Biology subjects

Singh, G.

Publications and source records attributed to Singh, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Evaluation of new adjuvants in enhancing the immune response to a candidate of Severe Fever with Thrombocytopenia Syndrome Virus vaccine.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging zoonotic disease caused by the tick-borne bunyavirus SFTSV. SFTSV is primarily transmitted by Haemaphysalis longicornis ticks and can cause a hemorrhagic fever-like illness characterized by high fever, thrombocytopenia, leukopenia, and multiorgan failure, with reported case-fatality rates ranging from 10% to over 30%. Despite its growing public health relevance, no licensed vaccines or specific antiviral therapies are currently available. Here, we evaluated a beta-propiolactone-inactivated SFTSV vaccine candidate based on strain YL1, formulated with benchmark adjuvants (Addavax and Alhydrogel) or experimental innate immune agonists, including Sendai virus-derived defective interfering RNA (SDI), a RIG-I agonist, and imidazoquinoline-poly(ethylene glycol)-cholesterol conjugate (IMDQ-P-C), a TLR7/8 agonist, alone or in combination. Using an extended prime-boost regimen, we examined adjuvant-dependent modulation of humoral immunity, antigen-specific cellular recall, antibody cross-reactivity, and functional protection following passive serum transfer and live-virus challenge in IFNAR-/- mice. All adjuvanted formulations induced detectable humoral responses, with Addavax and SDI eliciting the highest virus-specific binding and neutralizing antibody titers. Antigen-specific analyses identified the nucleoprotein (NP) as the dominant target of vaccine-induced immune memory. NP elicited robust antibody response and the broadest cytokine recall profile following ex vivo stimulation. This response was broader than that induced by the whole inactivated virus and was characterized by mixed Th1-associated, Th2-associated, and proinflammatory-associated features that varied across adjuvant formulations. In contrast, the head domain of the Gn glycoprotein elicited limited cellular recall responses, consistent with its relatively weak humoral immunogenicity after both priming and boosting. Nevertheless, sera from SDI and Addavax-adjuvanted groups displayed cross-reactivity with Gn from a heterologous SFTSV strain, suggesting broader antibody recognition across viral genotypes. Functionally, sera from SDI and Addavax-immunized mice conferred partial protection following passive transfer into IFNAR-/- recipients, as reflected by reduced viral loads, delayed disease onset, and prolonged survival after lethal SFTSV challenge. Together, these findings support the immunogenicity and protective potential of a BPL-inactivated SFTSV vaccine platform and identify NP as a major target of vaccine-induced immune memory. They further highlight the importance of adjuvant selection in shaping the magnitude, antigenic focus, and functional quality of vaccine-induced antiviral immunity.

microbiology↗

bioRxiv2026

Spatial profiling and neurovascular communication in the developing and adolescent cortex following prenatal alcohol exposure

Fetal alcohol spectrum disorders (FASD) constitute a wide range of developmental, cognitive, and behavioral impairments caused by prenatal alcohol exposure (PAE). Although neuronal and vascular consequences of PAE have been studied, how alcohol affects the cerebrovasculature within the framework of the neurovascular unit (NVU) across development remains poorly understood. At minimum, the NVU comprises neurons, astrocyte endfeet, and endothelial cells (ECs), which coordinate to maintain brain homeostasis. Here, we used the NanoString Digital Spatial Profiling platform to characterize spatial transcriptomic data from neurons, astrocytes, and ECs from PAE and saccharin (SAC) control cortices at embryonic day 18 (E18) and postnatal day 28 (P28). Differentially expressed genes were then used for Ingenuity Pathway Analysis (IPA) to identify altered biological pathways and perform comparison analyses across developmental time points, while CellChat was used to infer cell cell communication networks. We uncovered thousands of differentially expressed genes and numerous altered pathways and biological processes in PAE cortices across development. Both IPA and CellChat analyses implicated dysregulation of vascular and extracellular matrix (ECM) remodeling, cell adhesion, and neuroinflammatory signaling. CellChat further predicted the loss of several key bidirectional relationships and altered ligand-receptor interactions among neurovascular cell types at E18 and P28. Overall, these findings identify PAE associated alterations in neurovascular gene expression and intercellular signaling across development, providing potential mechanisms by which PAE may disrupt neurodevelopment.

molecular biology↗

bioRxiv2026

Loss of a conserved disulfide bond defines Penetration2-related immune myrosinases in Brassicaceae

