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Biology subjects

Su, S.

Publications and source records attributed to Su, S..

At least 19 recordsLinked to original sources

Lipid nanoparticle-mediated RNAi targeting of KRAS mutants sensitises colorectal cancer cells to chemotherapy

KRAS mutations, including G12D, G12V and G13D, are major oncogenic drivers in colorectal cancer (CRC) and are associated with therapeutic resistance. However, approved KRAS inhibitors remain focused on G12C subtype, leaving these prevalent variants without approved targeted therapies. Here, we developed a lipid nanoparticle (LNP)-based RNA interference (RNAi) strategy to target these three KRAS variants using a single small interfering RNA (siRNA) sequence. The developed siRNA-LNPs reduced KRAS mRNA and protein expression in HCT116 (G13D), SW620 (G12V) and LS180 (G12D) cells, but not in KRAS wild-type HT29 cells, suppressing the cellular proliferation, clonogenic survival and migration. Transcriptomic profiling revealed changes in KRAS associated signalling, including suppression of cell-cycle and DNA repair programmes, providing a rationale for combining siRNA silencing with the fluoropyrimidine chemotherapeutic agent 5-fluorouracil (5-FU). The combination produced synergistic effects across all three KRAS-mutant CRC cell models and enhanced the apoptosis in both monolayer cultures and 3D spheroids. Collectively, these findings provide proof of concept for this combination strategy and support its further investigation as a potential therapeutic approach for KRAS-mutant CRC.

molecular biology↗

Screening of Isolation and Culture Conditions of Lactic Acid Bacteria in Mongolian Horse Feces

ObjectiveThis study aimed to establish an efficient isolation, culture, and preservation system for lactic acid bacteria from Mongolian horse feces by systematically evaluating the effects of sampling methods, culture conditions, media types, and cryopreservation protocols. MethodsFecal samples were collected using rectal and natural defecation methods, and bacteria were isolated by the spread plate technique, with isolates subcultured and identified via 16S rRNA gene sequencing. The performance of five commercial media (A-E), aerobic versus anaerobic conditions, and different glycerol concentrations (10% and 30%), temperatures (-20 {degrees}C and -80 {degrees}C), and storage durations (7, 15, and 30 days) were compared. ResultsRectal sampling showed significantly higher lactic acid bacterial survival and greater species diversity (12 vs. 8). Anaerobic culture yielded substantially higher counts and diversity (707 strains, 12 species) compared to aerobic conditions (36 strains, 5 species). Medium C (M.R.S. AGAR) exhibited the best isolation performance, producing the highest number of strains (311) and species (11), with selective enrichment for both bacilli and cocci. Glycerol effectively improved strain survival during sample cryopreservation, with the optimal short-term storage ([≤]15 days) achieved at -20 {degrees}C with 30% glycerol. Functional screening of randomly selected strains from optimized conditions demonstrated promising growth, acid and bile salt tolerance, and antimicrobial activity. ConclusionRectal sampling combined with anaerobic incubation using Medium C is recommended for optimal isolation. For samples that cannot be processed immediately, short-term preservation at -20 {degrees}C with 30% glycerol prior to isolation is effective. This study provides practical technical references for the acquisition and preservation of equine intestinal lactic acid bacteria resources.

microbiology↗

LIFU-Responsive Nanocomplexes Deliver PDGF-BB mRNA for Plaques Stabilization via Neovascularization Modulation

