiy , Navankasattusas Sutip , Tandar Anwar , Ducker Gregory S. , Rutter Jared , Hong TingTing , Shaw Robin M. , Lui Charles , Welt Frederick G. , Drakos Stavros G.
Published: February 2025

Ischemic heart disease and acute myocardial infarction (AMI) is a leading cause of morbidity and mortality. Improvements have been made in coronary interventions to restore blood flow, but ischemia/reperfusion (I/R) injury significantly impacts clinical outcomes. We previously reported that activation of percutaneous mechanical unloading of the left ventricle (LV) with a transvalvular axial-flow device simultaneously with reperfusion improves myocardial salvage. However, the underlying mechanisms, potential adjuvant pharmacological interventions and the timing of the use of LV unloading as a cardioprotective approach in AMI are not well understood. This study investigated a) the mechanisms associated with improved myocardial salvage, b) a pharmacological intervention, and c) the timing of LV unloading. Following 90 minutes of ischemia, adult swine were subjected to reperfusion alone, simultaneous unloading with reperfusion, upfront unloading with delayed reperfusion, upfront reperfusion with delayed unloading, or reperfusion with concurrent use of esmolol and milrinone. Compared to controls, the simultaneous group had a 47% increase in myocardial salvage following AMI. This was associated with increased expression of neutrophil degranulation, macrophage activation, iNOS signaling, wound healing, and PPAR signaling. From these pathways,PPARG(peroxisome proliferator-activated receptor gamma) emerged as a potential cardioprotective gene that was uniquely overexpressed in the simultaneously unloaded and reperfused myocardium. Next, we showedPPARGagonism with rosiglitazone reduces mitochondrial oxygen demand in cardiomyocytes and in vivo, improves myocardial salvage following I/R injury inC57BL6/Jmice. Thiazolidinediones (TZDs), such as rosiglitazone could be investigated as therapies combined with simultaneous LV unloading and coronary interventions to mitigate reperfusion injury.

GRAPHICAL ABSTRACT
Reprogrammable 4D Tissue Engineering Hydrogel Scaffold via Reversible Ion Printing
Authors: Ding Aixiang , Tang Fang , Alsberg Eben
Published: February 2025

Shape changeable hydrogel scaffolds recapitulating morphological dynamism of native tissues have emerged as an elegant tool for future tissue engineering (TE) applications, due to their capability to create morphodynamical tissues with complex architectures. Hydrogel scaffolds capable of preprogrammable, reprogrammable and/or reversible shape transformations would widely expand the scope of possible temporal shape changes. Current morphable hydrogels are mostly based on multimaterial, multilayered structures, which involve complicated and time-consuming fabrication protocols, and are often limited to single unidirectional deformation. This work reports on the development of a transformable hydrogel system using a fast, simple, and robust fabrication approach for manipulating the shapes of soft tissues at defined maturation states. Simply by using an ion-transfer printing (ITP) technology (i.e., transferring Ca2+from an ion reservoir with filter paper and subsequent covering on a preformed alginate-derived hydrogel), a tunable Ca2+crosslinking density gradient across the hydrogel thickness has been incorporated, which enables preprogrammable deformations upon further swelling in cell culture media. Combining with a surface patterning technology, cell-laden constructs (bioconstructs) capable of morphing in multiple directions are deformed into sophisticated configurations. Not only can the deformed bioconstructs recover their original shapes by chemical treatment, but at user-defined times they can also be incorporated with new, different spatially controlled gradient crosslinking via the ITP process, conferring 3D bioconstruct shape reprogrammability. In this manner, unique “3D-to-3D” shape conversions have been realized. Finally, we demonstrated effective shape manipulation in engineered cartilage-like tissue constructs using this strategy. These morphable scaffolds may advance 4D TE by enabling more sophisticated spatiotemporal control over construct shape evolution.
Evolutionary Rescue Promotes Mutators
Authors: Tuffaha Marwa Z , Wahl Lindi M
Published: February 2025

The role of mutation rate in evolutionary rescue has been extensively explored, but little work has investigated how evolutionary rescue can promote mutators, lineages with higher mutation rates. We investigate the likelihood of evolutionary rescue on a mutator background that either emergesde novoor pre-exists in the population prior to a severe environmental change. If such an evolutionary rescue event occurs, the mutator lineage sweeps into the population, and thus the environmental stress has promoted mutators. Our findings indicate that mutation rate evolution can substantially boost rescue probabilities, but stronger mutators are most effective when the wildtype has a low mutation rate, while their advantage diminishes for higher wildtype mutation rates. Interestingly, at intermediate wildtype mutation rates, emerging mutators can be almost equally likely to sweep no matter how slowly or quickly the environment changes. However, at low wildtype mutation rates, mutators are only likely to sweep for very slow environmental changes due to the sequential nature of necessary mutations for such sweeps to occur. Finally, we show that pre-existing mutators can be significantly more likely to rescue the population compared to the wildtype, provided the wildtype’s mutation rate is relatively low. This research opens new avenues for investigating mutator dynamics in response to environmental stress.
Few-shot in-context learning with large language models for antibody characterization
Authors: Fung Sin-Hang , Zhang Zhenghao , Wang Ran , Miao Chen , Wong Brian Shing-Hei , Li Kelly Yichen , Hong Chenyang , Zhou Jingying , Yip Kevin Y. , Tsui Stephen Kwok-Wing , Cao Qin
Published: February 2025

