Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits

Cattle are important livestock that provide essential meat and milk resources. However, a comprehensive analysis of gene expression, alternative splicing (AS), and RNA editing across various organs and developmental stages in cattle has not been reported. This study aims to create a comprehensive transcriptomic BodyMap across various tissues and developmental stages, integrating this information into genomic predictions of beef production traits. We created a comprehensive transcriptomic BodyMap using 400 samples collected from 52 organs of newborn, young, and adult cattle, and estimated their contributions to genetic variance and genomic predictions for 23 beef production traits in 1476 beef cattle. We cataloged the expression of 25,530 annotated genes, 28,533 novel long non-coding RNAs (lncRNAs), 215,754 AS events, and 3,093,058 A-to-I RNA-editing sites. Integrating transcriptome BodyMap with 23 beef production traits, we found lncRNAs influenced traits like rib-eye area and carcass length, while RNA editing associated with chunk roll weight and daily gain. We observed trait-relevant tissues between different stages, including the differential expressed genes of cerebellum, longissimus muscle, and testis between newborn and adult stages are more relevant to beef production traits. The tissue-specific genes and development-associated genes in several tissues could improve the reliability of genomic prediction in beef production traits. We developed Cattle BodyMap Transcriptome Database (https://cattlegenomics.online/cattle_bodymap) to retrieve, analyze, and visualize gene expression, lncRNA, splicing and RNA editing data. Our results demonstrated the potential of using transcriptome data as a valuable resource for genomic selection and breeding programs in beef cattle. Additionally, our transcriptome BodyMap serves as a valuable resource for biological interpretation, functional validation, and genomic improvement in livestock.

genomics↗

bioRxiv2025

Ultrasound Transparent Neural Interfaces for Multimodal Interaction

Neural interfaces that unify diagnostic and therapeutic functionalities hold particular promise for advancing both fundamental neuroscience and clinical neurotechnology. Functional ultrasound imaging (fUSI) has recently emerged as a powerful modality for high-resolution, non-invasive monitoring of brain function and structure. However, conventional metal-based microelectrodes typically impede ultrasound propagation, limiting compatibility with fUSI. Here, we present flexible, ultrasound-transparent neural interfaces that retain practical metal thicknesses while achieving high acoustic transparency. We introduce a theoretical and simulation-based framework to investigate the conditions under which commonly used polymers and metals in neural interfaces can become acoustically transparent. Based on these insights, we propose design guidelines that maximize ultrasound transmission through soft neural interfaces. We experimentally validate our approach through immersion experiments and by demonstrating the acoustic transparency of a suitably engineered interface using fUSI in phantom and in vivo experiments. Finally, we discuss the potential extension of this approach to therapeutic focused ultrasound (FUS). This work establishes a foundation for the development of multimodal neural interfaces with enhanced diagnostic and therapeutic capabilities, enabling both scientific discovery and translational impact.

bioengineering↗

bioRxiv2025

Programmable translational inhibition by a molecular glue-oligonucleotide conjugate

Selective inhibition of mRNA translation is a promising strategy for modulating the activity of disease-associated genes, yet achieving both high potency and specificity remains challenging. Rocaglamide A (RocA), a molecular glue, inhibits translation by clamping eIF4A onto polypurine motifs found in many transcripts, thereby limiting RocAs specificity. Here, we developed RocASO, a chemical conjugate that links RocA to an antisense oligonucleotide (ASO) capable of base-pairing with defined mRNA sequences, thus directing RocAs clamping mechanism to chosen targets and enhancing overall potency and specificity. We show that RocASOs are compatible with various types of ASO modalities, including gapmers that induce the degradation of target RNAs. RocASOs were designed to effectively knock down endogenous genes (PTGES3, HSPA1B) and SARS-CoV-2 viral RNA, the latter conferring potent antiviral activity in cells. These findings establish RocASO as a versatile platform for programmable translational inhibition with therapeutic potential.