BackgroundPathological intraplaque neovascularization, vascular leakage, and fibrous cap thinning contribute to vulnerable atherosclerotic plaque rupture. Platelet- derived growth factor-BB (PDGF-BB) has been shown to promote pericyte recruitment, thereby stabilizing the microvascular structure, and to induce phenotypic modulation of vascular smooth muscle cells (VSMCs), which enhances fibrous cap thickness and reinforces plaque stability. Nevertheless, systemic protein delivery is limited by rapid clearance and potential off-target effects. MethodsWe developed PDGF-BB mRNA-loaded lipid nanoparticle-poly(lactic-co- glycolic acid) nanobubble complexes (LNPmRNA@PLGA) and used low-intensity focused ultrasound (LIFU) to enhance plaque-targeted delivery. Cellular uptake, PDGF- BB expression, vascular mural-cell responses, plaque histology, hemodynamics, and proteomic changes were evaluated in vitro and in ApoE-/-Fbn1C1041G+/- mice. ResultsLIFU enhanced nanocomplex uptake and PDGF-BB expression, promoted vascular smooth muscle cell proliferation, migration, and phenotypic switching, and increased pericyte coverage. In vivo, LIFU plus LNPmRNA@PLGA reduced the plaque vulnerability index by 78.2% and the neovascularization area by 67.3% compared with controls, while increasing collagen deposition and improving carotid hemodynamics. ConclusionsLIFU-responsive delivery of PDGF-BB mRNA stabilized vulnerable plaques by promoting neovessel maturation and strengthening the fibrous cap. This strategy provides a spatially controlled framework for therapeutic remodeling of high-risk atherosclerotic plaques. Research Perspective What New Question Does This Study Raise?O_LICan spatially controlled PDGF-BB mRNA delivery simultaneously mature intraplaque neovessels and reinforce the fibrous cap without the systemic effects associated with recombinant PDGF-BB? C_LI What Question Should Be Addressed Next?O_LIFuture studies should define the therapeutic window, durability, and long-term safety of LIFU-triggered PDGF-BB mRNA delivery in large-animal models that more closely reproduce human plaque rupture. C_LI

pharmacology and toxicology↗

A pesticide hijacks a neurohormonal circuit to block ovulation in insects

The global decline of insect populations threatens ecosystem stability, yet the hidden physiological impacts of sublethal pesticide exposure remain largely uncharted. Here we show that emamectin benzoate (EB), a widely used insecticide, suppresses female fertility not by disrupting egg development, but by specifically blocking ovulation. Through a systematic genetic screen in Drosophila, we identify the glutamate-gated chloride channel GluCl in a discrete set of octopaminergic neurons as the primary neural target. EB subverts the activity of this circuit, thereby impairing octopamine-dependent follicle rupture, suppressing ovarian ecdysteroid signaling, and altering oviduct muscle dynamics--three coordinated processes essential for egg release. Strikingly, this ovulatory blockade is recapitulated in diverse dipteran pests and disease-vector mosquitoes, revealing a conserved vulnerability. Our findings establish a neurohormonal mechanism by which a common agrochemical hijacks reproductive control, and they expose ovulation as a critical, hitherto unrecognized nexus between environmental chemicals and insect population dynamics. SignificanceSublethal pesticide exposure can profoundly alter insect physiology beyond acute toxicity, yet the underlying mechanisms remain unclear. Here, we show that emamectin benzoate (EB), a widely used avermectin insecticide, suppresses ovulation and female fecundity in Drosophila by disrupting octopaminergic signaling, follicle rupture, and oviduct muscle contraction. Mechanistically, EB acts through GluCl-dependent neural pathways to impair ovulation-related processes and reproductive muscle dynamics. Notably, these inhibitory effects are conserved across multiple dipteran species, suggesting that reproductive suppression represents a broader physiological consequence of EB exposure. Our findings reveal a previously unrecognized neuro-reproductive mechanism of pesticide action and provide new insight into how sublethal insecticide exposure may influence insect population dynamics.