Large language models (LLMs) exhibit the emergent ability of few-shot in-context learning (ICL), allowing them to learn from demonstrations in simple prompts without task-specific training. However, applying few-shot ICL to biological sequences for classification, especially in computational immunology, remains underexplored. Here, we apply few-shot ICL with 18 general-purpose LLMs across five families to three antibody characterization scenarios, including predicting antibody humanness, specificity, and isotype. We evaluate performance under zero-shot, few-shot, and few-shot Chain-of-Thought ICL settings. We propose similarity-based few-shot demonstration selection strategies, which significantly improve performance of few-shot ICL compared to random selection. In all three scenarios, few-shot ICL, with as few as 32 examples, matches or exceeds the performance of established machine learning (ML) models trained on large datasets using traditional feature encodings. In two of the evaluated scenarios, few-shot ICL even matches or outperforms ML models that use state-of-the-art protein language model-based embeddings. Moreover, combining few-shot ICL with fine-tuning further enhances performance. We also demonstrate the reproducibility and stability of few-shot ICL results. Our findings establish few-shot ICL as a powerful method for efficiently characterizing antibody properties without task-specific training, enabling a single model to perform multiple tasks immediately. Its simplicity and versatility make few-shot ICL a promising approach to antibody characterization for researchers from diverse backgrounds, especially those without coding knowledge.
Draft genome of the marineEntamoebaspecies reveals reduction in the gene family repertoire associated with pathogenicity and lateral gene transfer for adaptation to the marine environment
Authors: Kawano-Sugaya Tetsuro , Izumiyama Shinji , Nozaki Tomoyoshi
Published: February 2025

Entamoebais the amoebozoan parasite commonly found in the intestines of animals.E. marinais the first exception isolated from marine sediments, possibly adapting from animal intestines to the sea. However, the evolutionary process ofE. marinaremains uncertain due to the lack of a genome sequence. Here, we present thede novogenome and transcriptome ofE. marinausing Oxford Nanopore MinION and Illumina HiSeq/MiSeq. The genome ofE. marinais approximately 37.5 Mbp in length and consisted of 202 contigs, which is the second longest followed byE. invadens.E. marinashowed significant reduction in the major virulence-associated gene families, including cysteine proteases, lysosomal enzyme transporters, and surface galactose/N-acetylglucosamine-specific lectins, suggesting diversification, more specifically reduction of pathogenicity-related genes. Genome and RNA-seq analyses also indicated genes either conserved throughout eukaryotes or laterally transferred from prokaryotes, and potentially responsible for salt tolerance. Our study provides insights into the mechanism underlying the lifestyle changes in the evolution of parasitic eukaryotes.
Pex30-dependent membrane contacts sites maintain ER lipid homeostasis
Authors: Ferreira Joana Veríssimo , Ahmed Yara , Heunis Tiaan , Jain Aamna , Johnson Errin , Raeschle Markus , Ernst Robert , Vanni Stefano , Carvalho Pedro
Published: February 2025

In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment remains poorly understood. Here, we investigate how Pex30, a membrane protein localized to the endoplasmic reticulum (ER), regulates multiple MCS in budding yeast. We show that Pex30 is critical for the integrity of ER MCS with peroxisomes and vacuoles. This requires the Dysferlin domain (DysF) on Pex30 cytosolic tail. This domain binds to phosphatidic acid (PA) bothin vitroandin silico,and it is important for normal PA metabolismin vivo. The DysF domain is evolutionarily conserved and may play a general role in PA homeostasis across eukaryotes. We further show that ER-Vacuole MCS requires Pex30 C-terminal Domain of Unknown Function and that its activity is controlled by phosphorylation in response to metabolic cues. These findings provide new insights into the dynamic nature of MCS and their coordination with cellular metabolism.
A prioritized medium-throughput screen on human stem cell derived insulin secreting beta cells identifies FGF4, FGF5, FGF8F, FGF19 and FGF21 as protective factors
Authors: Chu Chieh Min Jamie , Kamal Sepehr , Huang Luo Ting , Bayly Carmen L. , Chen Sing-young , Omur Meltem E. , Wasserman Wyeth W. , Lynn Francis C. , Johnson James D.
Published: February 2025

Insulin is produced by pancreatic β cells, whose dysfunction and death are hallmarks of diabetes. Stem cell-derived β-like cells (SCβ cells) are a potential alternative to cadaveric islets for replacement therapy. However, SCβ cells face a multitude of stresses, including hypoxia, hyperglycemia, ER stress, inflammation, and autoimmunity that must be overcome for this treatment to cure diabetes. Pancreatic β cells and SCβ cells reside in complex microtissues (islets or spheroids) and can therefore be potentially modulated by hundreds of autocrine and paracrine signals. Here, we leveraged scRNAseq, bulk RNAseq, and bulk proteomics data from late stage SCβ cells and human islets to map potential ligand-receptor pairs in these tissues and generate a prioritized list of ligands for high-content SCβ cell survival screening. We tracked cell number with Hoechst 33342, cell death using propidium iodide incorporation, andINSactivity fromINS-EGFP knock-in reporter human embryonic stem cells over several days using high throughput imaging. Members of the fibroblast growth factor (FGF) family significantly prevented cytokine induced cell death, with the top validated hits being FGF4, FGF5, FGF19, FGF21, and FGF8F. These results have the potential to improve SCβ cell survival with pathways that are readily targetable and translatable to the clinic.
The role of MKI67 in the regulation of 60S pre-ribosome nucleolar export, transcripts, energy supply, and apoptosis
Authors: Iuchi Shiro , Paulo Joao A.
Published: February 2025