genomics↗

bioRxiv2025

Cell-resolved high-dimensional imaging analysis, therapeutic modeling, and a Phase Ib clinical study validate BCL-2 as a target across heterogeneous CRPC subtypes

BCL-2 has been implicated in prostate cancer (PCa) progression and development of castration-resistant disease (CRPC). However, it remains unclear how the BCL-2- and AR-expressing PCa cell populations evolve across the PCa continuum, how AR molecularly regulates BCL-2 and whether BCL-2 represents a common therapeutic target in heterogeneous CRPC. Importantly, BCL-2 inhibitors have yet to be approved for treating PCa patients. Here we first show the selective induction of BCL-2 by AR pathway inhibitors (ARPIs) in both patient specimens and xenograft models. Vectra-based quantitative multiplex immunofluorescence (qmIF) and image mass cytometry (IMC) analyses with single-cell resolution reveal markedly expanded BCL-2+ (AR+ or AR-) PCa cell populations in CRPC. Mechanistically, AR represses BCL-2 transcription through genomic binding via several AR binding sites and ARPIs relieve this repression, leading to BCL-2 upregulation. Comprehensive therapeutic studies in cells, organoids and xenografts establish that castration-induced BCL-2 is not merely associated with resistance but represents a shared and actionable vulnerability as the BCL-2 inhibitor ABT-199 potently suppressed the growth of multiple subtypes of CRPC. A Phase Ib clinical trial (NCT03751436) combining enzalutamide and BCL-2 inhibitor venetoclax demonstrated reduced circulating tumor cells in responding patients. Together, our findings elucidate the AR+/-BCL-2+/- PCa cell subpopulation dynamics during PCa progression, reveal a direct mechanistic link between AR inhibition and BCL-2-mediated resistance, and provide a strong rationale for targeting BCL-2 from the outset to eliminate emerging resistant subpopulations, inhibit treatment-induced cellular heterogeneity and plasticity, and improve therapeutic outcomes in CRPC.

cancer biology↗

bioRxiv2025

Thin Filament Interaction and Ca2+-Desensitization Effect of the C-Terminal End Peptide of Cardiac Troponin T Where Loss of Function Mutations Cause Hypertrophic Cardiomyopathy

BackgroundTroponin T (TnT) is the tropomyosin (Tm)-binding subunit of troponin with a central role in regulating cardiac muscle contractility. The recently identified Tm-binding site 3 in the highly conserved C-terminal end segment of TnT has a troponin I (TnI)-like inhibitory function. Conformational modulation by proteolytic removal of the N-terminal variable region of cardiac TnT (cTnT-ND) in adaptation to inotropy-afterload mismatch enhances the function of Tm-binding site 3 to adjust ventricular contractile kinetics and sustain stroke volume. Mutations in this segment of cTnT cause overactivation of cardiac muscle and hypertrophic cardiomyopathy (HCM). MethodsThe C-terminal end 14 amino acid peptide of cTnT (cTnT-C14) was analyzed for interactions with Tm, F-actin, and F-actin-Tm thin filament using localized surface plasmon resonance (LSPR). Wild-type and HCM mutant cTnT-C14 peptides were used to treat skinned cardiac muscle strips from wild-type and cTnT-ND transgenic mice to assess the effect on Ca{superscript 2}- activation of contraction. ResultscTnT-C14 peptide showed saturable binding to Tm and F-actin in LSPR with physiological affinity, which is significantly impaired by HCM mutation R278C, K280N or R286C. Treatment of wild-type mouse cardiac muscle strips with cTnT-C14 peptide produced a Ca2+- desensitization effect on myofilament activation, which was not seen with cTnT-ND mouse cardiac muscle strips implicating a prior utilization of the same mechanism. The HCM mutant peptides lost this function. ConclusionsThe findings demonstrate the function of the cTnT C-terminal end segment underlying the pathophysiology of the HCM mutations. Its preserved functionality in the form of free peptide presents a drug candidate for the treatment of heart failure.