O_LIThis study investigated whether PEN2/BGLU26 has uniquely evolved as an indole glucosinolate-hydrolysing myrosinase required for Arabidopsis thaliana pre-invasive immunity, or whether related myrosinases can replace its function when targeted to the same subcellular context. C_LIO_LIPEN2-homologous and other selected myrosinases from A. thaliana and Brassica rapa were expressed in the pen2-2 mutant background using a PEN2-like targeting strategy. The resulting lines were assessed by gene expression, protein accumulation, metabolite analysis and pathogen resistance assays. In parallel, targeted mutagenesis, structural comparison and phylogenetic analysis were used to examine molecular and evolutionary features of PEN2-related myrosinases. C_LIO_LIAtBGLU27 and BrBABG.a, but not AtBGLU18, AtBGLU23 or AtBGLU28, partially restored indole glucosinolate hydrolysis and resistance to Colletotrichum tropicale in pen2-2. Unlike AtPEN2, both enzymes acted mainly constitutively and showed distinct substrate preferences. PEN2, BGLU27 and BABG proteins lacked conserved post-translational modification sites, including residues associated with a conserved disulfide bond. Restoring this disulfide bond in AtPEN2 abolished its activity. C_LIO_LIPEN2-related myrosinases form an evolutionarily distinct BGLU lineage associated with indole glucosinolate metabolism in Brassicales. Loss of the conserved disulfide bond appears to be required for PEN2 activity, whereas additional PEN2-specific regulatory features are needed for pathogen-triggered, rather than constitutive, glucosinolate metabolism. C_LI

plant biology↗

bioRxiv2026

A human monoclonal antibody from hybrid immunity exhibits exceptional neutralization breadth against antigenically divergent contemporary Omicron JN.1 lineage variants

Hybrid immunity offers stronger and more durable antibody-mediated protection against symptomatic SARS-CoV-2 infection. In the present study, we report the development of a durable antibody response in an individual with hybrid immunity who also received three doses of the prototype COVID-19 vaccine. Polyclonal plasma antibody obtained from this donor also showed extraordinary neutralization breadth against contemporary Omicron variants. One of the functional monoclonal antibodies (ATHS-C30) isolated from this individual, representing the IGHV4-30 lineage-specific B cell with strong binding affinity to JN.1 spike protein, showed extraordinary neutralization breadth, including variants of Omicron lineages that emerged beyond JN.1, such as KP.2, KP.3.1.1, KP.3.2, KP.3.3, LB.1 and XEC. ATHS-C30 was found to bind RBD with high affinity and showed distinct epitope specificity to the other neutralizing mAbs isolated from the same donor through the epitope binning assay. Molecular modelling of the CDHR3 sequence using existing structures indicated that ATHSC-30 belongs to the class 4 antibody, a feature that contributes to breadth, while epitope conservation analysis indicated that the majority of RBD-interacting residues of ATHSC-30 are evolutionarily conserved. Taken together, our study indicate that ATHS-C30 forms the basis of development of a robust and broadly neutralizing antibody response in this individual with hybrid immunity, which overcomes the antigenic variation by targeting highly conserved and cryptic epitopes in destabilizing the spike structure. ImportanceSARS-CoV-2 continues to pose a significant public health threat, particularly to immunocompromised individuals and older adults with underlying comorbidities. Hybrid immunity to SARS-CoV-2 in vaccinated individuals leads to the development of B cells that are qualitatively superior to those that are expected to develop in only vaccinated individuals. In the present study, we found that among individuals with hybrid immunity who developed robust, durable antigen-specific antibody responses, one developed antibody response capable of broadly cross-neutralising contemporary Omicron variants. This was correlated with development of antigen-specific B cell lineage, such as IGHV4-30, that produced antibodies with potent and extraordinary neutralisation breadth against contemporary Omicron lineages, such as KP.2, KP.3.1.1, KP.3.2, KP.3.3, LB.1 and XEC. This is believed to be due to heterologous antigen exposures driving the development of an antigen-specific B cell repertoire that, in turn, facilitates immune imprinting capable of overcoming the ineffectiveness of antibodies to effectively neutralize newly emerging Omicron variants.

immunology↗

bioRxiv2026

Talk2QSP: Deriving Executable Scenarios from Unstructured Literature via Human-in-the-Loop Agents