neuroscience↗

Brain Structure Shapes Function through higher-order Functional Interactions

Brain function is deeply embedded within multiscale structural architecture. Conventional studies predominantly utilize pairwise connectivity networks to investigate structure-function relationships. However, this low-dimensional perspective overlooks multi-region collaborations for complex cognition. Consequently, whether and how anatomy constrains such higher-order functional networks remains unresolved. To address this pivotal question, we utilize an information-theoretic O-information approach to characterize higher-order functional interactions (HOIs). By reconstructing individual-level HOIs from multimodal structural networks, we directly validate the structural constraint on HOIs. The resulting reconstruction coefficients are defined as structural-functional constraint strength (SFCS), serving as a quantitative vehicle to decipher how anatomy shapes these higher-order networks. SFCS uncovers a highly heterogeneous structural constraint landscape across data modalities, spatial regions, and informational interaction modes. Crucially, individualized SFCS robustly predicts multi-domain cognitive phenotypes, showing higher sensitivity for informant-reported than patient-reported assessments. Finally, we show that this landscape undergoes pathological, mode-specific reorganization in Alzheimers disease. Cross-scale alignment with spatial transcriptomics further demonstrates that this macroscale network remodeling is coupled with microscale metabolic and regulatory gene pathways. Collectively, our findings not only validate the structural constraint on higher-order functional networks but also decipher its precise underlying mechanisms. This constraint paradigm plays a pivotal role in shaping diverse cognitive capabilities, while its pathological disruption in Alzheimers disease highlights the potential of SFCS as a biomarker for tracking neurodegenerative network impairments.

neuroscience↗

Rapid Intracellular Delivery of Human Heat Shock Protein 72 Prevents Memory Loss and Inhibits Neurodegeneration up to 9 Days After a Blast Injury

Traumatic brain injuries (TBIs) are increasingly prevalent among military service members and are associated with long-term neurological impairment and neurodegeneration. Heat shock protein 72 (HSP72) has demonstrated cytoprotective properties and has been shown to cross the blood brain barrier in rat models of blast injury, remaining in brain tissue for up to 12 hours. In this study, we evaluate engineered Fv-HSP72 variants for their ability to reduce neurodegeneration and preserve short-term memory following blast-induced TBI. Male Sprague-Dawley rats were assigned to 9 groups of n = 8 rats. Animals were either not exposed to blast (Sham), exposed to blast (Blast Only), blast exposed and given buffer (Vehicle), or blast exposed and treated with one of three Fv-HSP72 variants, dosed at 10 or 30mg/kg at 15m post-blast. Blast exposure was generated using an Advanced Blast Simulator (ABS) producing positive static pressure to model moderate to severe blast injury. Animals were euthanized 48 hours post injury for neurodegeneration and immunologic biomarker analysis. After selecting an effective Fv-HSP72 variant using the biomarker data, additional rats were divided into Sham, Vehicle, and Fv-HSP72 treatment groups to evaluate short-term memory function through the Novel Object Recognition (NOR) test on days 2 and 8 post-blast. Analysis of cortical and spinal cord tissues demonstrated a statistically significant reduction in expression of neurodegenerative markers of Tau phosphorylation and glial injury (GFAP) for rats receiving a single dose of our clinical candidate, RBB012-CTB. In fact, the drug drove astrogliosis toward a neuroprotective state in blast exposed rats. In the NOR assay, Fv-HSP72 treated rats showed improved recognition performance, indicating preservation of short-term memory function. With similar biomarker results obtained for a controlled cortical impact injury model published elsewhere (Chan et al. manuscript submitted), the analyses suggest Fv-HSP72 is neuroprotective following a blast injury as well. One sentence summaryThis study describes the effectiveness of a biologic agent, Fv-HSP72, in significantly preventing learning and memory loss in rats for up to 9 days after a blast injury.

neuroscience↗

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

The function of proteins, the building blocks of life, in health and disease depends not only on their 3D-conformational states but most importantly on the dynamic transition between states controlled by a wide array of post-translational modifications (PTMs). Recent major advances have been made in our ability to predict static 3D structures; however, understanding and predicting the impact of PTMs on protein conformational dynamics remains a major question and challenge in the field. Molecular dynamics (MD) simulation remains the major computational approach for studying protein dynamics. However, the high computational cost, lack of integration of PTMs as conditioning inputs and inefficient generation of continuous protein dynamics largely precludes PTM-regulated conformational dynamics and the study of slow conformational processes. To address this critical bottleneck, we developed ProteinFlux, a flow-matching generative framework that links PTM-conditioned conformational dynamics to evolutionary constraints encoded by PTM sites. Evolutionary information plays a critical role in capturing conformational dynamics beyond sequence identity, and PTM sites inherently encode evolutionary constraints critical to protein functional regulation. We therefore built FluxSite, a dual-modal PTM site predictor that integrates sequence evolutionary information and 3D structural features to generate a continuous conditional signal encoding conservation and functional importance for each predicted site. FluxSite achieves robust generalization across 18 PTM types and 30 disease-associated proteomes. ProteinFlux generates phosphorylation-conditioned, all-atom conformational trajectories across diverse protein fold classes, faithfully reproducing both thermodynamic properties such as free energy landscapes and kinetic features such as conformational transition pathways. It outperforms state-of-the-art predictors while achieving inference speeds several orders of magnitude faster than traditional MD. In addition, we introduce DynaMo-phos, a benchmark dataset of phosphorylated protein MD simulations. Together, ProteinFlux, FluxSite and DynaMo-phos provide a scalable, high-throughput platform for elucidating PTM-driven conformational mechanisms, with potential applications across allosteric drug design, functional annotation of disease-associated modifications and mechanism-guided therapeutic development.