physiology↗

bioRxiv2025

Microbial Tryptophan Metabolism Activates Host Lysosomal Activity to Facilitate Lipid Breakdown and Ameliorate Hepatic Steatosis

Lysosomes are central to lipid metabolism, yet how gut microbiota-derived metabolites regulate lysosomal function to influence host lipid homeostasis remains unknown. Here, we identify an evolutionarily conserved mechanism in which bacterial tryptophan metabolism activates lysosomal activity to promote lipid breakdown. By developing a lysosomal-responsive lipid reporter in C. elegans to screen for bacterial metabolic states that modulate host lipid storage, we discover that E. coli tryptophan catabolism via tryptophanase TnaA induces lysosomal lipid chaperone LBP-8, driving lipid mobilization. Moreover, tryptophan metabolites enhanced lysosomal acidification and degradation capacity, while genetic disruption of lysosomal regulators reversed these effects. Strikingly, bacterial tryptophan metabolism further promoted mitochondrial {beta}-oxidation through lysosomal lipase activity. This pathway was conserved in mammalian hepatocytes, where E. coli-derived tryptophan metabolites enhance lysosomal function and reduce lipid accumulation. In high-fat diet mice, restoring gut bacterial tryptophan metabolism alleviated hepatic steatosis. Our work uncovers microbiota-regulated lysosomal activation as a critical axis in lipid homeostasis, highlighting its potential as a therapeutic target for metabolic disorders linked to lysosomal dysfunction. SignificanceWe uncover a conserved mechanism by which microbial tryptophan metabolism enhances lysosomal function to maintain host lipid homeostasis. Specifically, we demonstrate that bacterial tryptophan catabolism--via the enzyme TnaA--promotes lysosomal acidification, proteolytic capacity, and structural remodeling in C. elegans, driving lipid breakdown through the lysosomal chaperone LBP-8. This activation boosts mitochondrial {beta}-oxidation and reduces lipid storage. Importantly, the same pathway operates in mammalian hepatocytes and in a high-fat diet mouse model, where restoring bacterial tryptophan metabolism markedly alleviates hepatic steatosis. Our findings bridge microbial metabolism and lysosomal dynamics, offering fresh insights into host-microbe crosstalk and metabolic regulation. HighlightsTnaA-mediated bacterial tryptophan catabolism promotes lipid mobilization via lysosomal chaperone. Bacterial tryptophan metabolites boost lysosomal function, lipid breakdown, and mitochondrial {beta}-oxidation. Conserved microbiota-lysosome-lipid axis from worms to mammalian liver. Restoring gut bacterial tryptophan metabolism alleviates hepatic steatosis in high-fat diet mice.

cell biology↗

bioRxiv2025

Pathogen Subversion of Neuro-Epidermal Signaling Impairs Lysosomal Function to Disrupt Collagen Homeostasis

The epidermis relies on collagen-rich extracellular matrices (ECMs) to maintain barrier integrity against pathogens. Lysosomes regulate cuticle collagen turnover, yet how neuronal signaling modulates epidermal lysosomal function and collagen organization during infection remains unclear. Using Pseudomonas aeruginosa PA14-Caenorhabditis elegans infection model, we demonstrate that pathogen-induced neuronal signaling disrupts epidermal lysosomal activity and collagen remodeling. PA14 infection triggers neurons to secrete NSIF-1 (Neuronal Secreted Immune Factor 1), which translocates to the epidermis and impairs lysosomal acidification, maturation, and degradation by suppressing the transcription factor ELT-3. This disruption leads to disorganized collagen structure, compromising cuticle integrity and host resistance. Genetic mutation of nsif-1 restores lysosomal function, enhances collagen density, and improves survival, while neuron-specific nsif-1 knockdown confirms its neuronal origin. Moreover, NSIF-1 inhibits ELT-3 nuclear localization, blocking its role in lysosomal-dependent ECM repair. Our study reveals a neuro-epidermal axis wherein pathogens exploit neuronal signals to disrupt lysosomal function and collagen homeostasis, identifying NSIF-1 and ELT-3 as potential targets to counteract infection-driven ECM dysregulation.