Quantitative Systems Pharmacology (QSP) models play an inherently interventional role in pharmaceutical research and development, functioning as executable causal systems for designing, evaluating, and replacing clinical trials. However, deploying QSP as an experimental planning engine remains constrained by the difficulty of translating unstructured literature descriptions of clinical or preclinical scenarios into reproducible, simulation-ready model interventions. Motivated by this issue, we propose an agent-based framework that operationalizes QSP models as intervention-ready experimental systems by automatically extracting and executing literature-derived scenarios. The framework combines semantic grounding of model entities with a large language model (LLM)-driven Scenario Extractor and a dual-agent Scenario Mapper. Rather than relying on opaque, single-shot reasoning, our pipeline converts free-text interventions into precise parameter configurations through discrete, verifiable work orders. Moreover, our dynamic Human-in-the-Loop (HITL) strategy empowers modelers to resolve biological ambiguities interactively. Across four diverse kinetic ordinary differential equation (ODE)/QSP models and seven Subject Matter Expert (SME)-curated literature scenarios, our model resolved all selected scenarios into correct executable parameter changes, including multi-dose interventions, unit conversions, no-op scenarios, and ambiguity-triggered HITL cases, demonstrating that structured collaboration between experts and agentic systems can resolve scenarios that standalone Systems Biology Markup Language (SBML) reasoning LLM calls or prior agentic efforts operating on processed SBML data handle unreliably.

systems biology↗

bioRxiv2026

A SRC-Annexin A2 axis that couples membrane repair to microRNA export during radiation stress in glioblastoma

Repair of ionizing-radiation (IR)-induced membrane damage is essential for cell survival, and Annexin A2 (ANXA2) mediates this repair by promoting shedding of microvesicles containing both damaged lipid and ANXA2. Here, we show that coupling this process to microRNA export contributes to radiation resistance of glioblastoma, the most common adult brain cancer. Structural modeling and mutational analysis identify that ANXA2 tyrosine 23 (Y23) phosphorylation, required for its IR-induced localization to damaged membranes, is also essential for binding miR-603, a critical regulator of glioblastoma cell state. This binding is required for IR-induced miR-603 export, indicating that the repair program recruiting ANXA2 also positions it to load miR-603 into microvesicles. Mutations that abolish ROS-induced sulfenylation and activation of SRC (SRC-C185A/C245A) suppressed ANXA2-Y23 phosphorylation, microvesicle shedding, and miR-603 export. The epistatic interaction between ANXA2-Y23A, SRC-C185A/C245A, and miR-603 delineates a therapeutically targetable radiation-response network that couples membrane repair with miRNA export.

cancer biology↗

bioRxiv2026

A conserved Pho4-Pho84 axis ubiquitously maintains intracellular phosphate homeostasis in yeast

Inorganic phosphate (Pi) is central to fundamental cellular processes and the metabolic economy, and is constantly acquired in order to maintain intracellular Pi levels. While much is known about cellular adaptation during Pi starvation, how intracellular Pi is maintained in Pi-replete conditions remains unclear. Here, using Saccharomyces cerevisiae, we uncover an essential role for the Pho4 transcription factor in maintaining intracellular Pi under Pi-replete conditions, via the high affinity Pho84 transporter. Basal Pho4-dependent output is required for intracellular Pi maintenance, and the loss of Pho4 results in decreased intracellular Pi. We uncover that the Pho4 dependent, high affinity Pi transporter Pho84 is the primary transporter required for this intracellular Pi maintenance in phosphate replete conditions, and is not compensated by other transporters. The loss of Pho4 or Pho84 decreases intracellular Pi, with reduced ATP and glycolysis, and decreased growth. Through comparative genomic and phylogenetic analyses we establish that Pho84 is universally conserved across fungi, and Pho84 alone is orthologous to the plant high-affinity phosphate transporter PHT1. Thus, Pho84 is a primary determinant of intracellular Pi homeostasis during phosphate replete growth, and Pi acquisition in replete conditions is built around high-affinity phosphate transport. These findings reiterate the importance of Pi acquisition via high-affinity transport for metabolic homeostasis, with implications for microbial fermentation-based applications.