bioinformatics↗

Rapid Intracellular Delivery of Human Heat Shock Protein 72 Inhibits Neurodegeneration and Oxidative Damage After a Traumatic Brain Injury

Fv-HSP72 is a rapid cell-penetrating human heat shock protein for the treatment of traumatic organ injuries. We have shown this re-engineered protein (HSP72) is capable of crossing the blood brain barrier (BBB) of rats suffering a controlled cortical impact (CCI) and remains in brain tissue for up to 12 hours; long after clearance from the cortex of uninjured rats. Peptide sequences unique to Fv-HSP72 allow for its differential detection from endogenous HSP72. Male Sprague-Dawley rats were divided into 10 groups of n=10 with those animals receiving a CCI subjected to a unilateral cortical contusion simulating a moderate to severe brain injury using an electronically controlled pneumatic impact device. Control groups were either uninjured (Sham), injured (TBI Only), or injured and given buffer (TBI+Vehicle). Rats treated with one of three Fv-HSP72 variants were dosed at 10 or 30mg/kg 15m post-impact, then sacrificed 48 hours later. Cortical tissues were extracted from the ipsilateral and contralateral hemispheres for biomarker analysis. Here we report results of our drug inhibiting neurodegeneration based on five biomarkers (NF-L, pNF-H, pTau [T181, T231, S396]). These results were statistically significant, especially for one of the Fv-HSP72 variants, when comparing differences both between treatment groups and within groups (i.e. when comparing ipsi-vs. contralateral hemispheres). Significant inhibition of oxidative stress (3-NT) and inflammatory (IL-6) biomarkers were also observed (both p<0.0001). With similar results obtained for a blast injury model being published elsewhere, the analyses suggest Fv-HSP72 is neuroprotective following a direct impact brain injury. One sentence summaryThis study describes the effectiveness of a biologic agent, Fv-HSP72, in significantly inhibiting neuronal tissue damage in the brain when administered after a direct cortical impact.

neuroscience↗

HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during liver aging

Age-associated functional decline is partly driven by progressive chromatin degeneration. Maintenance of chromatin integrity preserves cell identity and promotes healthy aging, but through different mechanisms in proliferating and non-proliferating cells. However, specific mechanisms of chromatin maintenance and their compensatory capacity in proliferating and non-proliferating cells are undefined. The histone chaperone HIRA deposits the histone variant H3.3 in a DNA replication-independent manner, leading to its accumulation in aging, non-proliferating cells. Here, we show that hepatocyte-specific loss of HIRA causes loss of cell identity, metabolic dysfunction, and accelerated fibrotic pathology with age. Transcriptomic and epigenomic analyses indicate that HIRA-H3.3 preserves chromatin integrity and sustains transcription of highly expressed genes, including cell identity genes. Partial hepatectomy, associated with induced proliferation, restores identity of HIRA knockout livers with compensatory deposition of canonical histones H3.1/2. Together, these results demonstrate that HIRA-mediated H3.3 deposition is essential for safeguarding cell identity and tissue function during aging of non-proliferating cells, but this function can be rescued by tissue regeneration and associated cell proliferation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/710643v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a2a26aorg.highwire.dtl.DTLVardef@154e5aeorg.highwire.dtl.DTLVardef@b315a7org.highwire.dtl.DTLVardef@152bca4_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Development of KASP Molecular Markers and Construction of Fingerprinting for Cowpea (Vigna unguiculata (L.) Walp) unguiculata Based on ddRAD-Seq