cell biology↗

bioRxiv2025

Sephin1 alleviates white matter injury by protecting oligodendrocyte after intracerebral hemorrhage

BackgroundWhite matter injury (WMI) caused by intracerebral hemorrhage (ICH) is a major neuropathological feature closely associated with neurological impairments such as motor and sensory dysfunction. Oligodendrocytes (OLs), which are responsible for repairing WMI, also suffer severe death resulting from the compression of hematoma and secondary neuroinflammation after ICH. Sephin1, a selective inhibitor of PPP1R15A, has been shown to reduce general protein synthesis and protect OLs by prolonging the integrated stress response (ISR). We aimed to evaluate the effectiveness of Sephin1 in protecting OLs in experimental ICH mice and primary OLs and microglia co-cultures. MethodsWe first determined the performance of ICH mice treated with Sephin1 or vehicle in multiple behavioral tests. To investigate dynamic changes in the number of OLs surrounding the hematoma after ICH, we labeled and tracked apoptotic, proliferating, and mature OLs using immunofluorescence staining. ResultsSephin1 treatment improved long-term neurological function after ICH, which was accompanied by a significant alleviation of WMI in the perihematomal region. Our data indicated that Sephin1 dramatically increased the population of OLs in the perihematomal region after ICH by inhibiting OL apoptosis and promoting OL proliferation. Moreover, Sephin1 treatment attenuated neuroinflammation after ICH by inhibiting microglial polarization to the M1 phenotype. In vitro, a co-culture model of primary OLs and microglia demonstrated that Sephin1 preserved the viability of OLs under pro-inflammatory conditions. ConclusionsOur observations suggest that Sephin1 is a promising therapeutic drug to preserve the OLs and alleviate WMI around the hematoma in ICH, highlighting its translational potential to improve long-term neurological recovery in hemorrhagic stroke.

neuroscience↗

bioRxiv2025

Seasonal dynamics of mixotrophic phytoplankton in a freshwater habitat revealed by single-cell sorting

The nutritional strategy of phago-mixotrophy among eukaryotic phytoplankton has been widely recognized and characterized across various taxonomic lineages. While their ecological role as bacterivores in different aquatic environments is acknowledged, establishing a clear connection between mixotrophic activities and taxonomy within natural communities remains challenging. In this study, we utilized fluorescence-activated single-cell sorting techniques in combination with microscopic observation to investigate the diversity and seasonal variations of bacteria-feeding mixotrophs in a freshwater habitat. We identified four groups of mixotrophic phytoplankton using both methods: Pedinellales (Dictyochophyceae), Cryptomonas (Cryptophyceae), Dinobryon (Chrysophyceae), and a single-chloroplast bearing group within Chlorophyta. These groups accounted for 58-96% and 54-95% of total mixotrophs identified by the two methods, respectively. Seasonal variations demonstrated that Pedinellales and Chlorophyta were more abundant in spring and summer/autumn, while Dinobryon was only present in winter when temperatures were lowest and light intensity was moderate. Our findings, with six classes and twelve genera identified as bacterivorous mixotrophs, highlight the promising potential of single-cell techniques in aquatic plankton ecology. This approach reveals the speciation and feeding activities of phago-mixotrophs in situ, thereby enhancing our understanding of their functional ecological roles within microbial food webs.

microbiology↗

bioRxiv2025

Cerebellum metastasis model of HER2-positive breast cancer unveils key role of IL34-induced Arg1+ macrophages.