systems biology↗

bioRxiv2026

Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish

Nanopore sequencing technologies are used widely in genomics research and their adoption continues to accelerate. 'Basecalling' is an essential step in the nanopore sequencing workflow, during which raw electrical signals are translated into nucleotide sequences. The current state-of-the-art basecaller, Oxford Nanopore Technologies (ONT) software 'Dorado,' relies on proprietary, platform-specific NVIDIA GPU optimisations bundled in the closed-source 'Koi' library. As a result, practical, high-speed basecalling is effectively restricted to a narrow class of supported hardware, limiting accessibility, portability, and innovation. We present (1) 'Openfish,' an open-source GPU-accelerated nanopore basecaller decoding library that provides a competitive alternative to ONT's proprietary Koi library; and (2) Slorado, a fully open-source basecalling framework that supports both DNA and RNA with equivalent accuracy to Dorado. Together, Openfish and Slorado remove the hardware lock-in that currently limits high-performance nanopore basecalling. Our framework scales efficiently across heterogeneous computing environments, from low-power embedded devices to GPU-equipped datacenters, without sacrificing speed or accuracy. Openfish and Slorado are available as free open-source packages for basecalling research, optimisation and deployment beyond the constraints of proprietary software and hardware ecosystems: Openfish: https://github.com/warp9seq/openfish, Slorado: https://github.com/BonsonW/slorado.

bioinformatics↗

bioRxiv2026

Compartmentalized cytokine networks and systemic immune remodeling in bovine mammary H5N1 infection.

Highly pathogenic avian influenza A H5N1 has recently expanded its mammalian host range; in 2024, genotype B3.13 emerged in U.S. dairy cattle with pronounced mammary tropism. In the past, Influenza A virus immunology has been characterized primarily in respiratory infection models, whereas this study delineates immune responses after intramammary infection. An intramammary H5N1 challenge in Jersey cows in the early dry-off period enabled integration of dose- and compartment-resolved (alveoli versus teat cistern) cytokine and chemokine profiles with peripheral leukocyte dynamics and H5/N1-specific antibody responses. Infection-induced quarter-restricted, monophasic inflammatory networks peaking at 3-7 days post-infection, coordinated peripheral myeloid expansion and IFN-{gamma}-competent lymphocyte activation, and rising antibody titers across quarters.

microbiology↗

bioRxiv2026

Pathogenesis of H5N1 Clade 2.3.4.4b in dry Jersey cows following intramammary inoculation shows within-host compartmentalization

Dairy cattle have emerged as a prolific amplifying host for highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b and a new source for cross-species and zoonotic transmission. Independent introductions of H5N1 with unclear exposure routes have been reported in several dairy herds across the U.S. These events escalate the pandemic potential of HPAIV H5N1 as transmission within and between mammalian species present opportunities for mammalian adapted H5N1 viruses to emerge. Although more than 1000 herds have been infected, bovine H5N1 influenza virus pathogenesis, transmission, and evolution in dairy cattle remains not well characterized. Working with H5N1-infected lactating cattle in high containment has been a major challenge due to the required infrastructure and logistics associated with housing, husbandry, and waste management for this model. Thus, developing alternative bovine models that maintain biological relevance while reducing operational complexity is warranted. Here, we evaluate the susceptibility of lactating Jersey cattle in the dry-off period, and characterize the effect of inoculation dose on the mammary pathogenicity of HPAIV H5N1 genotype B3.13. The results of this study demonstrate that dairy cows 21 days into the dry-off period are highly susceptible to HPAIV H5N1, recapitulating the severe clinical and pathological outcomes observed in infected lactating cows under experimental conditions and in field cases. We also observed an association between virus dose and the onset and severity of mastitis in individual udder-quarters. Overall, this study demonstrates that dry cows can provide a feasible model to study H5N1 virology, pathology, and humoral immunology in dairy cows.

microbiology↗

bioRxiv2026

MIF-mediated reprogramming of myeloid lineage within the glioma tumor microenvironment impacts the efficacy of immune stimulatory gene therapy