Cowpea (Vigna unguiculata (L.) Walp.) is a globally important legume crop. However, the scarcity of efficient molecular markers has hindered molecular breeding efforts and the protection of plant breeders rights. In this study, we employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterize the genetic diversity of 19 core cowpea germplasm accessions. We generated 791,621 SNPs, from which 13,469 high-quality SNPs were filtered. Population structure and phylogenetic analyses revealed that these accessions cluster into three distinct groups. To facilitate cost-effective and rapid genotyping, we developed a panel of KASP (Kompetitive Allele Specific PCR) markers. Through rigorous screening for polymorphism and stability, we identified six core KASP markers located in exonic regions. These six markers alone were sufficient to discriminate all 19 accessions. Based on these core markers, we constructed a unique DNA fingerprinting profile and assigned specific QR codes for each accession. This study demonstrates that extracting core KASP markers from ddRAD-seq data is a powerful strategy for germplasm identification. The developed fingerprinting system provides a robust, low-cost tool for seed purity testing, variety authentication, and marker-assisted selection in cowpea breeding programs.

plant biology↗

CellFluxV2: An Image Generative Foundation Model for Virtual Cell Modeling

Building a virtual cell that simulates cellular behavior in silico is a central goal of computational biology. We introduce CellFluxV2, an image-generative model that predicts how cell morphologies change in response to chemical and genetic perturbations. A core innovation of CellFluxV2 is to learn distribution-level transformations from unperturbed to perturbed cells within the same experimental batch using flow matching, enabling it to disentangle true perturbation effects from confounding batch effects. Incorporating three methodological advances, CellFluxV2 achieves up to a 77% improvement in image fidelity over diffusion- and GAN-based baselines, while maintaining biological fidelity comparable to ground-truth images. Scaling up CellFluxV2, we establish the first scaling laws in image-based virtual cell modeling, demonstrating that performance improves consistently with both dataset size and model capacity. Furthermore, the scaled-up model generalizes well to out-of-distribution perturbations and exhibits two novel capabilities: batch-effect correction and cell-state interpolation. Together, these results position CellFluxV2 as a powerful foundation model advancing the vision of a virtual cell, unlocking novel opportunities for in silico drug screening.

bioinformatics↗

STUltra: scalable and accurate integration for subcellular-level spatial omics data

High-resolution spatial transcriptomics (ST) is generating massive datasets involving multiple tissue sections, continuous developmental stages, or various disease conditions. Yet, their scale, biological heterogeneity, and substantial batch effects hinder data integration for further analysis, particularly the temporal interpretation of disease-associated spatial domains within tissue organization landscapes. Here, we present STUltra, a scalable hypergraph framework that integrates multi-sample ST data for precise domain detection and genome-wide association study (GWAS)-based disease trait mapping. From ST datasets, STUltra first constructs interval-sampled integrative hypergraphs, in which hyperedges capture tissue neighborhoods within the slices as well as shared biological contexts across the slices. It then combines a robust graph autoencoder with contrastive learning to learn batch-corrected, spatially informed embeddings for identifying spatial domains across the tissue sections. These embeddings are then coupled with GWAS statistics to map trait-associated signals onto the integrated tissue sub-structure landscapes spanning different sections, developmental stages, and disease conditions. STUltra substantially outperforms competing methods, especially being much faster, on diverse integration benchmarks, enabling efficient processing of datasets containing millions of spots. As a case study on a mouse embryo dataset, STUltra recovered continuous developmental programs and mapped congenital heart disease signals beyond cardiac regions to broader programs including vascular and mesenchymal domains. On a mouse Alzheimer's disease dataset, STUltra prioritized localized AD-associated genetic signals to microglia and a disease-expanded C1QA/HEXB-high astrocyte state. Together, STUltra provides a scalable framework to bridge the gap between spatiotemporal tissue structures and complex disease traits, facilitating discoveries from previously unrecognized molecular and cellular architectures across diverse contexts.