Brain metastases occur in up to 40% of Stage IV breast cancer patients. The cerebellum is a frequent location for metastases in HER2-positive breast cancer patients, but the mechanisms for this are unknown. Here, we developed a syngeneic, immunocompetent mouse model for breast cancer brain metastases by stereotactically injecting mouse HER2-overexpressing breast cancer organoids into the cerebellum. Growth of these cerebellar metastases was monitored by MRI and trastuzumab optical imaging using a near-infrared fluorophore conjugated to trastuzumab. Spatial transcriptomics identified interleukin-34 production by breast cancer cells inducing ARG1+ macrophages at the invading edge of the metastasis. Treatment with a blocking antibody to interleukin-34s receptor, CSF1R, produced tumor shrinkage. These findings have immediate translation potential as a CSF1R-blocking antibody is FDA-approved. Further, it demonstrates that cancer-associated inflammation bordering the brain metastasis promotes metastatic growth and offers a molecularly targeted strategy to treat inflammation in brain metastasis. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/660224v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@9f1a50org.highwire.dtl.DTLVardef@178acc5org.highwire.dtl.DTLVardef@196d803org.highwire.dtl.DTLVardef@3fe631_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus

Chrysophytes are nanoflagellate protists widespread in aquatic ecosystems with diverse trophic roles as primary producers and bacterivores. Molecular evidence suggests that chrysophytes are commonly infected by giant viruses but isolates of such virus-host systems have not been reported. Here, we describe the first cultivated chrysophyte-infecting virus, Chrysophyceae Clade H virus SA1 (ChrysoHV), isolated along with its phago-mixotrophic host alga from surface waters in the tropical North Pacific Ocean. The ChrysoHV capsid (290 {+/-} 40 nm diameter) is associated with a loose, sac-like membrane that extends its effective diameter (720 {+/-} 120 nm) and presents a long (1,200 {+/-} 240 nm), thin (20 {+/-} 2), flexible tail, a morphology unlike any virion yet described. The assembled genome is 1.19 Mbp. Phylogenetic analysis places ChrysoHV as the third cultivated member of the Aliimimivirinae subfamily in the Mimiviridae family of giant viruses. The ChrysoHV genome encodes two heliorhodopsins and one proteorhodopsin. Proteorhodopsins are well known light-driven proton pumps in bacteria but have not been previously reported in a viral genome. The predicted viral proteorhodopsin structure suggests it may not have a functional retinal binding site implying a light-independent function. The genome also encodes two ribosomal proteins and nine genes with closest known homologs in marine cyanobacteria, most annotated as encoding for proteins involved in nutrient uptake. This unusual virus could serve as a model system for exploring viral rhodopsin functions and its genome suggests that phagotrophic protists may serve as an intracellular market for gene exchange between infecting viruses and ingested bacterial prey. ImportanceChrysophytes are abundant eukaryotic phytoplankton with trophic strategies ranging from photosynthesis to phagotrophy. They serve as models of mixotrophy among aquatic protists, but no chrysophyte-infecting viruses had been isolated, leaving a gap in experimental virus-host systems for a major class of protists. This study reports on the characterization of the first isolated chrysophyte-infecting virus, ChrysoHV. The virion morphology is unusual, having a loose membranous sac around a large capsid and a long filamentous tail. The genome contains genes for ribosomal proteins, a rarity in eukaryotic viruses, and multiple genes with homologs in common marine bacteria, one of which is a type of rhodopsin never before reported in a virus. We hypothesize that phago-mixotrophs, through infections and ingestion, may facilitate lateral gene exchange between eukaryote-infecting viruses and bacteria, entities that might not otherwise directly interact. The results expand the observed morphological diversity among viruses and the catalog of known virus genes.

microbiology↗

bioRxiv2025

Increased Synapse Elimination by Inflammatory Cells Contributes to Long-lasting Post-Stroke Memory Dysfunction in Old Mice