MKI67 (Ki67) is expressed exclusively in proliferating cells in human tissues, rendering it as a valuable diagnostic marker for cancer. However, the function of this protein in cells remains unclear. In this study, we present the findings on the regulatory functions of MKI67 in conjunction with its partner proteins GNL2 and MDN1, which are involved in pre-ribosome processing, as well as the regulatory functions in its absence. In proliferating HEK293T cells, MKI67 binds contiguously to the chromatin in conjunction with GNL2 and MDN1, localizing most densely to the nucleolar periphery to regulate 60S pre-ribosome export. On the other hand, RNA-seq analysis reveals that these three proteins can independently regulate many target transcripts, but they often share their target transcripts, yet often regulate them at different expression levels. MDN1 depletion strongly downregulates RNA gene transcripts involved in ribosome biogenesis and splicing. In contrast, MKI67 depletion strongly upregulates transcripts of protein-coding genes, including synapse-specific proteins and the mitosis-related protein NEK7. Furthermore, MKI67 depletion coordinately up-or down-regulates the levels of transcripts of several pathways, thereby enabling MKI67-depleted cells to adapt to less active metabolic states. The underlying mechanism by which MKI67 depletion upregulates transcripts appears to involve attenuation of transcript levels in cooperation with mRNA degradation systems, as evidenced by analysis of NEK7 and UNC13A translations. In conclusion, the present results indicate that MKI67 contributes to proliferation via nucleolar export of 60S pre-ribosome particles and high energy supply. Conversely, its absence leads the cells to adapt to the senescent and differentiated conditions.
Neuropeptide CRH prevents premature differentiation of OPCs following CNS injury and in early postnatal development
Authors: Ries Clemens , Stark Tibor , Boulat Benoit , Ruhwedel Torben , Delling Jan Philipp , Infante Antonio Miralles , von Poblotzki Julia T. , Ulivi Alessandro , von Mücke-Heim Iven-Alex , Chang Simon , Sakimura Kenji , Itoi Keiichi , Nestvogel Dennis B. , Attardo Alessio , Czisch Michael , Nave Klaus-Armin , Möbius Wiebke , Dimou Leda , Deussing Jan M.
Published: February 2025

The role of neuropeptides and their receptors in oligodendrocyte progenitor cells (OPCs) has largely been overlooked so far. Here, we describe a new subpopulation of corticotropin-releasing hormone (CRH)-expressing OPCs that aggregate around acute brain injuries and exhibit an elevated capacity to differentiate into myelinating oligodendrocytes (OLs). We found that CRH expression in OPCs is rapidly inducedde novoas a transient response within the first 72 hours after injury. As target cells, we identified CRH receptor type 1 (CRHR1)-expressing OPCs which show a decreased differentiation velocity. We demonstrate that CRH/CRHR1 system inactivation increases the speed of OL generation compromising the long-term survival of OLs after acute injury. Furthermore, we prove that a CRH/CRHR1 system deficiency under non-injury conditions leads to increased early postnatal oligodendrogenesis and alterations in adult myelination. Altogether, we show that OPC-derived CRH not only actively influences the injury environment through the interaction with CRHR1-expressing OPCs, but also identify the G-protein coupled receptor CRHR1 as a critical modulator of oligodendrogenesis at early postnatal stages with lasting effects on adult myelination.
Sex Differences in VEGF and PDGF Ligand and Receptor Protein Expression during Adipose Tissue Expansion and Regression
Authors: Fang Yingye , Gonzales-Nieves Silvia , Cifarelli Vincenza , Imoukhuede P.I.
Published: February 2025

Inadequate angiogenesis in obesogenic adipose tissue (AT) has been implicated in disrupted adipogenesis and metabolic disorders. Yet, key cellular and molecular regulators of AT angiogenesis remain largely unidentified. This study sought to identify the dysregulated elements within the Vascular Endothelial Growth Factor (VEGF) and Platelet-Derived Growth Factor (PDGF) systems during obesity progression. We employ a mouse model, comprising both male and female mice, to investigate the changes in the VEGF/PDGF concentration and their receptor distribution in AT during short- and long-term weight gain and weight loss. Our results reveal pronounced sex-specific differences in obesity progression, with male and female mice exhibiting distinct angiogenic ligand and receptor profiles under identical dietary interventions. This data also lays the groundwork for developing computational models of VEGF/PDGF signaling networks in AT, allowing for the simulation of complex biological interactions and the prediction of therapeutic outcomes.
Capicua refines mossy fiber–CA3 axon targeting in the late postnatal hippocampus
Authors: van Bruggen Rebekah , Wang Mi , Tan Qiumin
Published: February 2025