Gliomas with mutant isocitrate dehydrogenase 1 (mIDH1) represent a distinct subgroup of brain tumors characterized by unique metabolic and immunological profiles compared to wildtype IDH1 (wtIDH1) gliomas. Despite recent progress, the cellular mechanisms underlying tumor progression and immune modulation in these subtypes remain poorly understood. In this study, we employed single-cell RNA sequencing (scRNA-seq) to characterize the cellular heterogeneity of wtIDH1 and mIDH1 gliomas, with a particular focus on myeloid cell populations. Our analyses revealed a marked reduction of monocyte-derived tumor-associated macrophages (Mo-TAMs) and lower expression of macrophage migration inhibitory factor (MIF) in mIDH1 gliomas, which was attributable to epigenetic reprogramming. Mechanistic studies using MIF and CD74 knockout mice demonstrated that the MIF-CD74 axis plays a crucial role in regulating the glioma immune microenvironment, thereby driving tumor growth and progression. Importantly, the combination of immune-stimulatory gene therapy (HSV1-thymidine kinase/Fms-like tyrosine kinase 3 ligand; TK/Flt3L) with MIF inhibition significantly extended survival in models of wtIDH1 glioma. These findings highlight the therapeutic potential of targeting the MIF-CD74 pathway and underscore the importance of integrating immunomodulatory strategies for the treatment of glioma. HighlightsO_LIMutant IDH1 gliomas exhibit fewer Mo-TAMs and increased Mg-TAMs C_LIO_LIMutant IDH1 gliomas have less MIF expression via epigenetic reprogramming. C_LIO_LIMesenchymal wtIDH1 glioma cells are main source of MIF. C_LIO_LIMIF inhibition plus immune stimulatory gene therapy extends survival wtIDH1 glioma. C_LI

cancer biology↗

bioRxiv2026

Cortical Field Model of Complex Spiral Traveling Waves

Complex spiral traveling waves observed experimentally occur across the cortex. The underlying mechanisms responsible for generating such mesoscopic activity are not well understood. Understanding how local cortical neuronal populations interact to produce emergent spiral dynamics during cognitive processing remains unknown. Therefore, to bridge this gap, a spatiotemporal cortical field rate model of local cortical circuits, composed of excitatory and three distinct time-scale inhibitory populations, is proposed. This model is extended to a two-dimensional cortical sheet, consisting of both nonlinear local interactions and diffusive global coupling, with distance-dependent axonal delays. Simulation results indicate mixed-mode oscillations occur in the local circuits, which may represent the coexistence of multiple rhythms and show the emergence of complex dynamics, such as rotating spirals with annihilation events. Spiral waves differentially respond to the strength of the grating input stimulus and exhibit working memory-like characteristics. Also hypothesize that local patterns, such as planar, source, sink, or concentric across the cortex, might be an inherent integral part of the spiral state dynamics.

neuroscience↗

bioRxiv2025

Somatic copy number mutations contribute to fitness in transplantation models of spontaneous human breast cancer metastasis

The contribution of somatic gene dosage mutations (CNA) to breast cancer metastasis remains poorly defined. Using 9 transplantable human neoadjuvant-naive triple-negative breast cancer xenografts, we studied the fitness of copy number clones in spontaneous metastasis from orthotopic transplant sites. Metastatic site preference was strongly patient-dependent, and the emergence of metastases exhibited a general trend toward slower growth at the orthotopic site. In our models, single-cell whole-genome sequencing of primary and metastatic sites showed that distant metastases were most often the result of minor prevalence clones at the orthotopic site, suggesting that some metastatic phenotypes may be weakly negatively fit at the primary site. We validated the existence of a fitness hierarchy of copy number clones using a previously established paradigm of remixing and retransplanting clones. Single-cell clone analysis of competitive repopulation and re-emergence of metastases showed that CNAs arising in cancer evolution can mediate metastatic fitness. Moreover, some clones displaying strong metastatic tendency exhibited weaker survival at the primary site, consistent with the notion that metastatic phenotypes could have a fitness cost at the primary site. Finally, we conducted RNA-seq analysis combined with DriverNet analysis to dissect the contribution of CNA-mediated versus genome-independent transcriptional states. CNA mutations appeared to contribute strongly to transcriptional differences between clones. Among clones of high metastatic potential, we observed CNA-mediated and CNA-independent convergence on pathways such as epithelial-mesenchymal transition (EMT), established as mediators of metastatic cell survival at distant sites. Taken together, our data point to a contribution of CNA-mediated cancer evolution to metastatic states and identify distant-site context as a key determinant of CNA-mediated fitness.

cancer biology↗

bioRxiv2025

The Multiple Approaches for Drug-Drug Interaction Extraction using Machine learning and transformer based Model