bioinformatics↗

Short trains of transcutaneous vagus nerve stimulation increase online corticospinal excitability and pupil size in humans

BackgroundTranscutaneous vagus nerve stimulation (tVNS) has emerged as a method for interrogating the role of the locus coeruleus (LC) norepinephrine system in human behavior. Tuning of excitability in the corticospinal tract is central to many cognitive and motor processes, but little is known about how the LC contributes to this tuning. In particular, no existing studies have examined the effect of tVNS on corticospinal excitability "online" during active stimulation, where the largest effects on pupil size are observed. MethodTo address this question, we delivered repeated 4-second trains of tVNS and sham stimulation and elicited MEPs during stimulation trains (online) and shortly after train offset (offline). Pupil size was concurrently recorded throughout each train. ResultsWe discovered that tVNS significantly increases corticospinal excitability compared to sham stimulation, but only when measured online and not offline. The excitatory effects on corticospinal excitability were greater in the latter half of tVNS trains. Pupil size was also significantly increased by tVNS compared to sham; however, the effect on pupil size peaked earlier during the tVNS trains compared to corticospinal excitability. In line with these distinct temporal profiles, changes in corticospinal excitability and pupil size were not significantly correlated, likely reflecting differences in the anatomical circuits underpinning each effect. ConclusionsThis work demonstrates for the first time that tVNS increases corticospinal excitability at rest, but the effect only emerges when corticospinal excitability is measured online during active tVNS. Implications for basic and clinical neuroscientific research are discussed.

neuroscience↗

An Enhanced Variant-Aware Deep Learning Model for Individual Gene Expression Prediction

Accurate prediction of gene expression from individual whole-genome sequences is critical for understanding disease mechanisms and advancing precision medicine. Current methods, however, struggle with individual-specific genetic variations and integrating detailed sequence context. To address this, we introduce GenomicVariExpress (GVE), a novel deep learning model that leverages a pre-trained sequence encoder and incorporates an Enhanced Variant Integration Module (EVIM). EVIM explicitly encodes and fuses multi-dimensional variant features, such as type, allele frequency, and predicted functional impact, enabling GVE to precisely capture how individual variations modulate gene expression. We evaluate GVE using paired whole-genome and RNA sequencing data from the GTEx Whole Blood cohort. Our experiments demonstrate GVE consistently achieves superior performance compared to state-of-the-art baselines. An ablation study confirms EVIMs critical contribution to this improved performance. Furthermore, analyses highlight GVEs enhanced biological interpretability and its superior performance across multiple tissues and for genes influenced by rare variants. GVE represents a significant step towards accurate, individual-level gene expression prediction, offering a powerful tool for genomic function research and personalized healthcare applications.

bioinformatics↗

Internal mechanosensory feedback modulates central pattern generation to coordinate ovulation in Drosophila