Proper brain wiring relies on the precise distribution of axonal projections to specific subcellular domains of their target neurons. These spatially confined connections establish the anatomical foundation for neural circuit assembly. The mossy fiber (MF)–CA3 pathway in the hippocampus is an excellent system to study the mechanisms underlying lamina-specific connectivity. In rodents, MF projections develop postnatally and reach their mature configuration by the end of the second postnatal week. MF axons synapse on the proximal segments of the dendrites but avoid the somas of CA3 pyramidal neurons. As dentate gyrus granule neurons are continuously generated and integrated into the existing hippocampal circuit throughout the postnatal period and adulthood, the mechanisms that guide MF axons to achieve lamina-specific targeting of these later-born granule neurons remain unclear. Here, we show that deletion of the neurodevelopmental disorder-associated protein capicua (CIC) results in abnormal MF targeting in the mouse hippocampus. Notably, this defect emerges after the second postnatal week and persists into adulthood, distinguishing it from classical MF guidance defects, which typically manifest during the first postnatal week. We also demonstrate that this miswiring is due to CIC loss in dentate gyrus granule neurons rather than CA3 pyramidal neurons. Single-nucleus transcriptomics and trajectory analysis reveal a loss of a mature granule neuron subtype and dysregulation of axon guidance genes that are normally downregulated as granule neurons mature. Our findings uncover a previously unrecognized role for CIC in hippocampus development and offer insights into the regulation of lamina-specific MF connectivity in the postnatal brain.
STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence
Authors: Vanicek Leah Rebecca , Fischer Ariane , Ruz Jurado Mariano , Procida-Kowalski Tara , Wilhelm Jochen , Merten Maximilian , Escher Felicitas , Kattih Badder , Puntmann Valentina , John David , Nagel Eike , Dimmeler Stefanie , Luxán Guillermo
Published: February 2025

Heart failure with preserved ejection fraction (HFpEF) accounts for half of heart failure cases and is characterised by reduced pericyte coverage. While the contributions of other cardiac cell types to HFpEF are well-studied, the role of pericytes remains less understood. Using murine single-nucleus RNA sequencing to study cardiac pericytes in HFpEF, we identified reducedSTAT3expression as a hallmark of HFpEF pericytes. Mechanistic studiesin vitrorevealed thatSTAT3deletion induces cellular senescence and impairs pericyte adhesion, recapitulating HFpEF-like characteristics. These findings suggest thatSTAT3is crucial for maintaining pericyte homeostasis and highlight its reduction as a potential driver of pericyte loss, a defining feature of HFpEF.
Exploring mutational possibilities of KPC variants to reach high level resistance to cefiderocol
Authors: Hanna Sidonie , La Kevin , Yoshii Yutaka , Gits-Muselli Maud , Meouche Imane El , Benhadid-brahmi Yasmine , Bonacorsi Stéphane , Birgy André
Published: February 2025

Introduction

Klebsiella pneumoniae carbapenemase (KPC)is one of the most widespread carbapenemases, with over 242 variants identified. Some, like KPC-33 (D179Y), resist both ceftazidime-avibactam (CZA) and cefiderocol but show only a moderate cefiderocol MIC increase. KPC’s success stems from its genetic adaptability, enabling mutation accumulation and necessitating proactive resistance monitoring. This study investigates the mutational possibilities for three KPC variants to develop high-level cefiderocol resistance.

Method

Using random mutagenesis and enrichment selection over a 10-day cefiderocol exposure at increasing concentration, we investigated the mutational potential of KPC-2, KPC-3, and KPC-33 to develop high-level cefiderocol resistance. Resistance mechanisms were then analyzed through phenotypic testing and sequencing.

Results

Random mutagenesis generated 10⁵, 10⁴, and 105mutants forblaKPC-2,blaKPC-3, andblaKPC-33, respectively. After ten days of increasing cefiderocol exposure, MICs rose significantly, with KPC-2 mutants reaching >32 mg/L. Phenotypic analysis revealed a common resistance profile across all tested mutants, with resistance to ceftazidime, ceftazidime-avibactam, cefixime, and piperacillin, but restored susceptibility to carbapenems and most other β-lactams. Sequencing identified key mutations (D179Y- D209V in KPC-2, L169P in KPC-3), while chromosomal changes, particularlycirA andybiX disruptions, played a crucial role in resistance evolution.