This research paper investigates a machine learning based approach for Drug-Drug Interaction (DDI) extraction for determining the side effects of multi drugs when prescribed simultaneously. In our proposed model we used TAC 2017 Dataset, which has Adverse Drug Reactions (ADRs) data for the classification ofdrug-drug interaction. TAC 2017 Dataset has various types of information which are related to drugs and their interactions. Our method uses Term Frequency-Inverse Document Frequency (TF-IDF) to transform the textual descriptions ofside effects for DDI into numerical feature vectors, followed by a Random Forest Classifier, Gradient Boosting, BioBERT, Support Vector Machine (SVM) Algorithms to predict the potential interactions between drug pairs. One of the key strength of the Random Forest approach is its ability to provide feature importance scores, which allows us to interpret which side effects are most influential in predicting drug interactions. The key advantage of Gradient Boosting is its high predictive performance combined with interpretability. It is able to handle complex, structured data efficiently. Additionally, the models decisions are more transparent, which is necessary in the biomedical domain. The advantageof SVM is its ability to handle high-dimensional data, capture complex non-linear interactions using kernel functions, and generalize with datasets, making it robust to over-fitting. BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining) is advantageous for DDI prediction due to its biomedical domain knowledge, contextual understanding of complex drug-related texts.These method captures the relevance and importance of each side effect of multi drugs and also generate pairs of drugs from the dataset. Our model demonstrates competitive performance in DDI prediction, which highlights the utility of text-based feature extraction combined with an interpretable ensemble learning model.

bioengineering↗

bioRxiv2025

Disease modulation by TIV vaccination during secondary pneumococcal infections in influenza-infected mice.

Secondary bacterial infections can significantly worsen the clinical course of influenza virus infections and are a leading cause of morbidity and mortality during seasonal influenza epidemics. Despite being a vaccine-preventable disease, influenza-related complications from secondary bacterial infections are an important cause of death, particularly among the elderly population. Streptococcus pneumoniae (Spn) is the most common agent responsible for influenza-related secondary bacterial infections. Influenza virus vaccination serves as an effective prophylactic strategy for preventing influenza and reducing the burden of influenza-associated pathology, including secondary bacterial infection. However, whether the protective effects of influenza virus vaccination differ in the context of a secondary Spn infection at the level of the host response remains poorly characterized. Here, we present a preclinical mouse model to examine the impact of influenza vaccination in scenarios involving single infections with influenza A virus H1N1 (NC99) or Spn serotype 1; simultaneous infection with both NC99 and Spn (coinfection), or NC99 infection followed by Spn infection seven days later (superinfection). A single dose of trivalent inactivated Influenza vaccine (TIV) is able to decrease infection lethality in both secondary bacterial infection scenarios. Protection is associated with reduction in both viral and bacterial titers, decreased production of pro-inflammatory cytokines, protection of alveolar macrophages, prevention of exacerbated lung neutrophil recruitment, modulation of neutrophil activation status and induction of lung eosinophil recruitment and activation. These findings underscore the importance of influenza vaccination in modulating disease progression and preventing morbidity and mortality associated with secondary bacterial infections.

microbiology↗

bioRxiv2025

Entropy of the resting state cortex in epilepsy

BackgroundEpilepsy has long been conceptualised as a disorder in which aberrant brain dynamics extend beyond the epileptogenic zone. Evidence demonstrates that loss of entropy is a generic feature of pathological dynamics in the brain, including the ictal state. However, the impact of recurrent seizures on entropy in the interictal state remains unknown. MethodsResting state magnetoencephalography (MEG) scans and resection masks of 32 individuals with epilepsy who had Engel I outcome post-surgery were retrospectively retrieved. Using co-registered FreeSurfer parcellations, we reconstructed the source localised MEG time series and computed sample entropy for 114 regions of interest. We then tested the association of entropy with the resected volume of the brain, and additional clinical variables including the age of seizure onset, seizure frequency and duration of epilepsy. To further understand the temporal relationship between seizure onset and entropy in the interictal state, we collected and computed sample entropy for week-long EEG traces from leucine-rich glioma inactivated 1 monoclonal antibody (LGI1-mAb) rodent models of autoimmune encephalitis (n=5) and control rats (n=5). ResultsIn individuals with epilepsy, a lower age of seizure onset was associated with lower mean sample entropy of the whole cortex (Spearmans rho =0.60, p<0.001; partial correlation =0.41, p=0.021). Entropy did not differ between the resected and non-resected regions of the brain. Furthermore, LGI1-mAb treated rodents showed a persistent decrease in sample entropy as compared to control rats, after the onset of seizures, and this difference was greatest during periods of highest seizure frequency (p<0.001). ConclusionRecurrent seizures are associated with a persistent decrease in entropy, even in the interictal state, and this decrease was found to be most profound and affecting the whole cortex in patients who had a lower age of seizure onset.