Old patients are more likely to experience memory dysfunction than young patients after a stroke. It has been reported that brain astrocytes and microglia cause excessive removal of synapses at the acute and subacute stages of stroke, and inhibition of their phagocytosis improved neurobehavioral outcomes. We hypothesized that memory dysfunction in old subjects is associated with increased synapse removal by inflammatory cells. Ischemic stroke was induced in young (2-month-old) and old (15-18-month-old) mice. Memory functions were analyzed by the Y-maze test weekly for 8 weeks and the novel object recognition (NOR) test at 7 days before and 8 weeks post-stroke. We have also created a tibia fracture 6 hours before stroke injury in young mice, to test if the activation of 7-nicotinic acetylcholine receptor (nAchRs) reduces inflammatory cells and synapse elimination. Brains were collected 8 weeks after the induction of ischemic stroke. Transcriptome changes, neuronal injuries, neuroinflammation, synapse removal, and neurite outgrowth were analyzed. We found that old mice developed long-term memory dysfunction after ischemic stroke, which was not seen in young mice. Old mice showed larger infarct volume, higher neuroinflammation, and more synapses engulfed by microglia/macrophages and astrocytes in the peri-atrophic region and hippocampi than young mice. More synapse-engulfing astrocytes than microglia/macrophages were present in the peri-atrophic region and the ipsilateral hippocampi, suggesting that reactive astrocytes contributed more than activated microglia/macrophages in synapse removal. Activation of 7-nAchRs in mice subjected to tibia fracture 6 hours before ischemic injury reduced synapse removal by microglia/macrophages and astrocytes in the hippocampi. Our study indicated that an increase in synaptic elements by inflammatory cells contributes to the long-lasting memory deficit after stroke in old mice. Astrocytes may contribute more than microglia/macrophages in synapse removal. Inhibition of neuroinflammation by activating 7-nAchRs can reduce synapse loss and thus may improve post-stroke memory function.

neuroscience↗

bioRxiv2025

Loss of meiotic double strand breaks triggers recruitment of recombination-independent pro-crossover factors in C. elegans spermatogenesis

A key event in meiosis is the conversion of a small subset of double strand breaks into interhomolog crossovers. In this study, we demonstrate that Caenorhabditis elegans male spermatogenesis has less robust mechanisms than hermaphrodite oogenesis for ensuring and limiting the conversion of double strand breaks into crossovers. This is not a consequence of differences in meiotic prophase timing, sex chromosome genotype, or the presence or absence of germline apoptosis. Using the cyclin-like crossover marker COSA-1, we show that males have a linear response in converting increasing numbers of double strand breaks into crossovers, suggesting weakened crossover homeostasis. While the topoisomerase SPO-11, responsible for initiating meiotic double strand breaks, has an extended period of activity in males as in hermaphrodites, we discovered that COSA-1 foci form at the very end of meiotic prophase in the absence of SPO-11 during spermatogenesis. These COSA-1-marked sites are also independent of homologous recombination, and Topoisomerases I and II. We find that the synaptonemal complex, which holds homologs in proximity, differently modulates COSA-1 enrichment to chromosomes in the absence of SPO-11 in males and hermaphrodites. Together, these findings suggest that males have less robust crossover control and that there are previously unrecognized lesions or structures at the end of meiotic prophase in spermatocytes that can accumulate CO markers. Author SummaryFormation of healthy gametes depends on the accurate partitioning of genetic material in the daughter cells through meiosis. A hallmark of meiosis is the establishment of crossovers, which arise from physical exchange of DNA between the parental chromosomes during homologous recombination. Recombination is initiated via the induction of physiological DNA damage by the topoisomerase SPO-11 and its auxiliary factors. Abrogating SPO-11 activity prevents crossover formation, resulting in random chromosome segregation and generation of aneuploid gametes. While the underlying mechanisms of crossover formation are conserved between the sexes, several pieces of evidence indicate extensive sexual dimorphism. In our work we describe novel features of C. elegans spermatogenesis that reveal significant differences in the regulation of recombination compared to oogenesis. We find that in spermatogenesis crossover-promoting proteins can be recruited to chromosomes even in the absence of SPO-11 activity, a phenomenon not observed in the oogenic hermaphrodite germ line. Furthermore, removal of some auxiliary factors required for physiological break formation during oogenesis does not prevent crossover designation in spermatocytes. We show that the synaptonemal complex, tasked with keeping homologous chromosomes in proximity, exerts opposing roles in males and hermaphrodites by promoting and limiting the recruitment of SPO-11-independent crossover factors, respectively.