Discussion

Our results show that the enriched mutations in KPC genes are not sufficient to confer high cefiderocol MICs, suggesting that, in the studied variants, no simple mutational pathway allows the KPC enzyme to efficiently hydrolyze cefiderocol. These findings underscore the interplay between enzymatic and iron transport mutations in cefiderocol resistance, highlighting the importance of surveillance to anticipate emerging resistance in KPC-producing pathogens.
Linguistic coupling between neural systems for speech production and comprehension during real-time dyadic conversations
Authors: Zada Zaid , Nastase Samuel A. , Speer Sebastian , Mwilambwe-Tshilobo Laetitia , Tsoi Lily , Burns Shannon , Falk Emily , Hasson Uri , Tamir Diana
Published: February 2025

The core use of human language is communicating complex ideas from one mind to another in everyday conversations. In conversations, comprehension and production processes are intertwined, as speakers soon become listeners, and listeners become speakers. Nonetheless, the neural systems underlying these faculties are typically studied in isolation using paradigms that cannot fully engage our capacity for interactive communication. Here, we used an fMRI hyperscanning paradigm to measure neural activity simultaneously in pairs of subjects engaged in real-time, interactive conversations. We used contextual word embeddings from a large language model to quantify the linguistic coupling between production and comprehension systems within and across individual brains. We found a highly overlapping network of regions involved in both production and comprehension spanning much of the cortical language network. Our findings reveal that shared representations for both processes extend beyond the language network into areas associated with social cognition. Together, these results suggest that the specialized neural systems for speech perception and production align on a common set of linguistic features encoded in a broad cortical network for language and communication.
Single nucleotide polymorphisms associated with cytotoxicity ofBacillus cereusgroup strains in Caco-2 cells
Authors: Prince Cassidy , Chung Taejung , Kimble Kayla , Chandross-Cohen Tyler , Wiedmann Martin , Johler Sophia , Kovac Jasna
Published: February 2025

Bacillus cereus sensu lato(s.l.) encompasses strains with diverse impacts, ranging from foodborne illness and anthrax to beneficial applications in agriculture and industry. While the risk of anthrax and emetic intoxication can be reliably predicted by the presence of specific virulence genes, predicting diarrheal foodborne illness risk based solely on enterotoxin gene presence has proven unreliable. In this study, we evaluated cytotoxicity against Caco-2 human gut cells using a diverse collection ofB. cereus s.l.isolates representing all eightpanCphylogenetic groups and conducted genomic analyses to identify predictive markers of cytotoxicity. Isolates frompanCgroups I, IV, and V exhibited significantly higher cytotoxicity compared to other groups, although individual isolates from otherpanCgroups have also been linked to illness. Logistic and random forest regression models revealed that while the presence of enterotoxin genes was a sensitive indicator of cytotoxicity, it lacked specificity. Logistic regression analysis identified 21 nonsynonymous single nucleotide polymorphisms (SNPs) within enterotoxin (Nhe and Hbl) gene sequences that were more effective predictors of cytotoxicity, providing higher specificity with comparable sensitivity. These SNPs achieved accuracy and precision values exceeding 0.7. Random forest models highlighted the importance ofpanCgroup, enterotoxin gene SNPs, and the presence of the fullhbloperon as key predictors of cytotoxicity. The strong sensitivity, specificity, and biological relevance of these SNPs position them as promising markers for improving strain-based risk assessment ofB. cereus s.l.

IMPORTANCE

Enterotoxin genes have been associated withB. cereus sensu lato(s.l.) diarrheal foodborne illness; however, their mere presence in a genome is an unreliable predictor of an isolate’s cytotoxicity towards human gut epithelial cells. To improve food safety risk assessment, more specific markers of cytotoxicity are required. In this study, we identified nonsynonymous SNPs within the coding sequences of the enterotoxins Nhe and Hbl. These SNPs offer potential targets for rapid molecular tests to identifyB. cereus s.l.isolates with an elevated food safety risk due to their capacity to inflict cytotoxic damage on human gut epithelial cells. Implementation of such markers upon validation could improve consumer safety while reducing food waste.
The sperm specific Na+,K+-ATPase α4 shows a highly structured and dynamic distribution at the sperm flagellum
Authors: Oishee Mumtarin J , McDermott Jeffrey P. , Sánchez Gladis , Blanco Gustavo
Published: February 2025

Na+,K+-ATPase α4 is a unique cell plasma membrane Na+and K+transporter of spermatozoa, which is essential for male fertility. Previous studies have shown that Na+,K+-ATPase α4 is highly expressed in the sperm flagellum; however, the spatial arrangement of Na+,K+-ATPase α4 at the subcellular level and its relationship to the functional state of the cells are unknown. We studied this here using stimulated emission depletion (STED) super-resolution microscopy. We show that, under non-capacitated conditions, Na+,K+-ATPase α4 is distributed in a trilinear pattern along the midpiece and as a scattered single line along the principal piece segment of the sperm flagellum. Under capacitated conditions, Na+,K+-ATPase α4 pattern undergoes remodelling and its distribution shifts into a single line along the entire length of the flagellum. On the other hand, Na+,K+-ATPase α1 the somatic isoform of Na+,K+-ATPase also present in sperm, exhibits a similar trilaminar localization at the flagellar midpiece but a bilinear pattern in the principal piece. This distribution, unlike that of Na+,K+-ATPase α4, does not change during sperm capacitation. These differences in the localization pattern and spatial dynamics of Na+,K+- ATPase isoform expression highlights the dissimilarities in the roles of both ion transporters. The specific modulation of Na+,K+-ATPase α4 distribution, combined with the unique role that it has in sperm function, stresses the importance of Na+,K+-ATPase α4 for male fertility.