Ovulation is a prerequisite for successful reproduction and requires precise coordination of muscle contractions, especially to propel eggs from the paired lateral oviducts into the common oviduct. Although internal mechanosensation is expected to provide critical feedback for this process, the sensorimotor circuitry and mechanisms by which sensory feedback shapes motoneuron activity and coordinates oviduct contractions are still poorly known. Here, in Drosophila, we identify a novel pair of multidendritic mechanosensory neurons (mdn-LO) in the lateral oviducts that express the mechanosensitive channels TMC (transmembrane channel-like protein), PPK (pickpocket), and Piezo. We show that TMC is essential for coordinated ovulation; tmc mutation or neuron-specific knockdown increases egg-jamming at the junction between the lateral and the common oviduct. In contrast, ppk or Piezo mutants display reduced egg-laying but no jamming. Calcium imaging reveals that the mdn-LO neurons are rhythmically activated by oviduct contractions, and chemogenetic stimulation of these neurons triggers muscle contractions. Genetic manipulations of the mdn-LO neurons disrupt egg passage and induce egg-jamming. The axons of the mdn-LO neurons form functional contacts with female-specific oviduct motoneurons in the abdominal neuromeres that express insulin-like peptide 7 (ILP7) and glutamate. Activation of mdn-LO neurons triggers Ca{superscript 2} activity in ILP7 motoneurons and elicits rhythmic oviduct contractions. Importantly, the ILP7 motoneurons exhibit spontaneous rhythmic Ca{superscript 2} activity that is modulated by oviduct contractions and egg movement. Furthermore, triggering activity in the ILP7 neurons induces egg-jamming. Finally, knockdown of ILP7 peptide affects the rate of ovulation, but plays no role in egg jamming, which instead is likely induced by colocalized glutamate. In summary, our study identifies a novel circuit, including the TMC-expressing mdn-LO neurons and a small set of ILP7 motoneurons, that organizes an innate behavior by coupling strategic sensory information and rhythmical motor output to ensure bilateral coordination of oviduct contractions to prevent egg jamming during oviposition. SignificanceOvulation requires precisely coordinated contractions of the lateral oviducts to propel eggs into the common oviduct without jamming. Yet the sensory cells and mechanotransduction channels that coordinate movement through the paired lateral oviducts remain unclear. Here, we identify a novel pair of lateral-oviduct multidendritic neurons (mdn-LO) that express the conserved mechanosensory channels TMC (transmembrane channel-like protein), PPK (pickpocket), and Piezo, and show that TMC is uniquely required to prevent egg jamming at the junction between the lateral and common oviducts. The mdn-LO neurons are activated by oviduct contractions and relay signals to female-specific glutamatergic motoneurons in the abdominal neuromere. These paired oviduct motoneurons are rhythmically active and regulate contractions of the lateral oviducts. Together, our findings demonstrate that TMC-mediated mechanosensory feedback fine-tunes motor output to ensure coordinated ovulation and successful reproduction.

neuroscience↗

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

Long-read RNA sequencing enables full-length transcript profiling and improved isoform resolution, but variable platforms and evolving chemistries demand careful benchmarking for reliable application. We present LongBench, a matched, multi-platform reference dataset spanning bulk, single-cell, and single-nucleus transcriptomics across eight human lung cancer cell lines with synthetic spike-in controls. LongBench in-corporates three state-of-the-art long-read protocols alongside Illumina short reads: Oxford Nanopore Technologies (ONT) PCR-cDNA, ONT direct RNA, and PacBio Kinnex. We systematically evaluate transcript capture, quantification accuracy, differential expression, isoform usage, variant detection, and allele-specific analyses. Our results show high concordance in gene-level differential analyses across protocols, but reduced consistency for transcript-level and isoform analyses due to length- and platform-dependent biases. Single-cell long-read data are highly concordant with bulk for high-confidence features, though single-nuclei data show reduced feature detection. LongBench provides one of the largest publicly available long-read benchmarking resources, enabling rigorous cross-platform evaluation and guiding technology selection for transcriptomic research.

genomics↗

Characterization of real B0 shim fields generated by higher order B0 shim systems of whole body human 3T and 7T MRI systems