neuroscience↗

bioRxiv2025

Mapping the miRNA Landscape of Gallbladder Cancer: Genome-Wide Insights and Functional Implications

Gallbladder cancer (GBC), the sixth most aggressive gastrointestinal cancer, exhibits complex molecular dysregulation involving microRNAs (miRNAs) that drive tumor progression. This study has comprehensively profiled genome-wide miRNA expression in GBC cells revealing 971 known miRNAs, and 27 novel miRNAs. We identified 388 significantly differentially expressed (DE) miRNAs (191 upregulated and 197 downregulated), providing valuable insights into the various complex molecular mechanisms underlying GBC pathogenesis. These DE miRNAs target key biological processes, including hormone-induced signaling pathways, cell adhesion molecules, apoptosis, ferroptosis, and cancer-associated pathways, particularly those linked to gastric cancer. Profiling of DE miRNAs in GBC cells presents opportunities for novel miRNA-based diagnostic and prognostic approaches in GBC. Notably, among the DE miRNAs, the miR-17[~]92 cluster was significantly suppressed in GBC cells. We also show that miR-17[~]92 cluster targets and destabilizes an S-phase licensing factor Cdt2 (an oncogene) in GBC cells. miR-17[~]92 mediated negative regulation of Cdt2 induces S-phase arrest, leading to checked proliferation and invasive capabilities of GBC cells specifically, without any significant effect on non-cancerous cells, presenting miR-17[~]92 as a potential miRNA therapeutic for GBC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/679165v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@243970org.highwire.dtl.DTLVardef@36f578org.highwire.dtl.DTLVardef@2dba37org.highwire.dtl.DTLVardef@1c9e1b_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cancer biology↗

bioRxiv2025

Aberrant cohesin function in Saccharomyces cerevisiae activates Mcd1 degradation to promote cell lethality

The cohesin complex is composed of core ring proteins (Smc1, Smc3 and Mcd1) and associated factors (Pds5, Scc3, and Rad61) that bind via Mcd1. Extrusion (looping from within a single DNA molecule) and cohesion (the tethering together of two different DNA molecules) underlie the many roles that cohesins play in chromosome segregation, gene transcription, DNA repair, chromosome condensation, replication fork progression, and genome organization. While cohesin functions flank the activities of critical cell checkpoints (including spindle assembly and DNA damage checkpoints), the extent to which checkpoints directly target cohesins, in response to aberrant cohesin function, remains unknown. Based on prior evidence that cells mutated for cohesin contain reduced Mcd1 protein, we tested whether loss of Mcd1 is based simply on cohesin instability or integrity. The results show that Mcd1 loss persists even in rad61 cells, which contain elevated levels of stable chromosome-bound cohesins, and also in scc2-4, which do not affect cohesin complex integrity. In fact, re-elevating Mcd1 levels suppresses the temperature-sensitive growth defects of all cohesin alleles tested, revealing that Mcd1 loss is a fundamental mechanism through which cohesins are inactivated to promote cell lethality. Our findings further reveal that cells that exhibit aberrant cohesin function employ E3 ligases (such as San1) to target Mcd1 for degradation. This mechanism of degradation appears unique in that Mcd1 is reduced during S phase, when Mcd1 levels typically peak and despite a dramatic upregulation in MCD1 transcription. We infer from these latter findings that cells contain a negative feedback mechanism used to maintain Mcd1 homeostasis. AUTHOR SUMMARYCohesins are central to almost all aspects of DNA regulation (chromosome segregation, gene transcription, DNA repair, chromosome condensation, replication fork progression, and genomic organization). Cohesin also play key roles in cell checkpoints: cohesin mutations activate the spindle assembly checkpoint while double strand DNA breaks can elicit a new round of cohesin establishment. In the current study, we provide evidence for a novel cohesin surveillance system that employs E3 ligases that directly target Mcd1, a core component of the cohesin ring structure, for degradation. We further describe a feedback mechanism through which cells dramatically induce MCD1 transcription to maintain Mcd1 homeostasis. Finally, we provide evidence that requires the re-evaluation of phenotypes associated with other cohesin gene mutations.

cell biology↗