Significance statement

This is the first demonstration of the highly structured nature of Na+,K+-ATPase in the plasma membrane of sperm, including the sperm specific Na+,K+-ATPase α4 isoform, which is key for male fertility, and the somatic Na+,K+-ATPase α1, which is present in all cells. Utilizing stimulated emission depletion (STED) super resolution microscopy, we discovered that Na+,K+- ATPase α4 and Na+,K+-ATPase α1 have different distributions along the sperm flagellum. Moreover, only Na+,K+-ATPase α4 undergoes remodelling during sperm capacitation. These specific patterns of localization that are dependent on the sperm functional state in combination with the different function and regulation of Na+,K+-ATPase isoforms highlights the sophisticated mechanisms that cells have evolved to fulfil their unique function.
Full inter-hemispheric integration sustained by a fraction of posterior callosal fibers
Authors: Santander Tyler , Bekir Selin , Paul Theresa , Simonson Jessica M , Wiemer Valerie M , Skinner Henri Etel , Hopf Johanna L , Rada Anna , Woermann Friedrich G , Kalbhenn Thilo , Giesbrecht Barry , Bien Christian G , Sporns Olaf , Gazzaniga Michael S , Volz Lukas J , Miller Michael B
Published: February 2025

The dynamic integration of the lateralized and specialized capacities of the two cerebral hemispheres constitutes a hallmark feature of human brain function. This inter-hemispheric exchange of information is thought to critically depend upon the corpus callosum. Classical anatomical descriptions of callosal organization outline a topographic gradient from front to back, such that specific transcallosal fibers support distinct aspects of integrated brain function. Here we present a challenge to this conventional model. Using neuroimaging data obtained from a new cohort of adult callosotomy patients, we leverage modern network neuroscience techniques to show - for the first time - that full inter-hemispheric integration can be achieved via a small proportion of posterior callosal fibers. Partial callosotomy patients with spared callosal fibers retained widespread patterns of inter-hemispheric functional connectivity and showed no signs of behavioral disconnection syndromes, even with only 1 cm of the splenium intact. Conversely, only complete corpus callosotomy patients demonstrated sweeping disruptions of inter-hemispheric network architectures, aligning with disconnection syndromes long-thought to reflect diminished information propagation and communication across the brain. These findings motivate a novel mechanistic understanding of synchronized inter-hemispheric neural activity for large-scale human brain function and behavior.
The “Podcast” ECoG dataset for modeling neural activity during natural language comprehension
Authors: Zada Zaid , Nastase Samuel A. , Aubrey Bobbi , Jalon Itamar , Michelmann Sebastian , Wang Haocheng , Hasenfratz Liat , Doyle Werner , Friedman Daniel , Dugan Patricia , Melloni Lucia , Devore Sasha , Flinker Adeen , Devinsky Orrin , Goldstein Ariel , Hasson Uri
Published: February 2025

Naturalistic electrocorticography (ECoG) data are a rare but essential resource for studying the brain’s linguistic capabilities. ECoG offers a high temporal resolution suitable for investigating processes at multiple temporal timescales and frequency bands. It also provides broad spatial coverage, often along critical language areas. Here, we share a dataset of nine ECoG participants with 1,330 electrodes listening to a 30-minute audio podcast. The richness of this naturalistic stimulus can be used for various research endeavors, from auditory perception to semantic integration. In addition to the neural data, we extract linguistic features of the stimulus ranging from phonetic information to large language model word embeddings. We use these linguistic features in encoding models that relate stimulus properties to neural activity. Finally, we provide detailed tutorials for preprocessing raw data, extracting stimulus features, and running encoding analyses that can serve as a pedagogical resource or a springboard for new research.
A neuro-immune axis of transcriptomic dysregulation within the subgenual anterior cingulate cortex in schizophrenia
Authors: Smith Rachel L. , Mihalik Agoston , Akula Nirmala , Auluck Pavan K. , Marenco Stefano , Raznahan Armin , Vértes Petra E. , McMahon Francis J.
Published: February 2025

Many genes are linked to psychiatric disorders, but genome-wide association studies (GWAS) and differential gene expression (DGE) analyses in post-mortem brain tissue often implicate distinct gene sets. This disconnect impedes therapeutic development, which relies on integrating genetic and genomic insights. We address this issue using a novel multivariate technique that reduces DGE bias by leveraging gene co-expression networks and controlling for confounds such as drug exposure. Deep RNA sequencing was performed in bulk post-mortem sgACC from individuals with bipolar disorder (BD; N=35), major depression (MDD; N=51), schizophrenia (SCZ; N=44), and controls (N=55). Toxicology data dimensionality was reduced using multiple correspondence analysis; case-control gene expression was then analyzed using 1) traditional DGE and 2) group regularized canonical correlation analysis (GRCCA) – a multivariate regression method that accounts for feature interdependence. Gene set enrichment analyses compared results with established neuropsychiatric risk genes, gene ontology pathways, and cell type enrichments. GRCCA revealed a significant association with SCZ (Pperm=0.001; no significant BD or MDD association), and the resulting gene weight vector correlated with DGE SCZ-control t-statistics (R=0.53;P<0.05). Both methods indicated down-regulation of immune and microglial genes and upregulation of ion transport and excitatory neuron genes. However, GRCCA - at both the gene and transcript level - showed stronger enrichments (FDR<0.05). Notably, GRCCA results were enriched for SCZ GWAS-implicated genes (FDR<0.05), while DGE results were not. These findings identify a SCZ-specific sgACC gene expression pattern that highlights SCZ risk genes and implicates neuro-immune pathways, thus demonstrating the utility of multivariate approaches to integrate genetic and genomic signals.
Glucosylceramide induced ectosomes propagate pathogenic α-synuclein in Parkinson’s disease
Authors: Jacquemyn Julie , Mariott Brian , Chang Jinlan , Lee Nathanael Y J , Atonal Luis F. Rubio , Green Ceili , Wong Jeremy , Chik Kennedi , Acevedo-Morantes Claudia , Chen Carol X.-Q. , Nicouleau Michael , You Zhipeng , Deneault Eric , Abdian Narges , Durcan Thomas M. , Jackson Jesse , Ioannou Maria S.
Published: February 2025