PurposeEnsuring optimal homogeneity of the static magnetic field (B0) is critically important for significantly enhancing the image quality, spectral resolution, and overall diagnostic accuracy of magnetic resonance imaging (MRI) and magnetic resonance spectroscopy/spectroscopic imaging (MRS/MRSI), especially at high and ultra-high field strengths. Achieving this goal relies on the deployment of advanced, higher-order shim hardware, which is indispensable for effective and precise B0 shimming. MethodsIn this study, we acquired B0 field maps to characterize the performance of each shim channel of vendor-provided B0 shim hardware integrated into whole body human 7T MRI system. To rigorously evaluate and compare the B0 field homogeneity achievable using these devices, we utilized spherical harmonic expansions to fit the measured B0 distributions for each shim channel in each of the investigated built-in B0 shim systems. This methodology enabled a systematic assessment of shim field "purity" and the effectiveness of different B0 shim configurations. ResultsWhile our analysis confirmed that the linear-order shim terms provided by the gradient coils maintained high purity, certain second-order shim terms and all third-order B0 shim coils of all vendors 7T whole body human MRI systems exhibit a high level of impurity and more specifically introduce substantial linear field components. These unintended linear contributions interfere with the linear shim fields provided by the gradient coils negating their corrective influence. As a result, the 3rd order B0 shim coils and some 2nd order B0 shim coil elements compromised the overall effectiveness of the B0 shimming process rather than improving it. Although pure higher order B0 shim fields were previously shown to substantially improve B0 field inhomogeneity, the vendor implemented versions of higher order B0 shim systems in current 7T whole-body human MRI scanners cannot achieve the desired level of uniformity and partly perform worse than first order B0 shimming. Substantial deviations between 2nd order and especially 3rd order real shim fields versus ideal shim fields demonstrate the necessity of real shim field calibration and call for improvement of future 2nd and 3rd order B0 shim coil design for human whole-body MRI scanners. Our findings offer valuable guidance for optimizing B0 shimming strategies at high and ultra-high field strengths, ultimately enhancing image quality. ConclusionRecent evaluations have demonstrated that certain second- and third-order shim coils, as implemented in current commercial 7T human whole-body MRI systems, introduce unintended lower-order (linear) field components. These field "impurities" substantially deviate from the desired higher-order spatial harmonics, thereby diminishing the orthogonality of the higher order B0 shim system. This in turn largely compromises the effectiveness of higher-order B0 shimming at whole-body 7T MRI scanners. These findings emphasize the necessity of conducting accurate shim field calibration to best utilize the current 7T B0 shim system configurations on one hand. On the other hand, improving the purity of these commercial B0 shim systems in the design phase to ensure that the higher-order terms accurately match their intended spherical harmonic profiles, particularly for the third-order shim terms--would largely enhance the achievable B0 field homogeneity at 7T. This improvement has directly clinically significant outcomes.

bioengineering↗

Combined Deletion of miR-27a and miR-27b Enhances Protection Against Diet-Induced Obesity

MicroRNAs (miRNAs) are frequently encoded within polycistronic clusters thought to function as coherent regulatory units, yet whether individual cluster members act cooperatively or exert distinct physiological effects remains unclear. miR-27a and miR-27b are closely related miRNAs located within separate paralogous miR-23/27/24 clusters, but their in vivo relationship is unresolved. Using isoform-specific knockout models generated by precise CRISPR-based excision of individual miRNA hairpins, we defined how miR-27a and miR-27b regulate adipose thermogenesis and systemic metabolism. High-fat feeding increased miR-27a/b expression and suppressed thermogenic gene programs in subcutaneous white adipose tissue. In primary beige and brown adipocytes, loss of either isoform produced modest activation of thermogenic programs, whereas combined deletion caused additive increases in Ucp1 expression and mitochondrial DNA content. Ex vivo heat production was significantly elevated in double-knockout adipose explants relative to wild-type and single-knockout controls. In vivo, double-knockout mice exhibited increased energy expenditure and, under high-fat diet conditions, reduced adiposity with improved glucose homeostasis compared with wild-type and single-knockout mice. In contrast to metabolic dysfunction reported following whole-cluster deletion, selective miR-27 loss reveals a protective thermogenic program. These findings demonstrate that miRNA clusters need not act as coherent regulatory modules and identify miR-27a/b as a cooperative thermogenic checkpoint with therapeutic implications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/666011v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7d6b74org.highwire.dtl.DTLVardef@199d56org.highwire.dtl.DTLVardef@1a87e48org.highwire.dtl.DTLVardef@fab51a_HPS_FORMAT_FIGEXP M_FIG C_FIG * CRISPR isoform-specific knockouts isolate miR-27a/b contributions to metabolism. *Dual miR-27a/b loss drives cooperative thermogenic activation. *Double knockouts enhance energy expenditure and metabolic fitness in diet-induced obesity. *miR-27a/b deletion reveals that clustered miRNAs can exert non-coherent regulatory roles.

physiology↗