genetics↗

bioRxiv2025

Scavenger Receptor class F member 2 is an intracellular receptor for Hepatitis B virus

Hepatitis B virus (HBV) infects hepatocytes by specific binding to the cell-surface receptor --sodium taurocholate cotransporting polypeptide (NTCP)--through the preS1 region of its large envelop protein, followed by a less well understood transport process across the cytoplasm to the nucleus. Here, we report that scavenger receptor class F member 2 (SCARF2), a single-pass transmembrane protein, functions as an intracellular receptor for HBV. SCARF2 binds to a preS1 region downstream of the NTCP binding site through its N-terminal EGF-like domains 4-6, and its proline-rich C-terminal domain also plays an indispensable role in the infection. The internalized HBV virions are transported to the cytoplasmic side of nuclear pore complexes (NPCs) within the SCARF2-containing endosomes. HBV capsid release from the endosomal vesicles is significantly impaired by knockdown of SCARF2. These results suggest a model that SCARF2 conveys HBV to the periphery of NPCs and ultimately leads to viral capsid release for nuclear entry.

microbiology↗

bioRxiv2025

Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections

Neuron typing in intact brain sections demands 3D imaging reconciling thickness compatibility with large-area coverage--a persistent challenge for RNA imaging methods limited by either restricted fields-of-view (<1 mm2) or thin-section constraints (<20 m). Here we introduce oblique thick light-sheet microscopy integrated with spatiotemporal 3D localization, enabling multiplexed RNA imaging across 50 m-thick tissue sections and centimeter-scale regions. The 45{degrees} illumination geometry achieves optical-interference-free imaging in >100 m-thick tissues during single-plane scans, while a spatiotemporal localization algorithm recovers submicron resolution by pinpointing fluorescence in situ hybridization (FISH) spots within volumetric excitation. This strategy reveals layer-spanning neuronal distributions and region-specific expression gradients unattainable with conventional RNA imaging approaches. By resolving the historical trade-off between imaging depth and spatial coverage, our platform advances whole-brain transcriptomics, enabling 3D neuron typing capability critical for deciphering brain-wide cellular architectures.

biophysics↗

bioRxiv2025

Development of a Novel Benzodiazepine to Delineate Peripheral GABA-A Signaling Mechanisms in Visceral Pain Syndromes

Background and AimsVisceral pain is a cardinal symptom of many disorders affecting the gut. Modulators of gamma-aminobutyric acid (GABA) such as benzodiazepines may attenuate colonic pain but the specific contribution of peripheral GABAA receptors remains unclear as these agents have prominent central effects. MethodsUsing medicinal chemistry optimization of the benzodiazepine scaffold, we developed a novel and potent benzodiazepine-based positive allosteric modulator (PAM) of GABAA receptors, Li633, with no significant central nervous system (CNS) penetration. ResultsThe locomotor activity of rats placed in an open field was unchanged with Li633 at doses up to 30 mg/kg, confirming its lack of a CNS effect. LI-633 produced robust potentiation of GABA-induced inward current, with EC50 values ranging from 8 nM (5{beta}2{gamma}2) to 128 nM (3{beta}2{gamma}2). In vitro electrophysiological studies confirmed its ability to reduce excitability of human dorsal root ganglion (DRG) neurons. LI-633 potentiated muscimol-induced GABAergic currents in rat DRG neurons in a dose-dependent manner, with an EC50 of 70.4 nM. In vivo, LI-633 significantly attenuated visceral hypersensitivity and pain behavior in a rat model of irritable bowel syndrome (IBS) and functional dyspepsia (FD). In the IBS model, administration of the drug also resulted in decreased excitability of colon-specific DRG neurons and significantly reduced the colonic afferent response to balloon distention as measured by recordings of neural activity in dorsal ganglia rootlets. ConclusionsThese findings highlight the potential of targeting peripheral GABAA receptors for pain management in IBS and other disorders associated with visceral hypersensitivity.