Intercellular transmission of α-synuclein contributes to Parkinson’s disease pathology. Yet, the mechanisms of α-synuclein spread are not fully understood. Here, we used live-cell microscopy to examine the impact of Parkinson’s disease associated lipid alterations on α-synuclein release. We discovered that increased glucosylceramides induce ectosome shedding from primary neurons, and from dopaminergic neurons derived from Parkinson’s disease patient iPSCs harboring mutations inGBA1(N370S, L444P and W378G) andLRRK2(G2019S and R1441H) compared to their isogenic control. We show that elevated glucosylceramide similarly increases vesicle release and uptake by other neurons in living mouse brains using 2-photon microscopy. Finally, we show that ectosomes are loaded with pathogenic α-synuclein and lead to the transmission of α-synuclein pathology to neighbouring neurons. These data reveal ectosomes as the predominant route for α-synuclein transmission that can only be appreciated by live-cell imaging technologies.
Hierarchical encoding of natural sounds mixtures in ferret auditory cortex
Authors: Landemard Agnès , Bimbard Célian , Boubenec Yves
Published: February 2025

Extracting relevant auditory signals from complex natural scenes is a fundamental challenge for the auditory system. Sounds from multiple sources overlap in time and frequency. In particular, dynamic “fore-ground” sounds are often masked by more stationary “background” sounds. Human auditory cortex exhibits a hierarchical organization where background-invariant representations are progressively enhanced along the processing stream, from primary to non-primary regions. However, we do not know whether this organizational principle is conserved across species and which neural mechanisms drive this invariance. To address these questions, we investigated background invariance in ferret auditory cortex using functional ultrasound imaging (fUSI), which enables large-scale, high-resolution recordings of hemodynamic responses. We measured responses across primary, secondary, and tertiary auditory cortical regions as ferrets passively listened to mixtures of natural sounds and their components in isolation. We found a hierarchical gradient of background invariance, mirroring findings in humans: responses in primary auditory cortex reflected contributions from both foreground and background sounds, while background invariance increased in higher-order auditory regions. Using a spectrotemporal filter-bank model, we found that in ferrets, this hierarchical structure could be largely explained by tuning to low-order acoustic features. However, this model failed to fully account for background invariance in human non-primary auditory cortex, suggesting that additional, higher-order mechanisms are crucial for background segregation in humans.
Optical Pooled Screening for the Discovery of Regulators of the Alternative Lengthening of Telomeres Pathway
Authors: Quintanilla Isabel , Azeroglu Benura , Sagar Md Abdul Kader , Stracker Travis H. , Lazzerini Denchi Eros , Pegoraro Gianluca
Published: February 2025

Telomere elongation is essential for the proliferation of cancer cells. Telomere length control is achieved by either the activation of the telomerase enzyme or the recombination-based Alternative Lengthening of Telomeres (ALT) pathway. ALT is active in about 10-15% of human cancers, but its molecular underpinnings remain poorly understood, preventing the discovery of potential novel therapeutic targets. Pooled CRISPR-based functional genomic screens enable the unbiased discovery of molecular factors involved in cancer biology. Recently, Optical Pooled Screens (OPS) have significantly extended the capabilities of pooled functional genomics screens to enable sensitive imaging-based readouts at the single cell level and large scale. To gain a better understanding of the ALT pathway, we developed a novel OPS assay that employs telomeric native DNA FISH (nFISH) as an optical quantitative readout to measure ALT activity. The assay uses standard OPS protocols for library preparation and sequencing. As a critical element, an optimized nFISH protocol is performed before in situ sequencing to maximize the assay performance. We show that the modified nFISH protocol faithfully detects changes in ALT activity upon CRISPR knock-out (KO) of theFANCMandBLMgenes which were previously implicated in ALT. Overall, the OPS-nFISH assay is a reliable method that can provide deep insights into the ALT pathway in a high-throughput format.
EID1, an F-box protein involved in phytochrome A-specific light signaling
Authors: Dieterle Monika , Zhou Yong-Chun , Schäfer Eberhard , Funk Markus , Kretsch Thomas
Published: July 2002

To perceive red and far-red light, plants have evolved specific photoreceptors called phytochromes. Even though the spectral properties of all phytochromes are very similar, they show a distinct mode of action. Here we describe EID1, a negatively acting component of the signaling cascade that shifts the responsiveness of the phytochrome A (phyA) signaling system associated with hypocotyl elongation from red to far-red wavelengths. EID1 is a novel nuclear F-box protein that contains a leucine zipper whose integrity is necessary for its biological function. EID1 most probably acts by targeting activated components of the phyA signaling pathway to ubiquitin-dependent proteolysis.
The Forkhead transcription factor UNC-130 is required for the graded spatial expression of the UNC-129 TGF-β guidance factor in C. elegans
Authors: Nash Bruce , Colavita Antonio , Zheng Hong , Roy Peter J. , Culotti Joseph G.
Published: July 2002

Secreted proteins required for cellular movements along the circumference of the body wall in Caenorhabditis elegansinclude UNC-6/netrin and the novel TGF-β UNC-129. Expression of these proteins is graded along the dorsoventral (D/V) axis, providing polarity information to guide migrations. Here we show that the graded expression of UNC-129 in dorsal but not ventral body muscles depends onunc-130, which encodes a Forkhead transcription factor. The phenotype of unc-130 mutants closely mimics the reported effects of ectopically expressing unc-129 in both dorsal and ventral body muscles (Colavita et al. 1998). This fits our present finding that unc-130 cell autonomously repressesunc-129 expression in the ventral body muscles. Thus the cell-specific effects of unc-130 on ventral, but not dorsal, body muscle expression of unc-129 accounts for the D/V polarity information required for UNC-129-mediated guidance. Genetic interactions between unc-130 and other guidance genes show that several molecular pathways function in parallel to guide the ventral to dorsal migration of distal tip cells (DTCs) and axonal growth cones inC. elegans. Genetic interactions confirm that UNC-129 does not require the only known type II TGF-β receptor in C. elegans(DAF-4) for its guidance functions. Also, unc-130 is partially required for male tail morphogenesis and for embryogenesis.
Structural basis of inhibition of CDK–cyclin complexes by INK4 inhibitors
Authors: Jeffrey Philip D. , Tong Lily , Pavletich Nikola P.
Published: July 2002

The cyclin-dependent kinases 4 and 6 (Cdk4/6) that drive progression through the G1 phase of the cell cycle play a central role in the control of cell proliferation, and CDK deregulation is a frequent event in cancer. Cdk4/6 are regulated by the D-type cyclins, which bind to CDKs and activate the kinase, and by the INK4 family of inhibitors. INK4 proteins can bind both monomeric CDK, preventing its association with a cyclin, and also the CDK-cyclin complex, forming an inactive ternary complex. In vivo, binary INK4–Cdk4/6 complexes are more abundant than ternary INK4–Cdk4/6–cyclinD complexes, and it has been suggested that INK4 binding may lead to the eventual dissociation of the cyclin. Here we present the 2.9-Å crystal structure of the inactive ternary complex between Cdk6, the INK4 inhibitor p18INK4c, and a D-type viral cyclin. The structure reveals that p18INK4c inhibits the CDK–cyclin complex by distorting the ATP binding site and misaligning catalytic residues. p18INK4c also distorts the cyclin-binding site, with the cyclin remaining bound at an interface that is substantially reduced in size. These observations support the model that INK4 binding weakens the cyclin's affinity for the CDK. This structure also provides insights into the specificity of the D-type cyclins for Cdk4/6.
Identification of Candidate Coding Region Single Nucleotide Polymorphisms in 165 Human Genes Using Assembled Expressed Sequence Tags
Authors: Garg Kavita , Green Philip , Nickerson Deborah A.
Published: July 2002

Using assembled expressed sequence tags (ESTs) from 50 different cDNA libraries, we have identified contigs that represent the complete coding sequences of 850 known human genes, and have scanned these for high quality sequence substitutions. We report the identification and characteristics of 201 candidate single nucleotide polymorphisms found in the coding sequences (cSNPs) of 165 of these genes. Using a conservative calculation, coding region nucleotide diversity (the average number of differences between any pair of chromosomes) was found to be 3 per 10,000 bp based on this data. This analysis reveals that assembled ESTs from multiple libraries may provide a rich source of comparative sequences to search for cSNPs in the human genome.
A Comparative Gene Map of the Horse (Equus caballus)
Authors: Caetano Alexandre R. , Shiue Yow-Ling , Lyons Leslie A. , O'Brien Steven J. , Laughlin Thomas F. , Bowling Ann T. , Murray James D.
Published: July 2002

A comparative gene map of the horse genome composed of 127 loci was assembled based on the new assignment of 68 equine type I loci and on data published previously. PCR primers based on consensus gene sequences conserved across mammalian species were used to amplify markers for assigning 68 equine type I loci to 27 horse synteny groups established previously with a horse-mouse somatic cell hybrid panel (SCHP, UC Davis). This increased the number of coding genes mapped to the horse genome by over 2-fold and allowed refinements of the comparative mapping data available for this species. In conjunction with 57 previous assignments of type I loci to the horse genome map, these data have allowed us to confirm the assignment of 24 equine synteny groups to their respective chromosomes, to provisionally assign nine synteny groups to chromosomes, and to further refine the genetic composition established with Zoo-FISH of two horse chromosomes. The equine type I markers developed in this study provide an important resource for the future development of the horse linkage and physical genome maps.