neuroscience↗

bioRxiv2025

Blind De Novo Design of Dual Cyclic Peptide Agonists Targeting GCGR and GLP1R

Agonists of the glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP1R) are key to treating metabolic diseases like type 2 diabetes and obesity, but often limited by being linear. Cyclic peptides offer greater stability and potential oral delivery, but their de novo design with computational methods as agonists is unproven. Here, we used the EvoBind AI platform to design cyclic peptide agonists for GCGR from sequence alone, without any structural templates or prior binding site information. EvoBind consistently identified the receptors activation surface, producing peptides that also activated GLP1R. Of three synthesised peptides, two showed potent dual activation of GCGR and GLP1R in cAMP assays, while all three activate GLP1R, with the 18-residue design achieving EC50 values of 32 nM (GLP1R) and 542 nM (GCGR), rivalling natural hormones. The designed sequences show no similarity to known agonists, and structural modelling indicates that they adopt novel binding modes compatible with active-state stabilisation. This is made possible by EvoBinds purely sequence-based, template-free approach, which enables the discovery of alternative solutions that are inaccessible to structure-guided methods. This study presents the first successful blind de novo design of a cyclic peptide agonist for a G protein-coupled receptor (GPCR), using only the receptor sequence as input. The findings highlight EvoBinds capacity to go beyond static binding, offering a generalisable strategy for therapeutic discovery through target-agnostic, sequence-driven peptide design.

bioinformatics↗

bioRxiv2025

GENERanno: A Genomic Foundation Model for Metagenomic Annotation

The rapid growth of genomic and metagenomic data has underscored the pressing need for advanced computational tools capable of deciphering complex biological sequences. In this study, we introduce Generanno, a compact yet powerful genomic foundation model (GFM) specifically optimized for metagenomic annotation. Trained on an extensive dataset comprising 715 billion base pairs (bp) of prokaryotic DNA, Generanno employs a transformer encoder architecture with 500 million parameters, enabling bidirectional attention over sequences up to 8192 bp at single-nucleotide resolution. This design addresses key limitations of existing methods, including the inability of traditional Hidden Markov Models (HMMs) to handle fragmented DNA sequences from multi-species microbial communities, as well as the suboptimal tokenization schemes of existing GFMs that compromise fine-grained analysis. At its core, Generanno excels in identifying coding regions from fragmented and mixed DNA sequences--a hallmark of metagenomic analysis. It achieves superior accuracy compared to traditional HMM-based methods (e.g., GLIMMER3, GeneMarkS2, Prodigal) and recent LLM-based approaches (e.g., GeneLM), while demonstrating robust generalization ability on archaeal genomes. Leveraging its advanced contextual understanding capability, Generanno further enables two essential functions: pseudogene prediction and taxonomic classification--both performed based solely on raw sequence data, without reliance on reference databases or comparative genomics. These functionalities collectively streamline the metagenomic analysis pipeline, significantly reducing preprocessing requirements and enabling end-to-end interpretation of sequencing data. Beyond its primary role in metagenomic annotation, Generanno also serves as a powerful GFM. To evaluate its broader utility, we curated the Prokaryotic Gener Tasks--a comprehensive benchmark suite specifically tailored for prokaryotic genomic analysis. It includes gene fitness prediction, antibiotic resistance identification, gene classification, and taxonomic classification, reflecting diverse aspects of functional genomics. On this benchmark, Generanno consistently outperforms existing GFMs such as DNABERT-2, NT-v2, and GenomeOcean, demonstrating strong generalization capabilities across a wide range of genomic tasks. Overall, Generanno provides a unified framework that integrates multiple critical functions for metagenomic annotation and beyond. By eliminating dependencies on external resources and offering rich contextual understanding of genomic sequences, this work delivers a foundational tool for advancing functional genomics in complex microbial communities. Implementation details and supplementary resources are available at https://github.com/GenerTeam/GENERanno.

genomics↗